Table 2.
LncRNAs known to interact with human chromatin remodeling complexes
| lncRNA (name UCSC) | Binding to | Type of lncRNA | Action | Refs. |
|---|---|---|---|---|
| SWI/SNF subunits (Histone dimer/nucleosome removal, nucleosome sliding) | ||||
| Evf2 (DLX6-AS1) | SMARCA4 | Antisense of DLX6 | Competing with transcription factor DLX1 for binding to BRG1 | [138] |
| UCA1 | SMARCA4 | Intergenic | Prevents binding to p21 promoter UCA1 expression regulated by ARID1A | [139, 140]$ |
| TUG1 | SMARCA4 | Intergenic, sharing promoter with MORC2 | Inhibiting BRG1 degradation (MORC2 has PARP1-mediated ATPase and chromatin remodeling activities important in the DNA-damage response [141]). | [142] |
| Myheart (Mhrt) | SMARCA4 | Antisense of MYH7 | Binding to BRG1 prevents DNA binding of SWI/SNF complex | [143] |
| CPS1‐IT1 | SMARCA4 | Intronic of CPS1 gene | Prevents binding to Cyr61 promoter region | [144]$ |
| NEAT1 | SMARCA2, SMARCA4 | Intergenic | Facilitates the organization of paraspeckle proteins (independent of SMARCA catalytic activity) | [145] |
| MALAT1 | SMARCA4 | intergenic | Complex with HDAC9 that represses vascular smooth muscle cell genes | [146] |
| LincRNA Cox2 | SMARCA4 | Antisense | Recruiting the SWI/SNF complex to inflammatory-response genes, e.g., Saa3 and Ccl5 | [147] |
| IL-7–AS | p300/SMARCA4 | Antisense | Recruiting HAT p300 followed by recruitment of SWI/SNF complex to activate inflammatory genes, (e.g., CCL2, CCL5, and IL-6) | [148] |
| LncFZD6 (BAALC-AS1) | SMARCA4 | Antisense, sharing promoter with FZD6 | Recruits SWI/SNF complex to FZD6 promoter, | [149]$ |
| lncTCF7 | SMARCA4 | antisense | Recruiting the SWI/SNF complex to the TCF7 promoter | [143] |
| lncBRM | SMARCA2 | Antisense | Associates with BRM and favors assembly of BRG1- BAF complexes in liver cancer stem cells | [18]$ |
| SWINGN (LINC00565/LINC00452) | SMARCB1 | Intergenic, sharing promoter with GAS6 | Transcriptional activation of several genes (e.g., GAS6, PDGFRB and COL1A1). | [17]$ |
| HOTAIR | SMARCB1, ARID1A | Intergenic, sharing promoter of HOXC11 | Affecting expression of transcriptional repressor gene SNAIL | [150]$ |
| MVIH (AK094613) | ARID1A | Intragenic, overlapping RPS24 exons | Affects CDKN1A transcription | [151]$ |
| DGCR5 | ARID1A | Intergenic | Promotes p21 expression | [152]$ |
| LINC00163 | ARID1A | Intergenic | Stimulation of TCF21 expression | [153]$ |
| uc.291* | ACTL6A | Intragenic at LRMDA gene | Prevents inhibition by ACTL6A on epidermal differentiation genes | [19] |
| CDKN2B-AS1 | BCL11A | Antisense | Inhibition of MAP4K1 | [20] |
| uc.57* | BCL11A | Intergenic upstream of BCL11A | Inhibition of PI3K/AKT and MAPK signaling pathways | [21]$ |
| Xist | SWI/SNF | Intergenic | Binding to SWI/SNF complex inhibits binding to Xi-genes regions | [154] |
| MANTIS | DNA | Intragenic, ANXA4 gene | Preventing SWI/SNF complex binding at ICAM-1 promoter region | [155] |
| SChLAP1 | DNA | intergenic | SMARCA4 associates frequently with primary transcripts including SChLAP1, preventing SWI/SNF complex binding | [16, 102, 156]$ |
| CASC15 | miR-221 | Intergenic | ceRNA ARID1A | [23]$ |
| DLEU1 | miR-490-3p | Intergenic sharing promoter of DLEU2 | ceRNA CDK1, CCND1 and SMARCD1 | [24]$ |
| INO80/SWR1 subunits (nucleosome replacement) | ||||
| LCTS5 (AC008610.1) | INO80 | Intergenic | Binding to INO80 inhibits binding to enhancer regions near lung cancer associated genes. | [31] |
