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https://www.readbyqxmd.com/read/29332189/the-arabidopsis-histone-chaperone-fact-is-required-for-stress-induced-expression-of-anthocyanin-biosynthetic-genes
#1
Alexander Pfab, Matthias Breindl, Klaus D Grasser
The histone chaperone FACT is involved in the expression of genes encoding anthocyanin biosynthetic enzymes also upon induction by moderate high-light and therefore contributes to the stress-induced plant pigmentation. The histone chaperone FACT consists of the SSRP1 and SPT16 proteins and associates with transcribing RNAPII (RNAPII) along the transcribed region of genes. FACT can promote transcriptional elongation by destabilising nucleosomes in the path of RNA polymerase II, thereby facilitating efficient transcription of chromatin templates...
January 13, 2018: Plant Molecular Biology
https://www.readbyqxmd.com/read/29329398/lenup-learning-nucleosome-positioning-from-dna-sequences-with-improved-convolutional-neural-networks
#2
Juhua Zhang, Wenbo Peng, Lei Wang
Motivation: Nucleosome positioning plays significant roles in proper genome packing and its accessibility to execute transcription regulation. Despite a multitude of nucleosome positioning resources available on line including experimental datasets of genome-wide nucleosome occupancy profiles and computational tools to the analysis on these data, the complex language of eukaryotic Nucleosome positioning remains incompletely understood. Results: Here, we address this challenge using an approach based on a state-of-the-art machine learning method...
January 10, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29328385/tormentic-acid-inhibits-il-1%C3%AE-induced-chondrocyte-apoptosis-by-activating-the-pi3k-akt-signaling-pathway
#3
Yang Yang, Yawei Wang, Meng Zhao, Haobo Jia, Bing Li, Dan Xing
Interleukin-1β (IL-1β) accelerates degradation of the cartilage matrix and induces apoptosis of chondrocytes. Tormentic acid (TA) is a triterpene isolated from the stem bark of the Vochysia divergens plant, which has been demonstrated to exert in vitro inhibitory activity against hepatocyte apoptosis. However, the effects of TA on IL‑1β‑induced apoptosis of human chondrocytes remain unclear. Therefore, the present study investigated the in vitro effects of TA on human osteoarthritic chondrocyte apoptosis cultivated in the presence of IL‑1β...
January 12, 2018: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29325627/epigenetic-mechanisms-underlying-nervous-system-diseases
#4
Irfan A Qureshi, Mark F Mehler
Epigenetic mechanisms act as control systems for modulating genomic structure and activity in response to evolving profiles of cell-extrinsic, cell-cell, and cell-intrinsic signals. These dynamic processes are responsible for mediating cell- and tissue-specific gene expression and function and gene-gene and gene-environmental interactions. The major epigenetic mechanisms include DNA methylation and hydroxymethylation; histone protein posttranslational modifications, nucleosome remodeling/repositioning, and higher-order chromatin reorganization; noncoding RNA regulation; and RNA editing...
2018: Handbook of Clinical Neurology
https://www.readbyqxmd.com/read/29325226/citrullinated-histone-h3-a-biomarker-of-neutrophil-extracellular-trap-formation-predicts-the-risk-of-venous-thromboembolism-in-cancer-patients
#5
Lisa-Marie Mauracher, Florian Posch, Kimberly Martinod, Ella Grilz, Thomas Däullary, Lena Hell, Christine Brostjan, Christoph Zielinski, Cihan Ay, Denisa D Wagner, Ingrid Pabinger, Johannes Thaler
BACKGROUND: Neutrophil extracellular traps (NETs) are decondensed chromatin fibers which might play a role in the prothrombotic state of cancer patients. OBJECTIVES: Here we investigated whether citrullinated histone H3 (H3Cit), a biomarker for NET formation, cell-free DNA (cfDNA), and nucleosomes predict venous thromboembolism (VTE) in cancer patients. PATIENTS/METHODS: Nine-hundred-forty-six patients with newly-diagnosed cancer or progression after remission were enrolled in this prospective observational cohort study...
