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Epigenetic regulation of chromosome

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https://www.readbyqxmd.com/read/28933030/phenotype-comparison-confirms-zmynd11-as-a-critical-gene-for-10p15-3-microdeletion-syndrome
#1
Birute Tumiene, Ž Čiuladaitė, E Preikšaitienė, R Mameniškienė, A Utkus, V Kučinskas
Proper epigenetic regulation processes are crucial in the normal development of the human brain. An ever-increasing group of neurodevelopmental disorders due to derangements of epigenetic regulation involve both microdeletion and monogenic syndromes. Some of these syndromes have overlapping clinical phenotypes due to haploinsufficiency-sensitive genes involved in microdeletions. It was shown recently that the ZMYND11 gene has important functions in epigenetic regulation as an unconventional transcription co-repressor of highly expressed genes, possibly acting in the repression of cryptic transcription from gene bodies...
September 21, 2017: Journal of Applied Genetics
https://www.readbyqxmd.com/read/28932904/a-computational-method-using-the-random-walk-with-restart-algorithm-for-identifying-novel-epigenetic-factors
#2
JiaRui Li, Lei Chen, ShaoPeng Wang, YuHang Zhang, XiangYin Kong, Tao Huang, Yu-Dong Cai
Epigenetic regulation has long been recognized as a significant factor in various biological processes, such as development, transcriptional regulation, spermatogenesis, and chromosome stabilization. Epigenetic alterations lead to many human diseases, including cancer, depression, autism, and immune system defects. Although efforts have been made to identify epigenetic regulators, it remains a challenge to systematically uncover all the components of the epigenetic regulation in the genome level using experimental approaches...
September 20, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28915715/epigenetic-regulation-during-the-differentiation-of-stem-cells-to-germ-cells
#3
REVIEW
Yuan-Chao Sun, Yong-Yong Wang, Wei Ge, Shun-Feng Cheng, Paul W Dyce, Wei Shen
Gametogenesis is an essential process to ensure the transfer of genetic information from one generation to the next. It also provides a mechanism by which genetic evolution can take place. Although the genome of primordial germ cells (PGCs) is exactly the same with somatic cells within an organism, there are significant differences between their developments. For example, PGCs eventually undergo meiosis to become functional haploid gametes, and prior to that they undergo epigenetic imprinting which greatly alter their genetic regulation...
August 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/28915635/dysregulation-of-an-x-linked-primate-specific-epididymal-microrna-cluster-in-unexplained-asthenozoospermia
#4
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...
August 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/28903899/the-application-of-next-generation-sequencing-techniques-in-studying-transcriptional-regulation-in-embryonic-stem-cells
#5
Ya-Jun Liu, Feng Zhang, Hong-de Liu, Xiao Sun
The mechanism of transcriptional regulation has been the focus of many studies in the post-genomic era. The development of sequencing-based technologies for chromatin profiling enables current researchers to experimentally measure chromatin properties. Moreover, many studies aim at annotating the state of the chromatin into broad categories based on observed chromatin features and/or DNA sequences, then associating the resultant distal regulatory regions with the correct target genes based on DNA sequences, and predicting the dependence of epigenetic features on genetic variation...
August 20, 2017: Yi Chuan, Hereditas
https://www.readbyqxmd.com/read/28903352/analysis-of-bos-taurus-and-sus-scrofa-x-and-y-chromosome-transcriptome-highlights-reproductive-driver-genes
#6
Faheem Ahmed Khan, Hui Liu, Hao Zhou, Kai Wang, Muhammad Tahir Ul Qamar, Nuruliarizki Shinta Pandupuspitasari, Zhang Shujun
The biology of sperm, its capability of fertilizing an egg and its role in sex ratio are the major biological questions in reproductive biology. To answer these question we integrated X and Y chromosome transcriptome across different species: Bos taurus and Sus scrofa and identified reproductive driver genes based on Weighted Gene Co-Expression Network Analysis (WGCNA) algorithm. Our strategy resulted in 11007 and 10445 unique genes consisting of 9 and 11 reproductive modules in Bos taurus and Sus scrofa, respectively...
