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chromatin remodeling

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https://www.readbyqxmd.com/read/28741893/when-epigenetics-meets-bioengineering-a-material-characteristics-and-surface-topography-perspective
#1
REVIEW
Lena Larsson, Sophia P Pilipchuk, William V Giannobile, Rogerio M Castilho
The field of tissue engineering and regenerative medicine (TE/RM) involves regeneration of tissues and organs using implantable biomaterials. The term epigenetics refers to changes in gene expression that are not encoded in the DNA sequence, leading to remodeling of the chromatin and activation or inactivation of gene expression. Recently, studies have demonstrated that these modifications are influenced not only by biological cues but also by mechanical and topographical signals. This review highlights the current knowledge on emerging approaches in TE/RM with a focus on the effect of materials and topography on the epigenetic expression pattern in cells with potential impacts on modulating regenerative biology...
July 25, 2017: Journal of Biomedical Materials Research. Part B, Applied Biomaterials
https://www.readbyqxmd.com/read/28741798/novel-orally-bioavailable-ezh1-2-dual-inhibitors-with-greater-antitumor-efficacy-than-an-ezh2-selective-inhibitor
#2
REVIEW
Daisuke Honma, Osamu Kanno, Jun Watanabe, Junzo Kinoshita, Makoto Hirasawa, Emi Nosaka, Machiko Shiroishi, Takeshi Takizawa, Isao Yasumatsu, Takao Horiuchi, Akira Nakao, Keisuke Suzuki, Tomonori Yamasaki, Katsuyoshi Nakajima, Miho Hayakawa, Takanori Yamazaki, Ajay Singh Yadav, Nobuaki Adachi
Polycomb repressive complex 2 (PRC2) methylates histone H3 lysine 27 and represses gene expression to regulate cell proliferation and differentiation. Enhancer of zeste homolog 2 (EZH2) or its close homolog EZH1 function as catalytic subunits of PRC2, so there are two PRC2 complexes containing either EZH2 or EZH1. Tumorigenic functions of EZH2 and its synthetic lethality with some subunits of SWItch/Sucrose Non-Fermentable (SWI/SNF) chromatin remodeling complexes have been observed. However, little is known about the function of EZH1 in tumorigenesis...
July 25, 2017: Cancer Science
https://www.readbyqxmd.com/read/28741130/epigenetic-involvement-in-etiopathogenesis-and-implications-in-treatment-of-systemic-lupus-erythematous
#3
REVIEW
Arron Munggela Foma, Saeed Aslani, Jafar Karami, Ahmadreza Jamshidi, Mahdi Mahmoudi
BACKGROUND: Recent researches in the field of genetics have extended our knowledge through the discovery of genetic factors associated with autoimmune diseases (AID). Genetics by itself, however, cannot elucidate all the uncertainties encountered in the etiopathology of AID. On the other hand, incomplete harmony in the prevalence of AID in identical twins suggests that non-genetic factors may play an important role in determining the disease susceptibility. Besides, epigenetics, which is defined by changes in gene expression without a corresponding change in the DNA sequences, has come in to provide new awareness in the disease etiopathology by bridging the genetic and epigenetic factors...
July 24, 2017: Inflammation Research: Official Journal of the European Histamine Research Society ... [et Al.]
https://www.readbyqxmd.com/read/28739803/chromatin-remodeling-swi-snf-complex-regulates-coenzyme-q6-synthesis-and-a-metabolic-shift-to-respiration-in-yeast
#4
Agape M Awad, Srivats Venkataramanan, Anish Nag, Anoop Raj Galivanche, Michelle C Bradley, Lauren Neves, Stephen Douglass, Catherine F Clarke, Tracy L Johnson
Despite its relatively streamlined genome, there are many important examples of regulated RNA splicing in Saccharomyces cerevisiae Here we report a role for the chromatin remodeler SWI/SNF in respiration, partially via the regulation of splicing. We find that a nutrient-dependent decrease in Snf2 leads to an increase in splicing of the PTC7 transcript. The spliced PTC7 transcript encodes a mitochondrial phosphatase regulator of biosynthesis of coenzyme Q6 (ubiquinone, or CoQ6), a mitochondrial redox-active lipid essential for electron and proton transport in respiration, and increased splicing of PTC7 increases CoQ6 levels...
