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Transcriptional elongation

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https://www.readbyqxmd.com/read/28213523/identification-of-regions-in-the-spt5-subunit-of-dsif-that-are-involved-in-promoter-proximal-pausing
#1
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/28211799/increased-expression-of-long-non-coding-rna-glidr-in-prostate-cancer
#2
Yingyi Zhang, Zhe Kong, Yalong Zhang, Wenhua Huang, Hai Wu, Xuechao Wan, Yao Li
Prostate cancer (PCa) was one of the most common cancers in males in China. Long non-coding RNAs (lncRNA), a class of non-coding RNAs with more than 200 nucleotides, played key roles in the progression of prostate cancer. GLIDR, a novel long intergenic ncRNA, was found to be upregulated in tumors compared to normal tissues by using publically databases. In the clinical validation cohort, our results showed GLIDR was significantly up-regulated in prostate cancer samples and cell lines. To explore the potential functions of the GLIDR, we constructed gene co-expression networks and applied GO analysis...
February 3, 2017: Cancer Biomarkers: Section A of Disease Markers
https://www.readbyqxmd.com/read/28211089/icariin-promotes-mouse-hair-follicle-growth-by-increasing-insulin-like-growth-factor-1-expression-in-dermal-papillary-cells
#3
Y-S Su, Z-X Fan, S-E Xiao, B-J Lin, Y Miao, Z-Q Hu, H Liu
BACKGROUND: Icariin is a major flavonoid isolated from Epimedium spp. leaves (Epimedium Herba), and has multiple pharmacological functions, including anti-angiogenesis, anti-oxidant, anti-inflammatory and immunoprotective effects. AIM: To investigate whether icariin can stimulate growth of hair follicles in mice and the underlying mechanism. METHODS: In vitro, the effect of icariin on hair growth was assessed by using a vibrissae hair follicle (VHF) organ-culture model...
February 16, 2017: Clinical and Experimental Dermatology
https://www.readbyqxmd.com/read/28210955/the-effects-of-igf-1-on-tnf-%C3%AE-treated-drg-neurons-by-modulating-atf3-and-gap-43-expression-via-pi3k-akt-s6k-signaling-pathway
#4
Lei Zhang, Yaping Yue, Meishuo Ouyang, Huaxiang Liu, Zhenzhong Li
Upregulation of the pro-inflammatory cytokine tumor necrosis factor α (TNF-α) is involved in the development and progression of numerous neurological disorders. Recent reports have challenged the concept that TNF-α exhibits only deleterious effects of pro-inflammatory destruction, and have raised the awareness that it may play a beneficial role in neuronal growth and function in particular conditions, which prompts us to further investigate the role of this cytokine. Insulin-like growth factor-1 (IGF-1) is a cytokine possessing powerful neuroprotective effects in promoting neuronal survival, neuronal differentiation, neurite elongation, and neurite regeneration...
February 16, 2017: Neurochemical Research
https://www.readbyqxmd.com/read/28209164/rnf40-regulates-gene-expression-in-an-epigenetic-context-dependent-manner
#5
Wanhua Xie, Sankari Nagarajan, Simon J Baumgart, Robyn Laura Kosinsky, Zeynab Najafova, Vijayalakshmi Kari, Magali Hennion, Daniela Indenbirken, Stefan Bonn, Adam Grundhoff, Florian Wegwitz, Ahmed Mansouri, Steven A Johnsen
BACKGROUND: Monoubiquitination of H2B (H2Bub1) is a largely enigmatic histone modification that has been linked to transcriptional elongation. Because of this association, it has been commonly assumed that H2Bub1 is an exclusively positively acting histone modification and that increased H2Bub1 occupancy correlates with increased gene expression. In contrast, depletion of the H2B ubiquitin ligases RNF20 or RNF40 alters the expression of only a subset of genes. RESULTS: Using conditional Rnf40 knockout mouse embryo fibroblasts, we show that genes occupied by low to moderate amounts of H2Bub1 are selectively regulated in response to Rnf40 deletion, whereas genes marked by high levels of H2Bub1 are mostly unaffected by Rnf40 loss...
