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https://www.readbyqxmd.com/read/29145630/yaf9-subunit-of-the-nua4-and-swr1-complexes-targets-histone-h3k27ac-through-its-yeats-domain
#1
Brianna J Klein, Salar Ahmad, Kendra R Vann, Forest H Andrews, Zachary A Mayo, Gaelle Bourriquen, Joseph B Bridgers, Jinyong Zhang, Brian D Strahl, Jacques Côté, Tatiana G Kutateladze
Yaf9 is an integral part of the NuA4 acetyltransferase and the SWR1 chromatin remodeling complexes. Here, we show that Yaf9 associates with acetylated histone H3 with high preference for H3K27ac. The crystal structure of the Yaf9 YEATS domain bound to the H3K27ac peptide reveals that the sequence C-terminal to K27ac stabilizes the complex. The side chain of K27ac inserts between two aromatic residues, mutation of which abrogates the interaction in vitro and leads in vivo to phenotypes similar to YAF9 deletion, including loss of SWR1-dependent incorporation of variant histone H2A...
November 14, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29145618/the-histone-variant-h2a-z-promotes-initiation-of-meiotic-recombination-in-fission-yeast
#2
Shintaro Yamada, Kazuto Kugou, Da-Qiao Ding, Yurika Fujita, Yasushi Hiraoka, Hiroshi Murakami, Kunihiro Ohta, Takatomi Yamada
Meiotic recombination is initiated by programmed formation of DNA double strand breaks (DSBs), which are mainly formed at recombination hotspots. Meiotic DSBs require multiple proteins including the conserved protein Spo11 and its cofactors, and are influenced by chromatin structure. For example, local chromatin around hotspots directly impacts DSB formation. Moreover, DSB is proposed to occur in a higher-order chromatin architecture termed 'axis-loop', in which many loops protrude from cohesin-enriched axis...
November 14, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29138493/suppression-of-srcap-chromatin-remodelling-complex-and-restriction-of-lymphoid-lineage-commitment-by-pcid2
#3
Buqing Ye, Benyu Liu, Liuliu Yang, Guanling Huang, Lu Hao, Pengyan Xia, Shuo Wang, Ying Du, Xiwen Qin, Pingping Zhu, Jiayi Wu, Nobuo Sakaguchi, Junyan Zhang, Zusen Fan
Lymphoid lineage commitment is an important process in haematopoiesis, which forms the immune system to protect the host from pathogen invasion. However, how multipotent progenitors (MPP) switch into common lymphoid progenitors (CLP) or common myeloid progenitors (CMP) during this process remains elusive. Here we show that PCI domain-containing protein 2 (Pcid2) is highly expressed in MPPs. Pcid2 deletion in the haematopoietic system causes skewed lymphoid lineage specification. In MPPs, Pcid2 interacts with the Zinc finger HIT-type containing 1 (ZNHIT1) to block Snf2-related CREBBP activator protein (SRCAP) activity and prevents the deposition of histone variant H2A...
November 15, 2017: Nature Communications
https://www.readbyqxmd.com/read/29126175/conventional-and-pioneer-modes-of-glucocorticoid-receptor-interaction-with-enhancer-chromatin-in-vivo
#4
Thomas A Johnson, Razvan V Chereji, Diana A Stavreva, Stephanie A Morris, Gordon L Hager, David J Clark
Glucocorticoid hormone plays a major role in metabolism and disease. The hormone-bound glucocorticoid receptor (GR) binds to a specific set of enhancers in different cell types, resulting in unique patterns of gene expression. We have addressed the role of chromatin structure in GR binding by mapping nucleosome positions in mouse adenocarcinoma cells. Before hormone treatment, GR-enhancers exist in one of three chromatin states: (i) Nucleosome-depleted enhancers that are DNase I-hypersensitive, associated with the Brg1 chromatin remodeler and flanked by nucleosomes incorporating histone H2A...
