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Epigenetic regulation of chromosome

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https://www.readbyqxmd.com/read/29352271/sex-disparity-in-cancer-roles-of-micrornas-and-related-functional-players
#1
REVIEW
Alessandra Carè, Maria Bellenghi, Paola Matarrese, Lucia Gabriele, Stefano Salvioli, Walter Malorni
A sexual dimorphism at the cellular level has been suggested to play a role in cancer onset and progression. In particular, very recent studies have unraveled striking differences between cells carrying XX or XY chromosomes in terms of response to stressful stimuli, indicating the presence of genetic and epigenetic differences determining sex-specific metabolic or phenotypic traits. Although this field of investigation is still in its infancy, available data suggest a key role of sexual chromosomes in determining cell life or death...
January 19, 2018: Cell Death and Differentiation
https://www.readbyqxmd.com/read/29352181/samhd1-is-recurrently-mutated-in-t-cell-prolymphocytic-leukemia
#2
Patricia Johansson, Ludger Klein-Hitpass, Axel Choidas, Peter Habenberger, Bijan Mahboubi, Baek Kim, Anke Bergmann, René Scholtysik, Martina Brauser, Anna Lollies, Reiner Siebert, Thorsten Zenz, Ulrich Dührsen, Ralf Küppers, Jan Dürig
T-cell prolymphocytic leukemia (T-PLL) is an aggressive malignancy with a median survival of the patients of less than two years. Besides characteristic chromosomal translocations, frequent mutations affect the ATM gene, JAK/STAT pathway members, and epigenetic regulators. We here performed a targeted mutation analysis for 40 genes selected from a RNA sequencing of 10 T-PLL in a collection of 28 T-PLL, and an exome analysis of five further cases. Nonsynonymous mutations were identified in 30 of the 40 genes, 18 being recurrently mutated...
January 19, 2018: Blood Cancer Journal
https://www.readbyqxmd.com/read/29339153/inhibition-of-cox-2-and-5-lox-regulates-the-progression-of-colorectal-cancer-by-promoting-pten-and-suppressing-pi3k-akt-pathway
#3
Jian Chang, Nan Tang, Qi Fang, Kongfan Zhu, Lei Liu, Xingcheng Xiong, Zhongchao Zhu, Bixiang Zhang, Mingzhi Zhang, Jing Tao
For colorectal cancer (CRC) patients, local and systemic inflammatory responses have been extensively reported to closely associate with patient survival. However, the specific signalling pathways responsible for carcinogenic responses are unclear. Phosphatase and tensin homolog deleted on chromosome 10 (PTEN) is a negative regulator of PI3K/AKT pathway that is gradually inactivated in cancers through mutation, loss of heterozygosity and others epigenetic mechanisms. In addition, COX and LOX metabolic pathways of arachidonic acid (AA) play a crucial role in promoting adenoma development...
January 12, 2018: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29338479/graphene-oxide-regulates-cox2-in-human-embryonic-kidney-293t-cells-via-epigenetic-mechanisms-dynamic-chromosomal-interactions
#4
Yuxiang Sun, Hui Dai, Shaopeng Chen, Ming Xu, Xuanyu Wang, Yajun Zhang, Shengmin Xu, An Xu, Jian Weng, Sijin Liu, Lijun Wu
To extend the applications of engineered nanomaterials, such as graphene oxide (GO), it is necessary to minimize cytotoxicity. However, the mechanisms underlying this cytotoxicity are unclear. Dynamic chromosomal interactions have been used to illustrate the molecular bases of gene expression, which offers a more sensitive and cutting-edge technology to elucidate complex biological processes associated with epigenetic regulations. In this study, the role of GO-triggered chromatin interactions in the activation of cox2, a hallmark of inflammation, was investigated in normal human cells...
January 16, 2018: Nanotoxicology
https://www.readbyqxmd.com/read/29335548/paternal-easirnas-regulate-parental-genome-dosage-in-arabidopsis
#5
German Martinez, Philip Wolff, Zhenxing Wang, Jordi Moreno-Romero, Juan Santos-González, Lei Liu Conze, Christopher DeFraia, R Keith Slotkin, Claudia Köhler
The regulation of parental genome dosage is of fundamental importance in animals and plants, as exemplified by X-chromosome inactivation and dosage compensation. The 'triploid block' is a classic example of dosage regulation in plants that establishes a reproductive barrier between species differing in chromosome number1,2. This barrier acts in the embryo-nourishing endosperm tissue and induces the abortion of hybrid seeds through a yet unknown mechanism 3 . Here we show that depletion of paternal epigenetically activated small interfering RNAs (easiRNAs) bypasses the triploid block in response to increased paternal ploidy in Arabidopsis thaliana...