February 16, 2017: Genome Biology
https://www.readbyqxmd.com/read/28199965/whole-exome-sequencing-identified-a-homozygous-brdt-mutation-in-a-patient-with-acephalic-spermatozoa
#6
Lin Li, Yanwei Sha, Xi Wang, Ping Li, Jing Wang, Kehkooi Kee, Binbin Wang
Acephalic spermatozoa is a very rare disorder of male infertility. Here, in a patient from from a consanguineous family, we have identified, by whole-exome sequencing, a homozygous mutation (c.G2783A, p.G928D) in the BRDT gene. The gene product, BRDT, is a testis-specific protein that is considered an important drug target for male contraception. The G928D mutation is in the P-TEFb binding domain, which mediates the interaction with transcription elongation factor and might affect the transcriptional activities of downstream genes...
February 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/28199109/the-nucleotide-selectivity-at-a-pre-insertion-checkpoint-of-t7-rna-polymerase-transcription-elongation
#7
Chao E, Baogen Duan, Jin Yu
Nucleotide selection is crucial for transcription fidelity control, in particular, for viral T7 RNA polymerase (RNAP) lack of proofreading activity. It has been recognized that multiple kinetic checkpoints exist prior to full nucleotide incorporation. In this work, we implemented intensive atomistic molecular dynamics (MD) simulations to quantify how strong the nucleotide selection is at the initial checkpoint of an elongation cycle of T7 RNAP. The incoming nucleotides bind into a pre-insertion site where a critical tyrosine residue locates nearby to assist the nucleotide selection...
February 15, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28191883/loap-is-a-broadly-conserved-antiterminator-protein-that-regulates-antibiotic-gene-clusters-in-bacillus-amyloliquefaciens
#8
Jonathan R Goodson, Steven Klupt, Chengxi Zhang, Paul Straight, Wade C Winkler
A valuable resource available in the search for new natural products is the diverse microbial life that spans the planet. A large subset of these microorganisms synthesize complex specialized metabolites exhibiting biomedically important activities. A limiting step to the characterization of these compounds is an elucidation of the genetic regulatory mechanisms that oversee their production. Although proteins that control transcription initiation of specialized metabolite gene clusters have been identified, those affecting transcription elongation have not been broadly investigated...
February 13, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/28190769/paf1-has-distinct-roles-in-transcription-elongation-and-differential-transcript-fate
#9
Harry Fischl, Françoise S Howe, Andre Furger, Jane Mellor
RNA polymerase II (Pol2) movement through chromatin and the co-transcriptional processing and fate of nascent transcripts is coordinated by transcription elongation factors (TEFs) such as polymerase-associated factor 1 (Paf1), but it is not known whether TEFs have gene-specific functions. Using strand-specific nucleotide resolution techniques, we show that levels of Paf1 on Pol2 vary between genes, are controlled dynamically by environmental factors via promoters, and reflect levels of processing and export factors on the encoded transcript...
February 16, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28188267/phosphorylation-of-spt5-by-cdkd-2-is-required-for-vip5-recruitment-and-normal-flowering-in-arabidopsis-thaliana
#10
Chengyuan Lu, Yongke Tian, Shiliang Wang, Yanhua Su, Ting Mao, Tongtong Huang, Qingqing Chen, Zuntao Xu, Yong Ding
The elongation factor suppressor of Ty 5 homolog (Spt5) is a regulator of transcription and histone methylation. In humans, phosphorylation of SPT5 by P-TEFb, a protein kinase composed of Cyclin-dependent kinase 9 (CDK9) and cyclin T, interacts with the RNA polymerase II-associated factor1 (PAF1) complex. However, the mechanism of SPT5 phosphorylation is not well understood in plants. Here, we examine the function of SPT5 in Arabidopsis thaliana, and find that spt5 mutant flowers early under long-day and short-day conditions...
February 10, 2017: Plant Cell
https://www.readbyqxmd.com/read/28184371/transcriptional-regulation-of-telomerase-reverse-transcriptase-tert-by-myc
#11
REVIEW
Ekta Khattar, Vinay Tergaonkar
Telomerase elongates telomeres and is crucial for maintaining genomic stability. While stem cells and cancer cells display high telomerase activity, normal somatic cells lack telomerase activity primarily due to transcriptional repression of telomerase reverse transcriptase (TERT), the catalytic component of telomerase. Transcription factor binding, chromatin status as well as epigenetic modifications at the TERT promoter regulates TERT transcription. Myc is an important transcriptional regulator of TERT that directly controls its expression by promoter binding and associating with other transcription factors...
