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gene regulation in eukaryotes

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https://www.readbyqxmd.com/read/28920762/measuring-dynamics-of-eukaryotic-transcription-initiation-challenges-insights-and-opportunities
#1
Zhengjian Zhang, Robert Tjian
Transcription of protein-encoding genes in eukaryotic cells is a dynamically coordinated process. Many of the key transcription regulators contain functionally essential intrinsically disordered regions (IDRs), the dynamic nature of which creates extra challenges to traditional biochemical analyses. Recent advances in single-molecule fluorescence imaging technology have enabled direct visualization of these rapid, complex and dynamic molecular interactions in real time.
September 18, 2017: Transcription
https://www.readbyqxmd.com/read/28920397/-effects-of-interleukin-34-expressed-by-human-bone-marrow-derived-mesenchymal-stem-cells-on-thp-1-cells
#2
Xueming Gao, Shun Zhang, Zhaojun Xu, Yan Shan, Zihong Wang, Ting Cai, Xue Jiang
To construct recombinant eukaryotic expression plasmid vector of human IL-34 gene, and to study the effects of IL-34 expressed by human bone marrow-derived mesenchymal stem cells (hBM-MSCs) on THP-1 cells. Full-length IL-34 encoding sequence was amplified by PCR. And this fragment was cloned into the plasmid pIRES2-EGFP. Western blotting and ELISA were used to analyze the expression of IL-34 in hBM-MSCs. THP-1 cells were cultured with hBM-MSCs medium containing IL-34 protein. Real-time PCR detected the effects of IL-34 on the expression of IL-10 and TNFα in THP-1 cells...
April 25, 2017: Sheng Wu Gong Cheng Xue Bao, Chinese Journal of Biotechnology
https://www.readbyqxmd.com/read/28918148/mammalian-target-of-rapamycin-signaling-and-ubiquitin-proteasome-related-gene-expression-in-3-different-skeletal-muscles-of-colostrum-versus-formula-fed-calves
#3
H Sadri, J Steinhoff-Wagner, Harald M Hammon, R M Bruckmaier, S Görs, H Sauerwein
The rates of protein turnover are higher during the neonatal period than at any other time in postnatal life. The mammalian target of rapamycin (mTOR) and the ubiquitin-proteasome system are key pathways regulating cellular protein turnover. The objectives of this study were (1) to elucidate the effect of feeding colostrum versus milk-based formula on the mRNA abundance of key components of the mTOR pathway and of the ubiquitin-proteasome system in skeletal muscle of neonatal calves and (2) to compare different muscles...
September 13, 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/28916784/p-body-proteins-regulate-transcriptional-rewiring-to-promote-dna-replication-stress-resistance
#4
Raphael Loll-Krippleber, Grant W Brown
mRNA-processing (P-) bodies are cytoplasmic granules that form in eukaryotic cells in response to numerous stresses to serve as sites of degradation and storage of mRNAs. Functional P-bodies are critical for the DNA replication stress response in yeast, yet the repertoire of P-body targets and the mechanisms by which P-bodies promote replication stress resistance are unknown. In this study we identify the complete complement of mRNA targets of P-bodies during replication stress induced by hydroxyurea treatment...
September 15, 2017: Nature Communications
https://www.readbyqxmd.com/read/28912271/the-complex-structure-and-function-of-mediator
#5
Thomas M Harper, Dylan J Taatjes
In eukaryotes, RNA polymerase II (pol II) transcribes all protein-coding genes and many non-coding RNAs. Whereas numerous factors contribute to the regulation of pol II activity, the Mediator complex is required for expression of most, if not all, pol II transcripts. Structural characterization of Mediator is challenging due to its large size (~20 subunits in yeast, 26 subunits in humans) and conformational flexibility. However, recent studies have revealed structural details at higher resolution. Here, we summarize recent findings and place in context with previous results, highlighting regions within Mediator that are important for regulating its structure and function...