November 8, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29116202/acetylated-histone-variant-h2a-z-is-involved-in-the-activation-of-neo-enhancers-in-prostate-cancer
#5
Fátima Valdés-Mora, Cathryn M Gould, Yolanda Colino-Sanguino, Wenjia Qu, Jenny Z Song, Kylie M Taylor, Fabian A Buske, Aaron L Statham, Shalima S Nair, Nicola J Armstrong, James G Kench, Kenneth M L Lee, Lisa G Horvath, Minru Qiu, Alexei Ilinykh, Nicole S Yeo-Teh, David Gallego-Ortega, Clare Stirzaker, Susan J Clark
Acetylation of the histone variant H2A.Z (H2A.Zac) occurs at active promoters and is associated with oncogene activation in prostate cancer, but its role in enhancer function is still poorly understood. Here we show that H2A.Zac containing nucleosomes are commonly redistributed to neo-enhancers in cancer resulting in a concomitant gain of chromatin accessibility and ectopic gene expression. Notably incorporation of acetylated H2A.Z nucleosomes is a pre-requisite for activation of Androgen receptor (AR) associated enhancers...
November 7, 2017: Nature Communications
https://www.readbyqxmd.com/read/29113076/gene-expression-analysis-of-the-effect-of-ischemic-infarction-in-whole-blood
#6
Ayako Takuma, Arata Abe, Yoshikazu Saito, Chikako Nito, Masayuki Ueda, Yoshiro Ishimaru, Hideki Harada, Keiko Abe, Kazumi Kimura, Tomiko Asakura
Given the abundance of stroke patients and deaths from stroke worldwide, many studies concerning the aftermath of stroke are being carried out. To reveal the precise effect of ischemic infarction, we conducted a comprehensive gene expression analysis. Alongside a middle cerebral artery occlusion (MCAO) Sprague-Dawley rat model, we used a group undergoing sham surgery for comparison, which was the same as MCAO surgery but without blood vessel occlusion. Subsequently, infarction of the brains of MCAO-treated rats occurred, but did not occur in the sham-treated rats...
November 5, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29099280/variant-histone-h2afv-reprograms-dna-methylation-during-early-zebrafish-development
#7
Bhavani Madakashira, Laura Corbett, Chi Zhang, Pier Paoli, John W Casement, Jelena Mann, Kirsten C Sadler, Derek A Mann
The DNA methylome is re-patterned during discrete phases of vertebrate development. In zebrafish, there are two waves of global DNA demethylation and re-methylation: the first occurs prior to gastrulation when the parental methylome is changed to the zygotic pattern and the second occurs after formation of the embryonic body axis, during organ specification. The occupancy of the histone variant H2A.Z and regions of DNA methylation are generally anti-correlated, and it has been proposed that H2A.Z restricts the boundaries of highly methylated regions...
November 3, 2017: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/29095668/sumo-modification-system-facilitates-the-exchange-of-histone-variant-h2a-z-2-at-dna-damage-sites
#8
Atsuhiko Fukuto, Masae Ikura, Tsuyoshi Ikura, Jiying Sun, Yasunori Horikoshi, Hiroki Shima, Kazuhiko Igarashi, Masayuki Kusakabe, Masahiko Harata, Naoki Horikoshi, Hitoshi Kurumizaka, Yoshiaki Kiuchi, Satoshi Tashiro
Histone exchange and histone post-translational modifications play important roles in the regulation of DNA metabolism, by re-organizing the chromatin configuration. We previously demonstrated that the histone variant H2A.Z-2 is rapidly exchanged at damaged sites after DNA double strand break induction in human cells. In yeast, the small ubiquitin-like modifier (SUMO) modification of H2A.Z is involved in the DNA damage response. However, whether the SUMO modification regulates the exchange of human H2A.Z-2 at DNA damage sites remains unclear...
November 2, 2017: Nucleus
https://www.readbyqxmd.com/read/29069602/the-histone-variant-h2a-z-is-a-master-regulator-of-the-epithelial-mesenchymal-transition
#9
Renae Domaschenz, Sebastian Kurscheid, Maxim Nekrasov, Shuyi Han, David J Tremethick
Epithelial-mesenchymal transition (EMT) is a profound example of cell plasticity that is crucial for embryonic development and cancer. Although it has long been suspected that chromatin-based mechanisms play a role in this process, no master regulator that can specifically regulate EMT has been identified to date. Here, we show that H2A.Z can coordinate EMT by serving as either an activator or repressor of epithelial or mesenchymal gene expression, respectively. Following induction of EMT by TGF-β, we observed an unexpected loss of H2A...
