Landes Highlights

New intrinsic RNA cleavage activity by multisubunit RNA polymerases

Pavel Čabart, Huiyan Jin, Liangtao Li, Craig D Kaplan

In addition to RNA synthesis, multisubunit RNA polymerases (msRNAPs) support enzymatic reactions such as intrinsic transcript cleavage. msRNAP active sites from different species appear to exhibit differential intrinsic transcript cleavage efficiency and have likely evolved to allow fine-tuning of the transcription process. A recent study by Dr Craig Kaplan and colleagues shows that a single amino-acid substitution in the trigger loop (TL) of Saccharomyces RNA polymerase II (Pol II, Rpb1 H1085Y), engenders a gain of intrinsic cleavage activity where the substituted tyrosine appears to participate in acid-base chemistry at alkaline pH for both intrinsic cleavage and nucleotidyl transfer. The researchers extensively characterized this TL substitution for each of these reactions by examining the responses of Pol II enzymes to catalytic metals, altered pH, and factor inputs. They demonstrated that transcrption factor II F (TFIIF) stimulation of the first phosphodiester bond formation by Pol II requires wild type TL function and that H1085Y substitution within the TL compromises or alters Pol II responsiveness to both transcription factor II B (TFIIB) and TFIIF. Finally, Mn2+ stimulation of H1085Y Pol II revealed possible allosteric effects of TFIIB on the active center and cooperation between TFIIB and TFIIF. The origin of a new activity in an otherwise highly constrained and conserved enzymatic active site nicely illustrates the possibility for unexpected changes providing raw material for the diversification of enzyme families. Taken together, this work extends the paradigm of the TL being a highly flexible and dynamic element central to multiple facets of msRNAP transcription.¹ (Fig. 1)

Figure 1. Čabart et al.

https://www.landesbioscience.com/journals/transcription/article/28869/

How Pol II CTD phosphorylation regulates transcription elongation

Elizabeth A Bowman, William Kelly

The eukaryote RNA polymerase II (Pol II) holoenzyme is a 12-subunit complex that transcribes protein coding genes and many non-coding RNA genes. Pol II activity is tightly regulated at three distinct phases: (1) initiation, which includes transcription start site selection, formation of the open complex, and production of the first few phosphodiester bonds in the RNA transcript; (2) elongation, or progression of RNA polymerase through a locus as it lengthens the RNA transcript; and (3) termination, or the release of polymerase when it reaches the end of the gene being transcribed. The transition between initiation and productive elongation during Pol II transcription is a well-appreciated point of regulation across many eukaryotes. Elongating Pol II is modified by phosphorylation of serine 2 (Ser2) on its carboxy terminal domain (CTD) by two kinases, Bur1/Ctk1 in yeast and Cdk9/Cdk12 in metazoans. A recent review by Drs Bowman and Kelly discusses the roles and regulation of these kinases and their relationship to Pol II elongation control. They focus on recent data from work in C. elegans that point out gaps in our current understanding of transcription elongation. Species-specific differences in Pol II regulation have been uncovered, and it is also becoming clear that differences in Ser2 phosphorylation can exist within a species as tissue-specific regulation. Thus, it will be important for future studies to begin to dissect mechanisms of Pol II elongation in distinct tissues.² (Fig. 2)

Figure 2. Bowman et al.

https://www.landesbioscience.com/journals/nucleus/article/29347/

Discovery of a lncRNA regulating autophagy

Di Ge, Lei Han, ShuYa Huang, Nan Peng, PengChong Wang, Zheng Jiang, Jing Zhao, Le Su, ShangLi Zhang, Yun Zhang, HsiangFu Kung, BaoXiang Zhao, JunYing Miao

MTOR (mechanistic target of rapamycin) controls many cellular processes, inluding apoptosis, autophagy, translation, energy metabolism and inflammation. MTOR is also involved in cancer and cardiovascular and neurological diseases. Modulating the MTOR signaling balance could thus be of great significance for numerous diseases. Since no chemical activators of MTOR have been found, the urgent challenge is to find novel MTOR downstream components. In previous studies, the small molecule, 3-benzyl-5-((2-nitrophenoxy) methyl)–dihydrofuran-2(3H)-one (3BDO) was shown to inhibit autophagy in human umbilical vein endothelial cells (HUVECs) and neuronal cells. In a new study, this same molecule was found to activate MTOR by targeting FKBP1A (FK506-binding protein 1A). The researchers, led by Drs Zhao and Miao, used 3BDO to detect novel factors downstream of the MTOR signaling pathway. Activation of MTOR by 3BDO increased the phosphorylation of TIA1 (TIA1 cytotoxic granule-associated RNA binding protein/T-cell-restricted intracellular antigen-1). By using several different techniques and methods, the authors could show that 3BDO could greatly decrease the level of a long noncoding RNA (lncRNA) derived from the 3‘ untranslated region of TGFB2 (transforming growth factor β2). The lncRNA is known as FLJ11812. TIA1 was found to be responsible for processing FLJ11812. Further experiments showed that the lncRNA FLJ11812 could bind the microRNA MIR4459, which is known to target ATG13 (autophagy-regulated 13). ATG13 protein levels were decreased along with 3BDO-decreased FLJ11812 levels. Taken together, this new study describes the lncRNA FLJ11812 as a new activator of MTOR, and highlights its role in autophagy.³ (Fig. 3)

Figure 3. Ge et al.

https://www.landesbioscience.com/journals/autophagy/article/28363/

MicroRNAs were initially formed from transposable element sequences

Justin T Roberts, Sara E Cardin, Glen M Borchert

MicroRNAs (miRNAs) are a recently discovered class of noncoding RNAs, known to play key roles in the regulation of gene expression. Despite being only ~20 nucleotides in length, these highly versatile molecules have been shown to be involved in diverse cellular processes such as development, basic cellular metabolism, apoptosis, and disease. Since miRNAs were first discovered in mammals in 2001, over 24,000 miRNAs have been characterized. However, the functions of the majority of these miRNAs remain largely undescribed. Several recent studies have suggested that characterization of the relationships between miRNAs and transposable elements (TEs) can help elucidate miRNA functionality. They have reported the initial formation of thousands of miRNA loci from TE sequences. In a recent review, Dr Glen Borchert and colleagues chronicle the findings of these reports, discuss the evolution of the field along with future directions, and examine how this information can be used to ascertain insights into miRNA transcriptional regulation. The author also speculate how this knowledge can be exploited to facilitate miRNA target prediction.⁴ (Fig. 4)

Figure 4. Roberts et al.

https://www.landesbioscience.com/journals/mge/article/29255/