September 14, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28911649/long-chain-bases-from-sea-cucumber-mitigate-endoplasmic-reticulum-stress-and-inflammation-in-obesity-mice
#6
Shiwei Hu, Jinhui Wang, Jingfeng Wang, Changhu Xue, Yuming Wang
Endoplasmic reticulum (ER) stress and inflammation can induce hyperglycemia. Long-chain bases (LCBs) from sea cucumber exhibit antihyperglycemic activities. However, their effects on ER stress and inflammation are unknown. We investigated the effects of LCBs on ER stress and inflammatory response in high-fat, fructose diet-induced obesity mice. Reactive oxygen species and free fatty acids were measured. Inflammatory cytokines in serum and their mRNA expressions in epididymal adipose tissues were investigated...
July 2017: Journal of Food and Drug Analysis
https://www.readbyqxmd.com/read/28911119/a-snorna-modulates-mrna-3-end-processing-and-regulates-the-expression-of-a-subset-of-mrnas
#7
Chunliu Huang, Junjie Shi, Yibin Guo, Weijun Huang, Shanshan Huang, Siqi Ming, Xingui Wu, Rui Zhang, Junjun Ding, Wei Zhao, Jie Jia, Xi Huang, Andy Peng Xiang, Yongsheng Shi, Chengguo Yao
mRNA 3' end processing is an essential step in gene expression. It is well established that canonical eukaryotic pre-mRNA 3' processing is carried out within a macromolecular machinery consisting of dozens of trans-acting proteins. However, it is unknown whether RNAs play any role in this process. Unexpectedly, we found that a subset of small nucleolar RNAs (snoRNAs) are associated with the mammalian mRNA 3' processing complex. These snoRNAs primarily interact with Fip1, a component of cleavage and polyadenylation specificity factor (CPSF)...
September 6, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28911096/distinct-regulation-of-alternative-polyadenylation-and-gene-expression-by-nuclear-poly-a-polymerases
#8
Weimin Li, Wencheng Li, Rakesh S Laishram, Mainul Hoque, Zhe Ji, Bin Tian, Richard A Anderson
Polyadenylation of nascent RNA by poly(A) polymerase (PAP) is important for 3' end maturation of almost all eukaryotic mRNAs. Most mammalian genes harbor multiple polyadenylation sites (PASs), leading to expression of alternative polyadenylation (APA) isoforms with distinct functions. How poly(A) polymerases may regulate PAS usage and hence gene expression is poorly understood. Here, we show that the nuclear canonical (PAPα and PAPγ) and non-canonical (Star-PAP) PAPs play diverse roles in PAS selection and gene expression...
September 6, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28903484/novel-role-of-fbxw7-circular-rna-in-repressing-glioma-tumorigenesis
#9
Yibing Yang, Xinya Gao, Maolei Zhang, Sheng Yan, Chengjun Sun, Feizhe Xiao, Nunu Huang, Xuesong Yang, Kun Zhao, Huangkai Zhou, Suyun Huang, Bo Xie, Nu Zhang
Background: Circular RNAs (circRNAs) are RNA transcripts that are widespread in the eukaryotic genome. Recent evidence indicates that circRNAs play important roles in tissue development, gene regulation, and carcinogenesis. However, whether circRNAs encode functional proteins remains elusive, although translation of several circRNAs was recently reported. Methods: CircRNA deep sequencing was performed by using 10 pathologically diagnosed glioblastoma samples and their paired adjacent normal brain tissues...
March 1, 2018: Journal of the National Cancer Institute
https://www.readbyqxmd.com/read/28902867/analysis-of-the-relationship-between-coexpression-domains-and-chromatin-3d-organization
#10
María E Soler-Oliva, Jose A Guerrero-Martínez, Valentina Bachetti, Jose C Reyes
Gene order is not random in eukaryotic chromosomes, and co-regulated genes tend to be clustered. The mechanisms that determine co-regulation of large regions of the genome and its connection with chromatin three-dimensional (3D) organization are still unclear however. Here we have adapted a recently described method for identifying chromatin topologically associating domains (TADs) to identify coexpression domains (which we term "CODs"). Using human normal breast and breast cancer RNA-seq data, we have identified approximately 500 CODs...
