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https://www.readbyqxmd.com/read/29235574/ten-principles-of-heterochromatin-formation-and-function
#1
REVIEW
Robin C Allshire, Hiten D Madhani
Heterochromatin is a key architectural feature of eukaryotic chromosomes, which endows particular genomic domains with specific functional properties. The capacity of heterochromatin to restrain the activity of mobile elements, isolate DNA repair in repetitive regions and ensure accurate chromosome segregation is crucial for maintaining genomic stability. Nucleosomes at heterochromatin regions display histone post-translational modifications that contribute to developmental regulation by restricting lineage-specific gene expression...
December 13, 2017: Nature Reviews. Molecular Cell Biology
https://www.readbyqxmd.com/read/29234324/long-non-coding-rnas-emerging-and-versatile-regulators-in-host-virus-interactions
#2
REVIEW
Xing-Yu Meng, Yuzi Luo, Muhammad Naveed Anwar, Yuan Sun, Yao Gao, Huawei Zhang, Muhammad Munir, Hua-Ji Qiu
Long non-coding RNAs (lncRNAs) are a class of non-protein-coding RNA molecules, which are involved in various biological processes, including chromatin modification, cell differentiation, pre-mRNA transcription and splicing, protein translation, etc. During the last decade, increasing evidence has suggested the involvement of lncRNAs in both immune and antiviral responses as positive or negative regulators. The immunity-associated lncRNAs modulate diverse and multilayered immune checkpoints, including activation or repression of innate immune signaling components, such as interleukin (IL)-8, IL-10, retinoic acid inducible gene I, toll-like receptors 1, 3, and 8, and interferon (IFN) regulatory factor 7, transcriptional regulation of various IFN-stimulated genes, and initiation of the cell apoptosis pathways...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/29233692/epigenetic-regulation-of-hibernation-associated-hp-20-and-hp-27-gene-transcription-in-chipmunk-liver
#3
Daisuke Tsukamoto, Michihiko Ito, Nobuhiko Takamatsu
The chipmunk hibernation-related proteins (HPs) HP-20 and HP-27 are components of a 140-kDa complex that dramatically decreases in the blood during hibernation. The HP-20 and HP-27 genes are expressed specifically in the liver and are downregulated in hibernating chipmunks. Hibernation-associated physiological changes are assumed to be under genetic control. Therefore, to elucidate the molecular mechanisms of hibernation, here we examined the mechanisms behind the altered HP-20 and HP-27 gene expression in nonhibernating versus hibernating chipmunks...
December 9, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29232016/characterization-of-h3-3-and-hira-expression-and-function-in-bovine-early-embryos
#4
Kun Zhang, Han Wang, Sandeep K Rajput, Joseph K Folger, George W Smith
Histone variant H3.3 is encoded by two distinct genes, H3F3A and H3F3B, that are closely associated with actively transcribed genes. H3.3 replacement is continuous and essential for maintaining correct chromatin structure during mouse oogenesis. Upon fertilization, H3.3 is incorporated to parental chromatin, and is required for blastocyst formation in mice. The H3.3 exchange process is facilitated by the chaperone HIRA, particularly during zygote development. We previously demonstrated that H3.3 is required for bovine early embryonic development; here, we explored the mechanisms of its functional requirement...
December 12, 2017: Molecular Reproduction and Development
https://www.readbyqxmd.com/read/29230532/rna-mediated-transgenerational-inheritance-in-ciliates-and-plants
#5
REVIEW
Zachary T Neeb, Mariusz Nowacki
In the age of next-generation sequencing (NGS) and with the availability of whole sequenced genomes and epigenomes, some attention has shifted from purely sequence-based studies to those of heritable epigenetic modifications. Transgenerational inheritance can be defined as heritable changes to the state of DNA that may be passed on to subsequent generations without alterations to the underlying DNA sequence. Although this phenomenon has been extensively studied in many systems, studies of transgenerational inheritance in mammals and other higher-level eukaryotes may be complicated by the fact that many epigenetic marks are reprogrammed during sexual reproduction...
