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Epigenetic regulation of chromosome

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https://www.readbyqxmd.com/read/28638443/dosage-compensation-and-sex-specific-epigenetic-landscape-of-the-x-chromosome-in-the-pea-aphid
#1
Gautier Richard, Fabrice Legeai, Nathalie Prunier-Leterme, Anthony Bretaudeau, Denis Tagu, Julie Jaquiéry, Gaël Le Trionnaire
BACKGROUND: Heterogametic species display a differential number of sex chromosomes resulting in imbalanced transcription levels for these chromosomes between males and females. To correct this disequilibrium, dosage compensation mechanisms involving gene expression and chromatin accessibility regulations have emerged throughout evolution. In insects, these mechanisms have been extensively characterized only in Drosophila but not in insects of agronomical importance. Aphids are indeed major pests of a wide range of crops...
2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/28636597/phase-separation-drives-heterochromatin-domain-formation
#2
Amy R Strom, Alexander V Emelyanov, Mustafa Mir, Dmitry V Fyodorov, Xavier Darzacq, Gary H Karpen
Constitutive heterochromatin is an important component of eukaryotic genomes that has essential roles in nuclear architecture, DNA repair and genome stability, and silencing of transposon and gene expression. Heterochromatin is highly enriched for repetitive sequences, and is defined epigenetically by methylation of histone H3 at lysine 9 and recruitment of its binding partner heterochromatin protein 1 (HP1). A prevalent view of heterochromatic silencing is that these and associated factors lead to chromatin compaction, resulting in steric exclusion of regulatory proteins such as RNA polymerase from the underlying DNA...
June 21, 2017: Nature
https://www.readbyqxmd.com/read/28630932/differential-intron-retention-in-jumonji-chromatin-modifier-genes-is-implicated-in-reptile-temperature-dependent-sex-determination
#3
Ira W Deveson, Clare E Holleley, James Blackburn, Jennifer A Marshall Graves, John S Mattick, Paul D Waters, Arthur Georges
In many vertebrates, sex of offspring is determined by external environmental cues rather than by sex chromosomes. In reptiles, for instance, temperature-dependent sex determination (TSD) is common. Despite decades of work, the mechanism by which temperature is converted into a sex-determining signal remains mysterious. This is partly because it is difficult to distinguish the primary molecular events of TSD from the confounding downstream signatures of sexual differentiation. We use the Australian central bearded dragon, in which chromosomal sex determination is overridden at high temperatures to produce sex-reversed female offspring, as a unique model to identify TSD-specific features of the transcriptome...
June 2017: Science Advances
https://www.readbyqxmd.com/read/28611266/retinoid-x-receptor-%C3%AE-dependent-hbv-minichromosome-remodeling-and-viral-replication
#4
Yan Zhang, Song He, Jin-Jun Guo, Hong Peng, Jia-Hao Fan, Qing-Ling Li
BACKGROUND AND AIM: The HBV covalently closed circular DNA (cccDNA) is organized into a minichromosome in the nuclei of infected hepatocytes through interactions with histone and nonhistone proteins. Retinoid X receptor α (RXRα), a liver-enriched nuclear receptor, participates in regulation of HBV replication and transcription through modulation of HBV enhancer 1 and core promoter activity. MATERIAL AND METHODS: This study investigated RXRα involvement in HBV cccDNA epigenetic modifications...
August 1, 2017: Annals of Hepatology
https://www.readbyqxmd.com/read/28608921/whole-exome-sequencing-reveals-critical-genes-underlying-metastasis-in-esophageal-squamous-cell-carcinoma
#5
Wei Dai, Josephine Mun Yee Ko, Sheyne Sta Ana Choi, Zhouyou Yu, Luwen Ning, Hong Zheng, Vinod Gopalan, Kin Tak Chan, Nikki Pui-Yue Lee, Kwok Wah Chan, Simon Ying-Kit Law, Alfred King-Yin Lam, Maria Li Lung
Esophageal squamous cell carcinoma (ESCC) is one of the most lethal cancers due to a high frequency of metastasis. However, little is known about the genomic landscape of metastatic ESCC. To identify the genetic alterations that underlie ESCC metastasis, whole-exome sequencing (WES) was performed for 41 primary tumors and 15 lymph nodes (LNs) with metastatic ESCC. Eleven cases included matched primary tumors, synchronous LN metastases and non-neoplastic mucosa. Approximately 50-76% of the mutations identified in primary tumors appeared in the synchronous LN metastases...
