keyword
MENU ▼
Read by QxMD icon Read
search

Promoter proximal pausing

keyword
https://www.readbyqxmd.com/read/28340332/super-elongation-complex-promotes-early-hiv-transcription-and-its-function-is-modulated-by-p-tefb
#1
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...
February 17, 2017: Transcription
https://www.readbyqxmd.com/read/28273906/identifying-novel-transcriptional-and-epigenetic-features-of-nuclear-lamina-associated-genes
#2
Feinan Wu, Jie Yao
Because a large portion of the mammalian genome is associated with the nuclear lamina (NL), it is interesting to study how native genes resided there are transcribed and regulated. In this study, we report unique transcriptional and epigenetic features of nearly 3,500 NL-associated genes (NL genes). Promoter regions of active NL genes are often excluded from NL-association, suggesting that NL-promoter interactions may repress transcription. Active NL genes with higher RNA polymerase II (Pol II) recruitment levels tend to display Pol II promoter-proximal pausing, while Pol II recruitment and Pol II pausing are not correlated among non-NL genes...
December 2017: Scientific Reports
https://www.readbyqxmd.com/read/28263964/total-rna-seq-to-identify-pharmacological-effects-on-specific-stages-of-mrna-synthesis
#3
Sarah A Boswell, Andrew Snavely, Heather M Landry, L Stirling Churchman, Jesse M Gray, Michael Springer
Pharmacological perturbation is a powerful tool for understanding mRNA synthesis, but identification of the specific steps of this multi-step process that are targeted by small molecules remains challenging. Here we applied strand-specific total RNA sequencing (RNA-seq) to identify and distinguish specific pharmacological effects on transcription and pre-mRNA processing in human cells. We found unexpectedly that the natural product isoginkgetin, previously described as a splicing inhibitor, inhibits transcription elongation...
March 6, 2017: Nature Chemical Biology
https://www.readbyqxmd.com/read/28245789/mechanisms-of-groucho-mediated-repression-revealed-by-genome-wide-analysis-of-groucho-binding-and-activity
#4
Michael Chambers, Wiam Turki-Judeh, Min Woo Kim, Kenny Chen, Sean D Gallaher, Albert J Courey
BACKGROUND: The transcriptional corepressor Groucho (Gro) is required for the function of many developmentally regulated DNA binding repressors, thus helping to define the gene expression profile of each cell during development. The ability of Gro to repress transcription at a distance together with its ability to oligomerize and bind to histones has led to the suggestion that Gro may spread along chromatin. However, much is unknown about the mechanism of Gro-mediated repression and about the dynamics of Gro targeting...
February 28, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28213523/identification-of-regions-in-the-spt5-subunit-of-dsif-that-are-involved-in-promoter-proximal-pausing
#5
Yijun Qiu, David S Gilmour
DRB-sensitivity inducing factor (DSIF(2), or Spt4/5) is a conserved transcription elongation factor that both inhibits and stimulates transcription elongation in metazoans. In Drosophila and vertebrates, DSIF together with negative elongation factor (NELF) associates with RNA polymerase II (Pol II) during early elongation and causes Pol II to pause in the promoter proximal region of genes. The mechanism of how DSIF establishes pausing is not known. We constructed Spt5 mutant forms of DSIF and tested their capacity to restore promoter proximal pausing to DSIF-depleted Drosophila nuclear extracts...
February 17, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28102758/p-tefb-finding-its-ways-to-release-promoter-proximally-paused-rna-polymerase-ii
#6
You Li, Min Liu, Lin-Feng Chen, Ruichuan Chen
The release of a paused Pol II depends on the recruitment of P-TEFb. Recent studies showed that both active P-TEFb and inactive P-TEFb (7SK snRNP) can be recruited to the promoter regions of global genes by different mechanisms. Here, we summarize the recent advances on these distinct recruitment mechanisms.
