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https://www.readbyqxmd.com/read/28446598/the-histone-variant-h2a-z-promotes-efficient-cotranscriptional-splicing-in-s-cerevisiae
#1
Lauren T Neves, Stephen Douglass, Roberto Spreafico, Srivats Venkataramanan, Tracy L Kress, Tracy L Johnson
In eukaryotes, a dynamic ribonucleic protein machine known as the spliceosome catalyzes the removal of introns from premessenger RNA (pre-mRNA). Recent studies show the processes of RNA synthesis and RNA processing to be spatio-temporally coordinated, indicating that RNA splicing takes place in the context of chromatin. H2A.Z is a highly conserved histone variant of the canonical histone H2A. In Saccharomyces cerevisiae, H2A.Z is deposited into chromatin by the SWR-C complex, is found near the 5' ends of protein-coding genes, and has been implicated in transcription regulation...
April 1, 2017: Genes & Development
https://www.readbyqxmd.com/read/28446597/the-histone-variant-h2a-z-promotes-splicing-of-weak-introns
#2
Kelly E Nissen, Christina M Homer, Colm J Ryan, Michael Shales, Nevan J Krogan, Kristin L Patrick, Christine Guthrie
Multiple lines of evidence implicate chromatin in the regulation of premessenger RNA (pre-mRNA) splicing. However, the influence of chromatin factors on cotranscriptional splice site usage remains unclear. Here we investigated the function of the highly conserved histone variant H2A.Z in pre-mRNA splicing using the intron-rich model yeast Schizosaccharomyces pombe Using epistatic miniarray profiles (EMAPs) to survey the genetic interaction landscape of the Swr1 nucleosome remodeling complex, which deposits H2A...
April 1, 2017: Genes & Development
https://www.readbyqxmd.com/read/28423325/rapid-genome-wide-recruitment-of-rna-polymerase-ii-drives-transcription-splicing-and-translation-events-during-t-cell-responses
#3
Kathrin Davari, Johannes Lichti, Christian Gallus, Franziska Greulich, N Henriette Uhlenhaut, Matthias Heinig, Caroline C Friedel, Elke Glasmacher
Activation of immune cells results in rapid functional changes, but how such fast changes are accomplished remains enigmatic. By combining time courses of 4sU-seq, RNA-seq, ribosome profiling (RP), and RNA polymerase II (RNA Pol II) ChIP-seq during T cell activation, we illustrate genome-wide temporal dynamics for ∼10,000 genes. This approach reveals not only immediate-early and posttranscriptionally regulated genes but also coupled changes in transcription and translation for >90% of genes. Recruitment, rather than release of paused RNA Pol II, primarily mediates transcriptional changes...
April 18, 2017: Cell Reports
https://www.readbyqxmd.com/read/28399446/enzyme-mediated-tagging-of-rna
#4
REVIEW
Lea Anhäuser, Andrea Rentmeister
RNA molecules can play diverse roles in the cell owing to their secondary structure dynamics and various binding modes. Studying localization and dynamics of RNA in vitro or in cells requires tagging with suitable reporter molecules-fluorophores being the most prominent ones. Enzymatic RNA labeling approaches are currently emerging as valuable alternatives to purely chemical synthesis and to binding- or hybridization-based RNA-imaging approaches. Different classes of enzymes allow for cotranscriptional or posttranscriptional installation of small functional groups in RNA...
April 8, 2017: Current Opinion in Biotechnology
https://www.readbyqxmd.com/read/28398514/distributed-biotin-streptavidin-transcription-roadblocks-for-mapping-cotranscriptional-rna-folding
#5
Eric J Strobel, Kyle E Watters, Yuri Nedialkov, Irina Artsimovitch, Julius B Lucks
RNA folding during transcription directs an order of folding that can determine RNA structure and function. However, the experimental study of cotranscriptional RNA folding has been limited by the lack of easily approachable methods that can interrogate nascent RNA structure at nucleotide resolution. To address this, we previously developed cotranscriptional selective 2΄-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq) to simultaneously probe all intermediate RNA transcripts during transcription by stalling elongation complexes at catalytically dead EcoRIE111Q roadblocks...