December 11, 2017: Chromosoma
https://www.readbyqxmd.com/read/29228602/fbxw8-dependent-degradation-of-mrfap1-in-anaphase-controls-mitotic-cell-death
#6
Duan-Zhuo Li, Shun-Fang Liu, Lan Zhu, Yu-Xing Wang, Yi-Xiang Chen, Jie Liu, Gang Hu, Xin Yu, Jian Li, Jin Zhang, Zhi-Xiang Wu, Han Lu, Wei Liu, Bin Liu
Mof4 family associated protein 1 (MRFAP1) is a 14 kDa nuclear protein, which involves in maintaining normal histone modification levels by negatively regulating recruitment of the NuA4 (nucleosome acetyltransferase of H4) histone acetyltransferase complex to chromatin. MRFAP1 has been identified as one of the most up-regulated proteins after NEDD8 (neural precursor cell expressed developmentally down-regulated 8) inhibition in multiple human cell lines. However, the biological function of MRFAP1 and the E3 ligase that targets MRFAP1 for destruction remain mysterious...
November 14, 2017: Oncotarget
https://www.readbyqxmd.com/read/29228394/the-psychiatric-risk-gene-transcription-factor-4-tcf4-regulates-neurodevelopmental-pathways-associated-with-schizophrenia-autism-and-intellectual-disability
#7
Marc P Forrest, Matthew J Hill, David H Kavanagh, Katherine E Tansey, Adrian J Waite, Derek J Blake
Background: Common genetic variants in and around the gene encoding transcription factor 4 (TCF4) are associated with an increased risk of schizophrenia. Conversely, rare damaging TCF4 mutations cause Pitt-Hopkins syndrome and have also been found in individuals with intellectual disability (ID) and autism spectrum disorder (ASD). Methods: Chromatin immunoprecipitation and next generation sequencing were used to identify the genomic targets of TCF4. These data were integrated with expression, epigenetic and disease gene sets using a range of computational tools...
December 8, 2017: Schizophrenia Bulletin
https://www.readbyqxmd.com/read/29227285/shifts-in-podocyte-histone-h3k27me3-regulate-mouse-and-human-glomerular-disease
#8
Syamantak Majumder, Karina Thieme, Sri N Batchu, Tamadher A Alghamdi, Bridgit B Bowskill, M Golam Kabir, Youan Liu, Suzanne L Advani, Kathryn E White, Laurette Geldenhuys, Karthik K Tennankore, Penelope Poyah, Ferhan S Siddiqi, Andrew Advani
Histone protein modifications control fate determination during normal development and dedifferentiation during disease. Here, we set out to determine the extent to which dynamic changes to histones affect the differentiated phenotype of ordinarily quiescent adult glomerular podocytes. To do this, we examined the consequences of shifting the balance of the repressive histone H3 lysine 27 trimethylation (H3K27me3) mark in podocytes. Adriamycin nephrotoxicity and subtotal nephrectomy (SNx) studies indicated that deletion of the histone methylating enzyme EZH2 from podocytes decreased H3K27me3 levels and sensitized mice to glomerular disease...
December 11, 2017: Journal of Clinical Investigation
https://www.readbyqxmd.com/read/29225971/biochemical-analysis-of-histone-succinylation
#9
Atsushi Yokoyama, Shogo Katsura, Akira Sugawara
Posttranslational modification (PTM) of proteins is used to regulate protein activity and stability. Histone PTMs are regarded as some of the most important, as they can directly regulate gene expression through chromatin reorganization. Recently, histone proteins were found to undergo succinylation, adding to other well-known PTMs such as acetylation, methylation, and phosphorylation. However, there is little information regarding the enzyme which catalyzes histone lysine succinylation. In fact, it is unclear whether this reaction is enzymatic...
