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. 2014 Sep 2;3:e02981. doi: 10.7554/eLife.02981

Nuclear envelope protein MAN1 regulates clock through BMAL1

Shu-Ting Lin 1,†, Luoying Zhang 1,†, Xiaoyan Lin 1,†,‡, Linda Chen Zhang 1, Valentina Elizabeth Garcia 1, Chen-Wei Tsai 1, Louis Ptáček 1,2, Ying-Hui Fu 1,*
Editor: Leslie C Griffith3
PMCID: PMC4150126  PMID: 25182847

Abstract

Circadian clocks serve as internal pacemakers that influence many basic homeostatic processes; consequently, the expression and function of their components are tightly regulated by intricate networks of feedback loops that fine-tune circadian processes. Our knowledge of these components and pathways is far from exhaustive. In recent decades, the nuclear envelope has emerged as a global gene regulatory machine, although its role in circadian regulation has not been explored. We report that transcription of the core clock component BMAL1 is positively modulated by the inner nuclear membrane protein MAN1, which directly binds the BMAL1 promoter and enhances its transcription. Our results establish a novel connection between the nuclear periphery and circadian rhythmicity, therefore bridging two global regulatory systems that modulate all aspects of bodily functions.

DOI: http://dx.doi.org/10.7554/eLife.02981.001

Research organism: D. melanogaster, mouse

eLife digest

If rodents, or indeed humans, are kept in constant darkness for a number of days, they continue to show patterns of sleep and wakefulness that repeat roughly every 24 hr. This internal ‘circadian rhythm’ controls many aspects of animal physiology, including body temperature, blood pressure, and hormone levels. It does so by regulating the expression of key genes: this means that the activity of the proteins encoded by these genes also varies in accordance with the circadian rhythm.

A second mechanism used by the body to coordinate gene expression on a large scale entails making adjustments to the membrane that surrounds the cell nucleus. This ‘nuclear envelope’ consists mainly of lipids, but it also contains proteins that bind DNA. These proteins regulate gene expression by controlling how easy it is for other proteins that activate or repress genes to gain access to specific DNA sequences.

Lin et al. now reveal that these mechanisms work together. The first evidence for this was the discovery that the levels of three specific nuclear envelope proteins influence, and are influenced by, circadian rhythms. In particular, two of these proteins control the activity of the third, which is known as MAN1. This protein in turn triggers the expression of a gene called BMAL1, which is one of the small number of ‘clock genes’ that are responsible for generating the internal circadian rhythm.

As well as adding to our knowledge of circadian biology and the nuclear envelope, this study reveals a mechanism by which cells can orchestrate the expression of large numbers of genes. Such mechanisms allow a wide range of physiological and behavioral processes to be co-ordinated.

DOI: http://dx.doi.org/10.7554/eLife.02981.002

Introduction

Most organisms, ranging from cyanobacteria to humans, are governed by their circadian rhythms: endogenous and self-sustained oscillations with a period of roughly 24 hr, which manifest in diverse metabolic, physiological, and behavioral processes (Ueda et al., 2005). This internal pacemaker is charged with two important roles: to perpetuate its own rhythms and to regulate the expression of genes that are under circadian control. In mammals, this internal pacemaker consists of a complex network of transcriptional regulations, at the core of which is transcription activators BMAL1 (also known as ARNTL1 or MOP3) and CLOCK, which form heterodimers and regulate gene expression. Up to 15% of the organism's genome is regulated in a circadian manner (Panda et al., 2002; Emery and Reppert, 2004; Zhang and Kay, 2010). Well-studied examples include the transcription repressors (PERIODs and CRYPTOCRHOMEs) that bind to CLOCK/BMAL1 and suppress their own transcription, thereby forming a feedback loop. Since the identification and cloning of the first mammalian clock gene, CLOCK, two decades ago (Vitaterna et al., 1994), the field of chronobiology has uncovered many additional players that regulate circadian rhythms on a transcriptional and/or post-transcriptional level, and many more such candidates are currently being evaluated.

Recently, mutations in nuclear envelope (NE) proteins have been shown to cause a surprisingly broad range of inherited diseases, thus shedding light on roles played by the NE in global regulations at cellular and organismal levels (Padiath et al., 2006; Dauer and Worman, 2009). These diseases (often referred to as nuclear envelopathies or laminopathies) can impact muscle, nerve, fat metabolism, bone formation, and others. NE consists of outer and inner nuclear membranes (connected by nuclear pore complexes) and nuclear lamina. The inner nuclear membrane proteins (such as MAN1, LBR, LAP2, etc) include approximately 60 putative transmembrane proteins specifically retained in the inner nuclear membrane and most of them are poorly characterized (Schirmer et al., 2005). In metazoan, nuclear lamina is a protein mesh-like structure composed of type V intermediate filament proteins lamins (including A, C, B1, B2, and B3 types) and sits primarily underneath the inner nuclear membrane (Zwerger and Medalia, 2013). The idea of nuclear envelope components as transcription regulators in mammals is relatively new, conceived from the observation that gene-rich chromosomes are generally located in more internal nuclear regions, whereas gene-poor chromosomes are relegated to the periphery (Spector, 2003). Many NE components such as inner nuclear membrane proteins, nuclear lamina, and the nuclear pore complex, harbor DNA-binding domains that are involved in anchoring chromatin to the periphery (Ulbert et al., 2006; Mekhail and Moazed, 2010). Functional relevance of these positional distinctions became apparent as studies with yeast and flies revealed that the NE can sequester factors that affect gene transcription in both repressive and, surprisingly, activating manners (Akhtar and Gasser, 2007). Although recent findings highlight the important functions of the nuclear periphery, its relationship with the circadian clock has not been probed. Given the increasing awareness of the global roles that these two systems play in myriad pathways, we set out to investigate the possibility that these seemingly separate pathways are connected and can work synergistically in regulating diverse functions.

Results

Nuclear envelope participates in circadian regulation

In order to investigate whether NE proteins are involved in circadian regulation, we began by focusing on lamin B1 since it has been shown to play a role in transcriptional regulation (Hutchison, 2002; Shevelyov et al., 2009). In vivo oscillation of lamin B1 (Lmnb1) expression patterns (both RNA and protein levels) were confirmed using mouse tissues from suprachiasmatic nuclei (SCN), kidney, and liver (Figure 1A,B). To test whether the level of lamin B1 affects the molecular clock, we examined the protein expression patterns for the core clock gene PERIOD2 (PER2) using Lmnb1 heterozygous knock out (homozygosity is lethal) and LMNB1 wild-type BAC transgenic mice (Vergnes et al., 2004; Heng et al., 2013). Oscillating PER2 expression patterns were phase delayed in Lmnb1 heterozygous knock out mice and phase advanced in LMNB1 BAC transgenic mice (overexpression) when compared to wild-type control mice (Figure 1C), suggesting that the level of lamin B1 can modulate circadian clock. However, neither Lmnb1 heterozygous knock out mice nor LMNB1 BAC transgenic mice demonstrated significant output behavioral change (Figure 1—figure supplement 1). To expand the investigation, we chose to include two additional NE proteins that are known to associate with lamin B1, LBR, and MAN1. We found that LBR and MAN1 expression also oscillate, albeit mildly for MAN1 (Figure 1D).

Figure 1. Lamin b1 regulates the circadian clock.

Expression levels of lamin b1 from SCN, kidney, and liver extracts in C57BL/6J mice (A and B). (A) mRNA levels of Lmnb1 and Gapdh were assayed at indicated circadian times (CT, n = 4). (B) Representative immunoblots show the levels of LMNB1, GAPDH, and β-ACTIN. (C) Representative immunoblots show PER2 (with intensity values indicated at the bottom) and LMNB1 abundance in Lmnb1+/Δ, wild-type and LMNB1BAC liver extracts. (D) Expression patterns of LMNB1, LBR, and MAN1 in C57BL/6 mouse livers at indicated Zeitgeber times (ZT) (n = 3). Quantifications (top panels) of Western blots (bottom panel) were obtained by using GAPDH as a loading control. Data represent means ± SD.

DOI: http://dx.doi.org/10.7554/eLife.02981.003

Figure 1.

Figure 1—figure supplement 1. Mice with altered LMNB1 levels do not exhibit altered behavioral rhythms.

Figure 1—figure supplement 1.

