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Heterochromatin

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https://www.readbyqxmd.com/read/28821184/repetitive-dna-in-the-catfish-genome-rdna-microsatellites-and-tc1-mariner-transposon-sequences-in-imparfinis-species-siluriformes-heptapteridae
#1
Juceli Gonzalez Gouveia, Ivan Rodrigo Wolf, Laurival Antonio Vilas-Boas, John Seymour Heslop-Harrison, Trude Schwarzacher, Ana Lúcia Dias
Physical mapping of repetitive DNA families in the karyotypes of fish is important to understand the organization and evolution of different orders, families, genera, or species. Fish in the genus Imparfinis show diverse karyotypes with various diploid numbers and ribosomal DNA (rDNA) locations. Here we isolated and characterized Tc1-mariner nucleotide sequences from Imparfinis schubarti, and mapped their locations together with 18S rDNA, 5S rDNA, and microsatellite probes in Imparfinis borodini and I. schubarti chromosomes...
September 1, 2017: Journal of Heredity
https://www.readbyqxmd.com/read/28820331/polo-like-kinase-1-plk1-dependent-phosphorylation-of-methylenetetrahydrofolate-reductase-mthfr-regulates-replication-via-histone-methylation
#2
Xueyan Li, Shanshan Nai, Yuehe Ding, Qizhi Geng, Bingtao Zhu, Kai Yu, Wei-Guo Zhu, Meng-Qiu Dong, Xiao-Dong Su, Xingzhi Xu, Jing Li
Methylenetetrahydrofolate reductase (MTHFR) is a key enzyme regulating the folate cycle and its genetic variations have been associated with various human diseases. Previously we identified that MTHFR is phosphorylated by cyclin-dependent kinase 1 (CDK1) at T34 and MTHFR underlies heterochromatin maintenance marked by H3K9me3 levels. Herein we demonstrate that pT34 creates a binding motif that docks MTHFR to the polo-binding domain (PBD) of polo-like kinase 1 (PLK1), a fundamental kinase that orchestrates many cell cycle events...
August 18, 2017: Cell Cycle
https://www.readbyqxmd.com/read/28819201/linker-histone-h1-prevents-r-loop-accumulation-and-genome-instability-in-heterochromatin
#3
Aleix Bayona-Feliu, Anna Casas-Lamesa, Oscar Reina, Jordi Bernués, Fernando Azorín
Linker histone H1 is an important structural component of chromatin that stabilizes the nucleosome and compacts the nucleofilament into higher-order structures. The biology of histone H1 remains, however, poorly understood. Here we show that Drosophila histone H1 (dH1) prevents genome instability as indicated by the increased γH2Av (H2AvS137P) content and the high incidence of DNA breaks and sister-chromatid exchanges observed in dH1-depleted cells. Increased γH2Av occurs preferentially at heterochromatic elements, which are upregulated upon dH1 depletion, and is due to the abnormal accumulation of DNA:RNA hybrids (R-loops)...
August 18, 2017: Nature Communications
https://www.readbyqxmd.com/read/28816576/a-demethylation-deficient-isoform-of-the-lysine-demethylase-kdm2a-interacts-with-pericentromeric-heterochromatin-in-an-hp1a-dependent-manner
#4
Dijana Lađinović, Jitka Novotná, Soňa Jakšová, Ivan Raška, Tomáš Vacík
Histone modifications have a profound impact on the chromatin structure and gene expression and their correct establishment and recognition is essential for correct cell functioning. Malfunction of histone modifying proteins is associated with developmental defects and diseases and detailed characterization of these proteins is therefore very important. The lysine specific demethylase KDM2A is a CpG island binding protein that has been studied predominantly for its ability to regulate CpG island-associated gene promoters by demethylating their H3K36me2...
August 17, 2017: Nucleus
https://www.readbyqxmd.com/read/28815537/from-heterochromatin-to-long-noncoding-rnas-in-drosophila-expanding-the-arena-of-gene-function-and-regulation
#5
Subhash C Lakhotia
Recent years have witnessed a remarkable interest in exploring the significance of pervasive noncoding transcripts in diverse eukaryotes. Classical cytogenetic studies using the Drosophila model system unraveled the perplexing attributes and "functions" of the "gene"-poor heterochromatin. Recent molecular studies in the fly model are likewise revealing the very diverse and significant roles played by long noncoding RNAs (lncRNAs) in development, gene regulation, chromatin organization, cell and nuclear architecture, etc...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28814448/carcinogen-susceptibility-is-regulated-by-genome-architecture-and-predicts-cancer-mutagenesis
#6
Pablo E García-Nieto, Erin K Schwartz, Devin A King, Jonas Paulsen, Philippe Collas, Rafael E Herrera, Ashby J Morrison
The development of many sporadic cancers is directly initiated by carcinogen exposure. Carcinogens induce malignancies by creating DNA lesions (i.e., adducts) that can result in mutations if left unrepaired. Despite this knowledge, there has been remarkably little investigation into the regulation of susceptibility to acquire DNA lesions. In this study, we present the first quantitative human genome-wide map of DNA lesions induced by ultraviolet (UV) radiation, the ubiquitous carcinogen in sunlight that causes skin cancer...
