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https://www.readbyqxmd.com/read/29929421/transcription-infidelity-and-genome-integrity-the-parallax-view
#1
Alasdair J E Gordon, Priya Sivaramakrishnan, Jennifer A Halliday, Christophe Herman
It was recently shown that removal of GreA, a transcription fidelity factor, enhances DNA break repair. This counterintuitive result, arising from unresolved backtracked RNA polymerase impeding DNA resection and thereby facilitating RecA-loading, leads to an interesting corollary: error-free full-length transcripts and broken chromosomes. Therefore, transcription fidelity may compromise genomic integrity.
June 21, 2018: Transcription
https://www.readbyqxmd.com/read/29895219/transcription-factors-in-eukaryotic-cells-can-functionally-regulate-gene-expression-by-acting-in-oligomeric-assemblies-formed-from-an-intrinsically-disordered-protein-phase-transition-enabled-by-molecular-crowding
#2
Mark C Leake
High-speed single-molecule fluorescence microscopy in vivo shows that transcription factors in eukaryotes can act in oligomeric clusters mediated by molecular crowding and intrinsically disordered protein. This finding impacts on the longstanding puzzle of how transcription factors find their gene targets so efficiently in the complex, heterogeneous environment of the cell.
June 12, 2018: Transcription
https://www.readbyqxmd.com/read/29889606/transcriptional-regulation-by-promoters-with-enhancer-function
#3
Lan T M Dao, Salvatore Spicuglia
Promoters with enhancer activity have been described recently. In this point of view, we will discuss current findings highlighting the commonality of this type of regulatory elements, their genetic and epigenetic characteristics, their potential biological roles in the regulation of gene expression and the underlining molecular mechanisms.
June 11, 2018: Transcription
https://www.readbyqxmd.com/read/29727262/aminoacyl-trna-synthetase-evolution-and-sectoring-of-the-genetic-code
#4
Daewoo Pak, Yunsoo Kim, Zachary F Burton
The genetic code sectored via tRNA charging errors, and the code progressed toward closure and universality because of evolution of aminoacyl-tRNA synthetase (aaRS) fidelity and translational fidelity mechanisms. Class I and class II aaRS folds are identified as homologs. From sequence alignments, a structurally conserved Zn-binding domain common to class I and class II aaRS was identified. A model for the class I and class II aaRS alternate folding pathways is posited. Five mechanisms toward code closure are highlighted: 1) aaRS proofreading to remove mischarged amino acids from tRNA; 2) accurate aaRS active site specification of amino acid substrates; 3) aaRS-tRNA anticodon recognition; 4) conformational coupling proofreading of the anticodon-codon interaction; and 5) deamination of tRNA wobble adenine to inosine...
May 30, 2018: Transcription
https://www.readbyqxmd.com/read/29624124/architecture-of-the-rna-polymerase-ii-elongation-complex-new-insights-into-spt4-5-and-elf1
#5
Haruhiko Ehara, Shun-Ichi Sekine
Transcription by RNA polymerase II (Pol II) is accomplished with the aid of numerous accessory factors specific to each transcriptional stage. The structure of the Pol II elongation complex (EC) bound with Spt4/5, Elf1, and TFIIS unveiled the sophisticated basal EC architecture essential for transcription elongation and other transcription-related events.
May 7, 2018: Transcription
https://www.readbyqxmd.com/read/29624107/rna-capping-by-mitochondrial-and-multi-subunit-rna-polymerases
#6
Christina Julius, Amber Riaz-Bradley, Yulia Yuzenkova
Recently, it was found that bacterial and eukaryotic transcripts are capped with cellular cofactors installed by their respective RNA polymerases (RNAPs) during transcription initiation. We now show that mitochondrial RNAP efficiently caps transcripts with ADP - containing cofactors. However, a functional role of universal RNAP - catalysed capping is not yet clear.