The period (A), activity level (B), and amplitude (C) of wheel-running rhythms under DD condition (n = 9–27, Student's t test, *p < 0.05). Error bars represent SEM.
DOI: http://dx.doi.org/10.7554/eLife.02981.004
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To determine if these NE genes passively receive cues from the core clock apparatus or if their protein products also actively play a role in maintaining circadian rhythms, we altered their protein levels in human osteosarcoma U2OS cells that express a luciferase reporter gene under the control of mouse Bmal1 promoter (Bmal1-Luc) and examined circadian period in cell culture (Vollmers et al., 2008). siRNA-induced reduction of LMNB1, LBR, and MAN1 in this cell-based system resulted in a longer circadian period (τ) (Figure 2A), whereas the over-expression of all three led to a shorter τ (Figure 2B). Cells transfected with LBR, LMNB1, and MAN1 siRNA lengthened τ by 54–69 min (n ≥ 4, *p < 0.05), when compared with control siRNA (τ = 27.39 ± 0.22 hr, n = 8) (Figure 2C). On the other hand, overexpression of FLAG-tagged LBR, LMNB1, or MAN1 shortened τ by 25.8–37.8 min (n ≥ 4, *p < 0.05) compared to empty vector controls (τ = 27.7 ± 0.15, Figure 2D). These changes in τ together with the altered phase of Lmnb1 heterozygous knock out mice and over-expressing mice suggest that these NE proteins participate in modulating circadian clock and therefore could impose significant impacts on downstream biological pathways.

Figure 2. LBR, LMNB1, and MAN1 are necessary for normal circadian rhythms.

Two representative traces of real-time bioluminescence analyses are shown for each, and Western blot verification of down-regulation or over-expression is demonstrated in the inset images. (A) Period was lengthened when LBR, LMNB1, or MAN1 was knocked down. (B) Over-expression of FLAG-tagged LBR (F-LBR), LMNB1 (F-LMNB1), or MAN1 (F-MAN1) shortened period compared to cells transfected with empty vector (ctrl). (C and D) Summary of period in (A and B). CRYPTOCRHOME2 (CRY2) and PER2 siRNA knockdowns served as positive controls. Data represent means ± SD.

DOI: http://dx.doi.org/10.7554/eLife.02981.005

Figure 2.

Figure 2—figure supplement 1. Over-expressing or knocking down nuclear envelope components alters circadian rhythms in flies.

Figure 2—figure supplement 1.

(A) Normalized locomotor activity profiles of flies over-expressing MAN1, Lam, or LBR during LD for 1 day followed by 4 days of DD. (B) Normalized locomotor activity profiles of flies with MAN1, Lam, or LBR knocked down by RNAi. White box indicates light period, black box indicates dark period, and gray box indicates subjective light period. Error bars represent SEM (n = 13–76).
DOI: http://dx.doi.org/10.7554/eLife.02981.006
Figure 2—figure supplement 2. The mRNA levels of nuclear envelope genes are reduced in the corresponding knockdown flies.

Figure 2—figure supplement 2.

Plots of relative mRNA abundance for MAN1, Lam, and LBR from whole head extracts of timGAL4/+;UASdicer2/+, timGAL4/UASMAN1RNAi;UASdicer2/+, timGAL4/+;UASdicer2/UASLamRNAi and timGAL4/UASLBRRNAi;UASdicer2/+ flies determined by qRT-PCR. Error bars represent SEM (n = 3–6). Significant differences indicated by asterisks (Student's t test, *p < 0.05, **p < 0.01, ***p < 0.001). The value of timGAL4/+;UASdicer2/+ for one experiment was set to 1.
DOI: http://dx.doi.org/10.7554/eLife.02981.007
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The effects of NE proteins on Drosophila circadian clock were also examined. Consistent with the mammalian data, over-expressing dLamin (dLam) (Padiath et al., 2006) in circadian neurons with cryptochrome (cry)GAL4-39 and cryGAL4-16 (Emery et al., 2000) in vivo resulted in substantially shortened periods of behavioral rhythms in constant darkness compared to GAL4 controls (but not to UASLMNB1/+, Table 1; Figure 2—figure supplement 1A). Knocking down dLam in circadian neurons lengthened the period (Table 2; Figure 2—figure supplement 1B). On the other hand, over-expressing dMAN1 and dLBR lengthened the period (Table 1; Figure 2—figure supplement 1A), while knocking down dMAN1 also lengthened period (Table 2; Figure 2—figure supplement 1B). Besides altering the period, most of these manipulations reduced the amplitude of behavioral rhythms as indicated by the reduced power values. In addition, we have assessed the mRNA levels of dMAN1, dLam, and dLBR to confirm knockdown (Figure 2—figure supplement 2). Taken together, these results indicate that NE proteins also participate in the regulation of fly clock.

Table 1.

Over-expressing NE genes alters the behavioral period in flies

DOI: http://dx.doi.org/10.7554/eLife.02981.008

Genotype Period (hr) Power Rhythmic% N
UASMAN1/+ 23.8 ± 0.0 90 ± 5 96 76
cryGAL4-39/UASMAN1 26.4 ± 0.3*,† 31 ± 6*,† 64 28
UASMAN1/+; cryGAL4-16/+ 26.8 ± 0.2*,† 40 ± 7*,† 66 32
UASLam/+ 23.9 ± 0.0 87 ± 6 93 55
cryGAL4-39/UASLam 23.8 ± 0.2† 33 ± 7*,† 73 22
UASLMNB1/+; cryGAL4-16/+ 24.4 ± 0.2† 5 ± 2*,† 26 31
UASLBR/+ 23.7 ± 0.0 59 ± 5 79 67
cryGAL4-39/UASLBR 25.6 ± 0.1*,† 44 ± 6† 79 33
UASLBR/+; cryGAL4-16/+ N/A 1 ± 0*,† 0 32
cryGAL4-39/+ 24.8 ± 0.1 86 ± 5 93 57
cryGAL4-16/+ 25.6 ± 0.1 86 ± 5 94 64
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*

One-way ANOVA compared to UAS control lines, p < 0.001.

†

One-way ANOVA compared to GAL4 control lines, p < 0.001.

Table 2.

Knocking-down NE genes lengthens the behavioral period in flies

DOI: http://dx.doi.org/10.7554/eLife.02981.009

Genotype Period (hr) Power %Rhythmic N
UASMAN1RNAi 24.4 ± 0.1 110 ± 10 100 14
UASMAN1RNAi;cryGAL4-39/+; UASdcr2/+ 26.3 ± 0.3*,† 29 ± 6*,† 80 15
UASMAN1RNAi; UASdcr2/+;cryGAL4-16/+ 27.9 ± 0.4*,† 39 ± 8*,† 69 16
UASLamRNAi/+ 23.6 ± 0.1 129 ± 12 100 16
cryGAL4-39/+; UASLamRNAi/UASdcr2 25.1 ± 0.4* 26 ± 17*,† 50 14
UASLamRNAi/UASdcr2; cryGAL4-16/+ 26.8 ± 0.1*,† 126 ± 17 100 13
UASLBRRNAi/+ 23.5 ± 0.0 112 ± 14 100 15
cryGAL4-39/UASLBRRNAi; UASdcr2/+ 24.9 ± 0.1 61 ± 12* 80 15
UASLBRRNAi/UASdcr2; cryGAL4-16/+ 24.6 ± 1.7 12 ± 4*,† 44 16
cryGAL4-39/+; UASdcr2/+ 24.9 ± 0.1 69 ± 12 88 16
UASdcr2/+;cryGAL4-16/+ 26.1 ± 0.1 87 ± 10 94 16
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*

One-way ANOVA compared to UASRNAi control lines, p < 0.05.

†

One-way ANOVA compared to control lines with GAL4 and UASdcr2, p < 0.05.

dicer2 (dcr2) is co-expressed to enhance the effects of RNAi.

Lamin B1 and LBR likely act through MAN1

We next explored the relationship of LBR, LMNB1, and MAN1 by examining mRNA and protein levels while knocking them down one at a time. Both LBR and LMNB1 knockdown significantly decreased the transcript level of MAN1 (by 15% and 40%, respectively) (Figure 3A). The effects of LBR or LMNB1 knockdown on MAN1 expression are even more dramatic at the protein level, with 54% and 44% reductions, respectively (Figure 3B). Moreover, knockdown of LBR expression reduces the amount of LMNB1 protein by 32%, which is consistent with the observation that reduction of LBR expression in the fibroblasts of patients harboring a heterozygous LBR mutation results in the abolition of LMNB1 protein (Gaudy-Marqueste et al., 2010), whereas a decrease in LMNB1 does not significantly affect LBR expression. MAN1 knockdown also does not change the expression of LBR and LMNB1, either at the mRNA or protein level (Figure 3). These results suggest that MAN1 is modulated by LBR and LMNB1, and thus the effects of LBR and LMNB1 on the clock are at least partially through MAN1. Therefore, we further investigated the effects of MAN1 on the molecular clock.