June 13, 2017: Journal of Pathology
https://www.readbyqxmd.com/read/28599293/dysregulation-of-an-x-linked-primate-specific-epididymal-microrna-cluster-in-unexplained-asthenozoospermia
#6
Xingrong Qing, Jian Shi, Tingting Dong, Chunlin Wu, Lian Hu, Honggang Li
Asthenoszoopermia, characterized by reduced sperm motility, is one of the primary forms of male infertility. Whereas most cases were diagnosed into unexplained asthenozoospermia (UA) because the etiology cannot be identified. In animal models, epigenetic dysregulation in epididymis can impair sperm maturation and result in asthenozoospermia. However, researches of epididymal epigenetic regulation on humans are impeded by the difficulty in obtaining epididymal tissues. We previously identified cell-free seminal microRNAs predominately derived from epididymis in human ejaculate...
May 23, 2017: Oncotarget
https://www.readbyqxmd.com/read/28594938/the-enemy-within-targeting-host-parasite-interaction-for-antileishmanial-drug-discovery
#7
REVIEW
Suzanne Lamotte, Gerald F Späth, Najma Rachidi, Eric Prina
The state of antileishmanial chemotherapy is strongly compromised by the emergence of drug-resistant Leishmania. The evolution of drug-resistant phenotypes has been linked to the parasites' intrinsic genome instability, with frequent gene and chromosome amplifications causing fitness gains that are directly selected by environmental factors, including the presence of antileishmanial drugs. Thus, even though the unique eukaryotic biology of Leishmania and its dependence on parasite-specific virulence factors provide valid opportunities for chemotherapeutical intervention, all strategies that target the parasite in a direct fashion are likely prone to select for resistance...
June 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28593035/smchd1-regulates-a-limited-set-of-gene-clusters-on-autosomal-chromosomes
#8
Amanda G Mason, Roderick C Slieker, Judit Balog, Richard J L F Lemmers, Chao-Jen Wong, Zizhen Yao, Jong-Won Lim, Galina N Filippova, Enrico Ne, Rabi Tawil, Bas T Heijmans, Stephen J Tapscott, Silvère M van der Maarel
BACKGROUND: Facioscapulohumeral muscular dystrophy (FSHD) is in most cases caused by a contraction of the D4Z4 macrosatellite repeat on chromosome 4 (FSHD1) or by mutations in the SMCHD1 or DNMT3B gene (FSHD2). Both situations result in the incomplete epigenetic repression of the D4Z4-encoded retrogene DUX4 in somatic cells, leading to the aberrant expression of DUX4 in the skeletal muscle. In mice, Smchd1 regulates chromatin repression at different loci, having a role in CpG methylation establishment and/or maintenance...
2017: Skeletal Muscle
https://www.readbyqxmd.com/read/28589860/gaussiancpg-a-gaussian-model-for-detection-of-cpg-island-in-human-genome-sequences
#9
Ning Yu, Xuan Guo, Alexander Zelikovsky, Yi Pan
BACKGROUND: As crucial markers in identifying biological elements and processes in mammalian genomes, CpG islands (CGI) play important roles in DNA methylation, gene regulation, epigenetic inheritance, gene mutation, chromosome inactivation and nuclesome retention. The generally accepted criteria of CGI rely on: (a) %G+C content is ≥ 50%, (b) the ratio of the observed CpG content and the expected CpG content is ≥ 0.6, and (c) the general length of CGI is greater than 200 nucleotides...
May 24, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28588028/the-lysine-methyltransferase-smyd2-methylates-the-kinase-domain-of-type-ii-receptor-bmpr2-and-stimulates-bone-morphogenetic-protein-signaling
#10
Shuman Gao, Zhiqiang Wang, Wencai Wang, Xueli Hu, Peilin Chen, Jiwen Li, Xin Hua Feng, Jiemin Wong, James X Du
Lysine methylation of chromosomal and nuclear proteins is a well-known mechanism of epigenetic regulation, but relatively little is known about the role of this protein modification in signal transduction. Using an RNAi-based functional screening of the SMYD family of lysine methyltransferases (KMTs), we identified SMYD2 as a KMT essential for robust bone morphogenic protein (BMP)- but not TGFβ-induced target gene expression in HaCaT keratinocyte cells. A role for SMYD2 in BMP-induced gene expression was confirmed by shRNA knockdown and CRISPR/Cas9-mediated knockout of SMYD2...
