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Transcriptional elongation

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https://www.readbyqxmd.com/read/28644379/physical-forces-may-cause-the-hoxd-gene-cluster-elongation
#1
Spyros Papageorgiou
Hox gene collinearity was discovered be Edward B. Lewis in 1978. It consists of the Hox1, Hox2, Hox3 ordering of the Hox genes in the chromosome from the telomeric to the centromeric side of the chromosome. Surprisingly, the spatial activation of the Hox genes in the ontogenetic units of the embryo follows the same ordering along the anterior-posterior embryonic axis. The chromosome microscale differs from the embryo macroscale by 3 to 4 orders of magnitude. The traditional biomolecular mechanisms are not adequate to comprise phenomena at so divergent spatial domains...
June 23, 2017: Biology
https://www.readbyqxmd.com/read/28641539/role-of-host-factors-on-the-regulation-of-tat-mediated-hiv-1-transcription
#2
Guillaume Mousseau, Susana T Valente
BACKGROUND: The viral transactivator Tat protein is a key modulator of HIV-1 replication, as it regulates transcriptional elongation from the integrated proviral genome. Tat recruits the human transcription elongation factor b, and other host proteins, such as the super elongation complex, to activate the cellular RNA polymerase II, normally stalled shortly after transcription initiation at the HIV promoter. By means of a complex set of interactions with host cellular factors, Tat determines the fate of viral activity within the infected cell...
June 22, 2017: Current Pharmaceutical Design
https://www.readbyqxmd.com/read/28637236/the-ribosome-assembly-gene-network-is-controlled-by-the-feedback-regulation-of-transcription-elongation
#3
Fernando Gómez-Herreros, Thanasis Margaritis, Olga Rodríguez-Galán, Vicent Pelechano, Victoria Begley, Gonzalo Millán-Zambrano, Macarena Morillo-Huesca, Mari Cruz Muñoz-Centeno, José E Pérez-Ortín, Jesús de la Cruz, Frank C P Holstege, Sebastián Chávez
Ribosome assembly requires the concerted expression of hundreds of genes, which are transcribed by all three nuclear RNA polymerases. Transcription elongation involves dynamic interactions between RNA polymerases and chromatin. We performed a synthetic lethal screening in Saccharomyces cerevisiae with a conditional allele of SPT6, which encodes one of the factors that facilitates this process. Some of these synthetic mutants corresponded to factors that facilitate pre-rRNA processing and ribosome biogenesis...
June 15, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28637181/crosstalk-between-histone-modifications-indicates-that-inhibition-of-arginine-methyltransferase-carm1-activity-reverses-hiv-latency
#4
Zheng Zhang, Bryan C Nikolai, Leah A Gates, Sung Yun Jung, Edward B Siwak, Bin He, Andrew P Rice, Bert W O'Malley, Qin Feng
In eukaryotic cells, the gene expression status is strictly controlled by epigenetic modifications on chromatin. The repressive status of chromatin largely contributes to HIV latency. Studies have shown that modification of histone H3K27 acts as a key molecular switch for activation or suppression of many cellular genes. In this study, we found that K27-acetylated histone H3 specifically recruited Super Elongation Complex (SEC), the transcriptional elongation complex essential for HIV-1 long terminal repeat (LTR)-mediated and general cellular transcription...
June 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28636937/the-conserved-rna-binding-cyclophilin-rct1-regulates-small-rna-biogenesis-and-splicing-independent-of-heterochromatin-assembly
#5
An-Yun Chang, Stephane E Castel, Evan Ernst, Hyun Soo Kim, Robert A Martienssen
RNAi factors and their catalytic activities are essential for heterochromatin assembly in S. pombe. This has led to the idea that siRNAs can promote H3K9 methylation by recruiting the cryptic loci regulator complex (CLRC), also known as recombination in K complex (RIKC), to the nucleation site. The conserved RNA-binding protein Rct1 (AtCyp59/SIG-7) interacts with splicing factors and RNA polymerase II. Here we show that Rct1 promotes processing of pericentromeric transcripts into siRNAs via the RNA recognition motif...