Figure 3. Knocking down LBR/LMNB1 reduces MAN1 mRNA and protein levels but not vice versa.

Figure 3.

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Assessing mRNA (A) and protein (B) levels of LBR, LMNB1, and MAN1 while knocking them down one at a time in U2OS cells via RNAi. (A) mRNA levels of LBR, LMNB1, and MAN1 in each of the three knockdown conditions were quantified using qRT-PCR (n = 14, *p < 0.05). (B) MAN1 was significantly down-regulated when LBR or LMNB1 was knocked down (n = 14 *p < 0.001). The error bars represent SEM (left panel). Representative immunoblots show the protein levels of LBR, LMNB1 and MAN1 (right panel).

DOI: http://dx.doi.org/10.7554/eLife.02981.010

MAN1 regulates the clock by promoting BMAL1 expression

A lengthened period due to decreased MAN1 may arise from altered regulation of core clock proteins and/or altered transcription of core clock genes. Either of these effects would result in disruptions of the stoichiometry and temporal control of the dynamics of the core circadian feedback loops. Given what is known regarding the role of NE proteins in transcriptional regulation, we tested whether reductions in MAN1 expression would affect the transcription of clock genes. We examined the circadian oscillation of core clock genes at the mRNA level and found that only BMAL1 showed a clear difference wherein overall mRNA levels were down-regulated to half the levels of controls (Figure 4). Western blots also showed lower expression of BMAL1 when MAN1 was knocked down (Figure 4—figure supplement 1). The non-oscillatory CLOCK showed no significant change of either transcript or protein levels (Figure 4, Figure 4—figure supplement 1). The conserved mRNA levels of REV-ERBα and RORα in MAN1 knockdown cells suggest that the reduced BMAL1 expression is not caused by altered transcriptional activation of REV-ERBα, a BMAL1 repressor, or transcriptional repression of RORα, a BMAL1 activator.

Figure 4. Knocking down MAN1 reduces the levels of BMAL1 mRNA.

Each graph shows cells transfected with MAN1 siRNA vs ctrl siRNA. Time 0 indicates the moment that U2OS cells were treated with dexamethasone (100 nM). Data are presented as means ± SEM, n = 3.

DOI: http://dx.doi.org/10.7554/eLife.02981.011

Figure 4.

Figure 4—figure supplement 1. Knocking down MAN1 reduces BMAL1 protein levels.

Figure 4—figure supplement 1.

(A) Time course evaluations of U2OS cells transfected with MAN1 siRNA showed robust reduction of BMAL1 protein levels compared to ctrl siRNA. CLOCK levels were unaffected by MAN1 abundance (n = 3). (B) The quantification results of (A) were graphed (n = 14). Error bars indicate SEM.
DOI: http://dx.doi.org/10.7554/eLife.02981.012
Figure 4—figure supplement 2. Over-expressing Bmal1 suppresses the period lengthening effect of MAN1 knockdown.

Figure 4—figure supplement 2.

Periods of Bmal1-Luc U2OS cells transfected with MAN1 siRNA or control (ctrl) siRNA together with either empty vector or varying amounts of Bmal1. Error bars represent SEM (n = 2–4, Student's t test).
DOI: http://dx.doi.org/10.7554/eLife.02981.013
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To confirm MAN1 regulates the clock by targeting BMAL1, we over-expressed Bmal1 in MAN1 knockdown U2OS Bmal1-Luc cells. Knocking down MAN1 lengthened the period in control cells as described above (Figure 2), whereas cells over-expressing sufficient Bmal1 did not demonstrate period lengthening compared to cells without MAN1 knockdown (Figure 4—figure supplement 2), suggesting that the lengthened period caused by MAN1 deficiency is due to reduction of BMAL1. Together, these results indicate that MAN1 functions to promote BMAL1 expression, and thus exerting effects on the clock.

Consistent with the cell culture data, over-expressing MAN1 in all clock cells in flies using a timeless (tim) GAL4 driver (Emery et al., 1998) resulted in a significantly increased level of cycle (cyc) mRNA, the Drosophila BMAL1 homologue (Rutila et al., 1998; Figure 5A). The mRNA level of core clock gene tim was also significantly elevated. In addition, we have assessed the levels of MAN1 mRNA to confirm over-expression (Figure 5B). We also examined the effect of knocking down MAN1 in clock cells but did not observe altered cyc mRNA levels (Figure 5—figure supplement 1).

Figure 5. MAN1 increases cyc mRNA levels.

(A) Plots of relative mRNA abundance vs CT for clock genes from whole head extracts of timGAL4/+ and timGAL4/UASMAN1 flies during the first day of DD determined by qRT-PCR (n = 2). Gray box indicates subjective light period and black box indicates dark period. Significant effect of genotypes (Two-way ANOVA) were found for cyc (p = 0.0278) and tim (p = 0.0161). For each time series, the value of the lowest time point was set to 1. (B) Plot of relative mRNA abundance for MAN1 from whole head extracts of timGAL4/+ and timGAL4/UASMAN1 flies determined by qRT-PCR (n = 6, Student's t test, ***p < 0.001). The value of timGAL4/+ in one experiment was set to 1. Error bars represent SEM.

DOI: http://dx.doi.org/10.7554/eLife.02981.014

Figure 5.

Figure 5—figure supplement 1. cyc transcript level is not altered in MAN1 knock-down flies.

Figure 5—figure supplement 1.

Plot of relative mRNA abundance for cyc from whole head extracts of timGAL4/+;UASdicer2/+ and timGAL4/UASMAN1RNAi;UASdicer2/+ flies determined by qRT-PCR. Error bars represent SEM (n = 6). The value of timGAL4/+;UASdicer2/+ for one experiment was set to 1.
DOI: http://dx.doi.org/10.7554/eLife.02981.015
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MAN1 enhances BMAL1 transcription

A luciferase reporter assay using HEK293 cells was used to further investigate the effect of MAN1 on BMAL1 transcription. MAN1 knockdown decreased Bmal1-Luc activity by 72% (Figure 6A), whereas overexpression of FLAG-MAN1 increased the luciferase activity by more than twofold vs cells transfected with empty vector (Figure 6B). Similar results were obtained with a longer, human BMAL1 promoter (Figure 6C). These data indicate that MAN1 may play a role in circadian regulation by activating the promoter of BMAL1.

Figure 6. MAN1 promotes BMAL1 transcriptional activity.

Figure 6.

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(A) Reduction of MAN1 transcripts (13 nM siRNA) reduced Bmal1 promoter activity (n = 3, *p < 0.001). (B) Over-expression of FLAG-tagged MAN1 (F-MAN1) enhanced Bmal1-Luc activity (n = 3, *p < 0.001). (C) Over-expression of FLAG-tagged MAN1 (F-MAN1) enhanced luciferase activities driven by mBmal1 promoter (530 bp) or hBMAL1 promoter (3.4 kb) (n = 3, *p < 0.05). Error bars represent SD.

DOI: http://dx.doi.org/10.7554/eLife.02981.016

Previously, MAN1 has been shown to exert antagonistic regulatory functions on signal transduction through its binding to R-SMADs (Osada et al., 2003; Raju et al., 2003; Hellemans et al., 2004; Lin et al., 2005; Pan et al., 2005; Cohen et al., 2007) and two types of R-SMADs are found in mammals: TGFβ-responsive (SMAD2 and SMAD3) and BMP-responsive (SMAD1, SMAD5, and SMAD8). To determine whether R-SMADs have an effect on BMAL1 transcription, we first expressed R-SMADs individually in HEK293 cells transfected with BMAL1-Luc to determine which R-SMAD/s is/are involved in regulating BMAL1 transcription. Expressing SMAD1, SMAD5, SMAD8, and SMAD3 had no significant effect on BMAL1 transcription but SMAD2 showed significant enhancing effect, suggesting a possible regulatory function by SMAD2 in BMAL1 regulation (Figure 7A). The enhancing action of SMAD2 was then examined together with MAN1 to determine whether there is interplay between MAN1 and SMAD2 on BMAL1 promoter activity. Intriguingly, MAN1 further augmented the enhancing effect of SMAD2 on BMAL1 in an additive manner, indicating that the positive regulatory function of MAN1 and SMAD2 on BMAL1 might be independent of each other (Figure 7B).