January 19, 2017: Transcription
https://www.readbyqxmd.com/read/28077616/different-modes-of-enhancer-specific-regulation-by-runt-and-even-skipped-during-drosophila-segmentation
#7
Saiyu Hang, J Peter Gergen
The initial metameric expression of the Drosophila sloppy paired 1 (slp1) gene is controlled by two distinct cis-regulatory DNA elements that interact in a nonadditive manner to integrate inputs from transcription factors encoded by the pair-rule segmentation genes. We performed chromatin immunoprecipitation on reporter genes containing these elements in different embryonic genotypes to investigate the mechanism of their regulation. The distal early stripe element (DESE) mediates both activation and repression by Runt...
March 1, 2017: Molecular Biology of the Cell
https://www.readbyqxmd.com/read/27928053/%C3%AF-38-dependent-promoter-proximal-pausing-by-bacterial-rna-polymerase
#8
Ivan Petushkov, Daria Esyunina, Andrey Kulbachinskiy
Transcription initiation by bacterial RNA polymerase (RNAP) requires a variable σ subunit that directs it to promoters for site-specific priming of RNA synthesis. The principal σ subunit responsible for expression of house-keeping genes can bind the transcription elongation complex after initiation and induce RNAP pausing through specific interactions with promoter-like motifs in transcribed DNA. We show that the stationary phase and stress response σ(38) subunit can also induce pausing by Escherichia coli RNAP on DNA templates containing promoter-like motifs in the transcribed regions...
December 7, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27889238/insights-into-nucleosome-organization-in-mouse-embryonic-stem-cells-through-chemical-mapping
#9
Lilien N Voong, Liqun Xi, Amy C Sebeson, Bin Xiong, Ji-Ping Wang, Xiaozhong Wang
Nucleosome organization influences gene activity by controlling DNA accessibility to transcription machinery. Here, we develop a chemical biology approach to determine mammalian nucleosome positions genome-wide. We uncovered surprising features of nucleosome organization in mouse embryonic stem cells. In contrast to the prevailing model, we observe that for nearly all mouse genes, a class of fragile nucleosomes occupies previously designated nucleosome-depleted regions around transcription start sites and transcription termination sites...
December 1, 2016: Cell
https://www.readbyqxmd.com/read/27729530/nascent-rna-sequencing-reveals-distinct-features-in-plant-transcription
#10
Jonathan Hetzel, Sascha H Duttke, Christopher Benner, Joanne Chory
Transcriptional regulation of gene expression is a major mechanism used by plants to confer phenotypic plasticity, and yet compared with other eukaryotes or bacteria, little is known about the design principles. We generated an extensive catalog of nascent and steady-state transcripts in Arabidopsis thaliana seedlings using global nuclear run-on sequencing (GRO-seq), 5'GRO-seq, and RNA-seq and reanalyzed published maize data to capture characteristics of plant transcription. De novo annotation of nascent transcripts accurately mapped start sites and unstable transcripts...
October 25, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27725713/systems-level-analysis-reveals-selective-regulation-of-aqp2-gene-expression-by-vasopressin
#11
Pablo C Sandoval, J'Neka S Claxton, Jae Wook Lee, Fahad Saeed, Jason D Hoffert, Mark A Knepper
Vasopressin-mediated regulation of renal water excretion is defective in a variety of water balance disorders in humans. It occurs in part through long-term mechanisms that regulate the abundance of the aquaporin-2 water channel in renal collecting duct cells. Here, we use deep DNA sequencing in mouse collecting duct cells to ask whether vasopressin signaling selectively increases Aqp2 gene transcription or whether it triggers a broadly targeted transcriptional network. ChIP-Seq quantification of binding sites for RNA polymerase II was combined with RNA-Seq quantification of transcript abundances to identify genes whose transcription is regulated by vasopressin...
