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Epigenetic regulation of chromosome

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https://www.readbyqxmd.com/read/28106784/microrna-29a-alleviates-bile-duct-ligation-exacerbation-of-hepatic-fibrosis-in-mice-through-epigenetic-control-of-methyltransferases
#1
Ya-Ling Yang, Feng-Sheng Wang, Sung-Chou Li, Mao-Meng Tiao, Ying-Hsien Huang
MicroRNA-29 (miR-29) is found to modulate hepatic stellate cells' (HSCs) activation and, thereby, reduces liver fibrosis pathogenesis. Histone methyltransferase regulation of epigenetic reactions reportedly participates in hepatic fibrosis. This study is undertaken to investigate the miR-29a regulation of the methyltransferase signaling and epigenetic program in hepatic fibrosis progression. miR-29a transgenic mice (miR-29aTg mice) and wild-type littermates were subjected to bile duct-ligation (BDL) to develop cholestatic liver fibrosis...
January 18, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28078514/the-molecular-basis-of-the-organization-of-repetitive-dna-containing-constitutive-heterochromatin-in-mammals
#2
REVIEW
Gohei Nishibuchi, Jérôme Déjardin
Constitutive heterochromatin is composed mainly of repetitive elements and represents the typical inert chromatin structure in eukaryotic cells. Approximately half of the mammalian genome is made of repeat sequences, such as satellite DNA, telomeric DNA, and transposable elements. As essential genes are not present in these regions, most of these repeat sequences were considered as junk DNA in the past. However, it is now clear that these regions are essential for chromosome stability and the silencing of neighboring genes...
January 11, 2017: Chromosome Research
https://www.readbyqxmd.com/read/28069706/dna-sequence-properties-that-predict-susceptibility-to-epiallelic-switching
#3
Marco Catoni, Jayne Griffiths, Claude Becker, Nicolae Radu Zabet, Carlos Bayon, Mélanie Dapp, Michal Lieberman-Lazarovich, Detlef Weigel, Jerzy Paszkowski
Transgenerationally heritable epialleles are defined by the stable propagation of alternative transcriptional states through mitotic and meiotic cell cycles. Given that the propagation of DNA methylation at CpG sites, mediated in Arabidopsis by MET1, plays a central role in epigenetic inheritance, we examined genomewide DNA methylation in partial and complete loss-of-function met1 mutants. We interpreted the data in relation to transgenerational epiallelic stability, which allowed us to classify chromosomal targets of epigenetic regulation into (i) single copy and methylated exclusively at CpGs, readily forming epialleles, and (ii) transposon-derived, methylated at all cytosines, which may or may not form epialleles...
January 9, 2017: EMBO Journal
https://www.readbyqxmd.com/read/28069135/epigenetic-control-of-gene-expression-in-maize
#4
J Huang, J S Lynn, L Schulte, S Vendramin, K McGinnis
Epigenetic gene regulation is important for proper development and gene expression in eukaryotes. Maize has a large and complex genome that includes abundant repetitive sequences which are frequently silenced by epigenetic mechanisms, making it an ideal organism to study epigenetic gene regulation. Epigenetic modifications are chromosome-bound, heritable changes to the genome that do not affect the DNA sequence, and can include DNA methylation, histone modification, and RNA processing. Our appreciation and understanding of epigenetic regulation has grown with the field since its inception ∼65 years ago...
2017: International Review of Cell and Molecular Biology
https://www.readbyqxmd.com/read/28064247/genome-wide-analysis-of-the-distinct-types-of-chromatin-interactions-in-arabidopsis-thaliana
#5
Jingjing Wang, Yincong Zhou, Xue Li, Xianwen Meng, Miao Fan, Hongjun Chen, Jitong Xue, Ming Chen
The three-dimensional shapes of chromosomes regulate gene expression and genome function. Our knowledge of the role of chromatin interaction is evolving rapidly. Here, we present a study of global chromatin interaction patterns in Arabidopsis thaliana. High-throughput experimental techniques have been developed to map long-range interactions within chromatin. We have integrated data from multiple experimental sources including Hi-C, BS-seq, ChIP-chip and ChIP-seq data for 17 epigenetic marks and 35 transcription factors...
