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https://www.readbyqxmd.com/read/28424740/essential-role-of-long-non-coding-rnas-in-de-novo-chromatin-modifications-the-genomic-address-code-hypothesis
#1
Ken Nishikawa, Akira R Kinjo
The epigenome, i.e., the whole of chromatin modifications, is transferred from mother to daughter cells during cell differentiation. When de novo chromatin modifications (establishment or erasure of, respectively, new or pre-existing DNA methylations and/or histone modifications) are made in a daughter cell, however, it has a different epigenome than its mother cell. Although de novo chromatin modification is an important event that comprises elementary processes of cell differentiation, its molecular mechanism remains poorly understood...
April 2017: Biophysical Reviews
https://www.readbyqxmd.com/read/28420606/epigenetic-regulation-and-related-diseases-during-placental-development
#2
Liu Fulin, Zhou Jin, Zhang Wei, Wang Hui
The placenta is vital to fetal growth and development, as it bridges the fetus and the mother. Genome-wide epigenetic regulations (e.g., DNA methylation, histone modifications, non-coding RNAs) participate in many aspects of placenta development, including decidua of the uterus, trophoblast cell adhesion and invasion, angiogenesis and placental imprinted gene expression. Environmental factors during pregnancy, such as heavy metals, chemical compounds, modern assisted reproductive technology and the nutrient conditions, may cause abnormal placental epigenetics...
April 20, 2017: Yi Chuan, Hereditas
https://www.readbyqxmd.com/read/28420141/coordinated-actions-of-micrornas-with-other-epigenetic-factors-regulate-skeletal-muscle-development-and-adaptation
#3
REVIEW
Marzia Bianchi, Alessandra Renzini, Sergio Adamo, Viviana Moresi
Epigenetics plays a pivotal role in regulating gene expression in development, in response to cellular stress or in disease states, in virtually all cell types. MicroRNAs (miRNAs) are short, non-coding RNA molecules that mediate RNA silencing and regulate gene expression. miRNAs were discovered in 1993 and have been extensively studied ever since. They can be expressed in a tissue-specific manner and play a crucial role in tissue development and many biological processes. miRNAs are responsible for changes in the cell epigenome because of their ability to modulate gene expression post-transcriptionally...
April 15, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28412585/the-promise-of-epigenetic-therapy-reprogramming-the-cancer-epigenome
#4
REVIEW
Andrew D Kelly, Jean-Pierre J Issa
Epigenetics refers to heritable molecular determinants of phenotype independent of DNA sequence. Epigenetic features include DNA methylation, histone modifications, non-coding RNAs, and chromatin structure. The epigenetic status of cells plays a crucial role in determining their differentiation state and proper function within multicellular organisms. Disruption of these processes is now understood to be a major contributor to cancer development and progression, and recent efforts have attempted to pharmacologically reverse such altered epigenetics...
April 13, 2017: Current Opinion in Genetics & Development
https://www.readbyqxmd.com/read/28407294/altered-tert-promoter-and-other-genomic-regulatory-elements-occurrence-and-impact
#5
Barbara Heidenreich, Rajiv Kumar
Study of genetic alterations, inherited or acquired, that increase the risk or drive cancers and many other diseases had remained mostly confined to coding sequences of the human genome. Data from genome wide associations studies, development of the Encyclopedia of DNA Elements (ENCODE), and a spurt in detection of driver somatic mutations have shifted focus towards noncoding regions of the human genome. The majority of genetic variants robustly associated with cancers and other syndromes identified through genome wide studies are located within noncoding regulatory regions of the genome...