January 15, 2018: Nature Genetics
https://www.readbyqxmd.com/read/29335544/transposon-derived-small-rnas-triggered-by-mir845-mediate-genome-dosage-response-in-arabidopsis
#6
Filipe Borges, Jean-Sébastien Parent, Frédéric van Ex, Philip Wolff, German Martínez, Claudia Köhler, Robert A Martienssen
Chromosome dosage has substantial effects on reproductive isolation and speciation in both plants and animals, but the underlying mechanisms are largely obscure 1 . Transposable elements in animals can regulate hybridity through maternal small RNA 2 , whereas small RNAs in plants have been postulated to regulate dosage response via neighboring imprinted genes3,4. Here we show that a highly conserved microRNA in plants, miR845, targets the tRNAMet primer-binding site (PBS) of long terminal repeat (LTR) retrotransposons in Arabidopsis pollen, and triggers the accumulation of 21-22-nucleotide (nt) small RNAs in a dose-dependent fashion via RNA polymerase IV...
January 15, 2018: Nature Genetics
https://www.readbyqxmd.com/read/29330288/epigenetically-regulated-chromosome-14q32-mirna-cluster-induces-metastasis-and-predicts-poor-prognosis-in-lung-adenocarcinoma-patients
#7
Margarita Gonzalez-Vallinas, Manuel Rodriguez-Paredes, Marco Albrecht, Carsten Sticht, Damian Stichel, Julian Gutekunst, Adriana Pitea, Steffen Sass, Francisco J Sánchez-Rivera, Justo L Bermejo, Jennifer Schmitt, Carolina De La Torre, Arne Warth, Fabian Theis, Nikola Mueller, Norbert Gretz, Thomas Muley, Michael Meister, Darjus F Tschaharganeh, Peter Schirmacher, Franziska Matthäus, Kai Breuhahn
Most lung cancer deaths are related to metastases, which indicates the necessity of detecting and inhibiting tumor cell dissemination. Here, we aimed to identify microRNAs (miRNAs) involved in metastasis of lung adenocarcinoma as prognostic biomarkers and therapeutic targets. To that end, lymph node metastasis-associated miRNAs were identified in The Cancer Genome Atlas (TCGA) lung adenocarcinoma patient cohort (sequencing data; n=449) and subsequently validated by RT-qPCR in an independent clinical cohort (n=108)...
January 12, 2018: Molecular Cancer Research: MCR
https://www.readbyqxmd.com/read/29325627/epigenetic-mechanisms-underlying-nervous-system-diseases
#8
Irfan A Qureshi, Mark F Mehler
Epigenetic mechanisms act as control systems for modulating genomic structure and activity in response to evolving profiles of cell-extrinsic, cell-cell, and cell-intrinsic signals. These dynamic processes are responsible for mediating cell- and tissue-specific gene expression and function and gene-gene and gene-environmental interactions. The major epigenetic mechanisms include DNA methylation and hydroxymethylation; histone protein posttranslational modifications, nucleosome remodeling/repositioning, and higher-order chromatin reorganization; noncoding RNA regulation; and RNA editing...
2018: Handbook of Clinical Neurology
https://www.readbyqxmd.com/read/29317751/methylation-in-mycobacterium-tuberculosis-is-lineage-specific-with-associated-mutations-present-globally
#9
Jody Phelan, Paola Florez de Sessions, Leopold Tientcheu, Joao Perdigao, Diana Machado, Rumina Hasan, Zahra Hasan, Indra L Bergval, Richard Anthony, Ruth McNerney, Martin Antonio, Isabel Portugal, Miguel Viveiros, Susana Campino, Martin L Hibberd, Taane G Clark
DNA methylation is an epigenetic modification of the genome involved in regulating crucial cellular processes, including transcription and chromosome stability. Advances in PacBio sequencing technologies can be used to robustly reveal methylation sites. The methylome of the Mycobacterium tuberculosis complex is poorly understood but may be involved in virulence, hypoxic survival and the emergence of drug resistance. In the most extensive study to date, we characterise the methylome across the 4 major lineages of M...
January 9, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29317619/phf8-histone-demethylase-deficiency-causes-cognitive-impairments-through-the-mtor-pathway
#10
Xuemei Chen, Shuai Wang, Ying Zhou, Yanfei Han, Shengtian Li, Qing Xu, Longyong Xu, Ziqi Zhu, Youming Deng, Lu Yu, Lulu Song, Adele Pin Chen, Juan Song, Eiki Takahashi, Guang He, Lin He, Weidong Li, Charlie Degui Chen
Epigenomic abnormalities caused by genetic mutation in epigenetic regulators can result in neurodevelopmental disorders, deficiency in neural plasticity and mental retardation. As a histone demethylase, plant homeodomain finger protein 8 (Phf8) is a candidate gene for syndromal and non-specific forms of X-chromosome-linked intellectual disability (XLID). Here we report that Phf8 knockout mice displayed impaired learning and memory, and impaired hippocampal long-term potentiation (LTP) without gross morphological defects...
