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https://www.readbyqxmd.com/read/28431042/cis-regulatory-divergence-in-gene-expression-between-two-thermally-divergent-yeast-species
#1
Xueying C Li, Justin C Fay
Gene regulation is a ubiquitous mechanism by which organisms respond to their environment. While organisms are often found to be adapted to the environments they experience, the role of gene regulation in environmental adaptation is not often known. In this study, we examine divergence in cis-regulatory effects between two Saccharomyces species, S. cerevisiae and S. uvarum, that have substantially diverged in their thermal growth profile. We measured allele specific expression (ASE) in the species' hybrid at three temperatures, the highest of which is lethal to S...
April 14, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28428255/nucleosome-nucleosome-interactions-via-histone-tails-and-linker-dna-regulate-nuclear-rigidity
#2
Yuta Shimamoto, Sachiko Tamura, Hiroshi Masumoto, Kazuhiro Maeshima
Cells, as well as the nuclei inside them, experience significant mechanical stress in diverse biological processes including contraction, migration, and adhesion. The structural stability of nuclei must therefore be maintained in order to protect genome integrity. Despite extensive knowledge on nuclear architecture and components, however, the underlying physical and molecular mechanisms remain largely unknown. We addressed this in the present study by subjecting isolated human cell nuclei to microneedle-based quantitative micromanipulation with a series of biochemical perturbations of the chromatin...
April 20, 2017: Molecular Biology of the Cell
https://www.readbyqxmd.com/read/28426042/antibodies-to-h2a-and-h2b-histones-from-the-sera-of-hiv-infected-patients-catalyze-site-specific-degradation-of-these-histones
#3
Svetlana V Baranova, Pavel S Dmitrienok, Nikita V Ivanisenko, Valentina N Buneva, Georgy A Nevinsky
Histones and their post-translational modifications have key roles in chromatin remodeling and gene transcription. Besides intranuclear functions, histones act as damage-associated molecules when they are released into the extracellular space. Administration of histones to animals leads to systemic inflammatory and toxic responses. Autoantibodies with enzymatic activities (abzymes) are distinctive features of some autoimmune and viral diseases. Electrophoretically homogeneous IgGs containing no canonical enzymes were isolated from the sera of HIV-infected patients by chromatography on several affinity sorbents including anti-histone Sepharose...
April 20, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28425915/competition-between-histone-and-transcription-factor-binding-regulates-the-onset-of-transcription-in-zebrafish-embryos
#4
Shai R Joseph, Máté Pálfy, Lennart Hilbert, Mukesh Kumar, Jens Karschau, Vasily Zaburdaev, Andrej Shevchenko, Nadine L Vastenhouw
Upon fertilization, the genome of animal embryos remains transcriptionally inactive until the maternal-to-zygotic transition. At this time, the embryo takes control of its development and transcription begins. How the onset of zygotic transcription is regulated remains unclear. Here, we show that a dynamic competition for DNA binding between nucleosome-forming histones and transcription factors regulates zebrafish genome activation. Taking a quantitative approach, we found that the concentration of non-DNA bound core histones sets the time for the onset of transcription...
April 20, 2017: ELife
https://www.readbyqxmd.com/read/28424519/mechanism-of-chromatin-remodelling-revealed-by-the-snf2-nucleosome-structure
#5
Xiaoyu Liu, Meijing Li, Xian Xia, Xueming Li, Zhucheng Chen
Chromatin remodellers are helicase-like, ATP-dependent enzymes that alter chromatin structure and nucleosome positions to allow regulatory proteins access to DNA. Here we report the cryo-electron microscopy structure of chromatin remodeller Switch/sucrose non-fermentable (SWI2/SNF2) from Saccharomyces cerevisiae bound to the nucleosome. The structure shows that the two core domains of Snf2 are realigned upon nucleosome binding, suggesting activation of the enzyme. The core domains contact each other through two induced Brace helices, which are crucial for coupling ATP hydrolysis to chromatin remodelling...