April 8, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28301768/theory-and-modeling-of-rna-structure-and-interactions-with-metal-ions-and-small-molecules
#6
Li-Zhen Sun, Dong Zhang, Shi-Jie Chen
In addition to continuous rapid progress in RNA structure determination, probing, and biophysical studies, the past decade has seen remarkable advances in the development of a new generation of RNA folding theories and models. In this article, we review RNA structure prediction models and models for ion-RNA and ligand-RNA interactions. These new models are becoming increasingly important for a mechanistic understanding of RNA function and quantitative design of RNA nanotechnology. We focus on new methods for physics-based, knowledge-based, and experimental data-directed modeling for RNA structures and explore the new theories for the predictions of metal ion and ligand binding sites and metal iondependent RNA stabilities...
March 15, 2017: Annual Review of Biophysics
https://www.readbyqxmd.com/read/28283057/super-enhancer-mediated-rna-processing-revealed-by-integrative-microrna-network-analysis
#7
Hiroshi I Suzuki, Richard A Young, Phillip A Sharp
Super-enhancers are an emerging subclass of regulatory regions controlling cell identity and disease genes. However, their biological function and impact on miRNA networks are unclear. Here, we report that super-enhancers drive the biogenesis of master miRNAs crucial for cell identity by enhancing both transcription and Drosha/DGCR8-mediated primary miRNA (pri-miRNA) processing. Super-enhancers, together with broad H3K4me3 domains, shape a tissue-specific and evolutionarily conserved atlas of miRNA expression and function...
March 9, 2017: Cell
https://www.readbyqxmd.com/read/28148777/sabotaging-of-the-oxidative-stress-response-by-an-oncogenic-noncoding-rna
#8
Nitin Mahajan, Hua-Jun Wu, Richard L Bennett, Catalina Troche, Jonathan D Licht, Jason D Weber, Leonard B Maggi, Michael H Tomasson
Overexpression of the multiple myeloma set domain (MMSET) Wolf-Hirschhorn syndrome candidate 1 gene, which contains an orphan box H/ACA class small nucleolar RNA, ACA11, in an intron, is associated with several cancer types, including multiple myeloma (MM). ACA11 and MMSET are overexpressed cotranscriptionally as a result of the t(4;14) chromosomal translocation in a subset of patients with MM. RNA sequencing of CD138(+) tumor cells from t(4;14)-positive and -negative MM patient bone marrow samples revealed an enhanced oxidative phosphorylation mRNA signature...
February 2017: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
https://www.readbyqxmd.com/read/28071751/transcriptional-pausing-at-the-translation-start-site-operates-as-a-critical-checkpoint-for-riboswitch-regulation
#9
Adrien Chauvier, Frédéric Picard-Jean, Jean-Christophe Berger-Dancause, Laurène Bastet, Mohammad Reza Naghdi, Audrey Dubé, Pierre Turcotte, Jonathan Perreault, Daniel A Lafontaine
On the basis of nascent transcript sequencing, it has been postulated but never demonstrated that transcriptional pausing at translation start sites is important for gene regulation. Here we show that the Escherichia coli thiamin pyrophosphate (TPP) thiC riboswitch contains a regulatory pause site in the translation initiation region that acts as a checkpoint for thiC expression. By biochemically probing nascent transcription complexes halted at defined positions, we find a narrow transcriptional window for metabolite binding, in which the downstream boundary is delimited by the checkpoint...
January 10, 2017: Nature Communications
https://www.readbyqxmd.com/read/28031484/identification-of-nad-capped-mrnas-in-saccharomyces-cerevisiae
#10
Robert W Walters, Tyler Matheny, Laura S Mizoue, Bhalchandra S Rao, Denise Muhlrad, Roy Parker
RNAs besides tRNA and rRNA contain chemical modifications, including the recently described 5' nicotinamide-adenine dinucleotide (NAD(+)) RNA in bacteria. Whether 5' NAD-RNA exists in eukaryotes remains unknown. We demonstrate that 5' NAD-RNA is found on subsets of nuclear and mitochondrial encoded mRNAs in Saccharomyces cerevisiae NAD-mRNA appears to be produced cotranscriptionally because NAD-RNA is also found on pre-mRNAs, and only on mitochondrial transcripts that are not 5' end processed. These results define an additional 5' RNA cap structure in eukaryotes and raise the possibility that this 5' NAD(+) cap could modulate RNA stability and translation on specific subclasses of mRNAs...