Figure 7. MAN1 and SMAD2 enhance BMAL1 transcription.

Figure 7.

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(A–D) Luciferase reporter activities in transfected HEK293 cells. Cells transfected with indicated constructs in the presence of the 3.4 kb hBMAL1 promoter for 48 hr and relative luciferase activities were measured in extracts and normalized to Renilla luciferase activities. Relative luciferase activities were shown on the y-axis. Values are means ± SEM, n = 3, **p < 0.01 compared to control. †p < 0.05, ††p < 0.01 compared to MAN1 0, one-way ANOVA with Newman–Keuls test.

DOI: http://dx.doi.org/10.7554/eLife.02981.017

Since BMAL1 transcription is regulated by RORα and REV-ERBα, we wondered whether the effect of MAN1 on BMAL1 is influenced by RORα/REV-ERBα. MAN1 increases BMAL1 transcription in the HEK293 luciferase reporter assay but this effect was overshadowed by the presence of either RORα or REV-ERBα, and the impact of RORα and REV-ERBα on BMAL1 was not influenced by the presence of MAN1 (Figure 7C). In addition, the effect of MAN1 was also not significantly altered by mutating the RORE sequence (+3 ∼ +13 and +39 ∼ +48) in the BMAL1 promoter (Figure 7D), which serves as the DNA binding target of RORα and REV-ERBα. Together, these data suggest that the effect of MAN1 on BMAL1 transcription is not through the RORE and does not require or impact RORα and REV-ERBα.

MAN1 binds to the BMAL1 promoter

Since MAN1 does not execute its function through RORE, we investigated the promoter region of BMAL1 to determine what is necessary for the enhancing effect of MAN1. A series of deletion constructs of the BMAL1 promoter were generated for luciferase assays and a 900 bp region (−795 ∼ +106) was identified to be the region harboring the necessary DNA sequence for the regulatory effect of MAN1 on BMAL1 (Figure 8A, Figure 8—figure supplement 1A).

Figure 8. MAN1 binds to the BMAL1 promoter to enhance its transcription.

(A) Luciferase activities of deleted hBMAL1-promoter constructs in the absence or presence of MAN1 expression vectors. n = 3, Student's t test, **p < 0.01, ***p < 0.001. (B and C) Luciferase activities of the 3.4 Kb hBMAL1-Luc in the presence of MAN1 constructs as indicated. n = 3, **p < 0.01, ***p < 0.001 compared to control; †p < 0.05; ††p < 0.001 compared to WT MAN1. (D) ChIP analysis of MAN1 (WT or DNA binding truncation) for 14 segments of hBMAL1 promoter region. Data represent pull-down relative to input. n = 6, †p < 0.05, compared to WT MAN1. One-way ANOVA with Newman–Keuls test. All data are presented as ratio of means ± SEM.

DOI: http://dx.doi.org/10.7554/eLife.02981.018

Figure 8.

Figure 8—figure supplement 1. Domain-specific interactions between MAN1 and the hBMAL1 promoter.

Figure 8—figure supplement 1.

(A) Schematic representation of the indicated constructs generated from the 3.4 kb hBMAL1 promoter and cloned into the luciferase reporter vector pGL3. Histogram of luciferase activity in HEK293 cells transfected with the deleted hBMAL1 promoter constructs in the absence or presence of MAN1 expression vectors. Cells transfected for 48 hr and relative luciferase activities measured in extracts and normalized to Renilla luciferase activities. Activities (relative luciferase activity) are shown on the y-axis. Values are means ± SEM, n = 3, Student's t test, **p < 0.01, ***p < 0.001 compared to control. (B) Schematic representation of the deletion constructs generated from the MAN1 expressing construct. (C) Sequences of constructs with point mutations generated from the MAN1 expressing construct.
DOI: http://dx.doi.org/10.7554/eLife.02981.019
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MAN1 has an N-terminal LAP2-Emerin-MAN1 (LEM) domain, two transmembrane segments in the middle, a unique DNA binding domain, and a C-terminal RNA recognition motif (RRM) that is required for its binding with R-SMADs (Caputo et al., 2006). We next examined the domain of MAN1 necessary for its effect on BMAL1. Two truncation constructs of MAN1 were generated, one without the DNA binding domain (amino acids 707–725) and the other without the RRM domain (amino acids 760–911) (Pan et al., 2005; Figure 8—figure supplement 1B). In addition, we utilized a substitution mutant of MAN1 (YV-DD) (Pan et al., 2005), containing two amino acid alterations in the RRM that nullify the ability of MAN1 to antagonize R-SMADs. These constructs were then used to test their transcriptional enhancing effect on BMAL1 promoters (either full length 3.4 kb or 2.4 kb [−2300 ∼ +105]). Intriguingly, the RRM truncation mutation lost the enhancing effect on the BMAL1 promoter (Figure 8B). The DNA binding domain truncation mutation also lost the activating effect on BMAL1, and this effect can be produced by simply mutating three positively charged amino acids (RKK) at amino acids 709–711 (Figure 8C, Figure 8—figure supplement 1C). These results imply that the effect of MAN1 on BMAL1 transcription requires potential DNA binding ability of MAN1 as well as interaction with a protein partner (possibly SMAD2) through RRM.

Since the DNA binding domain is required for the effect of MAN1 on the BMAL1 promoter, we next tested whether MAN1 directly binds to the BMAL1 promoter. Chromatin immunoprecipitation (ChIP) analysis revealed that the region −237 bp to +45 bp from transcriptional start site was pulled down by MAN1 indicating a direct interaction (Figure 8D). All together, these data suggest that MAN1 binds to the BMAL1 promoter region (−237 bp to +45 bp) to enhance its transcription.

Discussion

The nuclear envelope plays essential roles in diverse cellular functions including global regulation of gene expression. Interestingly, another global regulatory mechanism is the molecular clock that modulates our body and cellular daily rhythm. We sought to see whether there is cross talk between these two regulatory mechanisms. Our studies revealed that some components of nuclear envelope do show daily oscillations, indicating that nuclear envelope is subject to clock control. On the other hand, we found that one of the major transcription activators of the molecular clock, BMAL1, is regulated by one of the nuclear envelope proteins, MAN1. Thus, there is reciprocity between these two global regulatory mechanisms.

The nuclear envelope physically separates genomic DNA from the cytoplasm and functions as a signaling control center. An increasing number of human diseases are recognized to be caused by mutations in genes encoding nuclear envelope proteins and hence, termed ‘envelopathies’ (Dauer and Worman, 2009). Several inner nuclear membrane proteins are known to regulate critical signaling pathways and act as intranuclear regulators of signaling pathways that receive and transduce signals from extracellular cues. The nuclear lamina provides structural support for the nucleus and the nuclear envelope; however, lamins and their associated proteins are also involved in most of the nuclear processes. Lamin B1 is essential for brain development and is required for the integrity of the nuclear lamina (Padiath et al., 2006; Coffinier et al., 2011). Interestingly, no abnormality has been reported for the heterozygous Lmnb1 knock out mice (Stewart et al., 2007; Coffinier et al., 2011), and it is estimated that these heterozygous mice still express 70% of lamin b1 (SG Young, personal communication). Consistent with these reports, we did not find significant phenotype including circadian behavior change in these mice despite the clear phase shift on PER2 oscillation in the liver. It is possible that the oscillation of one or more additional core clock components are also altered by reduced lamin b1 level and these additional alterations can compensate the effect of PER2 phase shift on output behavior. Alternatively, it is also possible that the SCN clock is resilient to perturbations caused by reduced lamin b1 level, hence we can only observe alterations in peripheral clocks. Further investigation is necessary to reveal the mechanism leading to the findings we report here.