October 24, 2017: Cell Reports
https://www.readbyqxmd.com/read/29045007/chromatin-remodeling-factor-osino80-is-involved-in-regulation-of-gibberellin-biosynthesis-and-is-crucial-for-rice-plant-growth-and-development
#10
Chao Li, Yuhao Liu, Wen-Hui Sun, Yu Yu, Aiwu Dong
The phytohormone gibberellin (GA) plays essential roles in plant growth and development. Here, we report that OsINO80, a conserved ATP-dependent chromatin-remodeling factor in rice (Oryza sativa), functions in diverse biological processes and GA biosynthesis. OsINO80-knockdown mutants, derived from either T-DNA insertion or RNA interference, display typical GA-deficient phenotypes, including dwarfism, reduced cell length, late flowering, retarded seed germination and impaired reproductive development. Consistently, transcriptome analyses reveal that OsINO80 knockdown results in down-regulation by more than two-fold of over 1000 genes, including the GA biosynthesis genes CPS1 and GA3ox2, and the dwarf phenotype of OsINO80-knockdown mutants can be rescued by the application of exogenous GA3...
October 17, 2017: Journal of Integrative Plant Biology
https://www.readbyqxmd.com/read/29036602/n6-adenine-dna-methylation-is-associated-with-the-linker-dna-of-h2a-z-containing-well-positioned-nucleosomes-in-pol-ii-transcribed-genes-in-tetrahymena
#11
Yuanyuan Wang, Xiao Chen, Yalan Sheng, Yifan Liu, Shan Gao
DNA N6-methyladenine (6mA) is newly rediscovered as a potential epigenetic mark across a more diverse range of eukaryotes than previously realized. As a unicellular model organism, Tetrahymena thermophila is among the first eukaryotes reported to contain 6mA modification. However, lack of comprehensive information about 6mA distribution hinders further investigations into its function and regulatory mechanism. In this study, we provide the first genome-wide, base pair-resolution map of 6mA in Tetrahymena by applying single-molecule real-time (SMRT) sequencing...
November 16, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29036442/global-inhibition-of-transcription-causes-an-increase-in-histone-h2a-z-incorporation-within-gene-bodies
#12
Anahita Lashgari, Jean-François Millau, Pierre-Étienne Jacques, Luc Gaudreau
H2A.Z histone variant is an important regulator of gene transcription, which is enriched at regulatory regions but is also found within gene bodies. Recent evidence suggests that active recruitment of H2A.Z within gene bodies is required to induce gene repression. In contrast to this view, we show that global inhibition of transcription results in H2A.Z accumulation at gene transcription start sites, as well as within gene bodies. Our results indicate that accumulation of H2A.Z within repressed genes can also be a consequence of the repression of gene transcription rather than an active mechanism required to establish the repression...
October 3, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29034626/-sequence-analysis-and-expression-patterns-of-histone-h2a-variants-in-phytophthora-infestans
#13
Xiaowen Wang, Liyun Guo
In eukaryotic cells, DNA is packaged inside the nucleus together with histones to form nucleosomes. Each histone molecule contains two of each core histone subunits H2A, H2B, H3 and H4. Among core histones, the H2A family is of great interest due to the high diversity of specialized variants. These variants have shown important role in critical cellular processes. Epigenetic mechanism in oomycetes is barely known. Phytophthora infestans is a severe pathogen and a model species in oomycetes. In this study, we studied the sequence and expression pattern of H2A variants of P...
November 25, 2016: Sheng Wu Gong Cheng Xue Bao, Chinese Journal of Biotechnology
https://www.readbyqxmd.com/read/29021892/catching-global-interactions-in-vivo
#14
Yi Qiu, Suming Huang
Histone proteins and transcription factors (TFs) play critical roles in gene transcription and development of multicellular organisms. Although antibody mediated protein isolation couple with mass spectrometry approach has been a standard method to identify TF interacting partners and characterize their functional molecular complexes, it becomes urge to develop a robust method to functional characterize how these transcription factors act during biological process in the post-human genome project era. Here, Dr...
2017: Cell & Bioscience
https://www.readbyqxmd.com/read/28973436/dual-function-of-swc5-in-swr-remodeling-atpase-activation-and-histone-h2a-eviction
#15
Lu Sun, Ed Luk
The chromatin remodeler SWR deposits histone H2A.Z at promoters and other regulatory sites via an ATP-driven histone exchange reaction that replaces nucleosomal H2A with H2A.Z. Simultaneous binding of SWR to both H2A nucleosome and free H2A.Z induces SWR ATPase activity and engages the histone exchange mechanism. Swc5 is a conserved subunit of the 14-polypeptide SWR complex that is required for the histone exchange reaction, but its molecular role is unknown. We found that Swc5, although not required for substrate binding, is required for SWR ATPase stimulation, suggesting that Swc5 is required to couple substrate recognition to ATPase activation...