November 15, 2016: Plant & Cell Physiology
https://www.readbyqxmd.com/read/28059702/cdk-regulated-dimerization-of-m18bp1-on-a-mis18-hexamer-is-necessary-for-cenp-a-loading
#6
Dongqing Pan, Kerstin Klare, Arsen Petrovic, Annika Take, Kai Walstein, Priyanka Singh, Arnaud Rondelet, Alexander W Bird, Andrea Musacchio
Centromeres are unique chromosomal loci that promote the assembly of kinetochores, macromolecular complexes that bind spindle microtubules during mitosis. In most organisms, centromeres lack defined genetic features. Rather, they are specified epigenetically by a centromere-specific histone H3 variant, CENP-A. The Mis18 complex, comprising the Mis18α:Mis18β subcomplex and M18BP1, is crucial for CENP-A homeostasis. It recruits the CENP-A-specific chaperone HJURP to centromeres and primes it for CENP-A loading...
January 6, 2017: ELife
https://www.readbyqxmd.com/read/28053272/trans-generational-function-of-tetrahymena-piwi-protein-twi8p-at-distinctive-non-coding-rna-loci
#7
Brian M Farley, Kathleen Collins
Trans-generational transmission of genome-regulatory epigenetic information can determine phenotypes in the progeny of sexual reproduction. Sequence specificity of trans-generational regulation derives from small RNAs assembled into Piwi-protein complexes. Known targets of trans-generational regulation are primarily transposons and transposon-derived sequences. Here, we extend the scope of Piwi-mediated trans-generational regulation to include unique non-coding RNA loci. Ciliates such as Tetrahymena have a phenotypically silent germline micronucleus and an expressed somatic macronucleus, which is differentiated anew from a germline genome copy in sexual reproduction...
January 4, 2017: RNA
https://www.readbyqxmd.com/read/28033038/mgo3-and-gip1-act-synergistically-for-the-maintenance-of-centromeric-cohesion
#8
Morgane Batzenschlager, Anne-Catherine Schmit, Etienne Herzog, Joerg Fuchs, Veit Schubert, Guy Houlné, Marie-Edith Chabouté
The control of genomic maintenance during S phase is crucial in eukaryotes. It involves the establishment of sister chromatid cohesion, ensuring faithful chromosome segregation, as well as proper DNA replication and repair to preserve genetic information. In animals, nuclear periphery proteins - including inner nuclear membrane proteins and nuclear pore-associated components - are key factors which regulate DNA integrity. Corresponding functional homologues are not so well known in plants which may have developed specific mechanisms due to their sessile life...
December 29, 2016: Nucleus
https://www.readbyqxmd.com/read/28024084/targeting-the-histone-methyltransferase-g9a-activates-imprinted-genes-and-improves-survival-of-a-mouse-model-of-prader-willi-syndrome
#9
Yuna Kim, Hyeong-Min Lee, Yan Xiong, Noah Sciaky, Samuel W Hulbert, Xinyu Cao, Jeffrey I Everitt, Jian Jin, Bryan L Roth, Yong-Hui Jiang
Prader-Willi syndrome (PWS) is an imprinting disorder caused by a deficiency of paternally expressed gene(s) in the 15q11-q13 chromosomal region. The regulation of imprinted gene expression in this region is coordinated by an imprinting center (PWS-IC). In individuals with PWS, genes responsible for PWS on the maternal chromosome are present, but repressed epigenetically, which provides an opportunity for the use of epigenetic therapy to restore expression from the maternal copies of PWS-associated genes. Through a high-content screen (HCS) of >9,000 small molecules, we discovered that UNC0638 and UNC0642-two selective inhibitors of euchromatic histone lysine N-methyltransferase-2 (EHMT2, also known as G9a)-activated the maternal (m) copy of candidate genes underlying PWS, including the SnoRNA cluster SNORD116, in cells from humans with PWS and also from a mouse model of PWS carrying a paternal (p) deletion from small nuclear ribonucleoprotein N (Snrpn (S)) to ubiquitin protein ligase E3A (Ube3a (U)) (mouse model referred to hereafter as m(+)/p(ΔS-U))...
December 26, 2016: Nature Medicine
https://www.readbyqxmd.com/read/28018144/deciphering-the-epigenetic-code-in-embryonic-and-dental-pulp-stem-cells
#10
REVIEW
Dashzeveg Bayarsaihan
A close cooperation between chromatin states, transcriptional modulation, and epigenetic modifications is required for establishing appropriate regulatory circuits underlying self-renewal and differentiation of adult and embryonic stem cells. A growing body of research has established that the epigenome topology provides a structural framework for engaging genes in the non-random chromosomal interactions to orchestrate complex processes such as cell-matrix interactions, cell adhesion and cell migration during lineage commitment...