January 9, 2018: Nature Communications
https://www.readbyqxmd.com/read/29316023/sj%C3%A3-gren-s-syndrome-x-chromosome-dose-effect-an-epigenetic-perspective
#11
REVIEW
Jean-Luc C Mougeot, Braxton Noll, Farah K Bahrani Mougeot
Sjögren's syndrome (SS) is a chronic autoimmune disease affecting exocrine glands leading to mouth and eyes dryness. The extent to which epigenetic DNA methylation changes are responsible for an X-chromosome dose effect has yet to be determined. Our objectives were to (i) describe how epigenetic DNA methylation changes could explain an X-chromosome dose effect in SS for women with normal 46,XX genotype and (ii) determine the relevant relationships to this dose effect, between X-linked genes, genes controlling X-chromosome inactivation (XCI) and genes encoding associated transcription factors, all of which are differentially expressed and/or differentially methylated in the salivary glands of SS patients...
January 9, 2018: Oral Diseases
https://www.readbyqxmd.com/read/29305654/spontaneous-regression-of-neuroblastoma
#12
REVIEW
Garrett M Brodeur
Neuroblastomas are characterized by heterogeneous clinical behavior, from spontaneous regression or differentiation into a benign ganglioneuroma, to relentless progression despite aggressive, multimodality therapy. Indeed, neuroblastoma is unique among human cancers in terms of its propensity to undergo spontaneous regression. The strongest evidence for this comes from the mass screening studies conducted in Japan, North America and Europe and it is most evident in infants with stage 4S disease. This propensity is associated with a pattern of genomic change characterized by whole chromosome gains rather than segmental chromosome changes but the mechanism(s) underlying spontaneous regression are currently a matter of speculation...
January 5, 2018: Cell and Tissue Research
https://www.readbyqxmd.com/read/29281018/smchd1-haploinsufficiency-exacerbates-the-phenotype-of-a-transgenic-fshd1-mouse-model
#13
Jessica C de Greef, Yvonne D Krom, Bianca den Hamer, Lauren Snider, Yosuke Hiramuki, Rob F P van den Akker, Kelsey Breslin, Miha Pakusch, Daniela C F Salvatori, Bram Slütter, Rabi Tawil, Marnie E Blewitt, Stephen J Tapscott, Silvère M van der Maarel
In humans, a copy of the DUX4 retrogene is located in each unit of the D4Z4 macrosatellite repeat that normally comprises 8-100 units. The D4Z4 repeat has heterochromatic features and does not express DUX4 in somatic cells. Individuals with facioscapulohumeral muscular dystrophy (FSHD) have a partial failure of somatic DUX4 repression resulting in the presence of DUX4 protein in sporadic muscle nuclei. Somatic DUX4 derepression is caused by contraction of the D4Z4 repeat to 1-10 units (FSHD1) or by heterozygous mutations in genes responsible for maintaining the D4Z4 chromatin structure in a repressive state (FSHD2)...
December 21, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/29276809/new-advances-in-human-x-chromosome-status-from-a-developmental-and-stem-cell-biology
#14
Benjamin Patterson, Yoshiaki Tanaka, In-Hyun Park
Recent advances in stem cell biology have dramatically increased the understanding of molecular and cellular mechanism of pluripotency and cell fate determination. Additionally, pluripotent stem cells (PSCs), including embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs), arose as essential resources for disease modeling and cellular therapeutics. Despite these advancements, the epigenetic dysregulation in pluripotency such as the imprinting status, and X chromosome dosage compensation, and its consequences on future utility of PSCs yet remain unresolved...
December 2017: Tissue Engineering and Regenerative Medicine
https://www.readbyqxmd.com/read/29239787/deciphering-psoriasis-a-bioinformatic-approach
#15
Juan L Melero, Sergi Andrades, Lluís Arola, Antoni Romeu
BACKGROUND: Psoriasis is an immune-mediated, inflammatory and hyperproliferative disease of the skin and joints. The cause of psoriasis is still unknown. The fundamental feature of the disease is the hyperproliferation of keratinocytes and the recruitment of cells from the immune system in the region of the affected skin, which leads to deregulation of many well-known gene expressions. OBJECTIVE: Based on data mining and bioinformatic scripting, here we show a new dimension of the effect of psoriasis at the genomic level...