September 29, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28951178/h2a-z-represses-gene-expression-by-modulating-promoter-nucleosome-structure-and-enhancer-histone-modifications-in-arabidopsis
#16
Xiaozhuan Dai, Youhuang Bai, Lihua Zhao, Xianying Dou, Yanhui Liu, Lulu Wang, Yi Li, Weimin Li, Yanan Hui, Xinyu Huang, Zonghua Wang, Yuan Qin
Deposition of the histone variant H2A.Z at gene bodies regulates transcription by modifying chromatin accessibility in plants. However, the role of H2A.Z enrichment at the promoter and enhancer regions is unclear, and how H2A.Z interacts with other mechanisms of chromatin modification to regulate gene expression remains obscure. Here, we mapped genome-wide H2A.Z, H3K4me3, H3K27me3, Pol II, and nucleosome occupancy in Arabidopsis inflorescence. We showed that H2A.Z preferentially associated with H3K4me3 at promoters, while it was found with H3K27me3 at enhancers, and that H2A...
October 9, 2017: Molecular Plant
https://www.readbyqxmd.com/read/28925810/ube3a-mediated-regulation-of-imprinted-genes-and-epigenome-wide-marks-in-human-neurons
#17
S Jesse Lopez, Keith Dunaway, M Saharul Islam, Charles Mordaunt, Annie Vogel Ciernia, Makiko Meguro-Horike, Shin-Ichi Horike, David J Segal, Janine LaSalle
The dysregulation of genes in neurodevelopmental disorders that lead to social and cognitive phenotypes is a complex, multilayered process involving both genetics and epigenetics. Parent-of-origin effects of deletion and duplication of the 15q11-q13 locus leading to Angelman, Prader-Willi, and Dup15q syndromes are due to imprinted genes, including UBE3A, which is maternally expressed exclusively in neurons. UBE3A encodes a ubiquitin E3 ligase protein with multiple downstream targets, including RING1B, which in turn monoubiquitinates histone variant H2A...
September 19, 2017: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/28893714/transcriptional-regulation-of-the-ambient-temperature-response-by-h2a-z-nucleosomes-and-hsf1-transcription-factors-in-arabidopsis
#18
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 heat shock response in eukaryotes, the heat shock factors (HSFs), have undergone large-scale gene amplification in plants. While HSFs are central in heat stress responses, their role in the response to 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...
October 9, 2017: Molecular Plant
https://www.readbyqxmd.com/read/28893254/skip-controls-flowering-time-via-the-alternative-splicing-of-sef-pre-mrna-in-arabidopsis
#19
Zhibo Cui, Aizi Tong, Yiqiong Huo, Zhiqiang Yan, Weiqi Yang, Xianli Yang, Xiao-Xue Wang
BACKGROUND: Similar to other eukaryotes, splicing is emerging as an important process affecting development and stress tolerance in plants. Ski-interacting protein (SKIP), a splicing factor, is essential for circadian clock function and abiotic stress tolerance; however, the mechanisms whereby it regulates flowering time are unknown. RESULTS: In this study, we found that SKIP is required for the splicing of serrated leaves and early flowering (SEF) pre-messenger RNA (mRNA), which encodes a component of the ATP-dependent SWR1 chromatin remodeling complex (SWR1-C)...
September 11, 2017: BMC Biology
https://www.readbyqxmd.com/read/28883625/redundant-functions-for-nap1-and-chz1-in-h2a-z-deposition
#20
Raghuvar Dronamraju, Srinivas Ramachandran, Deepak K Jha, Alexander T Adams, Julia V DiFiore, Michael A Parra, Nikolay V Dokholyan, Brian D Strahl
H2A.Z is a histone H2A variant that contributes to transcriptional regulation, DNA damage response and limits heterochromatin spreading. In Saccharomyces cerevisiae, H2A.Z is deposited by the SWR-C complex, which relies on several histone chaperones including Nap1 and Chz1 to deliver H2A.Z-H2B dimers to SWR-C. However, the mechanisms by which Nap1 and Chz1 cooperate to bind H2A.Z and their contribution to H2A.Z deposition in chromatin is not well understood. Using structural modeling and molecular dynamics simulations, we identify a series of H2A...
September 7, 2017: Scientific Reports
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