January 17, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27999816/evidence-for-altered-canonical-wnt-signaling-in-the-trabecular-bone-of-elderly-postmenopausal-women-with-fragility-femoral-fracture
#11
Simona Bolamperti, Isabella Villa, Alice Spinello, Greta Manfredini, Emanuela Mrak, Umberto Mezzadri, Marco Ometti, Gianfranco Fraschini, Francesca Guidobono, Alessandro Rubinacci
Wnt signaling, a major regulator of bone formation and homeostasis, might be involved in the bone loss of osteoporotic patients and the consequent impaired response to fracture. Therefore we analyzed Wnt-related, osteogenic, and adipogenic genes in bone tissue of elderly postmenopausal women undergoing hip replacement for either femoral fracture or osteoarthritis. Bone specimens derived from the intertrochanteric region of the femurs of 25 women with fracture (F) and 29 with osteoarthritis without fracture (OA) were analyzed...
2016: BioMed Research International
https://www.readbyqxmd.com/read/27965595/cutting-a-long-intron-short-recursive-splicing-and-its-implications
#12
Theodore Georgomanolis, Konstantinos Sofiadis, Argyris Papantonis
Over time eukaryotic genomes have evolved to host genes carrying multiple exons separated by increasingly larger intronic, mostly non-protein-coding, sequences. Initially, little attention was paid to these intronic sequences, as they were considered not to contain regulatory information. However, advances in molecular biology, sequencing, and computational tools uncovered that numerous segments within these genomic elements do contribute to the regulation of gene expression. Introns are differentially removed in a cell type-specific manner to produce a range of alternatively-spliced transcripts, and many span tens to hundreds of kilobases...
2016: Frontiers in Physiology
https://www.readbyqxmd.com/read/27927177/initiator-trna-genes-template-the-3-cca-end-at-high-frequencies-in-bacteria
#13
David H Ardell, Ya-Ming Hou
BACKGROUND: While the CCA sequence at the mature 3' end of tRNAs is conserved and critical for translational function, a genetic template for this sequence is not always contained in tRNA genes. In eukaryotes and Archaea, the CCA ends of tRNAs are synthesized post-transcriptionally by CCA-adding enzymes. In Bacteria, tRNA genes template CCA sporadically. RESULTS: In order to understand the variation in how prokaryotic tRNA genes template CCA, we re-annotated tRNA genes in tRNAdb-CE database version 0...
December 8, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27856616/antisense-transcription-licenses-nascent-transcripts-to-mediate-transcriptional-gene-silencing
#14
Yunkun Dang, Jiasen Cheng, Xianyun Sun, Zhipeng Zhou, Yi Liu
In eukaryotes, antisense transcription can regulate sense transcription by induction of epigenetic modifications. We showed previously that antisense transcription triggers Dicer-independent siRNA (disiRNA) production and disiRNA locus DNA methylation (DLDM) in Neurospora crassa Here we show that the conserved exonuclease ERI-1 (enhanced RNAi-1) is a critical component in this process. Antisense transcription and ERI-1 binding to target RNAs are necessary and sufficient to trigger DLDM. Convergent transcription causes stalling of RNA polymerase II during transcription, which permits ERI-1 to bind nascent RNAs in the nucleus and recruit a histone methyltransferase complex that catalyzes chromatin modifications...
November 1, 2016: Genes & Development
https://www.readbyqxmd.com/read/27798597/cotranscriptional-folding-of-a-riboswitch-at-nucleotide-resolution
#15
Kyle E Watters, Eric J Strobel, Angela M Yu, John T Lis, Julius B Lucks
RNAs can begin to fold immediately as they emerge from RNA polymerase. During cotranscriptional folding, interactions between nascent RNAs and ligands are able to direct the formation of alternative RNA structures, a feature exploited by noncoding RNAs called riboswitches to make gene-regulatory decisions. Despite their importance, cotranscriptional folding pathways have yet to be uncovered with sufficient resolution to reveal how cotranscriptional folding governs RNA structure and function. To access cotranscriptional folding at nucleotide resolution, we extended selective 2'-hydroxyl acylation analyzed by primer-extension sequencing (SHAPE-seq) to measure structural information of nascent RNAs during transcription...