August 15, 2017: Oncotarget
https://www.readbyqxmd.com/read/28899949/the-future-genetics-advances-in-men1-therapeutic-approaches-and-management-strategies
#7
REVIEW
Sunita K Agarwal
The identification of the multiple endocrine neoplasia type 1 (MEN1) gene in 1997 has shown that germline heterozygous mutations in the MEN1 gene located on chromosome 11q13 predisposes to the development of tumors in the MEN1 syndrome. Tumor development occurs upon loss of the remaining normal copy of the MEN1 gene in MEN1-target tissues. Therefore, MEN1 is a classic tumor suppressor gene in the context of MEN1. This tumor suppressor role of the protein encoded by the MEN1 gene, menin, holds true in mouse models with germline heterozygous Men1 loss, wherein MEN1-associated tumors develop in adult mice after spontaneous loss of the remaining non-targeted copy of the Men1 gene...
October 2017: Endocrine-related Cancer
https://www.readbyqxmd.com/read/28895353/-circulating-long-noncoding-rnas-as-biomarkers-in-tumor-diagnosis
#8
Nan Jiang, Haihua Tian, Jinchang Pan, Zhaohui Gong
Long noncoding RNAs (lncRNAs) are involved in vital life processes of gene expression, epigenetic regulation and X-chromosome inactivation. lncRNAs are also closely associated with tumor initiation and progression. Moreover, lncRNAs may enter human circulation system in the form of microvesicle or exosome, or in combination with RNA binding protein. Interestingly, the circulating lncRNAs are widely existed in body fluids, such as blood and urine. We review the origin of circulating lncRNAs, and the detection methods as potential biomarkers...
June 25, 2017: Sheng Wu Gong Cheng Xue Bao, Chinese Journal of Biotechnology
https://www.readbyqxmd.com/read/28892047/a-system-for-detecting-high-impact-low-frequency-mutations-in-primary-tumors-and-metastases
#9
M Anjanappa, Y Hao, E R Simpson, P Bhat-Nakshatri, J B Nelson, S A Tersey, R G Mirmira, A A Cohen-Gadol, M R Saadatzadeh, L Li, F Fang, K P Nephew, K D Miller, Y Liu, H Nakshatri
Tumor complexity and intratumor heterogeneity contribute to subclonal diversity. Despite advances in next-generation sequencing (NGS) and bioinformatics, detecting rare mutations in primary tumors and metastases contributing to subclonal diversity is a challenge for precision genomics. Here, in order to identify rare mutations, we adapted a recently described epithelial reprograming assay for short-term propagation of epithelial cells from primary and metastatic tumors. Using this approach, we expanded minor clones and obtained epithelial cell-specific DNA/RNA for quantitative NGS analysis...
September 11, 2017: Oncogene
https://www.readbyqxmd.com/read/28887637/epigenetic-regulation-in-cell-senescence
#10
REVIEW
Li-Qin Cheng, Zhu-Qin Zhang, Hou-Zao Chen, De-Pei Liu
Cell senescence, which is an irreversible state of cell proliferative arrest, has emerged as a potentially important contributor to tissue dysfunction and organismal ageing. Cell senescence is triggered by a variety of senescence stressors, which affect gene expression and multiple signalling pathways that give rise to various senescence phenotypes. Epigenetic mechanisms, as critical regulators of chromosomal architecture and gene expression, have added an extra dimension to the molecular mechanisms of cell senescence...
September 8, 2017: Journal of Molecular Medicine: Official Organ of the "Gesellschaft Deutscher Naturforscher und Ärzte"
https://www.readbyqxmd.com/read/28884294/a-concise-review-of-microrna-exploring-the-insights-of-microrna-regulations-in-bacterial-viral-and-metabolic-diseases
#11
REVIEW
Ahsan Naveed, Sajjad Ur-Rahman, Sabahat Abdullah, Muhammad Ammar Naveed
MicroRNA (miRNA) is a small section of ribonucleic acid (RNA) that reduces the protein formation by making the pair of the complementary piece of mRNA. The genes of miRNA are present as transcriptional or polycistronic units in the chromosomes. The cellular multiplication, separation and existence like the multitude of genetic functions are affected by miRNA. Nearly 50% of identified miRNA are located in the residence in the intronic part of the genes. The mature miRNA is yielded in two steps. Drosha and RNA-induced silencing complex are the catalysts that play an important role in miRNA synthesis...