October 11, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27716820/gdown1-associates-efficiently-with-rna-polymerase-ii-after-promoter-clearance-and-displaces-tfiif-during-transcript-elongation
#12
Elizabeth DeLaney, Donal S Luse
Pausing during the earliest stage of transcript elongation by RNA polymerase II (Pol II) is a nearly universal control point in metazoan gene expression. The substoichiometric Pol II subunit Gdown1 facilitates promoter proximal pausing in vitro in extract-based transcription reactions, out-competes the initiation/elongation factor TFIIF for binding to free Pol II and co-localizes with paused Pol II in vivo. However, we have shown that Gdown1 cannot functionally associate with the Pol II preinitiation complex (PIC), which contains TFIIF...
2016: PloS One
https://www.readbyqxmd.com/read/27564129/tbp-loading-by-af4-through-sl1-is-the-major-rate-limiting-step-in-mll-fusion-dependent-transcription
#13
Hiroshi Okuda, Satoshi Takahashi, Akifumi Takaori-Kondo, Akihiko Yokoyama
Gene rearrangement of the mixed lineage leukemia (MLL) gene causes leukemia by inducing the constitutive expression of a gene subset normally expressed only in the immature haematopoietic progenitor cells. MLL gene rearrangements often generate fusion products of MLL and a component of the AF4 family/ENL family/P-TEFb (AEP) complex. MLL-AEP fusion proteins have the potential of constitutively recruiting the P-TEFb elongation complex. Thus, it is hypothesized that relieving the promoter proximal pausing of RNA polymerase II is the rate-limiting step of MLL fusion-dependent transcription...
October 17, 2016: Cell Cycle
https://www.readbyqxmd.com/read/27520065/rna-polymerase-ii-pausing-modulates-hematopoietic-stem-cell-emergence-in-zebrafish
#14
Qiwen Yang, Xiuli Liu, Ting Zhou, Jennifer Cook, Kim Nguyen, Xiaoying Bai
The promoter-proximal pausing of RNA polymerase II (Pol II) plays a critical role in regulating metazoan gene transcription. Despite the prevalence of Pol II pausing across the metazoan genomes, little is known about the in vivo effect of Pol II pausing on vertebrate development. We use the emergence of hematopoietic stem cells (HSCs) in zebrafish embryos as a model to investigate the role of Pol II pausing in vertebrate organogenesis. Disrupting Pol II pausing machinery causes a severe reduction of HSC specification, a defect that can be effectively rescued by inhibiting Pol II elongation...
September 29, 2016: Blood
https://www.readbyqxmd.com/read/27498870/high-resolution-mapping-of-rna-polymerases-identifies-mechanisms-of-sensitivity-and-resistance-to-bet-inhibitors-in-t-8-21-aml
#15
Yue Zhao, Qi Liu, Pankaj Acharya, Kristy R Stengel, Quanhu Sheng, Xiaofan Zhou, Hojoong Kwak, Melissa A Fischer, James E Bradner, Stephen A Strickland, Sanjay R Mohan, Michael R Savona, Bryan J Venters, Ming-Ming Zhou, John T Lis, Scott W Hiebert
Bromodomain and extra-terminal domain (BET) family inhibitors offer an approach to treating hematological malignancies. We used precision nuclear run-on transcription sequencing (PRO-seq) to create high-resolution maps of active RNA polymerases across the genome in t(8;21) acute myeloid leukemia (AML), as these polymerases are exceptionally sensitive to BET inhibitors. PRO-seq identified over 1,400 genes showing impaired release of promoter-proximal paused RNA polymerases, including the stem cell factor receptor tyrosine kinase KIT that is mutated in t(8;21) AML...
