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https://www.readbyqxmd.com/read/29101316/structural-basis-for-mutually-exclusive-co-transcriptional-nuclear-cap-binding-complexes-with-either-nelf-e-or-ars2
#1
Wiebke Manuela Schulze, Stephen Cusack
Pol II transcribes diverse classes of RNAs that need to be directed into the appropriate nuclear maturation pathway. All nascent Pol II transcripts are 5'-capped and the cap is immediately sequestered by the nuclear cap-binding complex (CBC). Mutually exclusive interactions of CBC with different partner proteins have been implicated in transcript fate determination. Here, we characterise the direct interactions between CBC and NELF-E, a subunit of the negative elongation factor complex, ARS2 and PHAX. Our biochemical and crystal structure results show that the homologous C-terminal peptides of NELF-E and ARS2 bind identically to CBC and in each case the affinity is enhanced when CBC is bound to a cap analogue...
November 3, 2017: Nature Communications
https://www.readbyqxmd.com/read/29050862/jak-stat-signaling-pathway-gene-expression-is-reduced-following-nelf-knockdown-in-gnrh-neurons
#2
Eun Kyung Ko, Lynn P Chorich, Megan E Sullivan, Richard S Cameron, Lawrence C Layman
Hypothalamic gonadotropin releasing hormone (GnRH) is crucial for the proper function of the hypothalamic-pituitary-gonadal (HPG) axis, subsequent puberty, and reproduction. When GnRH neuron migration or GnRH regulation is impaired, hypogonadotropic hypogonadism results. Mutations in the gene for nasal embryonic luteinizing hormone-releasing factor (NELF) have been identified in GnRH-deficient humans. NELF is a predominantly nuclear protein that may participate in gene transcription, but the genes NELF regulates are unknown...
October 16, 2017: Molecular and Cellular Endocrinology
https://www.readbyqxmd.com/read/28977633/oxidative-stress-rapidly-stabilizes-promoter-proximal-paused-pol-ii-across-the-human-genome
#3
Kyle A Nilson, Christine K Lawson, Nicholas J Mullen, Christopher B Ball, Benjamin M Spector, Jeffery L Meier, David H Price
Oxidative stress has pervasive effects on cells but how they respond transcriptionally upon the initial insult is incompletely understood. We developed a nuclear walk-on assay that semi-globally quantifies nascent transcripts in promoter-proximal paused RNA polymerase II (Pol II). Using this assay in conjunction with ChIP-Seq, in vitro transcription, and a chromatin retention assay, we show that within a minute, hydrogen peroxide causes accumulation of Pol II near promoters and enhancers that can best be explained by a rapid decrease in termination...
August 18, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28868519/dynamic-change-of-transcription-pausing-through-modulating-nelf-protein-stability-regulates-granulocytic-differentiation
#4
Xiuli Liu, Aishwarya A Gogate, Melodi Tastemel, Venkat S Malladi, Huiyu Yao, Kim Nguyen, Lily Jun-Shen Huang, Xiaoying Bai
The NELF complex is a metazoan-specific factor essential for establishing transcription pausing. Although NELF has been implicated in cell fate regulation, the cellular regulation of NELF and its intrinsic role in specific lineage differentiation remains largely unknown. Using mammalian hematopoietic differentiation as a model system, here we identified a dynamic change of NELF-mediated transcription pausing as a novel mechanism regulating hematopoietic differentiation. We found a sharp decrease of NELF protein abundance upon granulocytic differentiation and a subsequent genome-wide reduction of transcription pausing...
August 8, 2017: Blood Advances
https://www.readbyqxmd.com/read/28825619/thermodynamic-modeling-of-gas-transport-in-glassy-polymeric-membranes
#5
Matteo Minelli, Giulio Cesare Sarti
Solubility and permeability of gases in glassy polymers have been considered with the aim of illustrating the applicability of thermodynamically-based models for their description and prediction. The solubility isotherms are described by using the nonequilibrium lattice fluid (NELF) (model, already known to be appropriate for nonequilibrium glassy polymers, while the permeability isotherms are described through a general transport model in which diffusivity is the product of a purely kinetic factor, the mobility coefficient, and a thermodynamic factor...