September 13, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28902852/genome-wide-chromatin-mapping-with-size-resolution-reveals-a-dynamic-sub-nucleosomal-landscape-in-arabidopsis
#11
Daniel Antony Pass, Emily Sornay, Angela Marchbank, Margaret R Crawford, Konrad Paszkiewicz, Nicholas A Kent, James A H Murray
All eukaryotic genomes are packaged as chromatin, with DNA interlaced with both regularly patterned nucleosomes and sub-nucleosomal-sized protein structures such as mobile and labile transcription factors (TF) and initiation complexes, together forming a dynamic chromatin landscape. Whilst details of nucleosome position in Arabidopsis have been previously analysed, there is less understanding of their relationship to more dynamic sub-nucleosomal particles (subNSPs) defined as protected regions shorter than the ~150bp typical of nucleosomes...
September 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28902838/the-cryo-electron-microscopy-structure-of-human-transcription-factor-iih
#12
Basil J Greber, Thi Hoang Duong Nguyen, Jie Fang, Pavel V Afonine, Paul D Adams, Eva Nogales
Human transcription factor IIH (TFIIH) is part of the general transcriptional machinery required by RNA polymerase II for the initiation of eukaryotic gene transcription. Composed of ten subunits that add up to a molecular mass of about 500 kDa, TFIIH is also essential for nucleotide excision repair. The seven-subunit TFIIH core complex formed by XPB, XPD, p62, p52, p44, p34, and p8 is competent for DNA repair, while the CDK-activating kinase subcomplex, which includes the kinase activity of CDK7 as well as the cyclin H and MAT1 subunits, is additionally required for transcription initiation...
September 13, 2017: Nature
https://www.readbyqxmd.com/read/28900227/long-noncoding-rnas-in-the-model-species-brachypodium-distachyon
#13
Concetta De Quattro, Mario Enrico Pè, Edoardo Bertolini
Eukaryotic genomes are pervasively transcribed and only a small portion of the transcribed sequences belongs to protein coding genes. High-throughput sequencing technology contributed to consolidate this perspective, allowing the identification of numerous noncoding RNAs with key roles in biological processes. Long noncoding RNAs (lncRNAs) are transcripts longer than 200 nt with limited phylogenetic conservation, expressed at low levels and characterized by tissue/organ specific expression profiles. Although a large set of lncRNAs has been identified, the functional roles of lncRNAs are only beginning to be recognized and the molecular mechanism of lncRNA-mediated gene regulation remains largely unexplored, particularly in plants where their annotation and characterization are still incomplete...
September 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28900023/gene-expression-in-leishmania-is-regulated-predominantly-by-gene-dosage
#14
Stefano A Iantorno, Caroline Durrant, Asis Khan, Mandy J Sanders, Stephen M Beverley, Wesley C Warren, Matthew Berriman, David L Sacks, James A Cotton, Michael E Grigg
Leishmania tropica, a unicellular eukaryotic parasite present in North and East Africa, the Middle East, and the Indian subcontinent, has been linked to large outbreaks of cutaneous leishmaniasis in displaced populations in Iraq, Jordan, and Syria. Here, we report the genome sequence of this pathogen and 7,863 identified protein-coding genes, and we show that the majority of clinical isolates possess high levels of allelic diversity, genetic admixture, heterozygosity, and extensive aneuploidy. By utilizing paired genome-wide high-throughput DNA sequencing (DNA-seq) with RNA-seq, we found that gene dosage, at the level of individual genes or chromosomal "somy" (a general term covering disomy, trisomy, tetrasomy, etc...
September 12, 2017: MBio
https://www.readbyqxmd.com/read/28900015/structure-and-function-of-pif1-helicase
#15
REVIEW
Alicia K Byrd, Kevin D Raney
Pif1 family helicases have multiple roles in the maintenance of nuclear and mitochondrial DNA in eukaryotes. Saccharomyces cerevisiae Pif1 is involved in replication through barriers to replication, such as G-quadruplexes and protein blocks, and reduces genetic instability at these sites. Another Pif1 family helicase in S. cerevisiae, Rrm3, assists in fork progression through replication fork barriers at the rDNA locus and tRNA genes. ScPif1 (Saccharomyces cerevisiae Pif1) also negatively regulates telomerase, facilitates Okazaki fragment processing, and acts with polymerase δ in break-induced repair...