April 13, 2017: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/28400511/shprh-regulates-rrna-transcription-by-recognizing-the-histone-code-in-an-mtor-dependent-manner
#6
Deokjae Lee, Jungeun An, Young-Un Park, Hungjiun Liaw, Roger Woodgate, Jun Hong Park, Kyungjae Myung
Many DNA repair proteins have additional functions other than their roles in DNA repair. In addition to catalyzing PCNA polyubiquitylation in response to the stalling of DNA replication, SHPRH has the additional function of facilitating rRNA transcription by localizing to the ribosomal DNA (rDNA) promoter in the nucleoli. SHPRH was recruited to the rDNA promoter using its plant homeodomain (PHD), which interacts with histone H3 when the fourth lysine of H3 is not trimethylated. SHPRH enrichment at the rDNA promoter was inhibited by cell starvation, by treatment with actinomycin D or rapamycin, or by depletion of CHD4...
April 11, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28399646/long-non-coding-rna-bcar4-promotes-chondrosarcoma-cell-proliferation-and-migration-through-activation-of-mtor-signaling-pathway
#7
Xiaolong Shui, Chengwei Zhou, Wei Lin, Yang Yu, Yongzeng Feng, Jianzhong Kong
Chondrosarcoma is one of the common malignant histologic tumors, very difficult to treat, but the concrete cause and mechanism have not yet been elucidated. The present study aimed to investigate the functional involvement of BCAR4 in chondrosarcoma and its potentially underlying mechanism. QRT-PCR and western blot were used to determine the expression of BCAR4 and mTOR signaling pathway proteins both in chondrosarcoma tissues and cells. Chondrosarcoma cell proliferation and migration were assessed by MTT assay and transwell migration assay, respectively...
January 1, 2017: Experimental Biology and Medicine
https://www.readbyqxmd.com/read/28393112/chromatin-replication-transmitting-the-histone-code
#8
Han-Wen Chang, Vasily M Studitsky
Efficient overcoming of the nucleosomal barrier and accurate maintenance of associated histone marks during chromatin replication are essential for normal functioning of the cell. Recent studies revealed new protein factors and histone modifications contributing to overcoming the nucleosomal barrier, and suggested an important role for DNA looping in survival of the original histones during replication. These studies suggest new possible mechanisms for transmitting the histone code to next generations of cells...
February 2017: Journal of Nature and Science
https://www.readbyqxmd.com/read/28381576/dna-binding-properties-of-the-african-swine-fever-virus-pa104r-a-histone-like-protein-involved-in-viral-replication-and-transcription
#9
Gonçalo Frouco, Ferdinando B Freitas, João Coelho, Alexandre Leitão, Carlos Martins, Fernando Ferreira
African swine fever virus (ASFV) codes for a putative histone-like protein (pA104R) with extensive sequence homology to bacterial proteins that are implicated in genome replication and packaging. Functional characterization of purified recombinant pA104R revealed that it binds to ssDNA and dsDNA over a wide range of temperatures, pH values, salt concentrations and in an ATP-independent manner, with an estimated binding site size of about 14-16 nucleotides. Using site-directed mutagenesis, the arginine located in pA104R's DNA-binding domain, at position 69, was found to be relevant for an efficient DNA-binding activity...
April 5, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28379492/identification-and-dynamic-changes-of-rnas-isolated-from-raly-containing-ribonucleoprotein-complexes
#10
Annalisa Rossi, Albertomaria Moro, Toma Tebaldi, Nicola Cornella, Lisa Gasperini, Lorenzo Lunelli, Alessandro Quattrone, Gabriella Viero, Paolo Macchi
RALY is a member of the heterogeneous nuclear ribonucleoprotein family (hnRNP), a large family of RNA-binding proteins involved in many aspects of RNA metabolism. Although RALY interactome has been recently characterized, a comprehensive global analysis of RALY-associated RNAs is lacking and the biological function of RALY remains elusive. Here, we performed RIP-seq analysis to identify RALY interacting RNAs and assessed the role of RALY in gene expression. We demonstrate that RALY binds specific coding and non-coding RNAs and associates with translating mRNAs of mammalian cells...