September 7, 2017: Molecular Biotechnology
https://www.readbyqxmd.com/read/28883660/chromatin-remodeling-system-p300-hdac2-sin3a-is-involved-in-arginine-starvation-induced-hif-1%C3%AE-degradation-at-the-ass1-promoter-for-ass1-derepression
#12
Wen-Bin Tsai, Yan Long, Jeffrey T Chang, Niramol Savaraj, Lynn G Feun, Manfred Jung, Helen H W Chen, Macus Tien Kuo
Argininosuccinate synthetase 1 (ASS1) is the key enzyme that controls biosynthesis of arginine (Arg). ASS1 is silenced in many human malignancies therefore, these tumors require extracellular Arg for growth. The Arg-degrading recombinant protein, pegylated arginine deiminase (ADI-PEG20), has been in clinical trials for targeting Arg auxotrophic tumors by Arg starvation therapy. Resistance to Arg starvation is often developed through reactivation of ASS1 expression. We previously demonstrated that ASS1 silencing is controlled by HIF-1α and Arg starvation-reactivated ASS1 is associated with HIF-1α downregulation...
September 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28883545/copy-number-rather-than-epigenetic-alterations-are-the-major-dictator-of-imprinted-methylation-in-tumors
#13
Alex Martin-Trujillo, Enrique Vidal, Ana Monteagudo-Sa Nchez, Marta Sanchez-Delgado, Sebastian Moran, Jose Ramon Hernandez Mora, Holger Heyn, Miriam Guitart, Manel Esteller, David Monk
It has been postulated that imprinting aberrations are common in tumors. To understand the role of imprinting in cancer, we have characterized copy-number and methylation in over 280 cancer cell lines and confirm our observations in primary tumors. Imprinted differentially methylated regions (DMRs) regulate parent-of-origin monoallelic expression of neighboring transcripts in cis. Unlike single-copy CpG islands that may be prone to hypermethylation, imprinted DMRs can either loose or gain methylation during tumorigenesis...
September 7, 2017: Nature Communications
https://www.readbyqxmd.com/read/28882400/histone-modifications-a-review-about-the-presence-of-this-epigenetic-phenomenon-in-carcinogenesis
#14
REVIEW
Emanuely Silva Chrun, Filipe Modolo, Filipe Ivan Daniel
Among the epigenetic changes, histone acetylation has been recognized as a fundamental process that strongly affects gene expression regulation. Disrupt of this phenomenon has been linked to carcinogenesis. In this review, we analysed studies reporting the process of histone modification, the enzymes associated and affected genes concerning human malignancies and histone enzyme inhibitor drugs used in cancer treatment. Variable degrees of expression of HDACs (histone deacetylases) and HATs (histone acetyltransferases) are found in many human malignant tissues and the histones acetylation seems to influence different processes including the progression of cell cycle, the dynamics of chromosomes, DNA recombination, DNA repair and apoptosis...
June 28, 2017: Pathology, Research and Practice
https://www.readbyqxmd.com/read/28862742/transcription-factor-retention-on-mitotic-chromosomes-regulatory-mechanisms-and-impact-on-cell-fate-decisions
#15
REVIEW
Mahé Raccaud, David M Suter
During mitosis, gene transcription stops, and the bulk of DNA-binding proteins are excluded from condensed chromosomes. While most gene-specific transcription factors are largely evicted from mitotic chromosomes, a subset remains bound to specific and non-specific DNA sites. Here, we review the current knowledge on the mechanisms leading to the retention of a subset of transcription factors on mitotic chromosomes, and discuss the implications in gene expression regulation and their potential as an epigenetic mechanism controlling stem cell self-renewal and differentiation...