August 19, 2017: Membranes
https://www.readbyqxmd.com/read/28743741/cdk9-and-spt5-proteins-are-specifically-required-for-expression-of-herpes-simplex-virus-1-replication-dependent-late-genes
#6
Zhiyuan Zhao, Ka-Wei Tang, Isabella Muylaert, Tore Samuelsson, Per Elias
DNA replication greatly enhances expression of the herpes simplex virus 1 (HSV-1) γ2 late genes by still unknown mechanisms. Here, we demonstrate that 5,6-dichloro-1-β-d-ribofuranosylbenzimidazole (DRB), an inhibitor of CDK9, suppresses expression of γ2 late genes with an IC50 of 5 μm, which is at least 10 times lower than the IC50 value required for inhibition of expression of early genes. The effect of DRB could not be explained by inhibition of DNA replication per se or loading of RNA polymerase II to late promoters and subsequent reduction of transcription...
September 15, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28697339/oncogenic-activation-of-the-rna-binding-protein-nelfe-and-myc-signaling-in-hepatocellular-carcinoma
#7
Hien Dang, Atsushi Takai, Marshonna Forgues, Yotsowat Pomyen, Haiwei Mou, Wen Xue, Debashish Ray, Kevin C H Ha, Quaid D Morris, Timothy R Hughes, Xin Wei Wang
Global transcriptomic imbalance is a ubiquitous feature associated with cancer, including hepatocellular carcinoma (HCC). Analyses of 1,225 clinical HCC samples revealed that a large numbers of RNA binding proteins (RBPs) are dysregulated and that RBP dysregulation is associated with poor prognosis. We further identified that oncogenic activation of a top candidate RBP, negative elongation factor E (NELFE), via somatic copy-number alterations enhanced MYC signaling and promoted HCC progression. Interestingly, NELFE induces a unique tumor transcriptome by selectively regulating MYC-associated genes...
July 10, 2017: Cancer Cell
https://www.readbyqxmd.com/read/28578223/serpinb2-is-regulated-by-dynamic-interactions-with-pause-release-proteins-and-enhancer-rnas
#8
Lihua Shii, Li Song, Kelly Maurer, Zhe Zhang, Kathleen E Sullivan
The SERPINB2 gene is strongly upregulated in inflammatory states. In monocytes, it can constitute up to 1% of total cellular protein. It functions in protection from proteotoxic stress and plays a role in angioedema. The purpose of this study was to define the roles of enhancer RNAs embedded in the SERPIN gene complex. We found that the upstream enhancer RNAs upregulated SERPINB2 and the enhancer RNAs were expressed prior to those of SERPINB2 mRNA. Studies of the SERPINB2 promoter demonstrated the presence of an RNA polymerase II pause-inducing protein, NELF...
August 2017: Molecular Immunology
https://www.readbyqxmd.com/read/28336775/nelf-e-is-recruited-to-dna-double-strand-break-sites-to-promote-transcriptional-repression-and-repair
#9
Samah W Awwad, Enas R Abu-Zhayia, Noga Guttmann-Raviv, Nabieh Ayoub
Double-strand breaks (DSBs) trigger rapid and transient transcription pause to prevent collisions between repair and transcription machineries at damage sites. Little is known about the mechanisms that ensure transcriptional block after DNA damage. Here, we reveal a novel role of the negative elongation factor NELF in blocking transcription activity nearby DSBs. We show that NELF-E and NELF-A are rapidly recruited to DSB sites. Furthermore, NELF-E recruitment and its repressive activity are both required for switching off transcription at DSBs...