January 11, 2018: Journal of Thrombosis and Haemostasis: JTH
https://www.readbyqxmd.com/read/29323273/histone-octamer-rearranges-to-adapt-to-dna-unwrapping
#6
Silvija Bilokapic, Mike Strauss, Mario Halic
Nucleosomes, the basic units of chromatin, package and regulate expression of eukaryotic genomes. Although the structure of the intact nucleosome is well characterized, little is known about structures of partially unwrapped, transient intermediates. In this study, we present nine cryo-EM structures of distinct conformations of nucleosome and subnucleosome particles. These structures show that initial DNA breathing induces conformational changes in the histone octamer, particularly in histone H3, that propagate through the nucleosome and prevent symmetrical DNA opening...
January 2018: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/29323271/cryo-em-structures-of-the-human-ino80-chromatin-remodeling-complex
#7
Ricardo J Aramayo, Oliver Willhoft, Rafael Ayala, Rohan Bythell-Douglas, Dale B Wigley, Xiaodong Zhang
Access to chromatin for processes such as transcription and DNA repair requires the sliding of nucleosomes along DNA. This process is aided by chromatin-remodeling complexes, such as the multisubunit INO80 chromatin-remodeling complex. Here we present cryo-EM structures of the active core complex of human INO80 at 9.6 Å, with portions at 4.1-Å resolution, and reconstructions of combinations of subunits. Together, these structures reveal the architecture of the INO80 complex, including Ino80 and actin-related proteins, which is assembled around a single RUVBL1 (Tip49a) and RUVBL2 (Tip49b) AAA+ heterohexamer...
January 2018: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/29321480/domain-swapping-and-smyd1-interactions-with-the-pwwp-domain-of-human-hepatoma-derived-growth-factor
#8
Li-Ying Chen, Yen-Chieh Huang, Shih-Tsung Huang, Yin-Cheng Hsieh, Hong-Hsiang Guan, Nai-Chi Chen, Phimonphan Chuankhayan, Masato Yoshimura, Ming-Hong Tai, Chun-Jung Chen
The human hepatoma-derived growth factor (HDGF), containing the chromatin-associated N-terminal PWWP domain capable of binding the SMYD1 promoter, participates in various cellular processes and is involved in human cancers. We report the first crystal structures of the human HDGF PWWP domain (residues 1-100) in a complex with SMYD1 of 10 bp at 2.84 Å resolution and its apo form at 3.3 Å, respectively. The structure of the apo PWWP domain comprises mainly four β-strands and two α-helices. The PWWP domain undergoes domain swapping to dramatically transform its secondary structures, altering the overall conformation from monomeric globular folding into an extended dimeric structure upon DNA binding...
January 10, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29321305/arabidopsis-rna-polymerase-v-mediates-enhanced-compaction-and-silencing-of-geminivirus-and-transposon-chromatin-during-host-recovery-from-infection
#9
Tami Coursey, Elizabeth Regedanz, David M Bisaro
Plants employ RNA-directed DNA methylation (RdDM) and dimethylation of histone 3 lysine 9 (H3K9me2) to silence geminiviruses and transposable elements (TEs). We previously showed that canonical RdDM (Pol IV-RdDM) involving RNA polymerases IV and V (Pol IV and Pol V) is required for Arabidopsis thaliana to recover from infection with Beet curly top virus lacking a suppressor protein that inhibits methylation (BCTV L2-). Recovery, which is characterized by reduced viral DNA levels and symptom remission, allows normal floral development...
January 10, 2018: Journal of Virology
https://www.readbyqxmd.com/read/29321178/transcription-factor-dependent-anti-repressive-mammalian-enhancers-exclude-h3k27me3-from-extended-genomic-domains
#10
Madhurima Saxena, Adrianna K San Roman, Nicholas K O'Neill, Rita Sulahian, Unmesh Jadhav, Ramesh A Shivdasani
Compacted chromatin and nucleosomes are known barriers to gene expression; the nature and relative importance of other transcriptional constraints remain unclear, especially at distant enhancers. Polycomb repressor complex 2 (PRC2) places the histone mark H3K27me3 predominantly at promoters, where its silencing activity is well documented. In adult tissues, enhancers lack H3K27me3, and it is unknown whether intergenic H3K27me3 deposits affect nearby genes. In primary intestinal villus cells, we identified hundreds of tissue-restricted enhancers that require the transcription factor (TF) CDX2 to prevent the incursion of H3K27me3 from adjoining areas of elevated basal marking into large well-demarcated genome domains...
