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https://www.readbyqxmd.com/read/28632998/trna-structure-and-evolution-and-standardization-to-the-three-nucleotide-genetic-code
#1
Daewoo Pak, Robert Root-Bernstein, Zachary F Burton
Cloverleaf tRNA with a 75 nucleotide (nt) core is posited to have evolved from ligation of three 31 nt minihelices followed by symmetrical internal deletions of 9 nt within ligated acceptor stems. Statistical tests strongly support the model. Although the tRNA anticodon loop and T loop are homologs, their U-turns have been treated as distinct motifs. An appropriate comparison, however, shows that intercalation of D loop G19 between T loop bases 4 and 5 causes elevation of T loop base 5 and flipping of T loop bases 6 and 7 out of the 7 nucleotide loop...
June 20, 2017: Transcription
https://www.readbyqxmd.com/read/28598255/the-regulatory-role-of-mirnas-on-vdr-in-breast-cancer
#2
Tatyana Singh, Brian D Adams
Triple negative breast cancer has been associated with the lack of three hormone receptors; estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER-2). However, a host of other steroid hormone receptors such as vitamin D receptor (VDR) are present in triple negative breast cancers, and the role of these hormone receptors in breast tumorigenesis is unclear. The levels of microRNAs (miRNAs) are also expressed differently than in normal mammary epithelial cells. miRNAs are regulatory RNAs involved in various cellular functions, mainly gene silencing...
June 9, 2017: Transcription
https://www.readbyqxmd.com/read/28598254/archaeal-rna-polymerase-arrests-transcription-at-dna-lesions
#3
Alexandra M Gehring, Thomas J Santangelo
Transcription elongation is not uniform and transcription is often hindered by protein-bound factors or DNA lesions that limit translocation and impair catalysis. Despite the high degree of sequence and structural homology of the multi-subunit RNAPs, substantial differences in response to DNA lesions have been reported. Archaea encode only a single RNAP with striking structural conservation with eukaryotic RNAP II (Pol II). Here we demonstrate that the archaeal RNAP from Thermococcus kodakarensis is sensitive to a variety of DNA lesions that pause and arrest RNAP at or adjacent to the site of DNA damage...
June 9, 2017: Transcription
https://www.readbyqxmd.com/read/28598253/androgen-receptor-and-mir-206-regulation-in-prostate-cancer
#4
Fu Yee Gua, Brian D Adams
In the United States, prostate cancer is the second leading cause of cancer related deaths among men with an approximately 220,000 patients diagnosed with the disease in 2015. Prostate cancer is a hormone-driven tumor, and a common therapy is androgen-deprivation therapy (ADT) which involves anti-androgen treatments and/or castration therapy. Understanding the molecular basis for androgen-independent tumors is crucial towards developing new therapies for these patients. Understanding how androgen receptor itself functions, is an important first step in elucidating this process...
June 9, 2017: Transcription
https://www.readbyqxmd.com/read/28598252/mutation-of-nucleotides-around-the-1-position-of-type-3-polymerase-iii-promoters-the-effect-on-transcriptional-activity-and-start-site-usage
#5
Zongliang Gao, Alex Harwig, Ben Berkhout, Elena Herrera-Carrillo
Type 3 RNA Polymerase III (Pol III) promoters are widely used for the expression of small RNAs such as short hairpin RNA and guide RNA in the popular RNAi and CRISPR-Cas gene regulation systems. Although it is generally believed that type 3 Pol III promoters use a defined transcription start site (+1 position), most man-made promoter constructs contain local sequence alterations of which the impact on transcription efficiency and initiation accuracy is not known. For three human type 3 Pol III promoters (7SK, U6 and H1), we demonstrated that the nucleotides around the +1 position affect both the transcriptional efficiency and start site selection...
June 9, 2017: Transcription
https://www.readbyqxmd.com/read/28598247/a-long-range-flexible-billboard-model-of-gene-activation
#6
Christopher M Vockley, Ian C McDowell, Antony M D'Ippolito, Timothy E Reddy
Gene regulation is fundamentally important for the coordination of diverse biologic processes including homeostasis and responses to developmental and environmental stimuli. Transcription factor (TF) binding sites are one of the major functional subunits of gene regulation. They are arranged in cis-regulatory modules (CRMs) that can be more active than the sum of their individual effects. Recently, we described a mechanism of glucocorticoid (GC)-induced gene regulation in which the glucocorticoid receptor (GR) binds coordinately to multiple CRMs that are 10s of kilobases apart in the genome...