May 2017: EMBO Reports
https://www.readbyqxmd.com/read/28213523/identification-of-regions-in-the-spt5-subunit-of-drb-sensitivity-inducing-factor-dsif-that-are-involved-in-promoter-proximal-pausing
#10
Yijun Qiu, David S Gilmour
DRB sensitivity-inducing factor (DSIF 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 during early elongation and causes RNA polymerase 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...
March 31, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28112367/knockdown-of-cobra1-decreases-the-proliferation-and-migration-of-hepatocellular-carcinoma-cells
#11
Eman El Zeneini, Sarah Kamel, Mahmoud El-Meteini, Asma Amleh
Cofactor of BRCA1 (COBRA1) is one of the four subunits that make up the negative elongation factor (NELF) complex that is involved in the stalling of RNA polymerase II early during transcription elongation. As such, it regulates the expression of a substantial number of genes involved in cell cycle control, cellular metabolism and DNA repair. With no DNA binding domain, its capacity to modulate gene expression occurs via its ability to interact with different transcription factors. In the field of cancer, its role is not yet fully understood...
March 2017: Oncology Reports
https://www.readbyqxmd.com/read/27863397/targeting-gli-by-gant61-involves-mechanisms-dependent-on-inhibition-of-both-transcription-and-dna-licensing
#12
Ruowen Zhang, Jiahui Wu, Sylvain Ferrandon, Katie J Glowacki, Janet A Houghton
The GLI genes are transcription factors and in cancers are oncogenes, aberrantly and constitutively activated. GANT61, a specific GLI inhibitor, has induced extensive cytotoxicity in human models of colon cancer. The FOXM1 promoter was determined to be a transcriptional target of GLI1. In HT29 cells, inhibition of GLI1 binding at the GLI consensus sequence by GANT61 led to inhibited binding of Pol II, the pause-release factors DSIF, NELF and p-TEFb. The formation of R-loops (RNA:DNA hybrids, ssDNA), were reduced by GANT61 at the FOXM1 promoter...
December 6, 2016: Oncotarget
https://www.readbyqxmd.com/read/27833949/the-emerging-picture-of-cdk9-p-tefb-more-than-20-years-of-advances-since-pitalre
#13
REVIEW
Nikolas Ferreira Dos Santos Paparidis, Maxwell Castro Durvale, Fernanda Canduri
CDK9 is a prominent member of the transcriptional CDKs subfamily, a group of kinases whose function is to control the primary steps of mRNA synthesis and processing by eukaryotic RNA polymerase II. As a cyclin-dependent kinase, CDK9 activation in vivo depends upon its association with T-type cyclins to assemble the positive transcription elongation factor (P-TEFb). Although CDK9/P-TEFb phosphorylates the C-terminal domain of RNAP II in the same positions targeted by CDK7 (TFIIH) and CDK8 (Mediator), the former does not participate in the transcription initiation, but rather plays a unique role by driving the polymerase to productive elongation...
January 31, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/27803842/what-do-we-learn-from-the-murine-jacob-nsmf-gene-knockout-for-human-disease
#14
Christina Spilker, Katarzyna M Grochowska, Michael R Kreutz
Mutations in the NSMF gene have been related to Kallmann syndrome. Conflicting results have been reported on the subcellular localization of Jacob/NELF, the protein encoded by the NSMF gene. Some reports indicate an extracellular localization and a function as a guidance molecule for migration of GnRH-positive neurons from the olfactory placode to the hypothalamus. Other studies have shown protein transport of Jacob from synapse-to-nucleus and indicate a role of the protein in neuronal activity-dependent gene expression...
