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RNA Polymerase II

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https://www.readbyqxmd.com/read/29785964/mechanism-of-selective-recruitment-of-rna-polymerases-ii-and-iii-to-snrna-gene-promoters
#1
Oleksandr Dergai, Pascal Cousin, Jerome Gouge, Karishma Satia, Viviane Praz, Tracy Kuhlman, Philippe Lhôte, Alessandro Vannini, Nouria Hernandez
RNA polymerase II (Pol II) small nuclear RNA (snRNA) promoters and type 3 Pol III promoters have highly similar structures; both contain an interchangeable enhancer and "proximal sequence element" (PSE), which recruits the SNAP complex (SNAPc). The main distinguishing feature is the presence, in the type 3 promoters only, of a TATA box, which determines Pol III specificity. To understand the mechanism by which the absence or presence of a TATA box results in specific Pol recruitment, we examined how SNAPc and general transcription factors required for Pol II or Pol III transcription of SNAPc-dependent genes (i...
May 21, 2018: Genes & Development
https://www.readbyqxmd.com/read/29785027/targeting-g-quadruplex-dna-as-cognitive-function-therapy-for-atr-x-syndrome
#2
Norifumi Shioda, Yasushi Yabuki, Kouya Yamaguchi, Misaki Onozato, Yue Li, Kenji Kurosawa, Hideyuki Tanabe, Nobuhiko Okamoto, Takumi Era, Hiroshi Sugiyama, Takahito Wada, Kohji Fukunaga
Alpha-thalassemia X-linked intellectual disability (ATR-X) syndrome is caused by mutations in ATRX, which encodes a chromatin-remodeling protein. Genome-wide analyses in mouse and human cells indicate that ATRX tends to bind to G-rich sequences with a high potential to form G-quadruplexes. Here, we report that Atrx mutation induces aberrant upregulation of Xlr3b expression in the mouse brain, an outcome associated with neuronal pathogenesis displayed by ATR-X model mice. We show that ATRX normally binds to G-quadruplexes in CpG islands of the imprinted Xlr3b gene, regulating its expression by recruiting DNA methyltransferases...
May 21, 2018: Nature Medicine
https://www.readbyqxmd.com/read/29780264/methylation-and-gene-expression-of-bcat1-and-ikzf1-in-colorectal-cancer-tissues
#3
Maher Jedi, Graeme P Young, Susanne K Pedersen, Erin L Symonds
The genes BCAT1 and IKZF1 are hypermethylated in colorectal cancer (CRC), but little is known about how this relates to gene expression. This study assessed the relationship between methylation and gene expression of BCAT1 and IKZF1 in CRC and adjacent non-neoplastic tissues. The tissues were obtained at surgery from 36 patients diagnosed with different stages of CRC (stage I n = 8, stage II n = 13, stage III n = 10, stage IV n = 5). Methylated BCAT1 and IKZF1 were detected in 92% and 72% CRC tissues, respectively, with levels independent of stage ( P  > ...
2018: Clinical Medicine Insights. Oncology
https://www.readbyqxmd.com/read/29775646/the-rna-binding-protein-ars2-supports-hematopoiesis-at-multiple-levels
#4
Seerat Elahi, Shawn M Egan, G Aaron Holling, Rachel L Kandefer, Michael J Nemeth, Scott H Olejniczak
Recent biochemical characterization of Arsenic resistance protein 2 (Ars2) has established it as central to determining the fate of nascent RNA polymerase II (RNAPII) transcripts. Through interactions with the nuclear 5'-7-methylguanosine (7mG) cap binding complex (CBC), Ars2 promotes co-transcriptional processing coupled with nuclear export or degradation of several classes of RNAPII transcripts, allowing for gene expression programs that facilitate rapid and sustained proliferation of immortalized cells in culture...
May 15, 2018: Experimental Hematology
https://www.readbyqxmd.com/read/29774127/paf1-complex-interactions-with-setdb1-mediate-promoter-h3k9-methylation-and-transcriptional-repression-of-hoxa9-and-meis1-in-acute-myeloid-leukemia
#5
James Ropa, Nirmalya Saha, Zhiling Chen, Justin Serio, Wei Chen, Dattatreya Mellacheruvu, Lili Zhao, Venkatesha Basrur, Alexey I Nesvizhskii, Andrew G Muntean
The Polymerase Associated Factor 1 complex (PAF1c) is an epigenetic co-modifying complex that directly contacts RNA polymerase II (RNAPII) and several epigenetic regulating proteins. Mutations, overexpression and loss of expression of subunits of the PAF1c are observed in various forms of cancer suggesting proper regulation is needed for cellular development. However, the biochemical interactions with the PAF1c that allow dynamic gene regulation are unclear. We and others have shown that the PAF1c makes a direct interaction with MLL fusion proteins, which are potent oncogenic drivers of acute myeloid leukemia (AML)...