December 2016: Yale Journal of Biology and Medicine
https://www.readbyqxmd.com/read/28011933/epigenetic-and-transcriptional-regulation-of-irak-m-expression-in-macrophages
#11
Konstantina Lyroni, Andreas Patsalos, Maria G Daskalaki, Christina Doxaki, Birte Soennichsen, Mike Helms, Ioannis Liapis, Vassiliki Zacharioudaki, Sotirios C Kampranis, Christos Tsatsanis
During macrophage activation, expression of IL-1R-associated kinase (IRAK)-M is induced to suppress TLR-mediated responses and is a hallmark of endotoxin tolerance. Endotoxin tolerance requires tight regulation of genes occurring at the transcriptional and epigenetic levels. To identify novel regulators of IRAK-M, we used RAW 264.7 macrophages and performed a targeted RNA interference screen of genes encoding chromatin-modifying enzymes, signaling molecules, and transcription factors involved in macrophage activation...
December 23, 2016: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/27999969/functions-of-long-intergenic-non-coding-linc-rnas-in-plants
#12
Masashi Yamada
Whole transcriptome analyses in many organisms have revealed that most transcribed RNAs do not encode proteins. These non-coding RNAs likely contribute to the regulation of gene expression during the development of multicellular organisms. In eukaryotes, the roles of small RNAs, one class of non-coding RNAs, in transcriptional and post-transcriptional regulation have been well characterized. However, the functions of a second class of non-coding RNAs, long intergenic noncoding (linc) RNAs, are relatively unknown, especially in plants...
January 2017: Journal of Plant Research
https://www.readbyqxmd.com/read/27999094/the-epigenetic-landscape-of-alu-repeats-delineates-the-structural-and-functional-genomic-architecture-of-colon-cancer-cells
#13
Mireia Jordà, Anna Díez-Villanueva, Izaskun Mallona, Berta Martín, Sergi Lois, Víctor Barrera, Manel Esteller, Tanya Vavouri, Miguel A Peinado
Cancer cells exhibit multiple epigenetic changes with prominent local DNA hypermethylation and widespread hypomethylation affecting large chromosomal domains. Epigenome studies often disregard the study of repeat elements owing to technical complexity and their undefined role in genome regulation. We have developed NSUMA (Next-generation Sequencing of UnMethylated Alu), a cost-effective approach allowing the unambiguous interrogation of DNA methylation in more than 130,000 individual Alu elements, the most abundant retrotransposon in the human genome...
January 2017: Genome Research
https://www.readbyqxmd.com/read/27992376/myostatin-deficiency-in-mice-increases-global-gene-expression-at-the-dlk1-dio3-locus-in-the-skeletal-muscle
#14
Keisuke Hitachi, Kunihiro Tsuchida
Myostatin, a member of the transforming growth factor-beta superfamily, is a negative regulator of skeletal muscle growth and development. Myostatin inhibition leads to increased skeletal muscle mass in mammals; hence, myostatin is considered a potential therapeutic target for skeletal muscle wasting. However, downstream molecules of myostatin in the skeletal muscle have not been fully elucidated. Here, we identified the Dlk1-Dio3 locus at the mouse chromosome 12qF1, also called as the callipyge locus in sheep, as a novel downstream target of myostatin...
December 15, 2016: Oncotarget
https://www.readbyqxmd.com/read/27983975/current-status-of-potential-applications-of-repurposed-cas9-for-structural-and-functional-genomics-of-plants
#15
Kunal Seth, Harish
Redesigned Cas9 has emerged as a tool with various applications like gene editing, gene regulation, epigenetic modification and chromosomal imaging. Target specific single guide RNA (sgRNA) can be used with Cas9 for precise gene editing with high efficiency than previously known methods. Further, nuclease-deactivated Cas9 (dCas9) can be fused with activator or repressor for activation (CRISPRa) and repression (CRISPRi) of gene expression, respectively. dCas9 fused with epigenetic modifier like methylase or acetylase further expand the scope of this technique...