MAN1 belongs to the inner nuclear membrane LEM protein family (Worman, 2006; Bengtsson, 2007). LEM domains mediate the interaction with a chromatin-binding protein, barrier-to-autointegration factor (BAF), which has the ability to bind dsDNA, chromatin, histones, lamin binding proteins, and various transcription factors (Liu et al., 2003; Worman, 2006; Bengtsson, 2007). Therefore, LEM proteins have roles in gene regulation, chromatin organization, regulation of transcription factor activity at the nuclear periphery, and regulation of specific signal pathways. Both amino and carboxyl termini of MAN1 are nucleoplasmic domains. The amino-terminal nucleoplasmic region of MAN1 (including LEM) binds to the nuclear lamins and emerin in addition to BAF. It is also necessary for efficient localization of MAN1 to the inner nuclear membrane (Mansharamani and Wilson, 2005). The carboxyl-terminal nucleoplasmic region (residues 655–911) exhibits two globular domains (Pan et al., 2005; Caputo et al., 2006). The first globular domain contains a winged helix (including the sequence RKKMKKVWDR) which is mainly used for DNA binding and recognition. The second domain (amino acids 782–911) is an RRM-like protein interaction domain where it can interact with R-SMADs. The entire carboxy-terminal region of MAN1 was shown to participate in DNA binding, and this interaction is synergistic to the binding of MAN1 to different transcriptional regulators, including R-SMADs (Osada et al., 2003; Raju et al., 2003; Lin et al., 2005; Pan et al., 2005). Consistently, we found that both RRM and DNA binding domains are required for the activation of the BMAL1 promoter by MAN1. Also congruent with previous findings, we found that mutating three of the highly positively charged and conserved amino acids within the winged helix region is sufficient to dampen the activation efficiency of MAN1. In contrast to previous reports, we found that MAN1 further augments (but not antagonizes) the positive effect of SMAD2 on BMAL1. Consistent with this result, we also found that the substitution mutation YV-DD of MAN1 does not influence its effect on BMAL1 (though RRM domain is required). Collectively, these results suggest that the effects of MAN1 and SMAD2 on BMAL1 might not be completely independent to each other and that MAN1 might interact with SMAD2 in more than one way (presumably through other protein partners) to modulate transcription of target genes.

Many of our body functions manifest a daily rhythm which is maintained by the rhythmic regulation of approximately 15% of genes by the core molecular clock (Vollmers et al., 2009; Menet et al., 2012). However, cells must be flexible enough to allow for responses to exogenous and endogenous stimuli. This regulation is likely to be mediated not solely by the molecular clock, but also by many additional global and local mechanisms including at the level of chromatin and genome organization (Aguilar-Arnal et al., 2013; Hubner et al., 2013). Genetic loci associated with the nuclear lamina through large regions of chromatin (lamin associated domains–LADs) are associated with changes in transcriptional status (Peric-Hupkes et al., 2010). Circadian genes or genes involved in rhythmic processes display robust rhythmic expression patterns at the level of nascent mRNA and mRNA (Menet et al., 2012; Rodriguez et al., 2012), suggesting prominent contribution of transcriptional regulation to clock gene expression. Interestingly, genes harboring this expression pattern are dramatically enriched for specific function in transcriptional regulation and chromatin organization (Menet et al., 2012). These unbiased genome-wide transcriptome reports raised the possibility that components of nuclear envelope may modulate oscillation of clock genes at transcriptional levels. A recent study has also demonstrated that the molecular clock drives circadian changes in spatial and temporal chromosomal organization (Aguilar-Arnal et al., 2013). Indeed, our study links the nuclear periphery with circadian regulation via the regulatory effects of MAN1 on BMAL1 through transcription.

This effect is evident not only in mammalian systems, but also in flies, as over-expressing MAN1 resulted in significantly increased levels of cyc mRNA. MAN1 over-expression also increased tim mRNA levels, which may be at least partially due to increased cyc. Knocking down MAN1 did not alter cyc levels, possibly because the residual MAN1 is still sufficient to maintain normal cyc levels. However, this manipulation lengthened behavioral period, suggesting that MAN1 may target other clock components in addition to cyc. Over-expressing MAN1 and LBR in flies led to a lengthened behavioral period, while in U2OS cells, these manipulations resulted in moderate shortening of the period. On the other hand, over-expressing and knocking down Lam in flies shortened and lengthened the period, respectively, which is consistent with the mammalian data. These discrepancies reflect the differences between mammalian and insect clock, which has been implied in previous work as well (Lowrey et al., 2000; Preuss et al., 2004; Xu et al., 2005). Nevertheless, our results indicate that there is a conserved role for NE components in setting the clock in organisms ranging from invertebrates to humans.

Although only 22–30% of cycling mRNA is driven transcriptionally (Koike et al., 2012; Menet et al., 2012), demonstration of involvement of the nuclear envelope in regulation of the molecular circadian clock suggests one pathway through which the nuclear envelope may globally and temporally regulate large numbers of genes. Interestingly, expression of the genes for many nuclear envelope proteins also oscillates. This finding sheds new light on the interconnectedness of these biological processes and provides further insight into the mechanism whereby cellular, metabolic, physiological, and behavioral processes that oscillate are modulated in a highly coordinated manner.

Materials and methods

Plasmids

To generate FLAG-tagged proteins, human LBR, LMNB1, and MAN1 genes were subcloned into pCMV-Tag2A (Stratagene; La Jolla, CA). HA-tagged SMAD1, FLAG-MAN1 (YV-DD), and FLAG-MAN1 (1–759) were gifts from Dr Kunxin Luo (Pan et al., 2005). mBmal1-Luc was generated in Dr Satchidananda Panda's lab and kindly provided by Dr John Hogenesch (Vollmers et al., 2008), while the human BMAL1-luc construct was a generous gift from Dr Toru Takumi (Akashi and Takumi, 2005). Syrian hamster Bmal1 in pcDNA3.1 vector was provided by Dr David Weaver (Kume et al., 1999). pRL-TK was purchased from Promega (Madison, WI). Mutations of expression constructs were introduced by PCR, and all constructs used in this study were verified by sequencing.

LumiCycle analysis

A stable U2OS-B6 cell line that expresses a destabilized firefly luciferase gene under the control of the mBmal1 promoter was obtained from Dr Satchidananda Panda (Vollmers et al., 2008). siRNAs targeted to LBR, LMNB1, MAN1, or SMAD1 (10 nM, Invitrogen; Carlsbad, CA; see Supplementary file 1A) were individually transfected into 35-mm culture dishes using Lipofectamine RNAiMAX (Invitrogen). For overexpression of FLAG-tagged constructs, plasmid (2 µg) was distributed into each well along with FuGENE HD (4 μl, Roche; Switzerland). For co-transfection of MAN1 siRNA and Bmal1, Lipofectamine 2000 (Invitrogen) was used. 24 hr after transfection, cells were synchronized with 100 nM dexamethasone in serum-free DMEM containing 10 mM HEPES (pH 7.5) at 37°C for 2 hr. Following synchronization, the media were replaced with phenol red-free DMEM supplemented with 10 mM HEPES and 40 µM Luciferin-EF (Promega). Cells sealed with coverslips were incubated in a 32-channel LumiCycle (Actimetrics; Evanston, IL) to monitor real-time bioluminescence for 5 days. Data were analyzed using Lumicycle Analysis (Actimetrics).

Fly behavior experiments and analysis

To over-express NE, cryGAL4-39 and cryGAL4-16 (Emery et al., 2000) were crossed to MAN1GS2297 (Kyoto Stock Center; Japan), UASLam (Padiath et al., 2006) and LBRGS2162 (Kyoto Stock Center). To knock down NE, cryGAL4-39;UASdcr2 and UASdcr2;cryGAL4-16 were crossed to UASMAN1RNAi (3167R-1, NIG; Japan), UASLamRNAi (45,635, VDRC; Vienna) and UASLBRRNAi (KK110508, VDRC). For controls, the UAS and GAL4 lines were crossed to w1118 or yw strains. Male progenies were assayed for behavior.

Locomotor activity levels of flies were monitored using Trikinetics Activity Monitors (Waltham, MA) for 7 days of 12 hr light-12 hr dark (LD) conditions followed by 7 days of constant darkness (DD). For DD rhythmicity, chi-squared periodogram analyses were performed using Clocklab (Actimetrics). Rhythmic flies were defined as those in which the chi-squared power was ≥10 above the significance line. Period calculations also considered all flies with rhythmic power ≥10.

