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https://www.readbyqxmd.com/read/28446598/the-histone-variant-h2a-z-promotes-efficient-cotranscriptional-splicing-in-s-cerevisiae
#1
Lauren T Neves, Stephen Douglass, Roberto Spreafico, Srivats Venkataramanan, Tracy L Kress, Tracy L Johnson
In eukaryotes, a dynamic ribonucleic protein machine known as the spliceosome catalyzes the removal of introns from premessenger RNA (pre-mRNA). Recent studies show the processes of RNA synthesis and RNA processing to be spatio-temporally coordinated, indicating that RNA splicing takes place in the context of chromatin. H2A.Z is a highly conserved histone variant of the canonical histone H2A. In Saccharomyces cerevisiae, H2A.Z is deposited into chromatin by the SWR-C complex, is found near the 5' ends of protein-coding genes, and has been implicated in transcription regulation...
April 1, 2017: Genes & Development
https://www.readbyqxmd.com/read/28446597/the-histone-variant-h2a-z-promotes-splicing-of-weak-introns
#2
Kelly E Nissen, Christina M Homer, Colm J Ryan, Michael Shales, Nevan J Krogan, Kristin L Patrick, Christine Guthrie
Multiple lines of evidence implicate chromatin in the regulation of premessenger RNA (pre-mRNA) splicing. However, the influence of chromatin factors on cotranscriptional splice site usage remains unclear. Here we investigated the function of the highly conserved histone variant H2A.Z in pre-mRNA splicing using the intron-rich model yeast Schizosaccharomyces pombe Using epistatic miniarray profiles (EMAPs) to survey the genetic interaction landscape of the Swr1 nucleosome remodeling complex, which deposits H2A...
April 1, 2017: Genes & Development
https://www.readbyqxmd.com/read/28334816/dynamic-changes-in-chromatin-states-during-specification-and-differentiation-of-adult-intestinal-stem-cells
#3
Juri Kazakevych, Sergi Sayols, Berith Messner, Christina Krienke, Natalia Soshnikova
Epigenetic mechanisms, including chromatin structure, chromatin dynamics and histone modifications play an important role for maintenance and differentiation of pluripotent embryonic stem cells. However, little is known about the molecular mechanisms of adult stem cell specification and differentiation. Here, we used intestinal stem cells (ISCs) as a model system to reveal the epigenetic changes coordinating gene expression programs during these processes. We found that two distinct epigenetic mechanisms participate in establishing the transcriptional program promoting ISC specification from embryonic progenitors...
March 7, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28315825/effects-of-florida-red-tides-on-histone-variant-expression-and-dna-methylation-in-the-eastern-oyster-crassostrea-virginica
#4
Rodrigo Gonzalez-Romero, Victoria Suarez-Ulloa, Javier Rodriguez-Casariego, Daniel Garcia-Souto, Gabriel Diaz, Abraham Smith, Juan Jose Pasantes, Gary Rand, Jose M Eirin-Lopez
Massive algal proliferations known as Harmful Algal Blooms (HABs) represent one of the most important threats to coastal areas. Among them, the so-called Florida Red Tides (FRTs, caused by blooms of the dinoflagellate Karenia brevis and associated brevetoxins) are particularly detrimental in the southeastern U.S., causing high mortality rates and annual losses in excess of $40 million. The ability of marine organisms to cope with environmental stressors (including those produced during HABs) is influenced by genetic and epigenetic mechanisms, the latter resulting in phenotypic changes caused by heritable modifications in gene expression, without involving changes in the genetic (DNA) sequence...
March 7, 2017: Aquatic Toxicology
https://www.readbyqxmd.com/read/28301306/two-possible-modes-of-pioneering-associated-with-combinations-of-h2a-z-and-p300-cbp-at-nucleosome-occupied-enhancers
#5
Pierre Cauchy, Frederic Koch, Jean-Christophe Andrau
Pioneer transcription factors are defined by their ability to bind nucleosome-occupied regions. Here, we discuss the properties of nucleosomes bound by pioneers at enhancer regions. We describe how select pioneers bind nucleosome-occupied or -depleted enhancer sites. Importantly, by revisiting and expanding existing data sets, we show differential H2A.Z and p300/CBP association at bound enhancers, highlighting two possible pioneering modes.