April 25, 2018: Transcription
https://www.readbyqxmd.com/read/29406813/reading-cytosine-modifications-within-chromatin
#7
Elise A Mahé, Thierry Madigou, Gilles Salbert
Zinc-finger and homeodomain transcription factors have been shown in vitro to bind to recognition motifs containing a methylated CpG. However, accessing these motifs in vivo might be seriously impeded by the inclusion of DNA in nucleosomes and by the condensed structure adopted by chromatin formed on methylated DNA. Here, we discuss how oxidation of 5-methylcytosine into 5-hydroxymethylcytosine could provide the initial destabilizing clue for such transcription factors to get access to nucleosomal DNA and read epigenetic information...
February 6, 2018: Transcription
https://www.readbyqxmd.com/read/29372670/rna-polymerase-i-activation-and-hibernation-unique-mechanisms-for-unique-genes
#8
Carlos Fernández-Tornero
In yeast, transcription of ribosomal DNA (rDNA) by RNA polymerase I (Pol I) is regulated by unique mechanisms acting at the level of the enzyme. Under stress situations such as starvation, Pol I hibernates through dimerization. When growth conditions are restored, dimer disassembly and Rrn3 binding drive enzyme activation and subsequent recruitment to rDNA.
January 26, 2018: Transcription
https://www.readbyqxmd.com/read/29345523/hexim1-an-rna-controlled-protein-hub
#9
Annemieke A Michels, Olivier Bensaude
Hexim1 acts as a tumor suppressor and is involved in the regulation of innate immunity. It was initially described as a non-coding RNA-dependent regulator of transcription. Here, we detail how 7SK RNA binds to Hexim1 and turns it into an inhibitor of the positive transcription elongation factor (P-TEFb). In addition to its action on P-TEFb, it plays a role in a variety of different mechanisms: it controls the stability of transcription factor components and assists binding of transcription factors to their targets...
January 18, 2018: Transcription
https://www.readbyqxmd.com/read/29264963/breaking-the-mold-structures-of-the-rna-polymerase-i-transcription-complex-reveal-a-new-path-for-initiation
#10
Ashleigh J Jackobel, Yan Han, Yuan He, Bruce A Knutson
While structures of the RNA polymerase (Pol) II initiation complex have been resolved and extensively studied, the Pol I initiation complex remained elusive. Here, we review the recent structural analyses of the yeast Pol I transcription initiation complex that reveal several unique and unexpected Pol I-specific properties.
January 15, 2018: Transcription
https://www.readbyqxmd.com/read/29372672/rooted-trnaomes-and-evolution-of-the-genetic-code
#11
Daewoo Pak, Nan Du, Yunsoo Kim, Yanni Sun, Zachary F Burton
We advocate for a tRNA- rather than an mRNA-centric model for evolution of the genetic code. The mechanism for evolution of cloverleaf tRNA provides a root sequence for radiation of tRNAs and suggests a simplified understanding of code evolution. To analyze code sectoring, rooted tRNAomes were compared for several archaeal and one bacterial species. Rooting of tRNAome trees reveals conserved structures, indicating how the code was shaped during evolution and suggesting a model for evolution of a LUCA tRNAome tree...
2018: Transcription
https://www.readbyqxmd.com/read/29139335/shprh-as-a-new-player-in-ribosomal-rna-transcription-and-its-potential-role-in-homeostasis-of-ribosomal-dna-repeats
#12
Deokjae Lee, Jun Hong Park, Shinseog Kim, Seon-Gyeong Lee, Kyungjae Myung
There are hundreds of copies of rDNA repeats in mammalian chromosomes and the ratio of active, poised, or inactive rDNA is regulated in epigenetic manners. Recent studies demonstrated that a post-DNA replication repair enzyme, SHPRH affects rRNA transcription by recognizing epigenetic markers on rDNA promoters and unveiled potential links between DNA repair and ribosome biogenesis. This study suggests that SHPRH could be a link between mTOR-mediated epigenetic regulations and rRNA transcription, while concomitantly affecting genomic integrity...
2018: Transcription
https://www.readbyqxmd.com/read/29105534/transcription-pausing-biological-significance-of-thermal-fluctuations-biased-by-repetitive-genomic-sequences
#13
Masahiko Imashimizu, David B Lukatsky
Transcription of DNA by RNA polymerase (RNAP) takes place in a cell environment dominated by thermal fluctuations. How are transcription reactions including initiation, elongation, and termination on genomic DNA so well-controlled during such fluctuations? A recent statistical mechanical approach using high-throughput sequencing data reveals that repetitive DNA sequence elements embedded into a genomic sequence provide the key mechanism to functionally bias the fluctuations of transcription elongation complexes...