June 6, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28587678/smchd1-regulates-a-limited-set-of-gene-clusters-on-autosomal-chromosomes
#11
Amanda G Mason, Roderick C Slieker, Judit Balog, Richard J L F Lemmers, Chao-Jen Wong, Zizhen Yao, Jong-Won Lim, Galina N Filippova, Enrico Ne, Rabi Tawil, Bas T Heijmans, Stephen J Tapscott, Silvère M van der Maarel
BACKGROUND: Facioscapulohumeral muscular dystrophy (FSHD) is in most cases caused by a contraction of the D4Z4 macrosatellite repeat on chromosome 4 (FSHD1) or by mutations in the SMCHD1 or DNMT3B gene (FSHD2). Both situations result in the incomplete epigenetic repression of the D4Z4-encoded retrogene DUX4 in somatic cells, leading to the aberrant expression of DUX4 in the skeletal muscle. In mice, Smchd1 regulates chromatin repression at different loci, having a role in CpG methylation establishment and/or maintenance...
June 6, 2017: Skeletal Muscle
https://www.readbyqxmd.com/read/28577753/cocaine-induced-chromatin-modifications-associate-with-increased-expression-and-three-dimensional-looping-of-auts2
#12
Olivia Engmann, Benoit Labonté, Amanda Mitchell, Pavel Bashtrykov, Erin S Calipari, Chaggai Rosenbluh, Yong-Hwee E Loh, Deena M Walker, Dominika Burek, Peter J Hamilton, Orna Issler, Rachael L Neve, Gustavo Turecki, Yasmin Hurd, Andrew Chess, Li Shen, Isabelle Mansuy, Albert Jeltsch, Schahram Akbarian, Eric J Nestler
BACKGROUND: Exposure to drugs of abuse alters the epigenetic landscape of the brain's reward regions, such as the nucleus accumbens. We investigated how combinations of chromatin modifications affect genes that regulate responses to cocaine. We focused on Auts2, a gene linked to human evolution and cognitive disorders, which displays strong clustering of cocaine-induced chromatin modifications in this brain region. METHODS: We combined chromosome conformation capture, circularized chromosome conformation capture, and related approaches with behavioral paradigms relevant to cocaine phenotypes...
May 5, 2017: Biological Psychiatry
https://www.readbyqxmd.com/read/28558655/the-common-transcriptional-subnetworks-of-the-grape-berry-skin-in-the-late-stages-of-ripening
#13
Ryan Ghan, Juli Petereit, Richard L Tillett, Karen A Schlauch, David Toubiana, Aaron Fait, Grant R Cramer
BACKGROUND: Wine grapes are important economically in many countries around the world. Defining the optimum time for grape harvest is a major challenge to the grower and winemaker. Berry skins are an important source of flavor, color and other quality traits in the ripening stage. Senescent-like processes such as chloroplast disorganization and cell death characterize the late ripening stage. RESULTS: To better understand the molecular and physiological processes involved in the late stages of berry ripening, RNA-seq analysis of the skins of seven wine grape cultivars (Cabernet Franc, Cabernet Sauvignon, Merlot, Pinot Noir, Chardonnay, Sauvignon Blanc and Semillon) was performed...
May 30, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28532996/histone-methyltransferase-g9a-promotes-liver-cancer-development-by-epigenetic-silencing-of-tumor-suppressor-gene-rarres3
#14
Lai Wei, David Kung-Chun Chiu, Felice Ho-Ching Tsang, Dicky Cheuk-Ting Law, Carol Lai-Hung Cheng, Sandy Leung-Kuen Au, Joyce Man-Fong Lee, Carmen Chak-Lui Wong, Irene Oi-Lin Ng, Chun-Ming Wong
BACKGROUND AND AIMS: Hepatocellular carcinoma (HCC) is a major leading cause of cancer mortality worldwide. Epigenetic deregulation is a common trait of human HCC. G9s is an important epigenetics regulator. However, its roles in liver carcinogenesis remain to be investigated. METHODS: Gene expressions were determined by RNA-Seq and qRT-PCR. G9a knockdown and knockout cell lines were established by lentiviral-based shRNA and CRISPR/Cas9 gene editing system. Tumor promoting functions of G9a was studied by both in HCC cell lines and nude mice model...