June 20, 2017: Cell Reports
https://www.readbyqxmd.com/read/28636052/chemically-induced-degradation-of-cdk9-by-a-proteolysis-targeting-chimera-protac
#6
Caroline M Robb, Jacob I Contreras, Smit Kour, Margaret A Taylor, Mohammad Abid, Yogesh A Sonawane, Muhammad Zahid, Daryl J Murry, Amarnath Natarajan, Sandeep Rana
Cyclin-dependent kinase 9 (CDK9), a member of the cyclin-dependent protein kinase (CDK) family, is involved in transcriptional elongation of several target genes. CDK9 is ubiquitously expressed and has been shown to contribute to a variety of malignancies such as pancreatic, prostate and breast cancers. Here we report the development of a heterobifunctional small molecule proteolysis targeting chimera (PROTAC) capable of cereblon (CRBN) mediated proteasomal degradation of CDK9. In HCT116 cells, it selectively degrades CDK9 while sparing other CDK family members...
June 21, 2017: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/28631168/the-function-of-osbhlh068-is-partially-redundant-with-its-homolog-atbhlh112-in-the-regulation-of-the-salt-stress-response-but-has-opposite-functions-to-control-flowering-in-arabidopsis
#7
Hung-Chi Chen, Vicki Hsieh-Feng, Pei-Chun Liao, Wan-Hsing Cheng, Li-Yu Liu, Yun-Wei Yang, Ming-Hsin Lai, Men-Chi Chang
The homologous genes OsbHLH068 and AtbHLH112 have partially redundant functions in the regulation of the salt stress response but opposite functions to control flowering in Arabidopsis. The transcription factor (TF) basic/Helix-Loop-Helix (bHLH) is important for plant growth, development, and stress responses. OsbHLH068, which is a homologous gene of AtbHLH112 that is up-regulated under drought and salt stresses, as indicated by previous microarray data analysis. However, the intrinsic function of OsbHLH068 remains unknown...
June 19, 2017: Plant Molecular Biology
https://www.readbyqxmd.com/read/28627366/pqbp1-an-intrinsically-disordered-denatured-protein-at-the-crossroad-of-intellectual-disability-and-neurodegenerative-diseases
#8
REVIEW
Hitoshi Okazawa
PQBP1 (polyglutamine binding protein-1) is the earliest identified molecule among the group of disease-related intrinsically disordered/denatured proteins. PQBP1 interacts with splicing-related factors via the disordered/denatured domain and regulates post-transcriptional gene expression. The mutations cause intellectual disability due to decreased dendritic spines and abnormal expression of synapse molecules in neurons, and microcephaly due to elongated cell cycle time and abnormal expression of cell cycle proteins in neural stem progenitor cells...
June 13, 2017: Neurochemistry International
https://www.readbyqxmd.com/read/28624615/cell-size-dependent-transcription-of-flc-and-its-antisense-long-non-coding-rna-coolair-explain-cell-to-cell-expression-variation
#9
Robert Ietswaart, Stefanie Rosa, Zhe Wu, Caroline Dean, Martin Howard
Single-cell quantification of transcription kinetics and variability promotes a mechanistic understanding of gene regulation. Here, using single-molecule RNA fluorescence in situ hybridization and mathematical modeling, we dissect cellular RNA dynamics for Arabidopsis FLOWERING LOCUS C (FLC). FLC expression quantitatively determines flowering time and is regulated by antisense (COOLAIR) transcription. In cells without observable COOLAIR expression, we quantify FLC transcription initiation, elongation, intron processing, and lariat degradation, as well as mRNA release from the locus and degradation...
June 8, 2017: Cell Systems
https://www.readbyqxmd.com/read/28623956/differential-protein-expression-in-chicken-macrophages-and-heterophils-in-vivo-following-infection-with-salmonella-enteritidis
#10
Zuzana Sekelova, Hana Stepanova, Ondrej Polansky, Karolina Varmuzova, Marcela Faldynova, Radek Fedr, Ivan Rychlik, Lenka Vlasatikova
In this study we compared the proteomes of macrophages and heterophils isolated from the spleen 4 days after intravenous infection of chickens with Salmonella Enteritidis. Heterophils were characterized by expression of MMP9, MRP126, LECT2, CATHL1, CATHL2, CATHL3, LYG2, LYZ and RSFR. Macrophages specifically expressed receptor proteins, e.g. MRC1L, LRP1, LGALS1, LRPAP1 and a DMBT1L. Following infection, heterophils decreased ALB and FN1, and released MMP9 to enable their translocation to the site of infection...