June 9, 2017: Transcription
https://www.readbyqxmd.com/read/28548879/ras-and-rho-gtpase-regulation-of-pol-ii-transcription-a-shortcut-model-revisited
#7
Zhi-Liang Zheng
Transcriptional control is critical in relaying signals mediated by Ras and Rho family small GTPases to effect gene expression. In the classical model, signaling components such as MAP kinase target sequence-specific transcription factors, which in turn recruit RNA polymerase (Pol) II holoenzyme to the promoter and activate transcription. Findings in recent years have led to the proposal of a shortcut model in which the mediator components of the Pol II holoenzyme are regulated by signaling pathways. A very recent finding shows that an evolutionarily conserved Rho GTPase signaling pathway can directly modulate the Pol II C-terminal domain (CTD) phosphorylation by inhibiting the CTD phosphatase in yeast and Arabidopsis...
May 26, 2017: Transcription
https://www.readbyqxmd.com/read/28448767/transcriptional-control-of-yeast-ribosome-biogenesis-a-multifaceted-role-for-general-regulatory-factors
#8
Maria Cristina Bosio, Beatrice Fermi, Giorgio Dieci
In Saccharomyces cerevisiae, a group of more than 200 co-regulated genes (Ribi genes) is involved in ribosome biogenesis. This regulon has recently been shown to rely on a small set of transcriptional regulators (mainly Abf1, but also Reb1, Tbf1 and Rap1) previously referred to as general regulatory factors (GRFs) because of their widespread binding and action at many promoters and other specialized genomic regions. Intriguingly, Abf1 binding to Ribi genes is differentially modulated in response to distinct nutrition signaling pathways...
April 27, 2017: Transcription
https://www.readbyqxmd.com/read/28340332/super-elongation-complex-promotes-early-hiv-transcription-and-its-function-is-modulated-by-p-tefb
#9
Alona Kuzmina, Simona Krasnopolsky, Ran Taube
Early work on the control of transcription of the human immunodeficiency virus (HIV) laid the foundation for our current knowledge of how RNA Polymerase II is released from promoter-proximal pausing sites and transcription elongation is enhanced. The viral Tat activator recruits Positive Transcription Elongation Factor b (P-TEFb) and Super Elongation Complex (SEC) that jointly drive transcription elongation. While substantial progress in understanding the role of SEC in HIV gene transcription elongation has been obtained, defining of the mechanisms that govern SEC functions is still limited, and the role of SEC in controlling HIV transcription in the absence of Tat is less clear...
May 27, 2017: Transcription
https://www.readbyqxmd.com/read/28340330/same-same-but-different-the-evolution-of-tbp-in-archaea-and-their-eukaryotic-offspring
#10
Fabian Blombach, Dina Grohmann
Transcription factors TBP and TF(II)B assemble with RNA polymerase at the promoter DNA forming the initiation complex. Despite a high degree of conservation, the molecular binding mechanisms of archaeal and eukaryotic TBP and TF(II)B differ significantly. Based on recent biophysical data, we speculate how the mechanisms co-evolved with transcription regulation and TBP multiplicity.
May 27, 2017: Transcription
https://www.readbyqxmd.com/read/28301308/regenerating-muscle-with-arginine-methylation
#11
Roméo S Blanc, Stéphane Richard
Protein arginine methyltransferase (PRMT) is a family of nine proteins catalyzing the methylation of arginine residues. They were recently shown to be essential for proper regeneration of skeletal muscles. However, the mechanisms triggering the methylation event, as well as how the methylated substrates regulate muscle stem cell function and fate decision remain to be determined. This point-of-view will discuss the recent findings on the specific role of PRMT1, CARM1/PRMT4, PRMT5, and PRMT7 in muscle stem cell fate guidance, and shed light on the future challenges which could help defining the therapeutic potential of PRMT inhibitors against muscular disorders and aging...
May 27, 2017: Transcription
https://www.readbyqxmd.com/read/28301306/two-possible-modes-of-pioneering-associated-with-combinations-of-h2a-z-and-p300-cbp-at-nucleosome-occupied-enhancers
#12
Pierre Cauchy, Frederic Koch, Jean-Christophe Andrau
Pioneer transcription factors are defined by their ability to bind nucleosome-occupied regions. Here, we discuss the properties of nucleosomes bound by pioneers at enhancer regions. We describe how select pioneers bind nucleosome-occupied or -depleted enhancer sites. Importantly, by revisiting and expanding existing data sets, we show differential H2A.Z and p300/CBP association at bound enhancers, highlighting two possible pioneering modes.