July 24, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28738846/long-non-coding-rnas-as-novel-players-in-%C3%AE-cell-function-and-type-1-diabetes
#5
REVIEW
Aashiq H Mirza, Simranjeet Kaur, Flemming Pociot
BACKGROUND: Long non-coding RNAs (lncRNAs) are a sub-class within non-coding RNA repertoire that have emerged as crucial regulators of the gene expression in various pathophysiological conditions. lncRNAs display remarkable versatility and wield their functions through interactions with RNA, DNA, or proteins. Accumulating body of evidence based on multitude studies has highlighted the role of lncRNAs in many autoimmune and inflammatory diseases, including type 1 diabetes (T1D). This review highlights emerging roles of lncRNAs in immune and islet β cell function as well as some of the challenges and opportunities in understanding the pathogenesis of T1D and its complications...
July 24, 2017: Human Genomics
https://www.readbyqxmd.com/read/28737768/arid1a-mutated-ovarian-cancers-depend-on-hdac6%C3%A2-activity
#6
Benjamin G Bitler, Shuai Wu, Pyoung Hwa Park, Yang Hai, Katherine M Aird, Yemin Wang, Yali Zhai, Andrew V Kossenkov, Ana Vara-Ailor, Frank J Rauscher Iii, Weiping Zou, David W Speicher, David G Huntsman, Jose R Conejo-Garcia, Kathleen R Cho, David W Christianson, Rugang Zhang
ARID1A, encoding a subunit of the SWI/SNF chromatin-remodelling complex, is the most frequently mutated epigenetic regulator across all human cancers. ARID1A and TP53 mutations are typically mutually exclusive. Therapeutic approaches that correlate with this genetic characteristic remain to be explored. Here, we show that HDAC6 activity is essential in ARID1A-mutated ovarian cancers. Inhibition of HDAC6 activity using a clinically applicable small-molecule inhibitor significantly improved the survival of mice bearing ARID1A-mutated tumours...
July 24, 2017: Nature Cell Biology
https://www.readbyqxmd.com/read/28737171/brg1-swi-snf-dependent-regulation-of-the-wt1-transcriptional-landscape-mediates-epicardial-activity-during-heart-development-and-disease
#7
Joaquim Miguel Vieira, Sara Howard, Cristina Villa Del Campo, Sveva Bollini, Karina N Dubé, Megan Masters, Damien N Barnette, Mala Rohling, Xin Sun, Laura E Hankins, Daria Gavriouchkina, Ruth Williams, Daniel Metzger, Pierre Chambon, Tatjana Sauka-Spengler, Benjamin Davies, Paul R Riley
Epicardium-derived cells (EPDCs) contribute cardiovascular cell types during development and in adulthood respond to Thymosin β4 (Tβ4) and myocardial infarction (MI) by reactivating a fetal gene programme to promote neovascularization and cardiomyogenesis. The mechanism for epicardial gene (re-)activation remains elusive. Here we reveal that BRG1, the essential ATPase subunit of the SWI/SNF chromatin-remodelling complex, is required for expression of Wilms' tumour 1 (Wt1), fetal EPDC activation and subsequent differentiation into coronary smooth muscle, and restores Wt1 activity upon MI...