June 17, 2017: Veterinary Research
https://www.readbyqxmd.com/read/28623582/analysis-of-in-vivo-chromatin-and-protein-interactions-of-arabidopsis-transcript-elongation-factors
#11
Alexander Pfab, Wojciech Antosz, Philipp Holzinger, Astrid Bruckmann, Joachim Griesenbeck, Klaus D Grasser
A central step to elucidate the function of proteins commonly comprises the analysis of their molecular interactions in vivo. For nuclear regulatory proteins this involves determining protein-protein interactions as well as mapping of chromatin binding sites. Here, we present two protocols to identify protein-protein and chromatin interactions of transcript elongation factors (TEFs) in Arabidopsis. The first protocol (Subheading 3.1) describes protein affinity-purification coupled to mass spectrometry (AP-MS) that utilizes suspension cultured cells as experimental system...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28621431/adhesion-molecule-kirrel3-neph2-is-required-for-the-elongated-shape-of-myocytes-during-skeletal-muscle-differentiation
#12
Yael Tamir-Livne, Raeda Mubariki, Eyal Bengal
Kirrel/Neph proteins are evolutionarily conserved members of the immunoglobulin superfamily of adhesion proteins. Kirrel3 is the mouse orthologue of Dumbfounded (Duf), a family member that regulates myoblast pre-fusion events in Drosophila. Yet, the role of Kirrel3 in mammalian myogenesis has not been demonstrated. Experiments performed here indicate that the mouse Kirrel3 protein regulates morphological changes of myoblasts that are required for their subsequent fusion into multinucleated myotubes. We show that Kirrel3 is transiently expressed at the tips of myocytes during early myoblast differentiation and that its expression is dependent on the myogenic transcription factor, MyoD...
2017: International Journal of Developmental Biology
https://www.readbyqxmd.com/read/28619072/the-arabidopsis-swi-snf-protein-baf60-mediates-seedling-growth-control-by-modulating-dna-accessibility
#13
Teddy Jégu, Alaguraj Veluchamy, Juan S Ramirez-Prado, Charley Rizzi-Paillet, Magalie Perez, Anaïs Lhomme, David Latrasse, Emeline Coleno, Serge Vicaire, Stéphanie Legras, Bernard Jost, Martin Rougée, Fredy Barneche, Catherine Bergounioux, Martin Crespi, Magdy M Mahfouz, Heribert Hirt, Cécile Raynaud, Moussa Benhamed
BACKGROUND: Plant adaptive responses to changing environments involve complex molecular interplays between intrinsic and external signals. Whilst much is known on the signaling components mediating diurnal, light, and temperature controls on plant development, their influence on chromatin-based transcriptional controls remains poorly explored. RESULTS: In this study we show that a SWI/SNF chromatin remodeler subunit, BAF60, represses seedling growth by modulating DNA accessibility of hypocotyl cell size regulatory genes...
June 15, 2017: Genome Biology
https://www.readbyqxmd.com/read/28618313/a-mir4646-associated-methylation-locus-is-hypomethylated-in-adolescent-depression
#14
Adrian E Boström, Diana-Maria Ciuculete, Misty Attwood, Regina Krattinger, Lamia Nikontovic, Olga E Titova, Gerd A Kullak-Ublick, Jessica Mwinyi, Helgi B Schiöth
BACKGROUND: Studies of epigenetics and transcriptional activity in adolescents may provide knowledge about possible preventive strategies of depression. METHODS: We present a methylome-wide association study (MWAS) and cohort validation analysis of depression in adolescents, in two separate cohorts: discovery (n=93) and validation data set 1 (n=78). The genome-wide methylation pattern was measured from whole blood using the Illumina 450K array. A second validation cohort, validation data set 2, consists of post-mortem brain biopsies from depressed adults (n=58)...