May 27, 2017: Transcription
https://www.readbyqxmd.com/read/28301294/fubp-kh-domain-proteins-in-transcription-back-to-the-future
#13
Leonie M Quinn
Drosophila genetic studies demonstrate that cell and tissue growth regulation is a primary developmental function of P-element somatic inhibitor (Psi), the sole ortholog of FUBP family RNA/DNA-binding proteins. Psi achieves growth control through interaction with Mediator, observations that should put to rest controversy surrounding Pol II transcriptional functions for these KH domain proteins.
May 27, 2017: Transcription
https://www.readbyqxmd.com/read/28301293/signatures-of-dna-target-selectivity-by-ets-transcription-factors
#14
Gregory M K Poon, Hye Mi Kim
The ETS family of transcription factors is a functionally heterogeneous group of gene regulators that share a structurally conserved, eponymous DNA-binding domain. DNA target specificity derives from combinatorial interactions with other proteins as well as intrinsic heterogeneity among ETS domains. Emerging evidence suggests molecular hydration as a fundamental feature that defines the intrinsic heterogeneity in DNA target selection and susceptibility to epigenetic DNA modification. This perspective invokes novel hypotheses in the regulation of ETS proteins in physiologic osmotic stress, their pioneering potential in heterochromatin, and the effects of passive and pharmacologic DNA demethylation on ETS regulation...
May 27, 2017: Transcription
https://www.readbyqxmd.com/read/28301289/genome-wide-characterization-of-mediator-recruitment-function-and-regulation
#15
Sebastian Grünberg, Gabriel E Zentner
Mediator is a conserved and essential coactivator complex broadly required for RNA polymerase II (RNAPII) transcription. Recent genome-wide studies of Mediator binding in budding yeast have revealed new insights into the functions of this critical complex and raised new questions about its role in the regulation of gene expression.
May 27, 2017: Transcription
https://www.readbyqxmd.com/read/28301288/transcription-elongation
#16
Arkady Mustaev, Jeffrey Roberts, Max Gottesman
This review is focused on recent progress in understanding how Escherichia coli RNAP polymerase translocates along the DNA template and the factors that affect this movement. We discuss the fundamental aspects of RNAP translocation, template signals that influence forward or backward movement, and host or phage factors that modulate translocation.
May 27, 2017: Transcription
https://www.readbyqxmd.com/read/28379052/regulation-of-transcription-factors-by-sumoylation
#17
Emanuel Rosonina, Akhi Akhter, Yimo Dou, John Babu, Veroni S Sri Theivakadadcham
Transcription factors (TFs) are among the most frequently detected targets of sumoylation, and effects of the modification have been studied for about 200 individual TFs to date. TF sumoylation is most often associated with reduced target gene expression, which can be mediated by enhanced interactions with corepressors or by interference with protein modifications that promote transcription. However, recent studies show that sumoylation also regulates gene expression by controlling the levels of TFs that are associated with chromatin...
April 5, 2017: Transcription
https://www.readbyqxmd.com/read/28332923/different-types-of-pausing-modes-during-transcription-initiation
#18
Eitan Lerner, Antonino Ingargiola, Jookyung J Lee, Sergei Borukhov, Xavier Michalet, Shimon Weiss
In many cases, initiation is rate limiting to transcription. This due in part to the multiple cycles of abortive transcription that delay promoter escape and the transition from initiation to elongation. Pausing of transcription in initiation can further delay promoter escape. The previously hypothesized pausing in initiation was confirmed by two recent studies from Duchi et al. (1) and from Lerner, Chung et al. (2) In both studies, pausing is attributed to a lack of forward translocation of the nascent transcript during initiation...
March 23, 2017: Transcription
https://www.readbyqxmd.com/read/28453430/h2b-monoubiquitination-t-ub-or-not-t-ub-for-inducible-enhancers
#19
Gregory Segala, Didier Picard
Recently, we reported the unexpected finding that the monoubiquitination of histone H2B (H2Bub1) regulates inducible enhancers. Here, we propose a conceptual framework to reconcile the apparently discrepant roles of H2Bub1 in transcription initiation and elongation, and we discuss how H2Bub1 could regulate cellular processes linked to non-coding transcription.
March 15, 2017: Transcription
https://www.readbyqxmd.com/read/28151046/a-3d-puzzle-approach-to-building-protein-dna-structures
#20
Deborah M Hinton
Despite recent advances in structural analysis, it is still challenging to obtain a high-resolution structure for a complex of RNA polymerase, transcriptional factors, and DNA. However, using biochemical constraints, 3D printed models of available structures, and computer modeling, one can build biologically relevant models of such supramolecular complexes.
March 15, 2017: Transcription
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