July 24, 2017: Nature Communications
https://www.readbyqxmd.com/read/28736301/foxa-transcriptional-factor-modulates-insect-susceptibility-to-bacillus-thuringiensis-cry1ac-toxin-by-regulating-the-expression-of-toxin-receptor-abcc2-and-abcc3-genes
#8
Jianghuai Li, Yuemin Ma, Wanli Yuan, Yutao Xiao, Chenxi Liu, Jia Wang, Jianxin Peng, Rong Peng, Mario Soberón, Alejandra Bravo, Yongbo Yang, Kaiyu Liu
Cry toxins produced by Bacillus thuringiensis (Bt) are insecticidal proteins widely used in insect control. Recently, it was shown that ATP-binding cassette transporter proteins (ABC) such as ABCC2, ABCC3, ABCG1 and ABCA2 are implicated in the insecticidal action of Cry toxins as putative receptors. However, the transcriptional regulators involved in the expression of ABC transporter genes remain unknown. Sequence analysis of promoter regions of ABCC2 gene from Helicoverpa armigera and ABCC3 gene from Spodoptera litura Sl-HP cultured cells, revealed the potential participation of Forkhead box protein A (FOXA), a transcription factor that regulates the expression of genes through remodeling chromatin...
July 20, 2017: Insect Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/28735899/mot1-ino80c-and-nc2-function-coordinately-to-regulate-pervasive-transcription-in-yeast-and-mammals
#9
Yong Xue, Suman K Pradhan, Fei Sun, Constantinos Chronis, Nancy Tran, Trent Su, Christopher Van, Ajay Vashisht, James Wohlschlegel, Craig L Peterson, H T Marc Timmers, Siavash K Kurdistani, Michael F Carey
Pervasive transcription initiates from cryptic promoters and is observed in eukaryotes ranging from yeast to mammals. The Set2-Rpd3 regulatory system prevents cryptic promoter function within expressed genes. However, conserved systems that control pervasive transcription within intergenic regions have not been well established. Here we show that Mot1, Ino80 chromatin remodeling complex (Ino80C), and NC2 co-localize on chromatin and coordinately suppress pervasive transcription in S. cerevisiae and murine embryonic stem cells (mESCs)...
July 15, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28729363/brg1-brahma-related-gene-1-promotes-endothelial-mrtf-transcription-to-establish-embryonic-capillary-integrity
#10
Matthew T Menendez, E-Ching Ong, Brian T Shepherd, Vijay Muthukumar, Robert Silasi-Mansat, Florea Lupu, Courtney T Griffin
OBJECTIVE: The chromatin remodeling enzyme BRG1 (brahma-related gene 1) transcriptionally regulates target genes important for early blood vessel development and primitive hematopoiesis. However, because Brg1 deletion in vascular progenitor cells results in lethal anemia by embryonic day 10.5 (E10.5), roles for BRG1 in embryonic vascular development after midgestation are unknown. In this study, we sought to determine whether endothelial cell BRG1 regulates genes important for vascular development or maintenance later in embryonic development...
July 20, 2017: Arteriosclerosis, Thrombosis, and Vascular Biology
https://www.readbyqxmd.com/read/28725233/g-quadruplex-in-plants-a-ubiquitous-regulatory-element-and-its-biological-relevance
#11
REVIEW
Vikas Yadav, Hemansi, Nayun Kim, Narendra Tuteja, Puja Yadav
G quadruplexes (G4) are higher-order DNA and RNA secondary structures formed by G-rich sequences that are built around tetrads of hydrogen-bonded guanine bases. Potential G4 quadruplex sequences have been identified in G-rich eukaryotic non-telomeric and telomeric genomic regions. Upon function, G4 formation is known to involve in chromatin remodeling, gene regulation and has been associated with genomic instability, genetic diseases and cancer progression. The natural role and biological validation of G4 structures is starting to be explored, and is of particular interest for the therapeutic interventions for human diseases...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28723660/poly-adp-ribose-polymerase-inhibitors-as-radiosensitizers-a-systematic-review-of-pre-clinical-and-clinical-human-studies
#12
REVIEW
Paul Lesueur, François Chevalier, Jean-Baptiste Austry, Waisse Waissi, Hélène Burckel, Georges Noël, Jean-Louis Habrand, Yannick Saintigny, Florence Joly
BACKGROUND: Poly-(ADP-Ribose)-Polymerase (PARP) inhibitors are becoming important actors of anti-neoplasic agents landscape, with recent but narrow FDA's approvals for ovarian BRCA mutated cancers and prostatic cancer. Nevertheless, PARP inhibitors are also promising drugs for combined treatments particularly with radiotherapy. More than seven PARP inhibitors have been currently developed. Central Role of PARP in DNA repair, makes consider PARP inhibitor as potential radiosensitizers, especially for tumors with DNA repair defects, such as BRCA mutation, because of synthetic lethality...