September 12, 2017: Biochemical Society Transactions
https://www.readbyqxmd.com/read/28898250/effects-of-proteasome-inhibitor-mg-132-on-the-parasite-schistosoma-mansoni
#16
Enyara R Morais, Katia C Oliveira, Renato G de Paula, Alice M M Ornelas, Érika B C Moreira, Fernanda Rafacho Badoco, Lizandra G Magalhães, Sergio Verjovski-Almeida, Vanderlei Rodrigues
Proteasome is a proteolytic complex responsible for intracellular protein turnover in eukaryotes, archaea and in some actinobacteria species. Previous work has demonstrated that in Schistosoma mansoni parasites, the proteasome inhibitor MG-132 affects parasite development. However, the molecular targets affected by MG-132 in S. mansoni are not entirely known. Here, we used expression microarrays to measure the genome-wide changes in gene expression of S. mansoni adult worms exposed in vitro to MG-132, followed by in silico functional analyses of the affected genes using Ingenuity Pathway Analysis (IPA)...
2017: PloS One
https://www.readbyqxmd.com/read/28894236/genome-wide-functional-analysis-reveals-that-autophagy-is-necessary-for-growth-sporulation-deoxynivalenol-production-and-virulence-in-fusarium-graminearum
#17
Wuyun Lv, Chunyan Wang, Nan Yang, Yawei Que, Nicholas J Talbot, Zhengyi Wang
Autophagy is a conserved cellular recycling and trafficking pathway in eukaryotic cells and has been reported to be important in the virulence of a number of microbial pathogens. Here, we report genome-wide identification and characterization of autophagy-related genes (ATGs) in the wheat pathogenic fungus Fusarium graminearum. We identified twenty-eight genes associated with the regulation and operation of autophagy in F. graminearum. Using targeted gene deletion, we generated a set of 28 isogenic mutants...
September 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28893950/the-taf10-containing-tfiid-and-saga-transcriptional-complexes-are-dispensable-for-early-somitogenesis-in-the-mouse-embryo
#18
Paul Bardot, Stéphane D Vincent, Marjorie Fournier, Alexis Hubaud, Mathilde Joint, László Tora, Olivier Pourquié
During development, tightly regulated gene expression programs control cell fate and patterning. A key regulatory step in eukaryotic transcription is the assembly of the pre-initiation complex (PIC) at promoters. The PIC assembly has mainly been studied in vitro, and little is known about its composition during development. In vitro data suggests that TFIID is the general transcription factor that nucleates PIC formation at promoters. Here we show that TAF10, a subunit of TFIID and of the transcriptional co-activator SAGA, is required for the assembly of these complexes in the mouse embryo...
September 11, 2017: Development
https://www.readbyqxmd.com/read/28893714/transcriptional-regulation-of-the-ambient-temperature-response-by-h2a-z-nucleosomes-and-hsf1-transcription-factors-in-arabidopsis
#19
Sandra Cortijo, Varodom Charoensawan, Anna Brestovitsky, Ruth Buning, Charles Ravarani, Daniela Rhodes, John van Noort, Katja E Jaeger, Philip A Wigge
Temperature influences the distribution, range and phenology of plants. The key transcriptional activators of the heat shock response in eukaryotes, the heat shock factors (HSFs), have undergone a large-scale gene amplification in plants. While HSFs are central in heat stress responses, their role in ambient temperature changes is less well understood. We show here that the warm ambient temperature transcriptome is dependent upon the HSFA1 clade of Arabidopsis HSFs, which cause a rapid and dynamic eviction of H2A...
September 8, 2017: Molecular Plant
https://www.readbyqxmd.com/read/28893535/down-regulate-of-djrfc2-causes-tissues-hypertrophy-during-planarian-regeneration
#20
Qi Guo, Guixia Zhao, Jiajia Ni, Yanan Guo, Yizhe Zhang, Qingnan Tian, Shoutao Zhang
Planarians are an ideal model organism for regeneration research due to their amazing ability to regenerate. DNA replication is crucial for genome stability. Replication factor C (RFC), which is a replication factor C-like complex and plays an important role during DNA replication in eukaryotes, has been reported as a wound response factor during planarian regeneration. However, how RFC controls regeneration in planarians by regulating DNA replication remains to be explained. Here, we used a two-dimensional electrophoresis (2-DE) proteomic approach to identify differentially expressed proteins in intact and regenerated planarians...
September 8, 2017: Biochemical and Biophysical Research Communications
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