Quantitative real-time PCR (qRT-PCR)

RNeasy Mini Kit (Qiagen) was used to isolate total RNAs from synchronized U2OS-B6 cells that were collected at interval of 4 hr over the course of 48 hr. Purified RNA (2 µg) was applied in 20-μl reactions for RT primed with Oligo(dT)20 using Super-Script III First-Strand Synthesis System (Invitrogen). All qPCR reactions were carried out on a Rotor-Gene RG-3000 (Corbett Research; Netherland)/or 7900HT Fast Real-Time PCR System (Life technologies; Carlsbad, CA) using FastStart SYBR Green Master (Rox) (Roche). The templates were denatured at 95°C for 10 min, followed by forty cycles with 15 s at 95°C, 10 s at 58°C (Rotor-Gene) or 60 s at 60°C (HT7900 system and data acquisition at the end of this step), or 40 s at 72°C, and an additional 2 s for data acquisition (Rotor-Gene). The standard curve and delta–delta CT methods were used for quantification (Applied Biosystems; Carlsbad, CA). Primers used for expression analysis are listed in Supplementary file 1B. Primers used for ChIP assay are labeled as the nucleotide distance from the transcriptional start site (TSS) and +1 indicates the starting of TSS.

Fly heads were isolated at the indicated time points and total RNA was isolated with TRIzol reagent (Invitrogen). After the removal of contaminating genomic DNA by RQ1 DNase (Promega) digestion, total RNA was directly amplified with the QuantiTect SYBR green RT-PCR kit (QIAGEN). The following primers were used: for cyc, cyc_110.f 5′-GAGGTCTTCGTCGGAAAGG-3′ and cyc_347.r 5′-AAAGCACATGGGAATCATGG-3′; for tim, tim.f 5′-CTGGGGAGTGACCATGG-3′ and tim.r 5′-GCTGGAATCGCCACTG-3′; for dMAN1, dMAN1_148.f 5′-ATTTTGGCCTGTGACACTGC-3′ and dMAN1_303.r 5′-GAAGCCGCTCTGGATTAGC-3′; for dLam, dLam_446.f 5′-CGAGGAGCTCAAGAACAAGC-3′ and dLam_675_r. 5′-GCGACAGTGTCTCCTGTTCC-3′; for dLBR, dLBR_645.f 5′-CATTGACCACCAACACATCC-3′ and dLBR_825.r 5′-GTTATGCGTTTGCGAATGG-3′; for dActin, dActin.f1 5′-CTAACCTCGCCCTCTCCTCT-3′ and dActin.r1 5′-GCAGCCAAGTGTGAGTGTGT-3′. All other primers used for fly tissues are previously published (Lim et al., 2007; Kilman et al., 2009).

Mouse behavior experiment and analyses

Lmnb1+/Δ mice with a targeted disruption of the Lmnb1 gene (Vergnes et al., 2004) or LMNB1BAC mouse model overexpressing lamin B1 (Heng et al., 2013) was generated as previous described. The animals used here were derived from these mice and have been backcrossed to a C57BL/6J background for at least 10 generations. Wild-type littermates were used in pairs for subsequent experiments. Mice housed in light-tight, sound-attenuated cabinets were entrained to LD cycle for 14 days and then released into DD. Wheel-running activity of mice were monitored using Clocklab (Actimetrics). For DD rhythmicity, chi-squared periodogram analyses were performed using Clocklab. Experiments were approved by the Institutional Animal Care and Use Committee at University of California, San Francisco.

Western blot

Brains or livers were collected from mice that were entrained in LD cycle for 14 days and were then released into DD. Total cellular proteins were extracted from mouse brain or liver using RIPA buffer (150 mM NaCl, 1% NP-40, 0.1% SDS, 0.5% sodium deoxycholate, 20 mM Tris, pH 7.5, and 5 mM EDTA). Protein lysates from cells were prepared in SDS-PAGE loading buffer. Equal amounts of protein were resolved on 8% SDS-PAGE gels and then transferred to nitrocellulose membrane. After incubation with primary antibody at 4°C overnight, membranes were incubated with secondary antibodies at room temperature for 1 hr. The primary antibodies were anti-LBR rabbit polyclonal antibody (1:500; Abcam), anti-LMNB1 rabbit polyclonal antibody (1:1000; Abcam; England), anti-MAN1 rabbit polyclonal antibody (1:3000; from Dr Kunxin Luo) (Pan et al., 2005), anti-mPER2 rabbit polyclonal antibody (1:500; Alpha Diagnostic International; San Antonio, TX), anti-GAPDH mouse monoclonal antibody (1:5000; Chemicon; Billerica, MA), anti-BMAL1 goat polyclonal antibody (1:500; Santa Cruz; Dallas, TX), anti-CLOCK rabbit polyclonal antibody (1:1000; Santa Cruz), and anti-FLAG M2 antibody (1:5000; Sigma; St Louis, MO). The MAN1 antibody was generated by immunizing rabbits with C-terminal peptide (SHLRLRTGLTNSQGSS) of human MAN1 (1:1000; Covance and Agbio, Inc; Princeton, NJ). Secondary antibodies were conjugated either with IRDye 680 or IRDye 800 (LI-COR Biosciences; Lincoln, NE) and visualized with an Odyssey Infrared Imaging System (LI-COR Biosciences).

Luciferase assays

HEK293 cells were cultured in 24-well plates in DMEM containing 10% fetal bovine serum 24 hr prior to transient transfection with FuGENE HD (Roche) for overexpression (50–200 ng cDNA constructs), or Lipofectamine 2000 (Invitrogen) for siRNA knockdown (8–13 pmol, Invitrogen). All transfection mixtures included a Renilla luciferase plasmid (pRL-TK; 0.7 ng), as well as a reporter construct consisting of firefly luciferase driven by mouse Bmal1 or human BMAL1 promoter (50 ng). We assayed the Bmal1/BMAL1 promoter luciferase activity using the Dual-Luciferase Reporter Assay System (Promega), modifying the protocol to use 30 μl of luciferase substrate and Stop-n-Glo/substrate mix for each reaction. The luciferase activity was quantified with a TECAN GENios Pro Microplate Reader (TECAN; Switzerland) 48 hr after the initial transfection. Luciferase reporter vector used is pGL3-basic.

Chromatin immunoprecipitation (ChIP) assay

We performed ChIP assays using Millipore's EZ-ChIP assay kit (cat. # 17–371; Millipore; Billerica, MA) and protein-G sepharose. In brief, HEK293 cells were transfected with hBMAL1-luciferase (3.4 Kb) plus vector, FLAG-tagged WT or truncated DNA-binding constructs of MAN1 as indicated. Cell lysates were sonicated on ice using Branson digital sonifier #250 and 1% of cell lysate was taken as input sample. After incubation with FLAG M2 antibody (Sigma), antibody-loaded protein G agarose beads were washed with cold wash buffer six times followed by low-salt buffer, high salt wash buffer, LiCl wash buffer, and then once with TE (10 mM Tris–HCl at pH 8.0, 1 mM EDTA at pH 8.0). After washing, the beads were re-suspended in 100 μl of ChIP elution buffer supplemented with proteinase K and incubated for 2 hr at 65°C followed by 10 min at 95°C. The beads were spun down and the supernatant was saved. DNA was recovered from the spin column and resuspended in 50 μl of TE, and a 1 μl portion was used for qRT-PCR. The PCR products were analyzed by qRT-PCR and quantitated using 7900HT Fast Real-Time PCR System (Life technologies).

Statistics

Statistical analyses were performed using the unpaired Student's t test, one-way ANOVA with Newman–Keuls test, or two-way ANOVA (Prism5, GraphPad; La Jolla, CA). Data are presented as Mean ± SEM or SD. Significant differences (p < 0.05) are marked with asterisks in figures.

Acknowledgements

We thank Drs S Panda and J Hogenesch for mBmal1-luc construct; Dr T Takumi for hBMAL1-luc construct; Dr D Weaver for pcDNA3.1-Bmal1 construct; and Dr K Luo for MAN1 constructs, HA-SMAD1 construct, and MAN1 antibody.

Funding Statement

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Funding Information

This paper was supported by the following grants:

Additional information

Competing interests

LP: Reviewing editor, eLife.

The other authors declare that no competing interests exist.

Author contributions

S-TL, Conception and design, Acquisition of data, Analysis and interpretation of data, Drafting or revising the article, Contributed unpublished essential data or reagents.

LZ, Conception and design, Acquisition of data, Analysis and interpretation of data, Drafting or revising the article, Contributed unpublished essential data or reagents.

XL, Conception and design, Acquisition of data, Analysis and interpretation of data, Contributed unpublished essential data or reagents.

LCZ, Acquisition of data, Analysis and interpretation of data, Drafting or revising the article.

VEG, Acquisition of data, Analysis and interpretation of data.

C-WT, Acquisition of data, Analysis and interpretation of data.

LP, Conception and design, Analysis and interpretation of data, Drafting or revising the article, Contributed unpublished essential data or reagents.