September 1, 2017: FEBS Letters
https://www.readbyqxmd.com/read/28861108/gene-functioning-and-storage-within-a-folded-genome
#16
REVIEW
Sergey V Razin, Sergey V Ulianov
In mammals, genomic DNA that is roughly 2 m long is folded to fit the size of the cell nucleus that has a diameter of about 10 μm. The folding of genomic DNA is mediated via assembly of DNA-protein complex, chromatin. In addition to the reduction of genomic DNA linear dimensions, the assembly of chromatin allows to discriminate and to mark active (transcribed) and repressed (non-transcribed) genes. Consequently, epigenetic regulation of gene expression occurs at the level of DNA packaging in chromatin. Taking into account the increasing attention of scientific community toward epigenetic systems of gene regulation, it is very important to understand how DNA folding in chromatin is related to gene activity...
2017: Cellular & Molecular Biology Letters
https://www.readbyqxmd.com/read/28855255/single-molecule-force-spectroscopy-on-histone-h4-tail-cross-linked-chromatin-reveals-fiber-folding
#17
Artur Kaczmarczyk, Abdollah Allahverdi, Thomas B Brouwer, Lars Nordenskiöld, Nynke H Dekker, John van Noort
The eukaryotic genome is highly compacted into a protein-DNA complex called chromatin. The cell controls access of transcriptional regulators to chromosomal DNA via several mechanisms that act on chromatin-associated proteins and provide a rich spectrum of epigenetic regulation. Elucidating the mechanisms that fold chromatin fibers into higher-order structures is therefore key to understanding the epigenetic regulation of DNA accessibility. Here, using histone H4-V21C and histone H2A-E64C mutations, we employed single-molecule force spectroscopy to measure the unfolding of individual chromatin fibers that are reversibly cross-linked through the histone H4 tail...
August 30, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28854566/impact-of-transposable-elements-on-polyploid-plant-genomes
#18
Carlos M Vicient, Josep M Casacuberta
Background: The growing wealth of knowledge on whole-plant genome sequences is highlighting the key role of transposable elements (TEs) in plant evolution, as a driver of drastic changes in genome size and as a source of an important number of new coding and regulatory sequences. Together with polyploidization events, TEs should thus be considered the major players in evolution of plants. Scope: This review outlines the major mechanisms by which TEs impact plant genome evolution and how polyploidy events can affect these impacts, and vice versa...
August 1, 2017: Annals of Botany
https://www.readbyqxmd.com/read/28854222/rahu-is-a-mutant-allele-of-dnmt3c-encoding-a-dna-methyltransferase-homolog-required-for-meiosis-and-transposon-repression-in-the-mouse-male-germline
#19
Devanshi Jain, Cem Meydan, Julian Lange, Corentin Claeys Bouuaert, Nathalie Lailler, Christopher E Mason, Kathryn V Anderson, Scott Keeney
Transcriptional silencing by heritable cytosine-5 methylation is an ancient strategy to repress transposable elements. It was previously thought that mammals possess four DNA methyltransferase paralogs-Dnmt1, Dnmt3a, Dnmt3b and Dnmt3l-that establish and maintain cytosine-5 methylation. Here we identify a fifth paralog, Dnmt3c, that is essential for retrotransposon methylation and repression in the mouse male germline. From a phenotype-based forward genetics screen, we isolated a mutant mouse called 'rahu', which displays severe defects in double-strand-break repair and homologous chromosome synapsis during male meiosis, resulting in sterility...
August 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28842590/ddx3-localizes-to-the-centrosome-and-prevents-multipolar-mitosis-by-epigenetically-and-translationally-modulating-p53-expression
#20
Wei-Ju Chen, Wei-Ting Wang, Tsung-Yuan Tsai, Hao-Kang Li, Yan-Hwa Wu Lee
The DEAD-box RNA helicase DDX3 plays divergent roles in tumorigenesis, however, its function in mitosis is unclear. Immunofluorescence indicated that DDX3 localized to centrosome throughout the cell cycle and colocalized with centrosome-associated p53 during mitosis in HCT116 and U2OS cells. DDX3 depletion promoted chromosome misalignment, segregation defects and multipolar mitosis, eventually leading to G2/M delay and cell death. DDX3 prevented multipolar mitosis by inactivation and coalescence of supernumerary centrosomes...
August 25, 2017: Scientific Reports
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