2017: Frontiers in Cell and Developmental Biology
https://www.readbyqxmd.com/read/28182006/coordinate-activities-of-brd4-and-cdk9-in-the-transcriptional-elongation-complex-are-required-for-tgf%C3%AE-induced-nox4-expression-and-myofibroblast-transdifferentiation
#12
Talha Ijaz, Mohammad Jamaluddin, Yingxin Zhao, Yueqing Zhang, Jayson Jay, Celeste C Finnerty, David N Herndon, Ronald G Tilton, Allan R Brasier
Transdifferentiation of quiescent dermal fibroblasts to secretory myofibroblasts has a central role in wound healing and pathological scar formation. This myofibroblast transdifferentiation process involves TGFβ-induced de novo synthesis of alpha smooth muscle cell actin (αSMA)+ fibers that enhance contractility as well as increased expression of extracellular matrix (ECM) proteins, including collagen and fibronectin. These processes are mediated upstream by the reactive oxygen species (ROS)-producing enzyme Nox4, whose induction by TGFβ is incompletely understood...
February 9, 2017: Cell Death & Disease
https://www.readbyqxmd.com/read/28181542/elongation-factor-p-restricts-salmonella-s-growth-by-controlling-translation-of-a-mg-2-transporter-gene-during-infection
#13
Eunna Choi, Soomin Choi, Daesil Nam, Shinae Park, Yoontak Han, Jung-Shin Lee, Eun-Jin Lee
When a ribosome translates mRNA sequences, the ribosome often stalls at certain codons because it is hard to translate. Consecutive proline codons are such examples that induce ribosome stalling and elongation factor P (EF-P) is required for the stalled ribosome to continue translation at those consecutive proline codons. We found that EF-P is required for translation of the mgtB gene encoding a Mg(2+) transporter in the mgtCBR virulence operon from the intracellular pathogen Salmonella enterica serovar Typhimurium...
February 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28179136/expression-purification-and-characterization-of-the-human-mta2-rbbp7-complex
#14
Christoffer Brasen, Jerzy Dorosz, Anders Wiuf, Thomas Boesen, Osman Mirza, Michael Gajhede
The repressive Nucleosome Remodeling and histone Deacetylation (NuRD) complex remodels the chromatin structure by coupling ATP-dependent remodeling activity with histone deacetylase function and plays important roles in regulating gene transcription, DNA damage repair and chromatin assembly. The complex is composed of six subunits: Metastasis Associated proteins MTA1/2/3 initially recruit histone chaperones RBBP4/7 followed by the histone deacetylases HDAC1/2 forming a core complex. Further association of the CpG-binding protein MBD2/3, p66α/β and the ATP-dependent helicase CDH3/4 constitutes the NuRD complex...
February 4, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28169463/relationship-between-epigenetic-regulation-dietary-habits-and-the-developmental-origins-of-health-and-disease-theory
#15
REVIEW
Kazuki Mochizuki, Natsuyo Hariya, Kazue Honma, Toshinao Goda
Environmental stressors during developmental stages are hypothesized to increase the risk of developing metabolic diseases such as obesity, type 2 diabetes, hypertension, and psychiatric diseases during later life. This theory is known as the Developmental Origins of Health and Disease (DOHaD). Recent studies suggest that accumulation of environmental stress, including during developmental stages, is internalized as acquired information designated as "epigenetic memory." This epigenetic memory is generally indicated as DNA methylation and histone modifications in the chromatin...
February 7, 2017: Congenital Anomalies
https://www.readbyqxmd.com/read/28166983/maternal-recognition-of-pregnancy-and-implantation-are-not-associated-with-an-interferon-response-of-the-endometrium-to-the-presence-of-the-conceptus-in-dromedary-camel
#16
Ahmed Sabry Salah Abdoon, Corrine Giraud-Delville, Omaima Mohamed Kandil, Annelye Kerboeuf-Giraud, Caroline Eozénou, Anais Vitorino Carvalho, Skidmore Julian, Olivier Sandra
Maternal recognition of pregnancy (MRP) and implantation involve appropriate interactions between the elongating conceptus and the receptive endometrium that will condition development of the feto-placental unit to term. Molecular mechanisms that take place at the conceptus-endometrium interface during early pregnancy have been extensively investigated in domestic ungulates but they are still poorly understood in camelids including the dromedary camel (Camelus dromedarius), a domestic species with important economic and social roles in arid and semi-arid areas...