July 7, 2017: Oncotarget
https://www.readbyqxmd.com/read/28720707/intrinsically-disordered-chromatin-protein-nupr1-binds-to-the-c-terminal-region-of-polycomb-ring1b
#13
Patricia Santofimia-Castaño, Bruno Rizzuti, Ángel L Pey, Philippe Soubeyran, Miguel Vidal, Raúl Urrutia, Juan L Iovanna, José L Neira
Intrinsically disordered proteins (IDPs) are ubiquitous in eukaryotes, and they are often associated with diseases in humans. The protein NUPR1 is a multifunctional IDP involved in chromatin remodeling and in the development and progression of pancreatic cancer; however, the details of such functions are unknown. Polycomb proteins are involved in specific transcriptional cascades and gene silencing. One of the proteins of the Polycomb complex is the Ring finger protein 1 (RING1). RING1 is related to aggressive tumor features in multiple cancer types...
July 18, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28719581/phosphorylated-hbo1-at-uv-irradiated-sites-is-essential-for-nucleotide-excision-repair
#14
Hiroyuki Niida, Ryoichi Matsunuma, Ryo Horiguchi, Chiharu Uchida, Yuka Nakazawa, Akira Motegi, Koji Nishimoto, Satoshi Sakai, Tatsuya Ohhata, Kyoko Kitagawa, Shinichi Moriwaki, Hideo Nishitani, Ayako Ui, Tomoo Ogi, Masatoshi Kitagawa
HBO1, a histone acetyl transferase, is a co-activator of DNA pre-replication complex formation. We recently reported that HBO1 is phosphorylated by ATM and/or ATR and binds to DDB2 after ultraviolet irradiation. Here, we show that phosphorylated HBO1 at cyclobutane pyrimidine dimer (CPD) sites mediates histone acetylation to facilitate recruitment of XPC at the damaged DNA sites. Furthermore, HBO1 facilitates accumulation of SNF2H and ACF1, an ATP-dependent chromatin remodelling complex, to CPD sites. Depletion of HBO1 inhibited repair of CPDs and sensitized cells to ultraviolet irradiation...
July 18, 2017: Nature Communications
https://www.readbyqxmd.com/read/28718400/histone-h3g34r-mutation-causes-replication-stress-homologous-recombination-defects-and-genomic-instability-in-s-pombe
#15
Rajesh K Yadav, Carolyn M Jablonowski, Alfonso G Fernandez, Brandon R Lowe, Ryan A Henry, David Finkelstein, Kevin J Barnum, Alison L Pidoux, Yin-Ming Kuo, Jie Huang, Matthew J O'Connell, Andrew J Andrews, Arzu Onar-Thomas, Robin C Allshire, Janet F Partridge
Recurrent somatic mutations of H3F3A in aggressive pediatric high-grade gliomas generate K27M or G34R/V mutant histone H3.3. H3.3-G34R/V mutants are common in tumors with mutations in p53 and ATRX, an H3.3-specific chromatin remodeler. To gain insight into the role of H3-G34R, we generated fission yeast that express only the mutant histone H3. H3-G34R specifically reduces H3K36 tri-methylation and H3K36 acetylation, and mutants show partial transcriptional overlap with set2 deletions. H3-G34R mutants exhibit genomic instability and increased replication stress, including slowed replication fork restart, although DNA replication checkpoints are functional...