August 16, 2017: EMBO Journal
https://www.readbyqxmd.com/read/28810713/co-opted-megasatellite-dna-drives-evolution-of-secondary-night-vision-in-azara-s-owl-monkey
#7
Akihiko Koga, Hideyuki Tanabe, Yuriko Hirai, Hiroo Imai, Masanori Imamura, Takao Oishi, Roscoe Stanyon, Hirohisa Hirai
Owl monkeys (genus Aotus) are the only taxon in simian primates that consists of nocturnal or otherwise cathemeral species. Their night vision is superior to that of other monkeys, apes, and humans but not as good as that of typical nocturnal mammals. This incomplete night vision has been used to conclude that these monkeys only secondarily adapted to a nocturnal lifestyle, or to their cathemeral lifestyle that involves high night-time activity. It is known that the rod cells of many nocturnal mammals possess a unique nuclear architecture in which heterochromatin is centrally located...
July 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28808048/epigenetic-repression-of-line-1-elements-protects-drug-resistant-cells
#8
(no author information available yet)
H3K9me3-dependent heterochromatin formation maintains drug-tolerant persister (DTP) cell viability.
August 14, 2017: Cancer Discovery
https://www.readbyqxmd.com/read/28808009/a-protein-complex-regulates-rna-processing-of-intronic-heterochromatin-containing-genes-in-arabidopsis
#9
Cheng-Guo Duan, Xingang Wang, Lingrui Zhang, Xiansong Xiong, Zhengjing Zhang, Kai Tang, Li Pan, Chuan-Chih Hsu, Huawei Xu, W Andy Tao, Heng Zhang, Jian-Kang Zhu
In several eukaryotic organisms, heterochromatin (HC) in the introns of genes can regulate RNA processing, including polyadenylation, but the mechanism underlying this regulation is poorly understood. By promoting distal polyadenylation, the bromo-adjacent homology (BAH) domain-containing and RNA recognition motif-containing protein ASI1 and the H3K9me2-binding protein EDM2 are required for the expression of functional full-length transcripts of intronic HC-containing genes in Arabidopsis Here we report that ASI1 and EDM2 form a protein complex in vivo via a bridge protein, ASI1-Immunoprecipitated Protein 1 (AIPP1), which is another RNA recognition motif-containing protein...
August 14, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28806732/loss-of-the-chromatin-modifier-kdm2aa-causes-brafv600e-independent-spontaneous-melanoma-in-zebrafish
#10
Catherine M Scahill, Zsofia Digby, Ian M Sealy, Sonia Wojciechowska, Richard J White, John E Collins, Derek L Stemple, Till Bartke, Marie E Mathers, E Elizabeth Patton, Elisabeth M Busch-Nentwich
KDM2A is a histone demethylase associated with transcriptional silencing, however very little is known about its in vivo role in development and disease. Here we demonstrate that loss of the orthologue kdm2aa in zebrafish causes widespread transcriptional disruption and leads to spontaneous melanomas at a high frequency. Fish homozygous for two independent premature stop codon alleles show reduced growth and survival, a strong male sex bias, and homozygous females exhibit a progressive oogenesis defect. kdm2aa mutant fish also develop melanomas from early adulthood onwards which are independent from mutations in braf and other common oncogenes and tumour suppressors as revealed by deep whole exome sequencing...
August 14, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28794155/microrna-125b-is-a-key-epigenetic-regulatory-factor-that-promotes-nuclear-transfer-reprogramming
#11
Jingcheng Zhang, Pengxiang Qu, Chuan Zhou, Xin Liu, Xiaonan Ma, Mengyun Wang, Yongsheng Wang, Jianmin Su, Jun Liu, Yong Zhang
Somatic cell nuclear transfer (SCNT)-mediated reprogramming is a rapid, efficient, and sophisticated process that reprograms differentiated somatic cells to a pluripotent state. However, many factors in this elaborate reprogramming process remain largely unknown. Here, we report that the microRNA (miR) miR-125b is an important component of SCNT-mediated reprogramming. Luciferase reporter assay, quantitative PCR and Western blotting demonstrated that miR-125b directly binds the 3'-untranslated region of SUV39H1, encoding the histone-lysine N-methyltransferase SUV39H1, to downregulate histone H3 lysine-9 tri-methylation (H3K9me3) in SCNT embryos...