April 24, 2018: Oncotarget
https://www.readbyqxmd.com/read/29773845/aicar-inhibits-nf%C3%AE%C2%BAb-dna-binding-independently-of-ampk-to-attenuate-lps-triggered-inflammatory-responses-in-human-macrophages
#6
Johannes Kirchner, Bernhard Brüne, Dmitry Namgaladze
5-aminoimidazole-4-carboxamide-1-β-D-ribofuranoside (AICAR) is an established pharmacological activator of AMP-activated protein kinase (AMPK). Both, AICAR and AMPK were reported to attenuate inflammation. However, AICAR is known for many AMPK-independent effects, although the mechanisms remain incompletely understood. Here we report a potent suppression of lipopolysaccharide (LPS)-induced inflammatory gene expression by AICAR in primary human macrophages, which occurred independently of its conversion to AMPK-activating 5-aminoimidazole-4-carboxamide-1-β-D-ribofuranosyl monophosphate...
May 17, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29771641/inhabiting-plant-roots-nematodes-and-truffles-polyphilus-a-new-helotialean-genus-with-two-globally-distributed-species
#7
Samad Ashrafi, Dániel G Knapp, Damien Blaudez, Michel Chalot, Jose G Maciá-Vicente, Imre Zagyva, Abdelfattah A Dababat, Wolfgang Maier, Gábor M Kovács
Fungal root endophytes, including the common group of dark septate endophytes (DSEs), represent different taxonomic groups and potentially diverse life strategies. In this study, we investigated two unidentified helotialean lineages found previously in a study of DSE fungi of semiarid grasslands, from several other sites, and collected recently from a pezizalean truffle ascoma and eggs of the cereal cyst nematode Heterodera filipjevi. The taxonomic positions and phylogenetic relationships of 21 isolates with different hosts and geographic origins were studied in detail...
March 26, 2018: Mycologia
https://www.readbyqxmd.com/read/29771420/imp3-promotes-tnbc-stem-cell-property-through-mirna-34a-regulation
#8
Q-D Huang, S-R Zheng, Y-J Cai, D-L Chen, Y-Y Shen, C-Q Lin, X-Q Hu, X-H Wang, H Shi, G-L Guo
OBJECTIVE: To explore the expression and function of insulin-like growth factor II (IGFII) mRNA binding protein (IMP3) in the Triple Negative Breast Cancer (TNBC). MATERIALS AND METHODS: According to previously reported gene expression array, we found that IMP3 had significantly higher expression in the CD44+CD24-ESA+ cell cluster, tumor initiating cell or cancer stem cell (CSCs), compared to other tumor cells. Based on the GEO database (GEO accession No. GSE6883), we detected the mRNA levels of IMP 1,2 and 3 by quantitative polymerase chain reaction (q-PCR) in CD44+CD24-ESA+ cell cluster and other breast tumor cell clusters...
May 2018: European Review for Medical and Pharmacological Sciences
https://www.readbyqxmd.com/read/29771376/rna-dna-and-dna-dna-base-pairing-at-the-upstream-edge-of-the-transcription-bubble-regulate-translocation-of-rna-polymerase-and-transcription-rate
#9
Maria KIreeva, Cyndi Trang, Gayane Matevosyan, Joshua Turek-Herman, Vitaly Chasov, Lucyna Lubkowska, Mikhail Kashlev
Translocation of RNA polymerase (RNAP) along DNA may be rate-limiting for transcription elongation. The Brownian ratchet model posits that RNAP rapidly translocates back and forth until the post-translocated state is stabilized by NTP binding. An alternative model suggests that RNAP translocation is slow and poorly reversible. To distinguish between these two models, we take advantage of an observation that pyrophosphorolysis rates directly correlate with the abundance of the pre-translocated fraction. Pyrophosphorolysis by RNAP stabilized in the pre-translocated state by bacteriophage HK022 protein Nun was used as a reference point to determine the pre-translocated fraction in the absence of Nun...
May 16, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29768209/influenza-virus-mounts-a-two-pronged-attack-on-host-rna-polymerase-ii-transcription
#10
David L V Bauer, Michael Tellier, Mónica Martínez-Alonso, Takayuki Nojima, Nick J Proudfoot, Shona Murphy, Ervin Fodor
Influenza virus intimately associates with host RNA polymerase II (Pol II) and mRNA processing machinery. Here, we use mammalian native elongating transcript sequencing (mNET-seq) to examine Pol II behavior during viral infection. We show that influenza virus executes a two-pronged attack on host transcription. First, viral infection causes decreased Pol II gene occupancy downstream of transcription start sites. Second, virus-induced cellular stress leads to a catastrophic failure of Pol II termination at poly(A) sites, with transcription often continuing for tens of kilobases...