2016: Rare Diseases
https://www.readbyqxmd.com/read/27716820/gdown1-associates-efficiently-with-rna-polymerase-ii-after-promoter-clearance-and-displaces-tfiif-during-transcript-elongation
#15
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/27468311/gaga-factor-a-positive-regulator-of-global-gene-expression-modulates-transcriptional-pausing-and-organization-of-upstream-nucleosomes
#16
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/27353326/multiple-p-tefbs-cooperatively-regulate-the-release-of-promoter-proximally-paused-rna-polymerase-ii
#17
Xiaodong Lu, Xinxing Zhu, You Li, Min Liu, Bin Yu, Yu Wang, Muhua Rao, Haiyang Yang, Kai Zhou, Yao Wang, Yanheng Chen, Meihua Chen, Songkuan Zhuang, Lin-Feng Chen, Runzhong Liu, Ruichuan Chen
The association of DSIF and NELF with initiated RNA Polymerase II (Pol II) is the general mechanism for inducing promoter-proximal pausing of Pol II. However, it remains largely unclear how the paused Pol II is released in response to stimulation. Here, we show that the release of the paused Pol II is cooperatively regulated by multiple P-TEFbs which are recruited by bromodomain-containing protein Brd4 and super elongation complex (SEC) via different recruitment mechanisms. Upon stimulation, Brd4 recruits P-TEFb to Spt5/DSIF via a recruitment pathway consisting of Med1, Med23 and Tat-SF1, whereas SEC recruits P-TEFb to NELF-A and NELF-E via Paf1c and Med26, respectively...
August 19, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27282391/architecture-and-rna-binding-of-the-human-negative-elongation-factor
#18
Seychelle M Vos, David Pöllmann, Livia Caizzi, Katharina B Hofmann, Pascaline Rombaut, Tomasz Zimniak, Franz Herzog, Patrick Cramer
Transcription regulation in metazoans often involves promoter-proximal pausing of RNA polymerase (Pol) II, which requires the 4-subunit negative elongation factor (NELF). Here we discern the functional architecture of human NELF through X-ray crystallography, protein crosslinking, biochemical assays, and RNA crosslinking in cells. We identify a NELF core subcomplex formed by conserved regions in subunits NELF-A and NELF-C, and resolve its crystal structure. The NELF-AC subcomplex binds single-stranded nucleic acids in vitro, and NELF-C associates with RNA in vivo...
2016: ELife
https://www.readbyqxmd.com/read/27256882/chemical-genetic-discovery-of-parp-targets-reveals-a-role-for-parp-1-in-transcription-elongation
#19
Bryan A Gibson, Yajie Zhang, Hong Jiang, Kristine M Hussey, Jonathan H Shrimp, Hening Lin, Frank Schwede, Yonghao Yu, W Lee Kraus
Poly[adenosine diphosphate (ADP)-ribose] polymerases (PARPs) are a family of enzymes that modulate diverse biological processes through covalent transfer of ADP-ribose from the oxidized form of nicotinamide adenine dinucleotide (NAD(+)) onto substrate proteins. Here we report a robust NAD(+) analog-sensitive approach for PARPs, which allows PARP-specific ADP-ribosylation of substrates that is suitable for subsequent copper-catalyzed azide-alkyne cycloaddition reactions. Using this approach, we mapped hundreds of sites of ADP-ribosylation for PARPs 1, 2, and 3 across the proteome, as well as thousands of PARP-1-mediated ADP-ribosylation sites across the genome...
July 1, 2016: Science
https://www.readbyqxmd.com/read/27177472/mir-1236-regulates-hypoxia-induced-epithelial-mesenchymal-transition-and-cell-migration-invasion-through-repressing-senp1-and-hdac3
#20
Sung-Yuan Chen, Shu-Chun Teng, Tzu-Hao Cheng, Kou-Juey Wu
Intratumoral hypoxia induces epithelial-mesenchymal transition and promotes cancer metastasis. MicroRNAs (miRNAs) are endogenous, single-strand RNA molecules that regulate gene expression. MiRNAs control cell growth, proliferation, differentiation and cell death and may function as oncogenes or tumor suppressors. HDAC3 and SENP1 are two molecules involved in hypoxia-induced EMT and HIF-1α stability, respectively. In this report, we show that miR-1236 plays a critical role in hypoxia-induced EMT and metastasis...
August 1, 2016: Cancer Letters
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