Y-HF, Conception and design, Analysis and interpretation of data, Drafting or revising the article, Contributed unpublished essential data or reagents.

Ethics

Animal experimentation: All experiments were performed in accordance with the National Institutes of Health Guide for the Care and Use of Laboratory Animals and approved by Institutional Animal Care and Use Committee of University of California San Francisco. The protocol was approved by the Committee on the Ethics of Animal Experiments of the University of California San Francisco (AN089663-01).

Additional files

Supplementary file 1.

(A) Sequences of siRNAs used in the study. (B) qRT-PCR primer sequences for human clock genes.

DOI: http://dx.doi.org/10.7554/eLife.02981.020

elife02981s001.docx (81.3KB, docx)
DOI: 10.7554/eLife.02981.020

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eLife. 2014 Sep 2;3:e02981. doi: 10.7554/eLife.02981.021

Decision letter

Editor: Leslie C Griffith1

eLife posts the editorial decision letter and author response on a selection of the published articles (subject to the approval of the authors). An edited version of the letter sent to the authors after peer review is shown, indicating the substantive concerns or comments; minor concerns are not usually shown. Reviewers have the opportunity to discuss the decision before the letter is sent (see review process). Similarly, the author response typically shows only responses to the major concerns raised by the reviewers.

Thank you for sending your work entitled “Nuclear envelope protein MAN1 regulates clock through BMAL1” for consideration at eLife. Your article has been favorably evaluated by a Senior editor and 3 reviewers, one of whom is a member of our Board of Reviewing Editors.

The following individuals responsible for the peer review of your submission have agreed to reveal their identity: Leslie Griffith, BRE; Satchidananda Panda, reviewer.

The Reviewing editor and the other reviewers discussed their comments before we reached this decision, and the Reviewing editor has assembled the following comments to help you prepare a revised submission.

This paper provides a link between the nuclear envelope and the circadian clock and posits that the link is evolutionarily conserved, by suggesting that regulation of the clock by NE proteins, in particular MAN1, is present in both rodents and flies. The novelty of the study is high and the data are mostly clear and compelling. There are, however, a few weak links in the story which, if strengthened would make it quite compelling. The major issues are:

1) At the organismal/cellular level: The fly data generally are not completely convincing. It’s very easy to get RNAi phenotypes and a lot of times these don't map to the gene targeted. Phenotypes based on single RNAis, with no mutant data or experiments mapping the effect to the relevant gene, are not very convincing. In addition, the data in Table 1 for human LMB1 do not support what is stated in the text- there appears to be no change in period. Some genetic evidence that the RNAi phenotypes are actually due to changes in the relevant genes is required.

2) At the molecular mechanism level: The cell assay data are quite subtle. If the authors could show suppression of the long period of the NE knockdown cells (or knockout mouse fibroblasts) this would provide very strong evidence of the linkage the authors wish to make.

Reviewer #1:

This is a very interesting and novel study which suggests that NE proteins can directly modulate the circadian clock in both mammals and insects. Gene regulation by the nuclear envelope is a very new concept and connecting it to the clock is a potentially very important observation.

For the most part the data are very clear and consistent. The only piece of evidence that is less than clear is in Figure 1D. How do the authors draw the conclusion that MAN1 is cycling? It looks dead flat to me. Is there any evidence to suggest that the very small difference statistically significant? Ditto for LMNB1 and LBR. They are by eye a bit more convincing, but a quantitative treatment is required if they authors want to claim the protein cycles (which I am not sure they need to given the strength of the functional evidence- so what if the protein does not cycle in an extract of liver?).

Reviewer #2:

The manuscript demonstrates that nuclear envelope proteins contribute to the determination of circadian period. It focuses in particular on the MAN1 protein, showing that this is a positive regulator of BMAl1 transcription. Knockdown or overexpression of MAN1 or other nuclear envelope (NE) proteins, Lamin B1 and LBR, produces a small effect on circadian period in mammalian cultured cells. A more robust phenotype is seen with some of these manipulations in Drosophila although the directionality of the effect (short or long period) or the mechanism is not easily explained. Microarray studies have reported cyclic expression of nucleoporins, and not surprisingly, the authors report cyclic expression for a couple of other NE proteins. Overall, these are interesting observations although they do not quite provide a picture of how the nuclear envelope Figure in the clock mechanism. Additional comments are below:

Figure 1 should show quantification of multiple blots for PER2 cycling in the LaminB1 mutant and overexpression backgrounds (Figure 1C). Also, what happens to other clock proteins in these backgrounds?

Effects of knockdown and over-expression of NE proteins in mammalian cells are subtle. In mice heterozygous for a Lamin B1 mutation, or overexpressing LaminB1, PER2 oscillations appear to be altered, although this needs to be better documented, and is not linked to any overt rhythm. Period lengthening by overexpression of human MAN1 or LBR in Drosophila has a more robust effect, but then knockdown of MAN1 has the same effect. Given that the molecular mechanism is not known (see below for the inconclusive data regarding the effect on cyc), and mutant data are not shown (only a single RNAi for each gene, without any mapping of the RNAi effect) it is difficult to assess the significance of the fly data.

The text indicates that over-expression of human LMNB1 shortens the period in Drosophila, but this is not supported by the data in Table 1.

Given that knocking down MAN1 has no effect on cyc, the effect of overexpression could be non-physiological. Also, increased expression of cyc (through MAN1 overexpression) should not lengthen period as shown here, so it is unlikely that the effect on circadian period is going through cyc. Along the same lines, it would be good to know if the effects on circadian period in mammalian cells are going through BMal1. Does overexpression of BMal1 rescue the long period produced by knockdown of NE proteins?

Additive effects of SMAD and MAN1 suggest that they are acting independently, and not as part of the same pathway.

The studies mapping MAN1 interactions with the BMAL1 promoter are good, and indicate direct interaction.

Reviewer #3:

This manuscript offers a novel link between nuclear envelope components and circadian clock that is conserved from insects to mammals. The experiments are straightforward and well described. However, some gaps in data presentation need to be addressed.

Since the authors have access to the lamin mutant mice and flies with specific perturbation of Ne components, figure (a) showing the circadian behavior phenotype of these animals will substantially strengthen the manuscript. If the het mice lack any appreciable defect in free running circadian period, activity consolidation, phase angle of entrainment, such lack of phenotype may be explained in the discussion section. Circadian behavior phenotype of the flies should be shown in the main figures to strengthen the manuscript.

siRNA knockdown experiments on Bmal1:Luc expression should ideally have another promoter:Luc construct to rule out the possibility that the down regulation of Bmal1:luc signal is not due to general defect in nuclear integrity or overall transcription.

eLife. 2014 Sep 2;3:e02981. doi: 10.7554/eLife.02981.022

Author response

1) At the organismal/cellular level: The fly data generally are not completely convincing. It’s very easy to get RNAi phenotypes and a lot of times these don't map to the gene targeted. Phenotypes based on single RNAis, with no mutant data or experiments mapping the effect to the relevant gene, are not very convincing. In addition, the data in Table 1 for human LMB1 do not support what is stated in the text- there appears to be no change in period. Some genetic evidence that the RNAi phenotypes are actually due to changes in the relevant genes is required.

In our original submission, we showed that MAN1 mRNA level is reduced in flies expressing MAN1-RNAi. Here we have included additional data demonstrating that Lam and LBR mRNA levels are reduced in flies expressing Lam-RNAi and LBR-RNAi, respectively (Figure 2–figure supplement 2). This does not eliminate the possibility that the RNAi is also disrupting expression of other genes. However, given that we also observe circadian phenotypes when over-expressing these genes in flies, and that deficiency of these genes lead to disrupted circadian clock in the mammalian system, we believe it is highly likely that the circadian phenotypes associated with expressing RNAi constructs of MAN1/Lam/LBR in flies are due to reduction in the levels of these genes.

As for Lam over-expressing flies, the behavioral period is shorter than the GAL4 controls, which have long periods, but not shorter than UASLam control, which has a ∼24hr period. It is possible that there is a limit to how much Lam over-expression can shorten the period in flies. It may be able to shorten period to ∼24hr but cannot further shorten period to less than 24hr.

2) At the molecular mechanism level: The cell assay data are quite subtle. If the authors could show suppression of the long period of the NE knockdown cells (or knockout mouse fibroblasts) this would provide very strong evidence of the linkage the authors wish to make.