May 15, 2018: Cell Reports
https://www.readbyqxmd.com/read/29767265/knockdown-of-tnf%C3%A2-%C3%AE-alleviates-acute-lung-injury-in-rats-with-intestinal-ischemia-and-reperfusion-injury-by-upregulating-il%C3%A2-10-expression
#11
Zhen Yang, Xue-Rong Zhang, Qiong Zhao, Sheng-Lan Wang, Liu-Lin Xiong, Piao Zhang, Bing Yuan, Zi-Bing Zhang, Shu-Yuan Fan, Ting-Hua Wang, Yun-Hui Zhang
Intestinal ischemia and reperfusion (II/R) injury often triggers severe injury in remote organs, with the lungs being considered the main target. Excessive elevation of proinflammatory cytokines is a major contributor in the occurrence and development of II/R‑induced acute lung injury (ALI). Therefore, the present study aimed to investigate whether blocking tumor necrosis factor‑α (TNF‑α) expression could protect the lungs from injury following II/R, and to explore the possible underlying mechanism involving interleukin‑10 (IL‑10)...
May 14, 2018: International Journal of Molecular Medicine
https://www.readbyqxmd.com/read/29764463/lncmapk6-drives-mapk6-expression-and-liver-tic-self-renewal
#12
Guanqun Huang, Hui Jiang, Yueming He, Ye Lin, Wuzheng Xia, Yuanwei Luo, Min Liang, Boyun Shi, Xinke Zhou, Zhixiang Jian
BACKGROUND: Liver tumor initiating cells (TICs) have self-renewal and differentiate capacities, and largely contribute to tumor initiation, metastasis and drug resistance. MAPK signaling is a critical pathway in many biological processes, while its role in liver TICs hasn't been explored. METHODS: Online-available dataset was used for unbiased screening. Liver TICs were examined CD133 FACS or oncosphere formation. TIC self-renewal was detected by oncosphere formation and tumor initiation assay...
May 15, 2018: Journal of Experimental & Clinical Cancer Research: CR
https://www.readbyqxmd.com/read/29763375/chromosomal-architecture-and-placental-expression-of-the-human-growth-hormone-gene-family-are-targeted-by-pre-pregnancy-maternal-obesity
#13
Yan Jin, Hana Vakili, SongYan Liu, Savas Menticoglou, Margaret E Bock, Peter A Cattini
The human (h) placental lactogenic hormone chorionic somatomammotropin (CS) is highly produced during pregnancy and acts as a metabolic adaptor in response to maternal insulin resistance. Maternal obesity can exacerbate this "resistance" and a >75% decrease in CS RNA levels was observed in term placentas from obese versus lean women. The genes coding for hCS (hCS-A and hCS-B) and placental growth hormone (hGH-V) as well as the hCS-L pseudogene and pituitary growth hormone (GH) gene (hGH-N) are located at a single locus on chromosome 17...
May 15, 2018: American Journal of Physiology. Endocrinology and Metabolism
https://www.readbyqxmd.com/read/29760717/reduced-neuronal-transcription-of-escargot-the-drosophila-gene-encoding-a-snail-type-transcription-factor-promotes-longevity
#14
Alexander V Symonenko, Natalia V Roshina, Anna V Krementsova, Elena G Pasyukova
In recent years, several genes involved in complex neuron specification networks have been shown to control life span. However, information on these genes is scattered, and studies to discover new neuronal genes and gene cascades contributing to life span control are needed, especially because of the recognized role of the nervous system in governing homeostasis, aging, and longevity. Previously, we demonstrated that several genes that encode RNA polymerase II transcription factors and that are involved in the development of the nervous system affect life span in Drosophila melanogaster ...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/29759984/ndf-a-nucleosome-destabilizing-factor-that-facilitates-transcription-through-nucleosomes
#15
Jia Fei, Haruhiko Ishii, Marten A Hoeksema, Franz Meitinger, George A Kassavetis, Christopher K Glass, Bing Ren, James T Kadonaga
Our understanding of transcription by RNA polymerase II (Pol II) is limited by our knowledge of the factors that mediate this critically important process. Here we describe the identification of NDF, a nucleosome-destabilizing factor that facilitates Pol II transcription in chromatin. NDF has a PWWP motif, interacts with nucleosomes near the dyad, destabilizes nucleosomes in an ATP-independent manner, and facilitates transcription by Pol II through nucleosomes in a purified and defined transcription system as well as in cell nuclei...