January 10, 2018: Genes & Development
https://www.readbyqxmd.com/read/29320527/transcriptome-analysis-during-ripening-of-table-grape-berry-cv-thompson-seedless
#11
Iván Balic, Paula Vizoso, Ricardo Nilo-Poyanco, Dayan Sanhueza, Patricio Olmedo, Pablo Sepúlveda, Cesar Arriagada, Bruno G Defilippi, Claudio Meneses, Reinaldo Campos-Vargas
Ripening is one of the key processes associated with the development of major organoleptic characteristics of the fruit. This process has been extensively characterized in climacteric fruit, in contrast with non-climacteric fruit such as grape, where the process is less understood. With the aim of studying changes in gene expression during ripening of non-climacteric fruit, an Illumina based RNA-Seq transcriptome analysis was performed on four developmental stages, between veraison and harvest, on table grapes berries cv Thompson Seedless...
2018: PloS One
https://www.readbyqxmd.com/read/29318979/role-of-epigenetics-and-oxidative-stress-in-gliomagenesis
#12
Edgar Rangel-Lopez, Yesennia Sanchez-Perez, Ernesto Soto-Reyes, Claudia Maria Garcia-Cuellar, Bernardo Cacho-Diaz, Abel Santamaria
Malignant gliomas constitute more than 49% of all central nervous system (CNS) tumors and exhibit very poor prognosis. Two main events involved with the progression of gliomas are the deregulation of genes by genetic events and cellular damage elicited by the formation of reactive oxygen species (ROS). In gliomas, epigenetic abnormalities implicated in the deregulation of DNA methylation, nucleosome rearrangement, and acetylation of histones have been depicted. The overproduction of ROS has been implicated in the promotion of these modifications...
January 10, 2018: CNS & Neurological Disorders Drug Targets
https://www.readbyqxmd.com/read/29313808/regulation-of-trna-gene-transcription-by-the-chromatin-structure-and-nucleosome-dynamics
#13
REVIEW
Ashutosh Shukla, Purnima Bhargava
The short, non-coding genes transcribed by the RNA polymerase (pol) III, necessary for survival of a cell, need to be repressed under the stress conditions in vivo. The pol III-transcribed genes have adopted several novel chromatin-based regulatory mechanisms to their advantage. In the budding yeast, the sub-nucleosomal size tRNA genes are found in the nucleosome-free regions, flanked by positioned nucleosomes at both the ends. With their chromosomes-wide distribution, all tRNA genes have a different chromatin context...
December 4, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29310890/the-latest-twists-in-chromatin-remodeling
#14
REVIEW
Ralf Blossey, Helmut Schiessel
In its most restrictive interpretation, the notion of chromatin remodeling refers to the action of chromatin-remodeling enzymes on nucleosomes with the aim of displacing and removing them from the chromatin fiber (the effective polymer formed by a DNA molecule and proteins). This local modification of the fiber structure can have consequences for the initiation and repression of the transcription process, and when the remodeling process spreads along the fiber, it also results in long-range effects essential for fiber condensation...
January 5, 2018: Biophysical Journal
https://www.readbyqxmd.com/read/29309643/androgen-receptor-splice-variants-bind-to-constitutively-open-chromatin-and-promote-abiraterone-resistant-growth-of-prostate-cancer
#15
Yundong He, Ji Lu, Zhenqing Ye, Siyuan Hao, Liewei Wang, Manish Kohli, Donald J Tindall, Benyi Li, Runzhi Zhu, Liguo Wang, Haojie Huang
Androgen receptor (AR) splice variants (ARVs) are implicated in development of castration-resistant prostate cancer (CRPC). Upregulation of ARVs often correlates with persistent AR activity after androgen deprivation therapy (ADT). However, the genomic and epigenomic characteristics of ARV-dependent cistrome and the disease relevance of ARV-mediated transcriptome remain elusive. Through integrated chromatin immunoprecipitation coupled sequencing (ChIP-seq) and RNA sequencing (RNA-seq) analysis, we identified ARV-preferential-binding sites (ARV-PBS) and a set of genes preferentially transactivated by ARVs in CRPC cells...