November 22, 2017: Journal of Dermatological Science
https://www.readbyqxmd.com/read/29237550/the-effects-of-dna-methylation-on-human-psychology
#16
REVIEW
Farzeen Kader, Meenu Ghai, Leah Maharaj
DNA methylation is a fundamental epigenetic modification in the human genome; pivotal in development, genomic imprinting, X inactivation, chromosome stability, gene expression and methylation aberrations are involved in an array of human diseases. Methylation at promoters is associated with transcriptional repression, whereas gene body methylation is generally associated with gene expression. Extrinsic factors such as age, diets and lifestyle affect DNA methylation which consequently alters gene expression...
December 10, 2017: Behavioural Brain Research
https://www.readbyqxmd.com/read/29230394/acetylome-of-acinetobacter-baumannii-sk17-reveals-a-highly-conserved-modification-of-histone-like-protein-hu
#17
Jiahn-Haur Liao, Cheng-Han Tsai, Sanjay G Patel, Jhih-Tian Yang, I-Fan Tu, Matteo Lo Cicero, Magdalena Lipka-Lloyd, Wan-Ling Wu, Wen-Jie Shen, Meng-Ru Ho, Chi-Chi Chou, Garima R Sharma, Hiroki Okanishi, Louis Y P Luk, Yu-Hsuan Tsai, Shih-Hsiung Wu
Lysine acetylation is a prevalent post-translational modification in both eukaryotes and prokaryotes. Whereas this modification is known to play pivotal roles in eukaryotes, the function and extent of this modification in prokaryotic cells remain largely unexplored. Here we report the acetylome of a pair of antibiotic-sensitive and -resistant nosocomial pathogen Acinetobacter baumannii SK17-S and SK17-R. A total of 145 lysine acetylation sites on 125 proteins was identified, and there are 23 acetylated proteins found in both strains, including histone-like protein HU which was found to be acetylated at Lys13...
2017: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/29228278/zinc-finger-protein-274-regulates-imprinted-expression-of-transcripts-in-prader-willi-syndrome-neurons
#18
Maéva Langouët, Heather R Glatt-Deeley, Michael S Chung, Clémence M Dupont-Thibert, Elodie Mathieux, Erin C Banda, Christopher E Stoddard, Leann Crandall, Marc Lalande
Prader-Willi syndrome (PWS) is characterized by neonatal hypotonia, developmental delay and hyperphagia/obesity and is caused by the absence of paternal contribution to chromosome 15q11-q13. Using induced pluripotent stem cell (iPSC) models of PWS, we previously discovered an epigenetic complex that is comprised of the zinc-finger protein ZNF274 and the SET domain bifurcated 1 (SETDB1) histone H3 lysine 9 (H3K9) methyltransferase and that silences the maternal alleles at the PWS locus. Here, we have knocked out ZNF274 and rescued the expression of silent maternal alleles in neurons derived from PWS iPSC lines, without affecting DNA methylation at the PWS-Imprinting Center (PWS-IC)...
December 7, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/29222086/genome-wide-dna-methylation-profiling-using-the-methylation-dependent-restriction-enzyme-lpnpi
#19
Ruben Boers, Joachim Boers, Bas de Hoon, Christel Kockx, Zeliha Ozgur, Anco Molijn, Wilfred van IJcken, Joop Laven, Joost Gribnau
DNA methylation is a well-known epigenetic modification that plays a crucial role in gene regulation, but genome-wide analysis of DNA methylation remains technically challenging and costly. DNA methylation-dependent restriction enzymes can be used to restrict CpG methylation analysis to methylated regions of the genome only, which significantly reduces the required sequencing depth and simplifies subsequent bioinformatics analysis. Unfortunately, this approach has been hampered by complete digestion of DNA in CpG methylation-dense regions, resulting in fragments that are too small for accurate mapping...
December 8, 2017: Genome Research
https://www.readbyqxmd.com/read/29217590/a-mechanism-of-cohesin-dependent-loop-extrusion-organizes-zygotic-genome-architecture
#20
Johanna Gassler, Hugo B Brandão, Maxim Imakaev, Ilya M Flyamer, Sabrina Ladstätter, Wendy A Bickmore, Jan-Michael Peters, Leonid A Mirny, Kikuë Tachibana
Fertilization triggers assembly of higher-order chromatin structure from a condensed maternal and a naïve paternal genome to generate a totipotent embryo. Chromatin loops and domains have been detected in mouse zygotes by single-nucleus Hi-C (snHi-C), but not bulk Hi-C. It is therefore unclear when and how embryonic chromatin conformations are assembled. Here, we investigated whether a mechanism of cohesin-dependent loop extrusion generates higher-order chromatin structures within the one-cell embryo. Using snHi-C of mouse knockout embryos, we demonstrate that the zygotic genome folds into loops and domains that critically depend on Scc1-cohesin and that are regulated in size and linear density by Wapl...
December 7, 2017: EMBO Journal
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