August 16, 2016: Cell Reports
https://www.readbyqxmd.com/read/27492368/transcription-factors-gaf-and-hsf-act-at-distinct-regulatory-steps-to-modulate-stress-induced-gene-activation
#16
Fabiana M Duarte, Nicholas J Fuda, Dig B Mahat, Leighton J Core, Michael J Guertin, John T Lis
The coordinated regulation of gene expression at the transcriptional level is fundamental to development and homeostasis. Inducible systems are invaluable when studying transcription because the regulatory process can be triggered instantaneously, allowing the tracking of ordered mechanistic events. Here, we use precision run-on sequencing (PRO-seq) to examine the genome-wide heat shock (HS) response in Drosophila and the function of two key transcription factors on the immediate transcription activation or repression of all genes regulated by HS...
August 1, 2016: Genes & Development
https://www.readbyqxmd.com/read/27477907/engineered-covalent-inactivation-of-tfiih-kinase-reveals-an-elongation-checkpoint-and-results-in-widespread-mrna-stabilization
#17
Juan B Rodríguez-Molina, Sandra C Tseng, Shane P Simonett, Jack Taunton, Aseem Z Ansari
During transcription initiation, the TFIIH-kinase Kin28/Cdk7 marks RNA polymerase II (Pol II) by phosphorylating the C-terminal domain (CTD) of its largest subunit. Here we describe a structure-guided chemical approach to covalently and specifically inactivate Kin28 kinase activity in vivo. This method of irreversible inactivation recapitulates both the lethal phenotype and the key molecular signatures that result from genetically disrupting Kin28 function in vivo. Inactivating Kin28 impacts promoter release to differing degrees and reveals a "checkpoint" during the transition to productive elongation...
August 4, 2016: Molecular Cell
https://www.readbyqxmd.com/read/27468311/gaga-factor-a-positive-regulator-of-global-gene-expression-modulates-transcriptional-pausing-and-organization-of-upstream-nucleosomes
#18
Shih-Ying Tsai, Yuh-Long Chang, Krishna B S Swamy, Ruei-Lin Chiang, Der-Hwa Huang
BACKGROUND: Genome-wide studies in higher eukaryotes have revealed the presence of paused RNA polymerase II (RNA-Pol) at about 30-50 bp downstream of the transcription start site of genes involved in developmental control, cell proliferation and intercellular signaling. Promoter-proximal pausing is believed to represent a critical step in transcriptional regulation. GAGA sequence motifs have frequently been found in the upstream region of paused genes in Drosophila, implicating a prevalent binding factor, GAF, in transcriptional pausing...
2016: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/27447982/identification-of-parp-specific-adp-ribosylation-targets-reveals-a-regulatory-function-for-adp-ribosylation-in-transcription-elongation
#19
Mario Leutert, Deena M Leslie Pedrioli, Michael O Hottiger
In a recent issue of Science, Gibson et al. (2016) describe an in vitro chemical genetic approach that maps the specific ADP-ribosylation sites targeted by the ADP-ribosyltransferases PARP-1, PARP-2, and PARP-3 and demonstrate that PARP-1 regulates RNA polymerase II promoter-proximal pausing.
July 21, 2016: Molecular Cell
https://www.readbyqxmd.com/read/27432546/rna-polymerase-ii-promoter-proximal-pausing-in-mammalian-long-non-coding-genes
#20
Heeyoun Bunch, Brian P Lawney, Adam Burkholder, Duanduan Ma, Xiaofeng Zheng, Shmulik Motola, David C Fargo, Stuart S Levine, Yaoyu E Wang, Guang Hu
Mammalian genomes encode a large number of non-coding RNAs (ncRNAs) that greatly exceed mRNA genes. While the physiological and pathological roles of ncRNAs have been increasingly understood, the mechanisms of regulation of ncRNA expression are less clear. Here, our genomic study has shown that a significant number of long non-coding RNAs (lncRNAs, >1000 nucleotides) harbor RNA polymerase II (Pol II) engaged with the transcriptional start site. A pausing and transcriptional elongation factor for protein-coding genes, tripartite motif-containing 28 (TRIM28) regulates the transcription of a subset of lncRNAs in mammalian cells...
August 2016: Genomics
keyword
keyword
74751
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"