| HAND2‐AS1 (lncHand2) | INO80 | Antisense, sharing promoter with SCRG1 | Recruiting the INO80 complex to e.g. the BMP-R1A and Nkx1-2 promoter | [32, 33]$ |
| ANRIL | YY1 | Antisense in INK4 Locus | Recruitment of YY1 to promoter loci of IL6 and IL8 | [34] |
| Linc-YY1 | YY1 | Intragenic of YY | evict YY1/Polycomb repressive complex (PRC2) from target promoters | [35] |
| lncAKHE (AK056594) | YEATS4 | Intragenic of TRIM55 | activation of NOTCH2 signaling in hepatocellular carcinoma | [36]$ |
| DRAIC | UCHL5 | Intergenic | Promotes NFRKB (INO80G) ubiquitination-mediated degradation | [37]$ |
| CASC7 | miR-21 | Intergenic (in between CHRAC1-Ago2) | ceRNA ING3 | [41]$ |
| RNCR3 (LINC00599) | miR-185-5p | Intergenic | ceRNA BRD8 | [40]$ |
| TUG1 | miR-145 and YY1 | Intergenic, sharing promoter with MORC2 | Interference PRC2 complex | [157]$ |
| CR933609 | miRNA-5096 | Overlapping INO80D 3’UTR | ceRNA INO80D | [39]$ |
| SPAG5-AS1 | miR-769-5p | Antisense | ceRNA YY1 | [42] |
| HOTAIR | miR-1, miR-206 | Intergenic, sharing promoter of HOXC11 | ceRNA YY1 | [43]$ |
| LINC00899 | miR-744-3p | Intergenic | ceRNA YY1 | [44]$ |
| LINC00668 | miR-532-5p | Intergenic | ceRNA YY1 | [45]$ |
| Linc01134 | miR-324-5p | Intergenic | ceRNA IGF2BP1, increased stability YY1 expression | [158]$ |
| LncKdm2b (KDM2B-DT) | SRCAP | Antisense to Kdm2b | SRCAP complex recruitment to Zbtb3 gene, activating expression of this transcription factor | [59] |
| ISWI (nucleosome spacing, DNA repair) | ||||
| LncKdm2b (KDM2B-DT) | SATB1-ISWI | Antisense to Kdm2b | NURF complex directed to Zfp292 promoter via recruitment of chromatin organizer SATB1 (also capable of recruiting SWI/SNF complexes) | [58] |
| NMR (LINC01672) | BPTF | Intergenic | NURF complex recruitment promoting ERK1/2 signaling pathway | [60]$ |
| DLEU1 | SMARCA1 | Intergenic sharing promoter of DLEU2 | NURF complex recruitment activating of KPNA3 | [61]$ |
| NEXN-AS1 | BAZ1A | Antisense | Upregulation of NEXN expression, which is associated with atherosclerosis-related diseases | [62] |
| Lnc pRNA | BAZ2A | At intergenic spacer (IGS) sequences separating rDNA regions | Establishment of heterochromatin at ribosomal RNA genes (repression) e.g. RNA45SN2 (45S pre-rRNA) | [63, 159] |
| Paupar | TRIM28 | Intragenic of PAX6-AS1 | promotes KAP1 (H3K9me3 deposition) recruitment at a subset of distal targets, through formation Paupar-KAP1-PAX6 complex | [64] |
| BlackMamba (–) | HELLS | Intergenic upstream of KCNMA1 | Gene expression (e.g., RGS1, CCL17, CCL22, PAK2, and KCNMA1) in anaplastic large cell lymphoma | [65]$ |
| FGD5-AS1 | miR-302e | Antisense | ceRNA CDCA7 | [66]$ |
| CHD (chromodomain helicase DNA-binding, DNA repair; NuRD, histone deacetylation/demethylase complex) | ||||
| CHASERR (LINC01578) | CHD2 | Intergenic, upstream of CHD2 | Transcriptional interference between Chaserr and CHD2 results in negative feedback loop | [87] |
| MATN1-AS1 | miR-200b/c/429 | Antisense | ceRNA CHD1 | [91]$ |
| LINC01410 | miR-23c | Intergenic | ceRNA CHD7 | [92]$ |
| ANRIL | miR-34a | Antisense in INK4 Locus | ceRNA HDAC1 | [93]$ |
| SNHG15 | miR-490-3p | miRNA host gene | ceRNA HDAC2 | [94]$ |
| ARAP1-AS1 | miR-2110 | antisense | ceRNA HDAC2 | [95]$ |
| HOTAIR | miR-326 | Intergenic, sharing promoter of HOXC11 | ceRNA MTA2 | [96]$ |
*UltraConserved elements gene location at https://genome-test.gi.ucsc.edu/~hiram/hubs/GillBejerano/hg19/hg19.ultraConserved.bb. $Studies showing the role of lncRNA chromatin remodeling in cancer