December 2016: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/27779655/human-telomerase-reverse-transcriptase-regulation-by-dna-methylation-transcription-factor-binding-and-alternative-splicing-review
#16
REVIEW
Brittany A Avin, Christopher B Umbricht, Martha A Zeiger
The catalytic subunit of telomerase, human telomerase reverse transcriptase (hTERT), plays an essential role in telomere maintenance to oppose cellular senescence and, is highly regulated in normal and cancerous cells. Regulation of hTERT occurs through multiple avenues, including a unique pattern of CpG promoter methylation and alternative splicing. Promoter methylation affects the binding of transcription factors, resulting in changes in expression of the gene. In addition to expression level changes, changes in promoter binding can affect alternative splicing in a cotranscriptional manner...
December 2016: International Journal of Oncology
https://www.readbyqxmd.com/read/27605205/the-pol-ii-ctd-new-twists-in-the-tail
#17
REVIEW
Justyna Zaborowska, Sylvain Egloff, Shona Murphy
The C-terminal domain (CTD) of the large subunit of RNA polymerase (pol) II comprises conserved heptad repeats, and post-translational modification of the CTD regulates transcription and cotranscriptional RNA processing. Recently, the spatial patterns of modification of the CTD repeats have been investigated, and new functions of CTD modification have been revealed. In addition, there are new insights into the roles of the enzymes that decorate the CTD. We review these new findings and reassess the role of the pol II CTD in the regulation of gene expression...
September 6, 2016: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/27601672/structural-mechanism-for-the-recognition-and-ubiquitination-of-a-single-nucleosome-residue-by-rad6-bre1
#18
Laura D Gallego, Medini Ghodgaonkar Steger, Anton A Polyansky, Tobias Schubert, Bojan Zagrovic, Ning Zheng, Tim Clausen, Franz Herzog, Alwin Köhler
Cotranscriptional ubiquitination of histone H2B is key to gene regulation. The yeast E3 ubiquitin ligase Bre1 (human RNF20/40) pairs with the E2 ubiquitin conjugating enzyme Rad6 to monoubiquitinate H2B at Lys123. How this single lysine residue on the nucleosome core particle (NCP) is targeted by the Rad6-Bre1 machinery is unknown. Using chemical cross-linking and mass spectrometry, we identified the functional interfaces of Rad6, Bre1, and NCPs in a defined in vitro system. The Bre1 RING domain cross-links exclusively with distinct regions of histone H2B and H2A, indicating a spatial alignment of Bre1 with the NCP acidic patch...
September 20, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27582463/rna-binding-protein-dus16-plays-an-essential-role-in-primary-mirna-processing-in-the-unicellular-alga-chlamydomonas-reinhardtii
#19
Tomohito Yamasaki, Masayuki Onishi, Eun-Jeong Kim, Heriberto Cerutti, Takeshi Ohama
Canonical microRNAs (miRNAs) are embedded in duplexed stem-loops in long precursor transcripts and are excised by sequential cleavage by DICER nuclease(s). In this miRNA biogenesis pathway, dsRNA-binding proteins play important roles in animals and plants by assisting DICER. However, these RNA-binding proteins are poorly characterized in unicellular organisms. Here we report that a unique RNA-binding protein, Dull slicer-16 (DUS16), plays an essential role in processing of primary-miRNA (pri-miRNA) transcripts in the unicellular green alga Chlamydomonas reinhardtii In animals and plants, dsRNA-binding proteins involved in miRNA biogenesis harbor two or three dsRNA-binding domains (dsRBDs), whereas DUS16 contains one dsRBD and also an ssRNA-binding domain (RRM)...
September 20, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27518568/snapshot-transcription-elongation
#20
Christine E Cucinotta, Karen M Arndt
Transcription elongation is a key regulatory step in gene expression that is controlled by many proteins, and mechanisms, ranging from RNA Polymerase II pausing to cotranscriptional histone modifications.
August 11, 2016: Cell
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