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https://www.readbyqxmd.com/read/28177753/histone-h3-3-regulates-mitotic-progression-in-mouse-embryonic-fibroblasts
#1
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
#2
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 been reported during the day-night cycle. In this study, we generated genome wide maps of H2A.Z for day and night time harvested seedling tissues by combining chromatin immunoprecipitation and high-throughput sequencing...
February 2, 2017: Plant Signaling & Behavior
https://www.readbyqxmd.com/read/28144029/variants-of-core-histones-and-their-roles-in-cell-fate-decisions-development-and-cancer
#3
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...
February 1, 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
#4
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
#5
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...
December 25, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27992255/drosophila-h2a-and-h2a-z-nucleosome-sequences-reveal-different-nucleosome-positioning-sequence-patterns
#6
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...
December 19, 2016: 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
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
https://www.readbyqxmd.com/read/27643852/differential-deposition-of-h2a-z-in-combination-with-histone-modifications-within-related-genes-in-oryza-sativa-callus-and-seedling
#13
Kang Zhang, Wenying Xu, Chunchao Wang, Xin Yi, Wenli Zhang, Zhen Su
As a histone variant, H2A.Z is highly conserved among species and plays a significant role in diverse cellular processes. Here, we generated genome-wide maps of H2A.Z in Oryza sativa (rice) callus and seedling by combining chromatin immunoprecipitation using H2A.Z antibody and high-throughput sequencing. We found a significantly high peak and a small peak of H2A.Z distributed at the 5' and 3' ends of highly expressed genes, respectively. H2A.Z was also associated with inactive genes in both tissues. H3 lysine 4 trimethylation was associated with H2A...
January 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/27634286/genome-wide-positioning-of-bivalent-mononucleosomes
#14
Subhojit Sen, Kirsten F Block, Alice Pasini, Stephen B Baylin, Hariharan Easwaran
BACKGROUND: Bivalent chromatin refers to overlapping regions containing activating histone H3 Lys4 trimethylation (H3K4me3) and inactivating H3K27me3 marks. Existence of such bivalent marks on the same nucleosome has only recently been suggested. Previous genome-wide efforts to characterize bivalent chromatin have focused primarily on individual marks to define overlapping zones of bivalency rather than mapping positions of truly bivalent mononucleosomes. RESULTS: Here, we developed an efficacious sequential ChIP technique for examining global positioning of individual bivalent nucleosomes...
September 15, 2016: BMC Medical Genomics
https://www.readbyqxmd.com/read/27617756/characterization-of-mussel-h2a-z-2-a-new-h2a-z-variant-preferentially-expressed-in-germinal-tissues-from-mytilus
#15
Ciro Rivera-Casas, Rodrigo González-Romero, Ángel Vizoso-Vazquez, Manjinder S Cheema, M Esperanza Cerdán, Josefina Méndez, Juan Ausió, Jose M Eirin-Lopez
Histones are the fundamental constituents of the eukaryotic chromatin, facilitating the physical organization of DNA in chromosomes and participating in the regulation of its metabolism. The H2A family displays the largest number of variants among core histones, including the renowned H2A.X, macroH2A, H2A.B (Bbd), and H2A.Z. This latter variant is especially interesting because of its regulatory role and its differentiation into 2 functionally divergent variants (H2A.Z.1 and H2A.Z.2), further specializing the structure and function of vertebrate chromatin...
October 2016: Biochemistry and Cell Biology, Biochimie et Biologie Cellulaire
https://www.readbyqxmd.com/read/27578180/splice-variants-of-the-swr1-type-nucleosome-remodeling-factor-domino-have-distinct-functions-during-drosophila-melanogaster-oogenesis
#16
Kenneth Börner, Peter B Becker
SWR1-type nucleosome remodeling factors replace histone H2A by variants to endow chromatin locally with specialized functionality. In Drosophila melanogaster a single H2A variant, H2A.V, combines functions of mammalian H2A.Z and H2A.X in transcription regulation and the DNA damage response. A major role in H2A.V incorporation for the only SWR1-like enzyme in flies, Domino, is assumed but not well documented in vivo. It is also unclear whether the two alternatively spliced isoforms, DOM-A and DOM-B, have redundant or specialized functions...