April 19, 2017: Nature
https://www.readbyqxmd.com/read/28421450/the-level-of-proapoptotic-gene-transcripts-in-wheat-leaves-under-high-temperature-stress
#6
L V Topchieva, I A Nilova, A F Titov
Under exposure of wheat plants to high temperatures (33, 37, and 43°C), the level of transcripts of the genes encoding proapoptotic proteins-TaMCAII (encodes type II metacaspase) and TaBAX (functional homologue of the CDF1 gene of Arabidopsis thaliana)-in leaf cells increased. This process at temperatures of 37 and 43°C passed ahead of (in the case of TaBAX mRNA) or was accompanied by (in the case of TaMCAII mRNA) the emergence of signs of nucleosomal DNA degradation in leaves. The accumulation of malondialdehyde in the leaves of seedlings exposed to temperatures of 37 and 43°C coincided in time with a change in the TaMCAII gene expression and the emergence of signs of programmed cell death...
January 2017: Doklady. Biochemistry and Biophysics
https://www.readbyqxmd.com/read/28420746/the-mitochondrial-dna-mtdna-associated-protein-swib5-influences-mtdna-architecture-and-homologous-recombination
#7
Jonas Blomme, Olivier Van Aken, Jelle Van Leene, Teddy Jégu, Riet Maria De Rycke, Michiel De Bruyne, Jasmien Vercruysse, Jonah Nolf, Twiggy Van Daele, Liesbeth De Milde, Mattias Vermeersch, Catherine Colas des Francs-Small, Geert De Jaeger, Moussa Benhamed, A Harvey Millar, Dirk Inzé, Nathalie Gonzalez
In addition to the nucleus, mitochondria and chloroplasts in plant cells also contain genomes. Efficient DNA repair pathways are crucial in these organelles to fix damage resulting from endogenous and exogenous factors. Plant organellar genomes are complex compared to their animal counterparts and although several plant-specific mediators of organelle DNA repair have been reported, many regulators remain to be identified. Here, we show that a mitochondrial SWI/SNF (nucleosome remodeling) complex B protein, SWIB5, is capable of associating with mitochondrial DNA (mtDNA) in Arabidopsis thaliana...
April 18, 2017: Plant Cell
https://www.readbyqxmd.com/read/28419835/the-architecture-and-function-of-the-chromatin-replication-machinery
#8
REVIEW
Thomas Cr Miller, Alessandro Costa
Genomic DNA in eukaryotic cells is packaged into nucleosome arrays. During replication, nucleosomes need to be dismantled ahead of the advancing replication fork and reassembled on duplicated DNA. The architecture and function of the core replisome machinery is now beginning to be elucidated, with recent insights shaping our view on DNA replication processes. Simultaneously, breakthroughs in our mechanistic understanding of epigenetic inheritance allow us to build new models of how histone chaperones integrate with the replisome to reshuffle nucleosomes...
April 15, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28419383/cell-death-biomarkers-and-obstructive-sleep-apnea-implications-in-the-acute-coronary-syndrome
#9
Josep Miquel Bauça, Aina Yañez, Laura Fueyo, Mónica de la Peña, Javier Pierola, Alicia Sánchez-de-la-Torre, Olga Mediano, Valentín Cabriada-Nuño, María José Masdeu, Joaquin Teran-Santos, Joaquin Duran-Cantolla, Juan Fernando Masa, Jorge Abad, Manuel Sanchez-de-la-Torre, Ferran Barbé, Antònia Barceló
Background: Nucleosomes and cell-free DNA (dsDNA) have been suggested as promising biomarkers in cell death-related diseases, such as acute coronary syndrome (ACS). Currently, the impact of obstructive sleep apnea (OSA) in patients with ACS is unclear. Our aim was to evaluate the relationship between OSA, dsDNA and nucleosomes, and to assess their potential implication in the development of ACS. Methods: Up to 549 patients were included in the study and divided into 4 groups (145 ACS; 290 ACS+OSA; 62 OSA; 52 controls)...
April 17, 2017: Sleep
https://www.readbyqxmd.com/read/28418626/degradation-of-the-baf-complex-factor-brd9-by-heterobifunctional-ligands
#10
David Remillard, Dennis L Buckley, Joshiawa Paulk, Gerard L Brien, Matthew Sonnett, Hyuk-Soo Seo, Shiva Dastierdi, Martin Wühr, Sirano Dhe-Paganon, Scott A Armstrong, James E Bradner
The bromodomain-containing protein BRD9, a subunit of the human BAF (SWI/SNF) nucleosome remodeling complex, has emerged as an attractive therapeutic target in cancer. Despite the development of chemical probes targeting the BRD9 bromodomain, there is a limited understanding of BRD9 function beyond acetyl-lysine recognition. We have therefore created the first BRD9-directed chemical degraders, through iterative design and testing of heterobifunctional ligands that bridge the BRD9 bromodomain and the cereblon E3 ubiquitin ligase complex...