May 17, 2017: Journal of Affective Disorders
https://www.readbyqxmd.com/read/28611805/transcriptomic-analysis-in-strawberry-fruits-reveals-active-auxin-biosynthesis-and-signaling-in-the-ripe-receptacle
#15
Elizabeth Estrada-Johnson, Fabiana Csukasi, Carmen M Pizarro, José G Vallarino, Yulia Kiryakova, Amalia Vioque, Javier Brumos, Nieves Medina-Escobar, Miguel A Botella, José M Alonso, Alisdair R Fernie, José F Sánchez-Sevilla, Sonia Osorio, Victoriano Valpuesta
The role of auxin in ripening strawberry (Fragaria ×ananassa) fruits has been restricted to the early stages of development where the growth of the receptacle is dependent on the delivery of auxin from the achenes. At later stages, during enlargement of the receptacle, other hormones have been demonstrated to participate to different degrees, from the general involvement of gibberellins and abscisic acid to the more specific of ethylene. Here we report the involvement of auxin at the late stages of receptacle ripening...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28611249/a-herpesviral-immediate-early-protein-promotes-transcription-elongation-of-viral-transcripts
#16
Hannah L Fox, Jill A Dembowski, Neal A DeLuca
Herpes simplex virus 1 (HSV-1) genes are transcribed by cellular RNA polymerase II (RNA Pol II). While four viral immediate early proteins (ICP4, ICP0, ICP27, and ICP22) function in some capacity in viral transcription, the mechanism by which ICP22 functions remains unclear. We observed that the FACT complex (comprised of SSRP1 and Spt16) was relocalized in infected cells as a function of ICP22. ICP22 was also required for the association of FACT and the transcription elongation factors SPT5 and SPT6 with viral genomes...
June 13, 2017: MBio
https://www.readbyqxmd.com/read/28608935/cdk9-regulates-apoptosis-of-myoblast-cells-by-modulation-of-microrna-1-expression
#17
Vahideh Tarhriz, Kay-Dietrich Wagner, Zahra Masoumi, Ommoleila Molavi, Mohammad Saeid Hejazi, Hossein Ghanbarian
Cdk9 is the catalytic core of the positive transcription elongation factor b (P-TEFb) and regulates transcriptional elongation factors by phosphorylation of RNA pol II. Apart from its role on myogenic gene expression, Cdk9 regulation of muscle-specific microRNAs in the early stage of cardiomyogenesis is poorly understood. Here we demonstrate that Cdk9 not only regulates myogenic transcription factors, but also controls muscle-specific microRNAs. During cardiac differentiation of mouse embryonic stem cells, high Cdk9 expression preceded up-regulation of miR-1...
June 13, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/28605514/flipping-states-a-few-key-residues-decide-the-winning-conformation-of-the-only-universally-conserved-transcription-factor
#18
Da Shi, Dmitri Svetlov, Ruben Abagyan, Irina Artsimovitch
Transcription factors from the NusG family bind to the elongating RNA polymerase to enable synthesis of long RNAs in all domains of life. In bacteria, NusG frequently co-exists with specialized paralogs that regulate expression of a small set of targets, many of which encode virulence factors. Escherichia coli RfaH is the exemplar of this regulatory mechanism. In contrast to NusG, which freely binds to RNA polymerase, RfaH exists in a structurally distinct autoinhibitory state in which the RNA polymerase-binding site is buried at the interface between two RfaH domains...
June 10, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28601408/expression-of-ciliated-bronchial-epithelium-1-during-human-spermatogenesis
#19
Christiane Pleuger, Daniela Fietz, Katja Hartmann, Hans-Christian Schuppe, Wolfgang Weidner, Sabine Kliesch, Mark Baker, Moira K O'Bryan, Martin Bergmann
OBJECTIVE: To define the precise cellular localization of ciliated bronchial epithelium 1 (CBE1) in the human testis and test its relationship to impaired spermatogenesis. DESIGN: Gene expression analysis, and histologic and immunohistochemical evaluation. SETTING: University research laboratories and andrologic outpatient clinic. PATIENT(S): Forty-three human testicular biopsies: 12 biopsies showing normal spermatogenesis (NSP), 8 with maturation arrest at level of spermatocytes (STA), 8 with maturation arrest at level of spermatids (SDA), 4 with scattered elongating spermatids, and 12 with Sertoli cell-only syndrome, with an additional 5 semen samples from healthy donors...
June 7, 2017: Fertility and Sterility
https://www.readbyqxmd.com/read/28601220/structures-and-activities-of-the-elongator-complex-and-its-cofactors
#20
Olga Kolaj-Robin, Bertrand Séraphin
Elongator is a highly conserved eukaryotic protein complex consisting of two sets of six Elp proteins, while homologues of its catalytic subunit Elp3 are found in all the kingdoms of life. Although it was originally described as a transcription elongation factor, cumulating evidence suggests that its primary function is catalyzing tRNA modifications. In humans, defects in Elongator subunits are associated with neurological disorders and cancer. Although further studies are still required, a clearer picture of the molecular mechanism of action of Elongator and its cofactors has started to emerge within recent years that have witnessed significant development in the field...
2017: Enzymes
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