October 28, 2016: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/27979905/a-long-noncoding-rna-lincrna-tnfaip3-acts-as-a-coregulator-of-nf-%C3%AE%C2%BAb-to-modulate-inflammatory-gene-transcription-in-mouse-macrophages
#16
Shibin Ma, Zhenping Ming, Ai-Yu Gong, Yang Wang, Xiqiang Chen, Guoku Hu, Rui Zhou, Annemarie Shibata, Patrick C Swanson, Xian-Ming Chen
Long intergenic noncoding RNAs (lincRNAs) are long noncoding transcripts (>200 nt) from the intergenic regions of annotated protein-coding genes. We report here that the lincRNA gene lincRNA-Tnfaip3, located at mouse chromosome 10 proximal to the tumor necrosis factor α-induced protein 3 (Tnfaip3) gene, is an early-primary response gene controlled by nuclear factor-κB (NF-κB) signaling in murine macrophages. Functionally, lincRNA- Tnfaip3 appears to mediate both the activation and repression of distinct classes of inflammatory genes in macrophages...
December 15, 2016: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
https://www.readbyqxmd.com/read/27977688/regulation-of-the-human-telomerase-gene-tert-by-telomere-position-effect-over-long-distances-tpe-old-implications-for-aging-and-cancer
#17
Wanil Kim, Andrew T Ludlow, Jaewon Min, Jerome D Robin, Guido Stadler, Ilgen Mender, Tsung-Po Lai, Ning Zhang, Woodring E Wright, Jerry W Shay
Telomerase is expressed in early human development and then becomes silenced in most normal tissues. Because ~90% of primary human tumors express telomerase and generally maintain very short telomeres, telomerase is carefully regulated, particularly in large, long-lived mammals. In the current report, we provide substantial evidence for a new regulatory control mechanism of the rate limiting catalytic protein component of telomerase (hTERT) that is determined by the length of telomeres. We document that normal, young human cells with long telomeres have a repressed hTERT epigenetic status (chromatin and DNA methylation), but the epigenetic status is altered when telomeres become short...
December 2016: PLoS Biology
https://www.readbyqxmd.com/read/27964731/use-of-single-molecule-sequencing-for-comparative-genomics-of-an-environmental-and-a-clinical-isolate-of-clostridium-difficile-ribotype-078
#18
Katherine R Hargreaves, Anisha M Thanki, Bethany R Jose, Marco R Oggioni, Martha R J Clokie
BACKGROUND: How the pathogen Clostridium difficile might survive, evolve and be transferred between reservoirs within the natural environment is poorly understood. Some ribotypes are found both in clinical and environmental settings. Whether these strains are distinct from each another and evolve in the specific environments is not established. The possession of a highly mobile genome has contributed to the genetic diversity and ongoing evolution of C. difficile. Interpretations of genetic diversity have been limited by fragmented assemblies resulting from short-read length sequencing approaches and by a limited understanding of epigenetic regulation of diversity...
December 13, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27956470/epigenetic-regulation-of-the-sex-determination-gene-megi-in-polyploid-persimmon
#19
Takashi Akagi, Isabelle Marie Henry, Takashi Kawai, Luca Comai, Ryutaro Tao
Epigenetic regulation can add a flexible layer to genetic variation, potentially enabling long-term but reversible cis-regulatory changes to an allele while maintaining its DNA sequence. Here, we present a case in which alternative epigenetic states lead to reversible sex determination in the hexaploid persimmon Diospyros kaki. Previously, we elucidated the molecular mechanism of sex determination in diploid persimmon and demonstrated the action of a Y-encoded sex determinant pseudogene called OGI, which produces small-RNAs targeting the autosomal gene MeGI, resulting in separate male and female individuals (dioecy)...
December 12, 2016: Plant Cell
https://www.readbyqxmd.com/read/27955725/current-status-of-potential-applications-of-repurposed-cas9-for-structural-and-functional-genomics-of-plants
#20
Kunal Seth, Harish
Redesigned Cas9 has emerged as a tool with various applications like gene editing, gene regulation, epigenetic modification and chromosomal imaging. Target specific single guide RNA (sgRNA) can be used with Cas9 for precise gene editing with high efficiency than previously known methods. Further, nuclease-deactivated Cas9 (dCas9) can be fused with activator or repressor for activation (CRISPRa) and repression (CRISPRi) of gene expression, respectively. dCas9 fused with epigenetic modifier like methylase or acetylase further expand the scope of this technique...
November 25, 2016: Biochemical and Biophysical Research Communications
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