April 18, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28418026/the-cac2-subunit-is-essential-for-productive-histone-binding-and-nucleosome-assembly-in-caf-1
#11
Francesca Mattiroli, Yajie Gu, Jeremy L Balsbaugh, Natalie G Ahn, Karolin Luger
Nucleosome assembly following DNA replication controls epigenome maintenance and genome integrity. Chromatin assembly factor 1 (CAF-1) is the histone chaperone responsible for histone (H3-H4)2 deposition following DNA synthesis. Structural and functional details for this chaperone complex and its interaction with histones are slowly emerging. Using hydrogen-deuterium exchange coupled to mass spectrometry, combined with in vitro and in vivo mutagenesis studies, we identified the regions involved in the direct interaction between the yeast CAF-1 subunits, and mapped the CAF-1 domains responsible for H3-H4 binding...
April 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28413449/links-between-dna-methylation-and-nucleosome-occupancy-in-the-human-genome
#12
Clayton K Collings, John N Anderson
BACKGROUND: DNA methylation is an epigenetic modification that is enriched in heterochromatin but depleted at active promoters and enhancers. However, the debate on whether or not DNA methylation is a reliable indicator of high nucleosome occupancy has not been settled. For example, the methylation levels of DNA flanking CTCF sites are higher in linker DNA than in nucleosomal DNA, while other studies have shown that the nucleosome core is the preferred site of methylation. In this study, we make progress toward understanding these conflicting phenomena by implementing a bioinformatics approach that combines MNase-seq and NOMe-seq data and by comprehensively profiling DNA methylation and nucleosome occupancy throughout the human genome...
2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/28412501/regulation-of-baz1a-and-nucleosome-positioning-in-the-nucleus-accumbens-in-response-to-cocaine
#13
HaoSheng Sun, Diane M Damez-Werno, Kimberly N Scobie, Ning-Yi Shao, Caroline Dias, Jacqui Rabkin, Katherine N Wright, Ezekiell Mouzon, Mohamed Kabbaj, Rachael Neve, Gustavo Turecki, Li Shen, Eric J Nestler
Chromatin regulation, in particular ATP-dependent chromatin remodelers, have previously been shown to be important in the regulation of reward-related behaviors in animal models of mental illnesses. Here we demonstrate that BAZ1A, an accessory subunit of the ISWI family of chromatin remodeling complexes, is downregulated in the nucleus accumbens (NAc) of mice exposed repeatedly to cocaine and of cocaine-addicted humans. Viral-mediated overexpression of BAZ1A in mouse NAc reduces cocaine reward as assessed by CPP, but increases cocaine-induced locomotor activation...
April 12, 2017: Neuroscience
https://www.readbyqxmd.com/read/28411180/co-expression-of-sall4-with-hdac1-and-or-hdac2-is-associated-with-underexpression-of-pten-and-poor-prognosis-in-patients-with-hepatocellular-carcinoma
#14
Huanlin Wang, Kenichi Kohashi, Tomoharu Yoshizumi, Yukihiko Okumura, Yuki Tanaka, Masahiro Shimokawa, Takeshi Iwasaki, Shinichi Aishima, Yoshihiko Maehara, Yoshinao Oda
Spalt-like transcriptional factor 4 (SALL4), a stem marker, is re-activated in several cancers. A previous study has demonstrated that SALL4 interacts with the nucleosome remodeling deacetylase complex (NuRD), which contains histone deacetylase 1 (HDAC1) and histone deacetylase 2 (HDAC2). In this study we investigated the expression status of SALL4, HDAC1 and HDAC2 and their relationship with phosphatase and tensin homolog deleted on chromosome 10 (PTEN) by immunohistochemical analysis of the post-hepatectomy specimens of 135 patients with hepatocellular carcinoma (HCC) who were treated at our hospital...