January 4, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29305386/the-chromatin-remodeler-isw1-prevents-cag-repeat-expansions-during-transcription-in-saccharomyces-cerevisiae
#16
Melissa R Koch, Nealia C M House, Casey M Cosetta, Robyn M Jong, Christelle G Salomon, Cailin E Joyce, Elliot A Philips, Xiaofeng A Su, Catherine H Freudenreich
CAG/CTG trinucleotide repeats are unstable sequences that are difficult to replicate, repair, and transcribe due to their structure-forming nature. CAG repeats strongly position nucleosomes, however little is known about the chromatin remodeling needed to prevent repeat instability. In a Saccharomyces cerevisiae model system with CAG repeats carried on a yeast artificial chromosome, we discovered that the chromatin remodeler Isw1 is required to prevent CAG repeat expansions during transcription. CAG repeat expansions in the absence of Isw1 were dependent on both transcription-coupled repair (TCR) and base excision repair (BER)...
January 5, 2018: Genetics
https://www.readbyqxmd.com/read/29305013/transcription-insights-from-the-hiv-1-promoter
#17
Enrico Ne, Robert-Jan Palstra, Tokameh Mahmoudi
In this review, we cover transcription regulation of human immunodeficiency virus type 1 (HIV-1) gene expression, focusing on the invaluable contributions, made by HIV research over the years, toward the field of transcription. In this context, the HIV promoter can be considered to be a well-studied model promoter, which although a viral promoter, is subject to the same cellular regulatory mechanisms that modulate the transcriptional control of endogenous host cellular genes. The molecular control of HIV-1 transcription has been well studied and considerable knowledge toward development of alternative strategies for therapies aimed at eradicating both active but also latent HIV-1 has been obtained...
2018: International Review of Cell and Molecular Biology
https://www.readbyqxmd.com/read/29305001/epigenetic-regulation-of-adult-myogenesis
#18
Daniel C L Robinson, Francis J Dilworth
Skeletal muscle regeneration is an efficient stem cell-based repair system that ensures healthy musculature. For this repair system to function continuously throughout life, muscle stem cells must contribute to the process of myofiber repair as well as repopulation of the stem cell niche. The decision made by the muscle stem cells to commit to the muscle repair or to remain a stem cell depends upon patterns of gene expression, a process regulated at the epigenetic level. Indeed, it is well accepted that dynamic changes in epigenetic landscapes to control DNA accessibility and expression is a critical component during myogenesis for the effective repair of damaged muscle...
2018: Current Topics in Developmental Biology
https://www.readbyqxmd.com/read/29300974/the-elongation-factor-spn1-is-a-multi-functional-chromatin-binding-protein
#19
Sha Li, Adam R Almeida, Catherine A Radebaugh, Ling Zhang, Xu Chen, Liangqun Huang, Alison K Thurston, Anna A Kalashnikova, Jeffrey C Hansen, Karolin Luger, Laurie A Stargell
The process of transcriptional elongation by RNA polymerase II (RNAPII) in a chromatin context involves a large number of crucial factors. Spn1 is a highly conserved protein encoded by an essential gene and is known to interact with RNAPII and the histone chaperone Spt6. Spn1 negatively regulates the ability of Spt6 to interact with nucleosomes, but the chromatin binding properties of Spn1 are largely unknown. Here, we demonstrate that full length Spn1 (amino acids 1-410) binds DNA, histones H3-H4, mononucleosomes and nucleosomal arrays, and has weak nucleosome assembly activity...
December 30, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29300726/regulation-of-circadian-clock-transcriptional-output-by-clock-bmal1
#20
Alexandra J Trott, Jerome S Menet
The mammalian circadian clock relies on the transcription factor CLOCK:BMAL1 to coordinate the rhythmic expression of 15% of the transcriptome and control the daily regulation of biological functions. The recent characterization of CLOCK:BMAL1 cistrome revealed that although CLOCK:BMAL1 binds synchronously to all of its target genes, its transcriptional output is highly heterogeneous. By performing a meta-analysis of several independent genome-wide datasets, we found that the binding of other transcription factors at CLOCK:BMAL1 enhancers likely contribute to the heterogeneity of CLOCK:BMAL1 transcriptional output...
January 4, 2018: PLoS Genetics
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