August 9, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28792980/evolutionary-implications-of-heterochromatin-and-rdna-in-chromosome-number-and-genome-size-changes-during-dysploidy-a-case-study-in-reichardia-genus
#12
Sonja Siljak-Yakovlev, Bernard Godelle, Vlatka Zoldos, Joan Vallès, Teresa Garnatje, Oriane Hidalgo
In this study we showed that constitutive heterochromatin, GC-rich DNA and rDNA are implicated in chromosomal rearrangements during the basic chromosome number changing (dysploidy) in Reichardia genus. This small Mediterranean genus comprises 8-10 species and presents three basic chromosome numbers (x = 9, 8 and 7). To assess genome evolution and differentiation processes, studies were conducted in a dysploid series of six species: R. dichotoma, R. macrophylla and R. albanica (2n = 18), R. tingitana and R. gaditana (2n = 16), and R...
2017: PloS One
https://www.readbyqxmd.com/read/28790329/kdm4b-mediated-reduction-of-h3k9me3-and-h3k36me3-levels-improves-somatic-cell-reprogramming-into-pluripotency
#13
Jingwei Wei, Jisha Antony, Fanli Meng, Paul MacLean, Rebekah Rhind, Götz Laible, Björn Oback
Correct reprogramming of epigenetic marks is essential for somatic cells to regain pluripotency. Repressive histone (H) lysine (K) methylation marks are known to be stable and difficult to reprogram. In this study, we generated transgenic mice and mouse embryonic fibroblasts (MEFs) for the inducible expression of KDM4B, a demethylase that removes H3 K9 and H3K36 trimethylation (me3) marks (H3K9/36me3). Upon inducing Kdm4b, H3K9/36me3 levels significantly decreased compared to non-induced controls. Concurrently, H3K9me1 levels significantly increased, while H3K9me2 and H3K27me3 remained unchanged...
August 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28781121/repression-of-stress-induced-line-1-expression-protects-cancer-cell-subpopulations-from-lethal-drug-exposure
#14
Gulfem Dilek Guler, Charles Albert Tindell, Robert Pitti, Catherine Wilson, Katrina Nichols, Tommy KaiWai Cheung, Hyo-Jin Kim, Matthew Wongchenko, Yibing Yan, Benjamin Haley, Trinna Cuellar, Joshua Webster, Navneet Alag, Ganapati Hegde, Erica Jackson, Tracy Leah Nance, Paul Garrett Giresi, Kuan-Bei Chen, Jinfeng Liu, Suchit Jhunjhunwala, Jeff Settleman, Jean-Philippe Stephan, David Arnott, Marie Classon
Maintenance of phenotypic heterogeneity within cell populations is an evolutionarily conserved mechanism that underlies population survival upon stressful exposures. We show that the genomes of a cancer cell subpopulation that survives treatment with otherwise lethal drugs, the drug-tolerant persisters (DTPs), exhibit a repressed chromatin state characterized by increased methylation of histone H3 lysines 9 and 27 (H3K9 and H3K27). We also show that survival of DTPs is, in part, maintained by regulators of H3K9me3-mediated heterochromatin formation and that the observed increase in H3K9me3 in DTPs is most prominent over long interspersed repeat element 1 (LINE-1)...
August 14, 2017: Cancer Cell
https://www.readbyqxmd.com/read/28780664/unique-sequence-organization-and-small-rna-expression-of-a-selfish-b-chromosome
#15
Yue Li, Xueyuan A Jing, John C Aldrich, C Clifford, Jian Chen, Omar S Akbari, Patrick M Ferree
B chromosomes are found in numerous plants and animals. These nonessential, supernumerary chromosomes are often composed primarily of noncoding DNA repeats similar to those found within transcriptionally "silenced" heterochromatin. In order to persist within their resident genomes, many B chromosomes exhibit exceptional cellular behaviors, including asymmetric segregation into gametes and induction of genome elimination during early development. An important goal in understanding these behaviors is to identify unique B chromosome sequences and characterize their transcriptional contributions...
August 5, 2017: Chromosoma
https://www.readbyqxmd.com/read/28765174/role-of-telomeric-repeat-containing-rna-in-telomeric-chromatin-remodeling-during-the-early-expansion-of-human-embryonic-stem-cells
#16
Sicong Zeng, Lvjun Liu, Yi Sun, Guangxiu Lu, Ge Lin
This study aimed to explore the role of telomeric repeat-containing RNA (TERRA) in telomeric chromatin remodeling during the early expansion of human embryonic stem cells (hESCs). During the derivation of hESCs, histone demethylation in the telomeric region facilitates telomerase-mediated telomere elongation. An adequate telomere repeat is essential for hESCs to acquire and/or maintain the unlimited symmetric division, which suggests that there is a link between pluripotency and telomere maintenance. The present study found that the gradual decrease in TERRA levels and related TERRA foci were correlated with telomeric length elongation in the early expansion of hESCs...