April 4, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28374672/a-mutation-of-the-prdm9-mouse-hybrid-sterility-gene-carried-by-a-transgene
#11
O Mihola, Z Trachtulec
PRDM9 is a protein with histone-3-methyltransferase activity, which specifies the sites of meiotic recombination in mammals. Deficiency of the Prdm9 gene in the laboratory mouse results in complete arrest of the meiotic prophase of both sexes. Moreover, the combination of certain PRDM9 alleles from different mouse subspecies causes hybrid sterility, e.g., the male-specific meiotic arrest found in the (PWD/Ph × C57BL/6J)F1 animals. The fertility of all these mice can be rescued using a Prdm9-containing transgene...
2017: Folia Biologica (Praha)
https://www.readbyqxmd.com/read/28367113/transcriptome-analysis-reveals-altered-expression-of-memory-and-neurotransmission-associated-genes-in-the-rem-sleep-deprived-rat-brain
#12
Santosh C Narwade, Birendra N Mallick, Deepti D Deobagkar
Sleep disorders are associated with cognitive impairment. Selective rapid eye movement sleep (REMS) deprivation (REMSD) alters several physiological processes and behaviors. By employing NGS platform we carried out transcriptomic analysis in brain samples of control rats and those exposed to REMSD. The expression of genes involved in chromatin assembly, methylation, learning, memory, regulation of synaptic transmission, neuronal plasticity and neurohypophysial hormone synthesis were altered. Increased transcription of BMP4, DBH and ATP1B2 genes after REMSD supports our earlier findings and hypothesis...
2017: Frontiers in Molecular Neuroscience
https://www.readbyqxmd.com/read/28367077/protein-and-genetic-composition-of-four-chromatin-types-in-drosophila-melanogaster-cell-lines
#13
Lidiya V Boldyreva, Fyodor P Goncharov, Olga V Demakova, Tatyana Yu Zykova, Victor G Levitsky, Nikolay N Kolesnikov, Alexey V Pindyurin, Valeriy F Semeshin, Igor F Zhimulev
BACKGROUND: Recently, we analyzed genome-wide protein binding data for the Drosophila cell lines S2, Kc, BG3 and Cl.8 (modENCODE Consortium) and identified a set of 12 proteins enriched in the regions corresponding to interbands of salivary gland polytene chromosomes. Using these data, we developed a bioinformatic pipeline that partitioned the Drosophila genome into four chromatin types that we hereby refer to as aquamarine, lazurite, malachite and ruby. RESULTS: Here, we describe the properties of these chromatin types across different cell lines...
April 2017: Current Genomics
https://www.readbyqxmd.com/read/28359242/small-molecule-inhibitors-of-epigenetic-mutations-as-compelling-drug-targets-for-myelodysplastic-syndromes
#14
Bani Bandana Ganguly
BACKGROUND: Involvement of mutations in epigenetic mechanism in development of heterogeneous MDS and its evolution to AML has been understood with at least one mutation and median of 2-3 mutations of the landscapes of driver mutations in ~40 genes described >90% MDS patients. Exclusivity and cooperating effects of mutations have directed therapeutic implementation with hypomethylating agents and identified a number of first-in-class small molecules as inhibitors of mutational expression...
March 30, 2017: Current Cancer Drug Targets
https://www.readbyqxmd.com/read/28347254/epigenetic-perturbation-driving-asleep-telomerase-reverse-transcriptase-possible-therapeutic-avenues-in-carcinoma
#15
REVIEW
Ajay Kumar, Pritish Nilednu, Azad Kumar, Nilesh Kumar Sharma
In the last decade, implications of human telomerase reverse transcriptase (hTERT), a component of ribonucleoprotein telomerase in aging, senescence, and stem cell are highly evident. Besides, the activation of hTERT is also being documented several cancer types including carcinoma. The awakening of telomerase during carcinoma initiation and development is being seen with different perspectives including genetic and epigenetic tools and events. In view of several tumor progenitors genes (also referred as epigenetic mediators), telomerase is placed as key enzyme to achieve the carcinoma phenotype and sustain during the progression...