2017: Biochemistry Research International
https://www.readbyqxmd.com/read/29224150/bisulphite-sequencing-of-chromatin-immunoprecipitated-dna-bischip-seq
#10
Clare Stirzaker, Jenny Z Song, Aaron L Statham, Susan J Clark
Epigenetic regulation plays a critical role in gene expression, cellular differentiation, and disease. There is a complex interplay between the different layers of epigenetic information, including DNA methylation, nucleosome positions, histone modifications, histone variants, and other important epigenetic regulators. The different modifications do not act independently of each other and their relationship plays an important role in governing the regulation of the epigenome. Of these, DNA methylation is the best-studied epigenetic modification in mammals...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29224136/a-summary-of-the-biological-processes-disease-associated-changes-and-clinical-applications-of-dna-methylation
#11
Gitte Brinch Andersen, Jörg Tost
DNA methylation at cytosines followed by guanines, CpGs, forms one of the multiple layers of epigenetic mechanisms controlling and modulating gene expression through chromatin structure. It closely interacts with histone modifications and chromatin remodeling complexes to form the local genomic and higher-order chromatin landscape. DNA methylation is essential for proper mammalian development, crucial for imprinting and plays a role in maintaining genomic stability. DNA methylation patterns are susceptible to change in response to environmental stimuli such as diet or toxins, whereby the epigenome seems to be most vulnerable during early life...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29222117/pre-mrna-processing-includes-n6-methylation-of-adenosine-residues-that-are-retained-in-mrna-exons-and-the-fallacy-of-rna-epigenetics
#12
Robert B Darnell, Shengdong Ke, James E Darnell
By using a cell fraction technique that separates chromatin associated nascent RNA, newly completed nucleoplasmic mRNA and cytoplasmic mRNA, we have shown that residues in exons are methylated (m6A) in nascent pre-mRNA and remain methylated in the same exonic residues in nucleoplasmic and cytoplasmic mRNA. Thus, there is no evidence of a substantial degree of demethylation in mRNA exons that would correspond to so-called "epigenetic" demethylation. The turnover rate of mRNA molecules is faster depending on m6A content in HeLa cell mRNA suggesting specification of mRNA stability may be the major role of m6A exon modification...
December 8, 2017: RNA
https://www.readbyqxmd.com/read/29222089/core-binding-factor-%C3%AE-and-runx-transcription-factors-promote-adaptive-natural-killer-cell-responses
#13
Moritz Rapp, Colleen M Lau, Nicholas M Adams, Orr-El Weizman, Timothy E O'Sullivan, Clair D Geary, Joseph C Sun
Natural killer (NK) cells are innate lymphocytes that have features of adaptive immunity such as clonal expansion and generation of long-lived memory. Interleukin-12 (IL-12) signaling through its downstream transcription factor signal transducer and activator of transcription 4 (STAT4) is required for the generation of memory NK cells after expansion. We identify gene loci that are highly enriched for STAT4 binding using chromatin immunoprecipitation sequencing for STAT4 and the permissive histone mark H3K4me3 in activated NK cells...
December 8, 2017: Science Immunology
https://www.readbyqxmd.com/read/29221727/epigenetic-mechanisms-in-developmental-neurotoxicity
#14
REVIEW
M Raciti, S Ceccatelli
The constant interplay between environment (including both exogenous and endogenous factors) and epigenome (defined as the combination of chromatin, its covalent modifications and noncoding RNAs) triggers epigenetic events that, by modulating gene expression, capture information about changes in the environment. In this mini review, we will focus on the neurodevelopmental implications of exposure to adverse prenatal milieu with emphasis on mechanistic and functional aspects. Several neurotoxic insults have been shown to affect epigenetics with negative consequences on the development of the nervous system; among them are methylmercury, lead, arsenic and cadmium, as well as excess of glucocorticoids...
December 5, 2017: Neurotoxicology and Teratology
https://www.readbyqxmd.com/read/29220657/hnrnpk-recruits-pcgf3-5-prc1-to-the-xist-rna-b-repeat-to-establish-polycomb-mediated-chromosomal-silencing
#15
Greta Pintacuda, Guifeng Wei, Chloë Roustan, Burcu Anil Kirmizitas, Nicolae Solcan, Andrea Cerase, Alfredo Castello, Shabaz Mohammed, Benoît Moindrot, Tatyana B Nesterova, Neil Brockdorff
The Polycomb-repressive complexes PRC1 and PRC2 play a key role in chromosome silencing induced by the non-coding RNA Xist. Polycomb recruitment is initiated by the PCGF3/5-PRC1 complex, which catalyzes chromosome-wide H2A lysine 119 ubiquitylation, signaling recruitment of other PRC1 complexes, and PRC2. However, the molecular mechanism for PCGF3/5-PRC1 recruitment by Xist RNA is not understood. Here we define the Xist RNA Polycomb Interaction Domain (XR-PID), a 600 nt sequence encompassing the Xist B-repeat element...