August 1, 2017: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
https://www.readbyqxmd.com/read/28765164/selective-termination-of-lncrna-transcription-promotes-heterochromatin-silencing-and-cell-differentiation
#17
Leila Touat-Todeschini, Yuichi Shichino, Mathieu Dangin, Nicolas Thierry-Mieg, Benoit Gilquin, Edwige Hiriart, Ravi Sachidanandam, Emeline Lambert, Janine Brettschneider, Michael Reuter, Jan Kadlec, Ramesh Pillai, Akira Yamashita, Masayuki Yamamoto, André Verdel
Long non-coding RNAs (lncRNAs) regulating gene expression at the chromatin level are widespread among eukaryotes. However, their functions and the mechanisms by which they act are not fully understood. Here, we identify new fission yeast regulatory lncRNAs that are targeted, at their site of transcription, by the YTH domain of the RNA-binding protein Mmi1 and degraded by the nuclear exosome. We uncover that one of them, nam1, regulates entry into sexual differentiation. Importantly, we demonstrate that Mmi1 binding to this lncRNA not only triggers its degradation but also mediates its transcription termination, thus preventing lncRNA transcription from invading and repressing the downstream gene encoding a mitogen-activated protein kinase kinase kinase (MAPKKK) essential to sexual differentiation...
August 1, 2017: EMBO Journal
https://www.readbyqxmd.com/read/28763510/chromosomal-diversity-and-molecular-divergence-among-three-undescribed-species-of-neacomys-rodentia-sigmodontinae-separated-by-amazonian-rivers
#18
Willam Oliveira Da Silva, Julio Cesar Pieczarka, Malcolm Andrew Ferguson-Smith, Patricia Caroline Mary O'Brien, Ana Cristina Mendes-Oliveira, Iracilda Sampaio, Jeferson Carneiro, Cleusa Yoshiko Nagamachi
The Neacomys genus (Rodentia, Sigmodontinae) is distributed in the Amazon region, with some species limited to a single endemic area, while others may occur more widely. The number of species within the genus and their geographical boundaries are not known accurately, due to their high genetic diversity and difficulties in taxonomic identification. In this work we collected Neacomys specimens from both banks of the Tapajós River in eastern Amazon, and studied them using chromosome painting with whole chromosome probes of Hylaeamys megacephalus (HME; Rodentia, Sigmodontinae), and molecular analysis using haplotypes of mitochondrial genes COI and Cytb...
2017: PloS One
https://www.readbyqxmd.com/read/28761142/methylation-profile-of-a-satellite-dna-constituting-the-intercalary-g-c-rich-heterochromatin-of-the-cut-trough-shell-spisula-subtruncata-bivalvia-mactridae
#19
Daniel García-Souto, Brankica Mravinac, Eva Šatović, Miroslav Plohl, Paloma Morán, Juan J Pasantes
Tandemly repeated DNAs usually constitute significant portions of eukaryotic genomes. In bivalves, however, repetitive DNAs are habitually not widespread. In our search for abundant repetitive DNAs in trough shells, we discovered a novel satellite DNA, SSUsat, which constitutes at least 1.3% of the genome of Spisula subtruncata. As foreseen by the satellite DNA library hypothesis, we confirmed that this satellite DNA is also present in two other Mactridae species, showing a highly conserved nucleotide sequence together with a dramatic diminution in the number of repeats...
July 31, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28760201/impact-of-nucleic-acid-and-methylated-h3k9-binding-activities-of-suv39h1-on-its-heterochromatin-assembly
#20
Atsuko Shirai, Takayuki Kawaguchi, Hideaki Shimojo, Daisuke Muramatsu, Mayumi Ishida-Yonetani, Yoshifumi Nishimura, Hiroshi Kimura, Jun-Ichi Nakayama, Yoichi Shinkai
SUV39H is the major histone H3 lysine 9 (H3K9)-specific methyltransferase that targets pericentric regions and is crucial for assembling silent heterochromatin. SUV39H recognizes trimethylated H3K9 (H3K9me3) via its chromodomain (CD), and enriched H3K9me3 allows SUV39H to target specific chromosomal regions. However, the detailed targeting mechanisms, especially for naïve chromatin without preexisting H3K9me3, are poorly understood. Here we show that Suv39h1's CD (Suv39h1-CD) binds nucleic acids, and this binding is important for its function in heterochromatin assembly...
August 1, 2017: ELife
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