February 13, 2017: Transcription
https://www.readbyqxmd.com/read/28298436/chromatin-remodeler-chd4-represses-aberrant-expression-of-tbx3-and-sustains-self-renewal-of-embryonic-stem-cells
#6
Haixin Zhao, Zhijun Han, Xinyuan Liu, Junjie Gu, Fan Tang, Gang Wei, Ying Jin
The unique properties of embryonic stem cells (ESCs), unlimited self-renewal and pluripotent differentiation potential, are sustained by integrated genetic and epigenetic networks composed of a series of transcriptional factors and epigenetic modulators. However, molecular mechanisms underlying the function of these regulators are not fully elucidated. Chd4, an ATPase subunit of the nucleosome remodeling and deacetylase (NuRD) complex, is highly expressed in ESCs. However, its function in the regulation of ESC properties remains elusive...
March 15, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28295392/erecta-signaling-controls-arabidopsis-inflorescence-architecture-through-chromatin-mediated-activation-of-pre1-expression
#7
Hanyang Cai, Lihua Zhao, Lulu Wang, Man Zhang, Zhenxia Su, Yan Cheng, Heming Zhao, Yuan Qin
Flowering plants display a remarkable diversity in inflorescence architecture, and pedicel length is one of the key contributors to this diversity. In Arabidopsis thaliana, the receptor-like kinase ERECTA (ER) mediated signaling pathway plays important roles in regulating inflorescence architecture by promoting cell proliferation. However, the regulating mechanism remains elusive in the pedicel. Genetic interactions between ERECTA signaling and the chromatin remodeling complex SWR1 in the control of inflorescence architecture were studied...
March 13, 2017: New Phytologist
https://www.readbyqxmd.com/read/28258158/dual-role-of-the-histone-variant-h2a-z-in-transcriptional-regulation-of-stress-response-genes
#8
Weronika Sura, Michał Kabza, Wojciech M Karlowski, Tomasz Bieluszewski, Marta Kuś-Slowinska, Łukasz Pawełoszek, Jan Sadowski, Piotr A Ziolkowski
The influence of the histone variant H2A.Z on transcription remains a long-standing conundrum. Here, by analyzing the actin-related protein6 mutant, which is impaired in H2A.Z deposition, and by H2A.Z profiling in stress conditions, we investigated the impact of this histone variant on gene expression in Arabidopsis thaliana. We demonstrate that the arp6 mutant exhibits anomalies in response to osmotic stress. Indeed, stress-responsive genes are overrepresented amongst those hyperactive in arp6. In wild-type plants, these genes exhibit high levels of H2A...
March 3, 2017: Plant Cell
https://www.readbyqxmd.com/read/28177753/histone-h3-3-regulates-mitotic-progression-in-mouse-embryonic-fibroblasts
#9
Aysegul Ors, Christophe Papin, Bertrand Favier, Yohan Roulland, Defne Dalkara, Mehmet Ozturk, ALi Hamiche, Stefan Dimitrov, Kiran Padmanabhan
H3.3 is a histone variant, which marks transcription start sites as well as telomeres and heterochromatic sites on the genome. H3.3 presence is thought to positively correlate with transcriptional status of its target genes. Using a conditional genetic strategy against H3.3B combined with short hairpin RNAs against H3.3A, we essentially depleted all H3.3 gene expression in mouse embryonic fibroblasts. Following nearly complete loss of H3.3 in cells, our transcriptomic analyses show very little impact on global gene expression as well as on histone variant H2A...
February 1, 2017: Biochemistry and Cell Biology, Biochimie et Biologie Cellulaire
https://www.readbyqxmd.com/read/28151037/differential-deposition-of-h2a-z-in-rice-seedling-tissue-during-the-day-night-cycle
#10
Kang Zhang, Wenying Xu, Chunchao Wang, Xin Yi, Zhen Su
Chromatin structure has an important role in modulating gene expression. The incorporation of histone variants into the nucleosome leads to important changes in the chromatin structure. The histone variant H2A.Z is highly conserved between different species of fungi, animals, and plants. However, dynamic changes to H2A.Z in rice have not been reported during the day-night cycle. In this study, we generated genome wide maps of H2A.Z for day and night time in harvested seedling tissues by combining chromatin immunoprecipitation and high-throughput sequencing...