2018: Transcription
https://www.readbyqxmd.com/read/29099315/alternative-mrna-processing-sites-decrease-genetic-variability-while-increasing-functional-diversity
#14
Didier Auboeuf
Recent large-scale RNA sequencing efforts have revealed the extensive diversity of mRNA molecules produced from most eukaryotic coding genes, which arises from the usage of alternative, cryptic or non-canonical splicing and intronic polyadenylation sites. The prevailing view regarding the tremendous diversity of coding gene transcripts is that mRNA processing is a flexible and more-or-less noisy process leading to a diversity of proteins on which natural selection can act depending on protein-mediated cellular functions...
2018: Transcription
https://www.readbyqxmd.com/read/29099304/orphan-cpg-islands-as-alternative-promoters
#15
Shrutii Sarda, Sridhar Hannenhalli
CpG islands (CGIs) are associated with ∼60% of mammalian promoters. Most unmethylated CGIs exhibit transcriptional activity, which has led to their co-option as promoters by retrogenes. CGIs may also serve as alternative promoters for downstream genes with methylated promoters, with implications on aberrant activation of oncogenes in cancer phenotypes.
2018: Transcription
https://www.readbyqxmd.com/read/28992423/housekeeping-and-tissue-specific-cis-regulatory-elements-recipes-for-specificity-and-recipes-for-activity
#16
Marta Russo, Gioacchino Natoli, Serena Ghisletti
Cell type-specific and housekeeping enhancers and promoters collectively control the transcriptional output of mammalian cells. Recent data clarify how DNA sequence features on the one hand control functional coupling of promoters with selected enhancers, and on the other impart high level of activity to a broad range of regulatory elements.
2018: Transcription
https://www.readbyqxmd.com/read/28990856/gaining-insight-into-plant-gene-transcription-using-smfish
#17
Susan Duncan, Stefanie Rosa
Single molecule RNA fluorescent in situ hybridization (smFISH) enables gene transcription to be assessed at the cellular level. In this point of view article, we describe our recent smFISH research in the model plant Arabidopsis thaliana and discuss how this technique could further knowledge of plant gene transcription in the future.
2018: Transcription
https://www.readbyqxmd.com/read/28980882/super-enhancers-new-analyses-and-perspectives-on-the-low-hanging-fruit
#18
Feda H Hamdan, Steven A Johnsen
Significant attention has recently been given to a class of enhancers termed "super enhancers", while implying that "typical enhancers" are less important. In this report, we examine criteria for identification of super enhancers and address the need to evaluate the differences between BRD4-occupied "typical" and "super" enhancers.
2018: Transcription
https://www.readbyqxmd.com/read/28980880/spurious-transcription-and-its-impact-on-cell-function
#19
Joseph T Wade, David C Grainger
Most RNA polymerases can initiate transcription from diverse DNA template sequences with relatively few outright sequence restraints. Recent reports have demonstrated that failure to subdue the promiscuity of RNA polymerase in vivo can severely impede cell function. This phenomenon appears common to all cell types with undesirable effects ranging from growth inhibition in prokaryotes to cancer in higher organisms. Here we discuss similarities and differences in strategies employed by cells to minimise spurious transcription across life's domains...
2018: Transcription
https://www.readbyqxmd.com/read/28980873/emerging-roles-of-transcriptional-programs-in-autophagy-regulation
#20
Jun-Ichi Sakamaki, Jaclyn S Long, Maria New, Tim Van Acker, Sharon A Tooze, Kevin M Ryan
Autophagy is an essential cellular process that degrades cytoplasmic organelles and components. Precise control of autophagic activity is achieved by context-dependent signaling pathways. Recent studies have highlighted the involvement of transcriptional programs during autophagic responses to various signals. Here, we summarize the current understanding of the transcriptional regulation of autophagy.
2018: Transcription
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