July 18, 2017: ELife
https://www.readbyqxmd.com/read/28717667/haploinsufficiency-of-bcl11a-associated-with-cerebellar-abnormalities-in-2p15p16-1-deletion-syndrome
#16
Hiroko Shimbo, Takayuki Yokoi, Noriko Aida, Seiji Mizuno, Hiroshi Suzumura, Junichi Nagai, Kazumi Ida, Yumi Enomoto, Chihiro Hatano, Kenji Kurosawa
BACKGROUND: Chromosome 2p15p16.1 deletion syndrome is a rare genetic disorder characterized by intellectual disability (ID), neurodevelopmental delay, language delay, growth retardation, microcephaly, structural brain abnormalities, and dysmorphic features. More than 30 patients with 2p15p16.1 microdeletion syndrome have been reported in the literature. METHODS: Molecular analysis was performed using microarray-based comparative genomic hybridization (array CGH)...
July 2017: Molecular Genetics & Genomic Medicine
https://www.readbyqxmd.com/read/28717195/stability-of-the-phf10-subunit-of-pbaf-signature-module-is-regulated-by-phosphorylation-role-of-%C3%AE-trcp
#17
Victor V Tatarskiy, Yuriy P Simonov, Dmitrii S Shcherbinin, Alexander V Brechalov, Sofia G Georgieva, Nataliya V Soshnikova
The PBAF chromatin-remodeling complexes are multi-protein machines, regulating expression of genes involved in proliferation and differentiation. PHF10 is a subunit of the PBAF essential for its association with chromatin. Mammalian PHF10 is expressed as four ubiquitous isoforms, which are alternatively incorporated in the complex and differ by their influence on transcription of target genes. PHF10 have different domain structure and two of them (PHF10-S isoforms) lack C-terminal PHD domains, which enables their phosphorylation by CK-1...
July 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28716950/analysis-of-small-critical-regions-of-swi1-conferring-prion-formation-maintenance-and-transmission
#18
Stephanie Valtierra, Zhiqiang Du, Liming Li
Saccharomyces cerevisiae contains several prion elements, which are epigenetically transmitted as self-perpetuating protein conformations. One such prion is [SWI(+) ], whose protein determinant is Swi1, a subunit of the SWI/SNF chromatin-remodeling complex. We previously reported that [SWI(+) ] formation results in a partial loss-of-function phenotype of poor growth in non-glucose media and abolishment of multicellularity. We also showed that the first 38 amino acids of Swi1 propagated [SWI(+)]. We show here that a region as small as the first 32 amino acids of Swi1 (Swi11-32) can decorate [SWI(+)] aggregation and stably maintain and transmit [SWI(+)] independently of full-length Swi1...
July 17, 2017: Molecular and Cellular Biology
https://www.readbyqxmd.com/read/28716689/brg1-and-smarcal1-transcriptionally-co-regulate-drosha-dgcr8-and-dicer-in-response-to-doxorubicin-induced-dna-damage
#19
Ketki Patne, Radhakrishnan Rakesh, Vijendra Arya, Upasana Bedi Chanana, Ramesh Sethy, Pynskhem Bok Swer, Rohini Muthuswami
Recent investigations have emphasized the role of miRNA biogenesis proteins in the synthesis of non-coding RNA when double-strand DNA breaks are induced by ionizing radiations. However, the role of these ncRNA and their regulation in response to doxorubicin-induced DNA damage is not known. In this paper, BRG1 and SMARCAL1, members of the ATP-dependent chromatin remodelling family, are shown to co-regulate the transcription of DROSHA, DGCR8, and DICER in response to double-strand DNA breaks induced by doxorubicin...
July 14, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28716547/cellular-senescence-regulated-by-swi-snf-complex-subunits-through-p53-p21-and-p16-prb-pathway
#20
Ling He, Ying Chen, Jianguo Feng, Weichao Sun, Shun Li, Mengting Ou, Liling Tang
SWI/SNF complex is an evolutionarily well-conserved chromatin-remodeling complex, which is implicated in the nucleosomes removing or sliding, impacting on the DNA repair, replication and genes expression regulation. The SWI/SNF complex consists up to 12 protein subunits. The catalytic subunits are BRG1 or BRM, which are exclusive ATPase subunits. BRG1 has been reported to play an important role in cellular senescence. However, The function of non-catalytic subunits involved in cellular senescence is rarely investigated...
July 14, 2017: International Journal of Biochemistry & Cell Biology
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