May 19, 2017: Journal of Hepatology
https://www.readbyqxmd.com/read/28523538/mecp2-a-modulator-of-neuronal-chromatin-organization-involved-in-rett-syndrome
#15
Alexia Martínez de Paz, Juan Ausió
From an epigenetic perspective, the genomic chromatin organization of neurons exhibits unique features when compared to somatic cells. Methyl CpG binding protein 2 (MeCP2), through its ability to bind to methylated DNA, seems to be a major player in regulating such unusual organization. An important contribution to this uniqueness stems from the intrinsically disordered nature of this highly abundant chromosomal protein in neurons. Upon its binding to methylated/hydroxymethylated DNA, MeCP2 is able to recruit a plethora of interacting protein and RNA partners...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28512193/dna-replication-timing-during-development-anticipates-transcriptional-programs-and-parallels-enhancer-activation
#16
Joseph C Siefert, Constantin Georgescu, Jonathan D Wren, Amnon Koren, Christopher L Sansam
In dividing cells, DNA replication occurs in a precise order, but many questions remain regarding the mechanisms of replication timing establishment and regulation. We now have generated genome-wide, high-resolution replication timing maps throughout zebrafish development. Unexpectedly, in the rapid cell cycles preceding the midblastula transition, a defined timing program was present that predicted the initial wave of zygotic transcription. Replication timing was thereafter progressively and continuously remodeled across the majority of the genome, and epigenetic changes involved in enhancer activation frequently paralleled developmental changes in replication timing...
May 16, 2017: Genome Research
https://www.readbyqxmd.com/read/28502113/epigenetic-modifications-of-the-vh-region-after-djh-recombination-in-pro-b-cells
#17
Yanying Dong, Caijun Wu, Xiaohui Zhao, Ping Zhang, Hua Zhang, Mingzhe Zheng, Shichang Li, Junna Jiao, Xiaozhuo Yu, Zhuangwei Lv, Yanhong Ji
The variable region of murine immunoglobulin heavy chain (Igh) is assembled by sequential DH -JH and VH -DJH recombination. The accessibility of Igh locus determines the order of rearrangement. Because of the large number of VH genes and lack of a suitable model, the epigenetic modifications of VH genes after DJH recombination have not previously been characterized. Here, we employed two v-Abl pro-B cell lines, in which Igh locus is in germline and DJH -recombined configuration, respectively. The DJH junction displays the characteristics of recombination center, such as high levels of activation-associated histone modifications and recombination activating gene protein (RAG) binding in DJH -rearranged pro-B cells, which extend the recombination center model proposed for germline Igh locus...
May 14, 2017: Immunology
https://www.readbyqxmd.com/read/28501516/is-dual-inhibition-of-metalloenzymes-hdac-8-and-mmp-2-a-potential-pharmacological-target-to-combat-hematological-malignancies
#18
REVIEW
Sk Abdul Amin, Nilanjan Adhikari, Tarun Jha
For the last three decades, metalloenzymes such as histone deacetylases (HDACs) and matrix metalloproteinases (MMPs) have been identified in promoting solid as well as hematological carcinogenesis. Histone deacetylase 8 (HDAC-8), a class I HDAC enzyme, may serve as 'epigenetic player' that affects in the regulation of transcription factors and alters the structure of chromosome associated with tumorigenesis. It is established that the influence of MMP-2 in invasion, metastasis and angiogenenic events of hematological malignancies may be suppressed by HDAC inhibitors through reversion-inducing-cysteine-rich protein with kazal motifs (RECK) protein...
May 10, 2017: Pharmacological Research: the Official Journal of the Italian Pharmacological Society
https://www.readbyqxmd.com/read/28486493/characterization-of-joining-sites-of-a-viral-histone-h4-on-host-insect-chromosomes
#19
Sunil Kumar, Jin-Kyo Jung, Yonggyun Kim
A viral histone H4 (CpBV-H4) is encoded in a polydnavirus, Cotesia plutellae bracovirus (CpBV). It plays a crucial role in parasitism of an endoparasitoid wasp, C. plutellae, against diamondback moth, Plutella xylostella, by altering host gene expression in an epigenetic mode by its N-terminal tail after joining host nucleosomes. Comparative transcriptomic analysis between parasitized and nonparasitized P. xylostella by RNA-Seq indicated that 1,858 genes were altered at more than two folds in expression levels at late parasitic stage, including 877 up-regulated genes and 981 down-regulated genes...
2017: PloS One
https://www.readbyqxmd.com/read/28485726/gene-body-5-hydroxymethylation-is-associated-with-gene-expression-changes-in-the-prefrontal-cortex-of-depressed-individuals
#20
J A Gross, A Pacis, G G Chen, M Drupals, P-E Lutz, L B Barreiro, G Turecki
5-Hydroxymethylcytosine (5hmC) is a recently characterized epigenetic mark that is particularly abundant in brain tissue and that regulates gene transcription. We have recently begun to understand the important role of 5hmC in brain development, plasticity and disease, but there are currently little data on 5hmC alterations in psychiatric illnesses. Here we report what we believe to be the first genome-wide analysis of 5hmC in the depressed brain. Using AbaSI sequencing, we investigated 5hmC in the prefrontal cortex of depressed (N=19) and psychiatrically healthy controls (N=19)...
May 9, 2017: Translational Psychiatry
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