March 1, 2017: Theriogenology
https://www.readbyqxmd.com/read/28165739/discovery-of-novel-disruptor-of-silencing-telomeric-1-like-dot1l-inhibitors-using-a-target-specific-scoring-function-for-the-s-adenosyl-l-methionine-sam-dependent-methyltransferase-family
#17
Yulan Wang, Linjuan Li, Bidong Zhang, Jing Xing, Shijie Chen, Wei Wan, Yakai Song, Hao Jiang, Hualiang Jiang, Cheng Luo, Mingyue Zheng
The disruptor of telomeric silencing 1-like (DOT1L) protein is a histone H3K79 methyltransferase that plays a key role in transcriptional elongation and cell cycle regulation and is required for the development and maintenance of MLL-rearranged mixed lineage leukemia. Much effort has been dedicated towards discovering novel scaffold DOT1L inhibitors using different strategies. Here, we report the development and application of a target-specific scoring function, the SAM score, for S-adenosyl-L-methionine (SAM)-dependent methyltransferases, for the discovery of novel DOT1L inhibitors...
February 6, 2017: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28161635/effect-of-tcea3-on-the-differentiation-of-bovine-skeletal-muscle-satellite-cells
#18
Yue Zhu, Hui-Li Tong, Shu-Feng Li, Yun-Qin Yan
Bovine muscle-derived satellite cells (MDSCs) are important for animal growth. In this study, the effect of transcription elongation factor A3 (TCEA3) on bovine MDSC differentiation was investigated. Western blotting, immunofluorescence assays, and cytoplasmic and nuclear protein isolation and purification techniques were used to determine the expression pattern and protein localization of TCEA3 in bovine MDSCs during in vitro differentiation. TCEA3 expression was upregulated using the CRISPR/Cas9 technique to study its effects on MDSC differentiation in vitro...
February 2, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28155919/obtaining-spontaneously-beating-cardiomyocyte-like-cells-from-adipose-derived-stromal-vascular-fractions-cultured-on-enzyme-crosslinked-gelatin-hydrogels
#19
Gang Yang, Zhenghua Xiao, Xiaomei Ren, Haiyan Long, Kunlong Ma, Hong Qian, Yingqiang Guo
Heart failure often develops after acute myocardial infarction because the injured myocardial tissue fails to recover or regenerate. Stem cell transplantation using adult cell sources, such as adipose-derived stromal vascular fraction (SVF), draws extensive attention. In this study, SVF cells were isolated from rat adipose tissue and cultivated on enzyme-crosslinked gelatin hydrogels. Morphological features of cell development and spontaneous beating behavior from these cells were observed and recorded. Cardiac phenotypes were characterized via immunofluorescence staining, and the expression of cardiac-specific genes was measured via RT-PCR...
February 3, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28154185/heterochromatin-protein-1%C3%AE-is-a-novel-epigenetic-repressor-of-human-embryonic-%C3%AF%C2%B5-globin-gene-expression
#20
Yadong Wang, Ying Wang, Lingling Ma, Min Nie, Junyi Ju, Ming Liu, Yexuan Deng, Bing Yao, Tao Gui, Xinyu Li, Chan Guo, Chi Ma, Renxiang Tan, Quan Zhao
Production of hemoglobin during development is tightly regulated. For example, expression from the human β-globin gene locus, comprising β-, δ-, ϵ-, and γ-globin genes, switches from ϵ-globin to γ-globin during embryonic development and then from γ-globin to β-globin after birth. Expression of human ϵ-globin in mice has been shown to ameliorate anemia caused by β-globin mutations, including those causing β-thalassemia and sickle cell disease (SCD), raising the prospect that reactivation of ϵ-globin expression could be used in managing these conditions in humans...
February 1, 2017: Journal of Biological Chemistry
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