December 7, 2017: Molecular Cell
https://www.readbyqxmd.com/read/29220647/snapshot-lysine-methylation-beyond-histones
#16
Kyle K Biggar, Zhentian Wang, Shawn S-C Li
Lysine methylation is a prevalent post-translational modification (PTM) used by the cell to reversibly regulate protein function. Although it has been extensively studied in the context of histones and the associated chromatin, the remaining methyllysine proteome remains largely unexplored. This SnapShot provides an overview of the current state of lysine methylation research and its emergence as a dynamic PTM occurring on histone and non-histone proteins.
December 7, 2017: Molecular Cell
https://www.readbyqxmd.com/read/29217127/epigenome-in-early-mammalian-development-inheritance-reprogramming-and-establishment
#17
REVIEW
Qianhua Xu, Wei Xie
Drastic epigenetic reprogramming takes place during preimplantation development, leading to the conversion of terminally differentiated gametes to a totipotent embryo. Deficiencies in remodeling of the epigenomes can cause severe developmental defects, including embryonic lethality. However, how chromatin modifications and chromatin organization are reprogrammed upon fertilization in mammals has long remained elusive. Here, we review recent progress in understanding how the epigenome is dynamically regulated during early mammalian development...
December 4, 2017: Trends in Cell Biology
https://www.readbyqxmd.com/read/29214996/the-role-of-cdx2-as-a-lineage-specific-transcriptional-repressor-for-pluripotent-network-during-the-first-developmental-cell-lineage-segregation
#18
Daosheng Huang, Guoji Guo, Ping Yuan, Amy Ralston, Lingang Sun, Mikael Huss, Tapan Mistri, Luca Pinello, Huck Hui Ng, Guocheng Yuan, Junfeng Ji, Janet Rossant, Paul Robson, Xiaoping Han
The first cellular differentiation event in mouse development leads to the formation of the blastocyst consisting of the inner cell mass (ICM) and trophectoderm (TE). The transcription factor CDX2 is required for proper TE specification, where it promotes expression of TE genes, and represses expression of Pou5f1 (OCT4). However its downstream network in the developing embryo is not fully characterized. Here, we performed high-throughput single embryo qPCR analysis in Cdx2 null embryos to identify CDX2-regulated targets in vivo...
December 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29213033/-epigenetic-modifications-of-chromatin-in-epilepsy-a-potential-mechanism-of-pharmacoresistance
#19
L S Sokhranyaeva, V A Aniol, N V Gulyaeva
Pharmacoresistance in epilepsy is an important problem from both clinical and fundamental perspectives. The existent hypotheses of pharmacoresistance are based on long term plastic rebuilding of the epileptic brain. One of potential mechanisms mediating such protracted changes are alterations of gene expression induced by epigenetic modifications of chromatin in brain cells of epileptic patients. Recently, changes in DNA methylation and histone post-translational modifications were reported in brain tissues of patients with pharmacoresistant epilepsy...
2017: Zhurnal Nevrologii i Psikhiatrii Imeni S.S. Korsakova
https://www.readbyqxmd.com/read/29212285/bancr-a-novel-oncogenic-long-non-coding-rna-in-human-cancers
#20
REVIEW
Yifan Zou, Jianfa Li, Yincong Chen, Huizhong Xiao, Fuyou Zhang, Dan Yu, Kewang Luo
Long non-coding RNAs account for large proportion of non-coding transcripts in human genomes. Though they lack of open reading framework and cannot encode protein, they can control endogenous gene expression though regulating cell life activities. They serve as transcriptional modulator, posttranscriptional processor, chromatin remodeler and splicing regulator during the process of gene modification. Moreover, long non-coding RNAs were regarded as potential tumor markers for cancer diagnosis and prognosis. BANCR was identified as a cancer-promoting long non-coding RNA in melanoma tissues...
November 7, 2017: Oncotarget
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