Thank you for the suggestion. We have added new data demonstrating that Bmal1 over-expression suppresses the effect of MAN1 knockdown on circadian period in U2OS cells (Figure 4–figure supplement 2).

Reviewer #1:

This is a very interesting and novel study which suggests that NE proteins can directly modulate the circadian clock in both mammals and insects. Gene regulation by the nuclear envelope is a very new concept and connecting it to the clock is a potentially very important observation.

For the most part the data are very clear and consistent. The only piece of evidence that is less than clear is in Figure 1D. How do the authors draw the conclusion that MAN1 is cycling? It looks dead flat to me. Is there any evidence to suggest that the very small difference statistically significant? Ditto for LMNB1 and LBR. They are by eye a bit more convincing, but a quantitative treatment is required if they authors want to claim the protein cycles (which I am not sure they need to given the strength of the functional evidence- so what if the protein does not cycle in an extract of liver?).

Quantification of the Western blot is shown in Figure 1D top panel. The reviewer is correct that the oscillation for MAN1 is mild. However, the subsequent functional data strengthened our original idea that MAN1 could be the link between NE and the molecular clock.

Reviewer #2:

The manuscript demonstrates that nuclear envelope proteins contribute to the determination of circadian period. It focuses in particular on the MAN1 protein, showing that this is a positive regulator of BMAl1 transcription. Knockdown or overexpression of MAN1 or other nuclear envelope (NE) proteins, Lamin B1 and LBR, produces a small effect on circadian period in mammalian cultured cells. A more robust phenotype is seen with some of these manipulations in Drosophila although the directionality of the effect (short or long period) or the mechanism is not easily explained. Microarray studies have reported cyclic expression of nucleoporins, and not surprisingly, the authors report cyclic expression for a couple of other NE proteins. Overall, these are interesting observations although they do not quite provide a picture of how the nuclear envelope Figure in the clock mechanism. Additional comments are below:

Figure 1 should show quantification of multiple blots for PER2 cycling in the LaminB1 mutant and overexpression backgrounds (Figure 1C). Also, what happens to other clock proteins in these backgrounds?

We have included quantification of PER2 Western in Figure 1C. We did not examine other clock proteins at the time of experimentation and thought that PER2 was the most logical representative clock protein for us to test. Unfortunately, the tissue samples were lost in a freezer breakdown in the lab and the mouse lines have been cryopreserved. Although we would like to examine the other clock proteins as well, it would take tremendous amount of time and effort to re-derive these animals and perform the experiments

Effects of knockdown and over-expression of NE proteins in mammalian cells are subtle. In mice heterozygous for a Lamin B1 mutation, or overexpressing LaminB1, PER2 oscillations appear to be altered, although this needs to be better documented, and is not linked to any overt rhythm.

From the Western blot in Figure 1C, the peak PER2 oscillation time for heterozygous Lmnb1 is CT 0 vs CT 20 for WT, and the peak time for LMNBBAC is clearly CT 16. Either way, there is a 4 hr phase shift compared to control. Although we did not show the same shift in wheel-running rhythm, we reason that this may be due to the resilience of the SCN clock to perturbations. Therefore we can only observe alterations in peripheral clocks. It is also possible that other molecular changes in addition to PER2 can somehow neutralize the behavior rhythm. We have added this discussion in the text.

Period lengthening by overexpression of human MAN1 or LBR in Drosophila has a more robust effect, but then knockdown of MAN1 has the same effect. Given that the molecular mechanism is not known (see below for the inconclusive data regarding the effect on cyc), and mutant data are not shown (only a single RNAi for each gene, without any mapping of the RNAi effect) it is difficult to assess the significance of the fly data.

Please see point 1 (General) above. As addressed earlier, we have added additional data validating that Lam and LBR are knocked down by RNAi. It is true that not all changes are consistent between mammals and fly, and there is still need for future investigation to understand the differences between these two systems. We have added discussion in the text regarding this point.

The text indicates that over-expression of human LMNB1 shortens the period in Drosophila, but this is not supported by the data in Table 1.

We apologize for not making this clear in the original submission. When comparing cryGAL-39/UASLam to cryGAL4-39/+, or UASLam/+;cryGAL4-16/+ to cryGAL4-16/+, there are shortened periods. We have modified the text to clarify this.

Given that knocking down MAN1 has no effect on cyc, the effect of overexpression could be non-physiological. Also, increased expression of cyc (through MAN1 overexpression) should not lengthen period as shown here, so it is unlikely that the effect on circadian period is going through cyc.

We agree that over-expression of MAN1 in flies drives MAN1 much higher than the endogenous level, which may be “non-physiological”, but regardless, it demonstrates in this in vivo system, that increasing MAN1 results in increased cyc expression, consistent with what we demonstrate in cell culture, i.e. increasing MAN1 leads to increased Bmal1 expression. We were not able to demonstrate that knocking down MAN1 reduces cyc in vivo as we showed for Bmal1 in vitro, but we believe this is probably because in vivo knockdown is not as efficient as in vitro, and/or that the in vivo system is more resilient to perturbations compared to in vitro. Thus we do believe that Bmal1/cyc is a target of MAN1 in the clock, although it may not be the only target. When MAN1 is over-expressed in flies, the period is lengthened and cyc appears to be the clock gene that exhibits the largest changes, leading us to suspect that under the condition of MAN1 over-expression, cyc is the primary target of MAN1 in the clock. However, it is certainly possible that MAN1 is also targeting other clock genes. When MAN1 is knocked down in flies, cyc is not affected while period is still lengthened, suggesting that under MAN1 deficient condition, some other clock genes are altered which contribute to the period phenotype. Therefore, we can only draw the conclusion that in MAN1 knock-down flies, the period phenotype is not going through cyc, but we cannot draw the same conclusion for MAN1 over-expressing flies.

Along the same lines, it would be good to know if the effects on circadian period in mammalian cells are going through BMal1. Does overexpression of BMal1 rescue the long period produced by knockdown of NE proteins?

Thank you for the suggestion. As mentioned above in point 2 (General), we have included new data to address this question (Figure 4–figure supplement 2).

Additive effects of SMAD and MAN1 suggest that they are acting independently, and not as part of the same pathway.

We agree with the reviewer that this would seem to be the case at first. However, since MAN1’s enhancing effect on BMAL1 requires its RRM domain which is the SMAD interacting domain and the only SMAD that has effect on BMAL1 is SMAD2. For these reasons, MAN1 and SMAD2 may not be acting completely independently.

The studies mapping MAN1 interactions with the BMAL1 promoter are good, and indicate direct interaction.

Reviewer #3:

This manuscript offers a novel link between nuclear envelope components and circadian clock that is conserved from insects to mammals. The experiments are straightforward and well described. However, some gaps in data presentation need to be addressed.

Since the authors have access to the lamin mutant mice and flies with specific perturbation of Ne components, figure (a) showing the circadian behavior phenotype of these animals will substantially strengthen the manuscript. If the het mice lack any appreciable defect in free running circadian period, activity consolidation, phase angle of entrainment, such lack of phenotype may be explained in the discussion section.

Neither Lamin b1 heterozygous mutant nor Lamin B1 over-expressing mice show altered wheel-running rhythms (Figure 1–figure supplement 1). We have included these data along with relevant discussion in the revised manuscript.

Circadian behavior phenotype of the flies should be shown in the main figures to strengthen the manuscript.

We have added a new figure to demonstrate the behavioral profiles of flies with NE over-expressed or knocked-down (Figure 2–figure supplement 1).

siRNA knockdown experiments on Bmal1:Luc expression should ideally have another promoter:Luc construct to rule out the possibility that the down regulation of Bmal1:luc signal is not due to general defect in nuclear integrity or overall transcription.

For in vitro transcription assay, Renilla-luc was always used as internal control. Since Renilla-luc was not affected by siRNA, we believe that the effect we observed for Bmal-luc is not due to the general defect in nuclear integrity or overall transcription. In addition, the new data of Bmal1 overexpression rescuing the period change in U2OS cells further demonstrates that the down regulation of Bmal1:luc signal is not due to general defect in nuclear integrity or overall transcription.

Associated Data

    This section collects any data citations, data availability statements, or supplementary materials included in this article.

    Supplementary Materials

    Supplementary file 1.

    (A) Sequences of siRNAs used in the study. (B) qRT-PCR primer sequences for human clock genes.

    DOI: http://dx.doi.org/10.7554/eLife.02981.020

    elife02981s001.docx (81.3KB, docx)
    DOI: 10.7554/eLife.02981.020

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