April 11, 2017: Human Pathology
https://www.readbyqxmd.com/read/28410129/epigenetics-of-reproductive-infertility
#15
Laxmidhar Das, Sabnam Parbin, Nibedita Pradhan, Chahat Kausar, Samir K Patra
Infertility is a complex pathophysiological condition. It may caused by specific or multiple physical and physiological factors, including abnormalities in homeostasis, hormonal imbalances and genetic alterations. In recent times various studies implicated that, aberrant epigenetic mechanisms are associated with reproductive infertility. There might be transgenerational effects associated with epigenetic modifications of gametes and studies suggest the importance of alterations in epigenetic modification at early and late stages of gametogenesis...
June 1, 2017: Frontiers in Bioscience (Scholar Edition)
https://www.readbyqxmd.com/read/28408607/crystal-structure-of-the-overlapping-dinucleosome-composed-of-hexasome-and-octasome
#16
Daiki Kato, Akihisa Osakabe, Yasuhiro Arimura, Yuka Mizukami, Naoki Horikoshi, Kazumi Saikusa, Satoko Akashi, Yoshifumi Nishimura, Sam-Yong Park, Jumpei Nogami, Kazumitsu Maehara, Yasuyuki Ohkawa, Atsushi Matsumoto, Hidetoshi Kono, Rintaro Inoue, Masaaki Sugiyama, Hitoshi Kurumizaka
Nucleosomes are dynamic entities that are repositioned along DNA by chromatin remodeling processes. A nucleosome repositioned by the switch-sucrose nonfermentable (SWI/SNF) remodeler collides with a neighbor and forms the intermediate "overlapping dinucleosome." Here, we report the crystal structure of the overlapping dinucleosome, in which two nucleosomes are associated, at 3.14-angstrom resolution. In the overlapping dinucleosome structure, the unusual "hexasome" nucleosome, composed of the histone hexamer lacking one H2A-H2B dimer from the conventional histone octamer, contacts the canonical "octasome" nucleosome, and they intimately associate...
April 14, 2017: Science
https://www.readbyqxmd.com/read/28408574/nucleosomes-in-contact
#17
EDITORIAL
Valda Vinson
No abstract text is available yet for this article.
April 14, 2017: Science
https://www.readbyqxmd.com/read/28408367/variability-in-chromatin-architecture-and-associated-dna-repair-at-genomic-positions-containing-somatic-mutations
#18
Byungho Lim, Jihyeob Mun, Yong Sung Kim, Seon-Young Kim
Dynamic chromatin structures result in differential chemical reactivity to mutational processes throughout the genome. To identify chromatin features responsible for mutagenesis, we compared chromatin architecture around single-nucleotide variants (SNV), insertion/deletions (indels) and their context-matched, non-mutated positions. We found epigenetic differences between genomic regions containing missense SNV and those containing frameshift indels across multiple cancer types. Levels active histone marks were higher around frameshift indels than around missense SNV, whereas repressive histone marks exhibited the reverse trend...
April 13, 2017: Cancer Research
https://www.readbyqxmd.com/read/28406749/nucleosome-repositioning-during-differentiation-of-a-human-myeloid-leukemia-cell-line
#19
Vladimir B Teif, Jan-Philipp Mallm, Tanvi Sharma, David B Mark Welch, Karsten Rippe, Roland Eils, Jörg Langowski, Ada L Olins, Donald E Olins
Cell differentiation is associated with changes in chromatin organization and gene expression. In this study, we examine chromatin structure following differentiation of the human myeloid leukemia cell line (HL-60/S4) into granulocytes with retinoic acid (RA) or into macrophage with phorbol ester (TPA). We performed ChIP-seq of histone H3 and its modifications, analyzing changes in nucleosome occupancy, nucleosome repeat length, eu-/heterochromatin redistribution and properties of epichromatin (surface chromatin adjacent to the nuclear envelope)...
March 4, 2017: Nucleus
https://www.readbyqxmd.com/read/28406741/bridging-the-dynamics-and-organization-of-chromatin-domains-by-mathematical-modeling
#20
Soya Shinkai, Tadasu Nozaki, Kazuhiro Maeshima, Yuichi Togashi
The genome is three-dimensionally organized in the cell, and the mammalian genome DNA is partitioned into submegabase-sized chromatin domains. Genome functions are regulated within and across the domains according to their organization, whereas the chromatin itself is highly dynamic. However, the details of such dynamic organization of chromatin domains in living cells remain unclear. To unify chromatin dynamics and organization, we recently demonstrated that structural information of chromatin domains in living human cells can be extracted from analyses of the subdiffusive nucleosome movement using mathematical modeling...
April 13, 2017: Nucleus
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