September 1, 2016: Development
https://www.readbyqxmd.com/read/27569210/smyd3-mediated-h2a-z-1-methylation-promotes-cell-cycle-and-cancer-proliferation
#17
Cheng-Hui Tsai, Yun-Ju Chen, Chia-Jung Yu, Shiou-Ru Tzeng, I-Chen Wu, Wen-Hung Kuo, Ming-Chieh Lin, Nei-Li Chan, Kou-Juey Wu, Shu-Chun Teng
SMYD3 methyltransferase is nearly undetectable in normal human tissues but highly expressed in several cancers, including breast cancer, although its contributions to pathogenesis in this setting are unclear. Here we report that histone H2A.Z.1 is a substrate of SMYD3 that supports malignancy. SMYD3-mediated dimethylation of H2A.Z.1 at lysine 101 (H2A.Z.1K101me2) increased stability by preventing binding to the removal chaperone ANP32E and facilitating its interaction with histone H3. Moreover, a microarray analysis identified cyclin A1 as a target coregulated by SMYD3 and H2A...
October 15, 2016: Cancer Research
https://www.readbyqxmd.com/read/27501381/observing-mitotic-division-and-dynamics-in-a-live-zebrafish-embryo
#18
Stefanie M Percival, John M Parant
Mitosis is critical for organismal growth and differentiation. The process is highly dynamic and requires ordered events to accomplish proper chromatin condensation, microtubule-kinetochore attachment, chromosome segregation, and cytokinesis in a small time frame. Errors in the delicate process can result in human disease, including birth defects and cancer. Traditional approaches investigating human mitotic disease states often rely on cell culture systems, which lack the natural physiology and developmental/tissue-specific context advantageous when studying human disease...
July 15, 2016: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/27495811/the-arabidopsis-hnrnp-q-protein-lif2-and-the-prc1-subunit-lhp1-function-in-concert-to-regulate-the-transcription-of-stress-responsive-genes
#19
Anne Molitor, David Latrasse, Matthias Zytnicki, Philippe Andrey, Nicole Houba-Hérin, Mélanie Hachet, Christophe Battail, Stefania Del Prete, Adriana Alberti, Hadi Quesneville, Valerie Gaudin
LHP1-INTERACTING FACTOR2 (LIF2), a heterogeneous nuclear ribonucleoprotein involved in Arabidopsis thaliana cell fate and stress responses, interacts with LIKE HETEROCHROMATIN PROTEIN1 (LHP1), a Polycomb Repressive Complex1 (PRC1) subunit. To investigate LIF2-LHP1 functional interplay, we mapped their genome-wide distributions in wild-type, lif2, and lhp1 backgrounds, under standard and stress conditions. Interestingly, LHP1-targeted regions form local clusters, suggesting an underlying functional organization of the plant genome...
August 5, 2016: Plant Cell
https://www.readbyqxmd.com/read/27487198/single-molecule-observation-reveals-spontaneous-protein-dynamics-in-the-nucleosome
#20
Jongseong Kim, Sijie Wei, Jaehyoun Lee, Hongjun Yue, Tae-Hee Lee
Structural dynamics of a protein molecule is often critical to its function. Single-molecule methods provide efficient ways to investigate protein dynamics, although it is very challenging to achieve a millisecond or higher temporal resolution. Here we report spontaneous structural dynamics of the histone protein core in the nucleosome based on a single-molecule method that can reveal submillisecond dynamics by combining maximum likelihood estimation and fluorescence correlation spectroscopy. The nucleosome, comprising ∼147 bp DNA and an octameric histone protein core consisting of H2A, H2B, H3, and H4, is the fundamental packing unit of the eukaryotic genome...
September 1, 2016: Journal of Physical Chemistry. B
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