March 4, 2017: Plant Signaling & Behavior
https://www.readbyqxmd.com/read/28144029/variants-of-core-histones-and-their-roles-in-cell-fate-decisions-development-and-cancer
#11
REVIEW
Marcus Buschbeck, Sandra B Hake
Histone variants endow chromatin with unique properties and show a specific genomic distribution that is regulated by specific deposition and removal machineries. These variants - in particular, H2A.Z, macroH2A and H3.3 - have important roles in early embryonic development, and they regulate the lineage commitment of stem cells, as well as the converse process of somatic cell reprogramming to pluripotency. Recent progress has also shed light on how mutations, transcriptional deregulation and changes in the deposition machineries of histone variants affect the process of tumorigenesis...
May 2017: Nature Reviews. Molecular Cell Biology
https://www.readbyqxmd.com/read/28123501/identification-of-the-molecular-mechanisms-underlying-dilated-cardiomyopathy-via-bioinformatic-analysis-of-gene-expression-profiles
#12
Hu Zhang, Zhuo Yu, Jianchao He, Baotong Hua, Guiming Zhang
In the present study, gene expression profiles of patients with dilated cardiomyopathy (DCM) were re-analyzed with bioinformatics tools to investigate the molecular mechanisms underlying DCM. Gene expression dataset GSE3585 was downloaded from Gene Expression Omnibus, which included seven heart biopsy samples obtained from patients with DCM and five healthy controls. Differential analysis was performed using a Limma package in R to screen for differentially expressed genes (DEGs). Functional enrichment analysis was subsequently conducted for DEGs using the Database for Annotation, Visualization and Integration Discovery...
January 2017: Experimental and Therapeutic Medicine
https://www.readbyqxmd.com/read/28025392/ino80-represses-osmostress-induced-gene-expression-by-resetting-promoter-proximal-nucleosomes
#13
Eva Klopf, Heiko A Schmidt, Sandra Clauder-Münster, Lars M Steinmetz, Christoph Schüller
The conserved INO80 chromatin remodeling complex is involved in regulation of DNA damage repair, replication and transcription. It is commonly recruited to the transcription start region and contributes to the establishment of promoter-proximal nucleosomes. We find a substantial influence of INO80 on nucleosome dynamics and gene expression during stress induced transcription. Transcription induced by osmotic stress leads to genome-wide remodeling of promoter proximal nucleosomes. INO80 function is required for timely return of evicted nucleosomes to the 5΄ end of induced genes...
April 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/27992255/drosophila-h2a-and-h2a-z-nucleosome-sequences-reveal-different-nucleosome-positioning-sequence-patterns
#14
Doo Yang, Ilya Ioshikhes
Nucleosomes are implicated in transcriptional regulation as well as in packing and stabilizing the DNA. Nucleosome positions affect the transcription by impeding or facilitating the binding of transcription factors. The DNA sequence, especially the periodic occurrences of dinucleotides, is a major factor that affects the nucleosome positioning. We analyzed the Drosophila DNA sequences bound by H2A and H2A.Z nucleosomes. Periodic patterns of dinucleotides (weak-weak/strong-strong or purine-purine/pyrimidine-pyrimidine) were identified as WW/SS and RR/YY nucleosome positioning sequence (NPS) patterns...
April 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/27974215/cumulative-impact-of-polychlorinated-biphenyl-and-large-chromosomal-duplications-on-dna-methylation-chromatin-and-expression-of-autism-candidate-genes
#15
Keith W Dunaway, M Saharul Islam, Rochelle L Coulson, S Jesse Lopez, Annie Vogel Ciernia, Roy G Chu, Dag H Yasui, Isaac N Pessah, Paul Lott, Charles Mordaunt, Makiko Meguro-Horike, Shin-Ichi Horike, Ian Korf, Janine M LaSalle
Rare variants enriched for functions in chromatin regulation and neuronal synapses have been linked to autism. How chromatin and DNA methylation interact with environmental exposures at synaptic genes in autism etiologies is currently unclear. Using whole-genome bisulfite sequencing in brain tissue and a neuronal cell culture model carrying a 15q11.2-q13.3 maternal duplication, we find that significant global DNA hypomethylation is enriched over autism candidate genes and affects gene expression. The cumulative effect of multiple chromosomal duplications and exposure to the pervasive persistent organic pollutant PCB 95 altered methylation of more than 1,000 genes...