May 14, 2018: Genes & Development
https://www.readbyqxmd.com/read/29757712/genetic-variability-of-ganoderma-zonatum-infecting-palms-in-florida
#16
Monica L Elliott, Elizabeth A Des Jardin, Johana V Ortiz, Tommy Macias
Ganoderma zonatum is a lethal pathogen of palms (Arecaceae) in Florida (USA) because it degrades the wood of the lowest section of the palm trunk. This fungus is widespread throughout Florida, where it has been observed on over 60 species of palms. The authors examined the genetic variability of 25 isolates of G. zonatum obtained in Florida from 12 different palm species and representing 17 unique property locations in eight counties to determine if G. zonatum represents a species complex. The three genomic regions examined were the nuc rDNA ITS1-5...
March 2, 2018: Mycologia
https://www.readbyqxmd.com/read/29754318/four-new-species-of-metschnikowia-and-the-transfer-of-seven-candida-species-to-metschnikowia-and-clavispora-as-new-combinations
#17
Cletus P Kurtzman, Christie J Robnett, Eleanor Basehoar, Todd J Ward
From comparisons of ITS1-5.8S-ITS2 and gene sequences for nuclear D1/D2 LSU rRNA, nuclear SSU (18S) rRNA, translation elongation factor 1-α (EF1-α) and RNA polymerase II subunit 2 (RPB2), the following four new ascosporogenous yeast species were resolved and are described as Metschnikowia anglica (NRRL Y-7298T [type strain], CBS 15342, MycoBank MB 823167), Metschnikowia leonuri (NRRL Y-6546T , CBS 15341, MB 823166), Metschnikowia peoriensis (NRRL Y-5942T , CBS 15345, MB 823164) and Metschnikowia rubicola (NRRL Y-6064T , CBS 15344, MB 823165)...
May 12, 2018: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/29752751/intact-arabidopsis-rpb1-functions-in-stem-cell-niches-maintenance-and-cell-cycling-control
#18
Qian-Qian Zhang, Li Ying, Zhao-Ying Fu, Xun-Biao Liu, Kai Yuan, Ying Fang, Yan Liu, Gang Li, Xian-Sheng Zhang, Kang Chong, Lei Ge
Plant meristem activity depends on accurate execution of transcriptional networks required for establishing optimum functioning of stem cell niches. An Arabidopsis mutant card1-1 (constitutive auxin response with DR5:GFP) that encodes a truncated RPB1 (RNA Polymerase II's largest subunit) with shortened C-terminal domain (CTD) was identified. Phosphorylation of the CTD repeats of RPB1 is coupled to transcription in eukaryotes. Here we uncover that the truncated CTD of RPB1 disturbed cell cycling and enlarged the size of shoot and root meristem...
May 12, 2018: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/29748575/controlling-nuclear-rna-levels
#19
REVIEW
Manfred Schmid, Torben Heick Jensen
RNA turnover is an integral part of cellular RNA homeostasis and gene expression regulation. Whereas the cytoplasmic control of protein-coding mRNA is often the focus of study, we discuss here the less appreciated role of nuclear RNA decay systems in controlling RNA polymerase II (RNAPII)-derived transcripts. Historically, nuclear RNA degradation was found to be essential for the functionalization of transcripts through their proper maturation. Later, it was discovered to also be an important caretaker of nuclear hygiene by removing aberrant and unwanted transcripts...
May 10, 2018: Nature Reviews. Genetics
https://www.readbyqxmd.com/read/29747586/selective-modulation-of-local-linkages-between-active-transcription-and-oxidative-demethylation-activity-shapes-cardiomyocyte-specific-gene-body-epigenetic-status-in-mice
#20
Mayumi Oda, Shunichi Wakabayashi, N Ari Wijetunga, Shinsuke Yuasa, Hirokazu Enomoto, Ruri Kaneda, Sung Han Yoon, Nishant Mittal, Qiang Jing, Masako Suzuki, John M Greally, Keiichi Fukuda, Shinji Makino
BACKGROUND: Cell-type-specific genes exhibit heterogeneity in genomic contexts and may be subject to different epigenetic regulations through different gene transcriptional processes depending on the cell type involved. The gene-body regions (GBRs) of some cardiomyocyte (CM)-specific genes are long and highly hypomethylated in CMs. To explore the cell-type specificities of epigenetic patterns and functions, multiple epigenetic modifications of GBRs were compared among CMs, liver cells and embryonic stem cells (ESCs)...
May 10, 2018: BMC Genomics
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