March 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28343628/functional-architectures-of-local-and-distal-regulation-of-gene-expression-in-multiple-human-tissues
#16
Xuanyao Liu, Hilary K Finucane, Alexander Gusev, Gaurav Bhatia, Steven Gazal, Luke O'Connor, Brendan Bulik-Sullivan, Fred A Wright, Patrick F Sullivan, Benjamin M Neale, Alkes L Price
Genetic variants that modulate gene expression levels play an important role in the etiology of human diseases and complex traits. Although large-scale eQTL mapping studies routinely identify many local eQTLs, the molecular mechanisms by which genetic variants regulate expression remain unclear, particularly for distal eQTLs, which these studies are not well powered to detect. Here, we leveraged all variants (not just those that pass stringent significance thresholds) to analyze the functional architecture of local and distal regulation of gene expression in 15 human tissues by employing an extension of stratified LD-score regression that produces robust results in simulations...
April 6, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28343540/histone-code-aberrancies-in-small-cell-lung-cancer
#17
EDITORIAL
Eric E Gardner, John T Poirier, Charles M Rudin
No abstract text is available yet for this article.
April 2017: Journal of Thoracic Oncology
https://www.readbyqxmd.com/read/28342734/integration-of-microbiome-and-epigenome-to-decipher-the-pathogenesis-of-autoimmune-diseases
#18
REVIEW
Beidi Chen, Luxi Sun, Xuan Zhang
The interaction between genetic predisposition and environmental factors are of great significance in the pathogenesis and development of autoimmune diseases (AIDs). The human mucosa is the most frequent site that interacts with the exterior environment, and commensal microbiota at the gut and other human mucosal cavities play a crucial role in the regulation of immune system. Growing evidence has shown that the compositional and functional changes of mucosal microbiota are closely related to AIDs. Gut dysbiosis not only influence the expression level of Toll-like receptors (TLRs) of antigen presenting cells, but also contribute to Th17/Treg imbalance...
March 23, 2017: Journal of Autoimmunity
https://www.readbyqxmd.com/read/28337379/long-intergenic-non-coding-rna-00152-promotes-renal-cell-carcinoma-progression-by-epigenetically-suppressing-p16-and-negatively-regulates-mir-205
#19
Yongjun Wang, Jianzhen Liu, Hongzhong Bai, Yi Dang, Pei Lv, Shucai Wu
Long non-coding RNAs (lncRNAs) have been reported to play important roles in the tumorigenesis and development of several human cancers. Long intergenic non-coding RNA 152 (LINC00152) is significantly up-regulated in some solid tumors. However, the role of LINC00152 in the pathogenesis and development of renal cell carcinoma (RCC) remains largely unclear. In the study, we showed that LINC00152 expression was up-regulated in RCC tissues compared with adjacent normal tissues and revealed that LINC00152 expression was positively correlated with lymph node metastasis, higher TNM stage, and poor over survival (OS) time in RCC patients...
2017: American Journal of Cancer Research
https://www.readbyqxmd.com/read/28332701/the-epigenetic-landscape-related-to-reactive-oxygen-species-formation-in-the-cardiovascular-system
#20
REVIEW
Thomas Kietzmann, Andreas Petry, Antonina Shvetsova, Joachim M Gerhold, Agnes Görlach
Cardiovascular diseases are the leading cause of death worldwide. Reactive oxygen species (ROS) can act as damaging molecules but also represent central hubs in cellular signalling networks. Increasing evidence indicates that ROS play an important role in the pathogenesis of cardiovascular diseases, although the underlying mechanisms and consequences of pathophysiological elevated ROS in the cardiovascular system are still not completely resolved. More recently, alterations of the epigenetic landscape which can affect DNA methylation, post-translational histone modifications, ATP-dependent alterations to chromatin and non-coding RNA transcripts, have been considered to be of increasing importance in the pathogenesis of cardiovascular diseases...
March 23, 2017: British Journal of Pharmacology
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