December 13, 2016: Cell Reports
https://www.readbyqxmd.com/read/27896813/transcriptional-and-post-transcriptional-regulation-of-histone-variant-h2a-z-during-sea-urchin-development
#16
Mihai Hajdu, Jasmine Calle, Andrea Puno, Aminat Haruna, César Arenas-Mena
Histone variant H2A.Z promotes chromatin accessibility at transcriptional regulatory elements and is developmentally regulated in metazoans. We characterize the transcriptional and post-transcriptional regulation of H2A.Z in the purple sea urchin Strongylocentrotus purpuratus. H2A.Z depletion by antisense translation-blocking morpholino oligonucleotides during early development causes developmental collapse, in agreement with its previously demonstrated general role in transcriptional multipotency. During H2A...
December 2016: Development, Growth & Differentiation
https://www.readbyqxmd.com/read/27854013/an-assay-for-measuring-histone-variant-exchange-within-nucleosomes-in-vitro
#17
Liette Laflamme, Benoit Guillemette, Luc Gaudreau
The incorporation of histone variants into specific chromatin regions is a mechanism by which cells can regulate many important biological processes. One such example is H2A.Z, a highly conserved variant of H2A that is incorporated in genomic regulatory regions and contributes to control gene expression. H2A.Z variant exchange involves the removal of H2A-H2B dimers from a preassembled nucleosome and their replacement with H2A.Z-H2B dimers. A specific family of chromatin remodeling complexes, homologous to the yeast Swr1 complex, have been shown to be capable of this histone exchange activity both in vivo and in vitro...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27697661/possible-role-of-intragenic-dna-hypermethylation-in-gene-silencing-of-the-tumor-suppressor-gene-nr4a3-in-acute-myeloid-leukemia
#18
Ryo Shimizu, Tomoya Muto, Kazumasa Aoyama, Kwangmin Choi, Masahiro Takeuchi, Shuhei Koide, Nagisa Hasegawa, Yusuke Isshiki, Emi Togasaki, Chika Kawajiri-Manako, Yuhei Nagao, Shokichi Tsukamoto, Shio Sakai, Yusuke Takeda, Naoya Mimura, Chikako Ohwada, Emiko Sakaida, Tohru Iseki, Daniel T Starczynowski, Atsushi Iwama, Koutaro Yokote, Chiaki Nakaseko
Expression of the tumor suppressor gene NR4A3 is silenced in the blasts of acute myeloid leukemia (AML), irrespective of the karyotype. Although the transcriptional reactivation of NR4A3 is considered to have a broad-spectrum anti-leukemic effect, the therapeutic modalities targeting this gene have been hindered by our minimal understanding of the transcriptional mechanisms regulating its expression, particularly in human AML. Here we show the role of intragenic DNA hypermethylation in reducing the expression of NR4A3 in AML...
September 26, 2016: Leukemia Research
https://www.readbyqxmd.com/read/27692985/monoubiquitination-of-histone-h2b-blocks-eviction-of-histone-variant-h2a-z-from-inducible-enhancers
#19
Gregory Segala, Marcela A Bennesch, Deo Prakash Pandey, Nicolas Hulo, Didier Picard
Covalent modifications of histones play a crucial role in the regulation of gene expression. Histone H2B monoubiquitination has mainly been described as a regulator of transcription elongation, but its role in transcription initiation is poorly documented. We investigated the role of this histone mark (H2Bub1) on different inducible enhancers, in particular those regulated by estrogen receptor α, by loss- and gain-of-function experiments with the specific E3-ubiquitin ligase complex of H2B: RNF20/RNF40. RNF20/RNF40 overexpression causes repression of the induced activity of these enhancers...
October 20, 2016: Molecular Cell
https://www.readbyqxmd.com/read/27666591/ccp1-homodimer-mediates-chromatin-integrity-by-antagonizing-cenp-a-loading
#20
Qianhua Dong, Feng-Xiang Yin, Feng Gao, Yuan Shen, Faben Zhang, Yang Li, Haijin He, Marlyn Gonzalez, Jinpu Yang, Shu Zhang, Min Su, Yu-Hang Chen, Fei Li
CENP-A is a centromere-specific histone 3 variant essential for centromere specification. CENP-A partially replaces canonical histone H3 at the centromeres. How the particular CENP-A/H3 ratio at centromeres is precisely maintained is unknown. It also remains unclear how CENP-A is excluded from non-centromeric chromatin. Here, we identify Ccp1, an uncharacterized NAP family protein in fission yeast that antagonizes CENP-A loading at both centromeric and non-centromeric regions. Like the CENP-A loading factor HJURP, Ccp1 interacts with CENP-A and is recruited to centromeres at the end of mitosis in a Mis16-dependent manner...
October 6, 2016: Molecular Cell
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