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https://www.readbyqxmd.com/read/29667547/new-markers-for-predicting-fertility-of-the-male-gametes-in-the-post-genomic-age
#1
Savina Dipresa, Luca De Toni, Carlo Foresta, Andrea Garolla
A number of test have been proposed to assess male fertility potential, ranging from routine testing by light microscopic method for evaluating semen samples, to screening test for DNA integrity aimed to look at sperm chromatin abnormalities. Spermatozoa are an extremely differentiated cell, they have critical functions for embryo development and heredity, in addiction to delivering a haploid paternal genome to the oocyte. Towards this goal certain requirements must always be met. The ability of spermatozoa to perform its reproductive function taking place in the spermatogenesis, a highly specialized process depending on multiple factors with effect on male fertility...
April 18, 2018: Protein and Peptide Letters
https://www.readbyqxmd.com/read/29667342/middle-down-characterization-of-the-cell-cycle-dependence-of-histone-h4-post-translational-modifications-and-proteoforms
#2
Tingting Jiang, Michael E Hoover, Matthew V Holt, Michael A Freitas, Alan G Marshall, Nicolas L Young
Post-translational modifications (PTMs) of histones are important epigenetic regulatory mechanisms that are often dysregulated in cancer. We employ middle-down proteomics to investigate the PTMs and proteoforms of histone H4 during cell cycle progression. We use pH gradient weak cation exchange-hydrophilic interaction liquid chromatography (WCX-HILIC) for on-line liquid chromatography-mass spectrometry analysis to separate and analyze the proteoforms of histone H4. This provides enhanced separation of proteoforms, including positional isomers, and simplifies downstream data analysis...
April 17, 2018: Proteomics
https://www.readbyqxmd.com/read/29666907/three-dimensional-analysis-of-nuclear-heterochromatin-distribution-during-early-development-in-the-rabbit
#3
Amélie Bonnet-Garnier, Kiên Kiêu, Tiphaine Aguirre-Lavin, Krisztina Tar, Pierre Flores, Zichuan Liu, Nathalie Peynot, Martine Chebrout, András Dinnyés, Véronique Duranthon, Nathalie Beaujean
Changes to the spatial organization of specific chromatin domains such as constitutive heterochromatin have been studied extensively in somatic cells. During early embryonic development, drastic epigenetic reprogramming of both the maternal and paternal genomes, followed by chromatin remodeling at the time of embryonic genome activation (EGA), have been observed in the mouse. Very few studies have been performed in other mammalian species (human, bovine, or rabbit) and the data are far from complete. During this work, we studied the three-dimensional organization of pericentromeric regions during the preimplantation period in the rabbit using specific techniques (3D-FISH) and tools (semi-automated image analysis)...
April 18, 2018: Chromosoma
https://www.readbyqxmd.com/read/29666150/epigenetics-and-epitranscriptomics-in-temporal-patterning-of-cortical-neural-progenitor-competence
#4
REVIEW
Ki-Jun Yoon, Caroline Vissers, Guo-Li Ming, Hongjun Song
During embryonic brain development, neural progenitor/stem cells (NPCs) sequentially give rise to different subtypes of neurons and glia via a highly orchestrated process. To accomplish the ordered generation of distinct progenies, NPCs go through multistep transitions of their developmental competence. The molecular mechanisms driving precise temporal coordination of these transitions remains enigmatic. Epigenetic regulation, including changes in chromatin structures, DNA methylation, and histone modifications, has been extensively investigated in the context of cortical neurogenesis...
April 17, 2018: Journal of Cell Biology
https://www.readbyqxmd.com/read/29666116/critical-influences-on-the-pathogenesis-of-follicular-lymphoma
#5
Ralf Küppers, Freda K Stevenson
The development of follicular lymphoma (FL) from a founder B cell with an upregulation of BCL2, via the t(14;18) translocation, to a proliferating clone, poised to undergo further transformation to an aggressive lymphoma, illustrates the opportunistic Darwinian process of tumorigenesis. Protection against apoptosis allows an innocent cell to persist and divide, with dangerous accumulation of further mutational changes, commonly involving inactivation of chromatin-modifying genes. But this is not all. FL cells reflect normal B cells in relying on expression of surface Ig...
April 17, 2018: Blood
https://www.readbyqxmd.com/read/29665865/integrative-analysis-reveals-functional-and-regulatory-roles-of-h3k79me2-in-mediating-alternative-splicing
#6
Tianbao Li, Qi Liu, Nick Garza, Steven Kornblau, Victor X Jin
BACKGROUND: Accumulating evidence suggests alternative splicing (AS) is a co-transcriptional splicing process not only controlled by RNA-binding splicing factors, but also mediated by epigenetic regulators, such as chromatin structure, nucleosome density, and histone modification. Aberrant AS plays an important role in regulating various diseases, including cancers. METHODS: In this study, we integrated AS events derived from RNA-seq with H3K79me2 ChIP-seq data across 34 different normal and cancer cell types and found the higher enrichment of H3K79me2 in two AS types, skipping exon (SE) and alternative 3' splice site (A3SS)...
April 17, 2018: Genome Medicine
https://www.readbyqxmd.com/read/29665673/cooperative-instruction-of-signaling-and-metabolic-pathways-on-the-epigenetic-landscape
#7
Jung-Ae Kim
Cells cope with diverse intrinsic and extrinsic stimuli in order to make adaptations for survival. The epigenetic landscape plays a crucial role in cellular adaptation, as it integrates the information generated from stimuli. Signaling pathways induced by stimuli communicate with chromatin to change the epigenetic landscape through regulation of epigenetic modifiers. Metabolic dynamics altered by these stimuli also affect the activity of epigenetic modifiers. Here, I review the current understanding of epigenetic regulation via signaling and metabolic pathways...
April 11, 2018: Molecules and Cells
https://www.readbyqxmd.com/read/29660196/genome-wide-hi-c-analysis-reveals-extensive-hierarchical-chromatin-interactions-in-rice
#8
Qianli Dong, Ning Li, Xiaochong Li, Zan Yuan, Dejian Xie, Xiaofei Wang, Jianing Li, Yanan Yu, Jinbin Wang, Baoxu Ding, Zhibin Zhang, Changping Li, Yao Bian, Ai Zhang, Ying Wu, Bao Liu, Lei Gong
The non-random spatial packing of chromosomes in the nucleus plays critical roles in orchestrating gene expression and genome function. Here, we present a Hi-C analysis of the chromatin interaction patterns in rice (Oryza sativa L.) at hierarchical architectural levels. We confirm that rice chromosomes occupy their own territories with certain preferential inter-chromosomal associations. Moderate compartment delimitation and extensive TADs (Topologically Associated Domains) were determined to be associated with heterogeneous genomic compositions and epigenetic marks in the rice genome...
April 16, 2018: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/29660033/phosphorylation-of-xeroderma-pigmentosum-group-c-regulates-ultraviolet-induced-dna-damage-repair
#9
Palak Shah, Baozhong Zhao, Lei Qiang, Yu-Ying He
Nucleotide excision repair (NER) is the most versatile DNA repair system that removes bulky DNA damage induced by various endogenous and exogenous factors, including UV radiation. Defects in NER can lead to the xeroderma pigmentosum (XP) syndrome, mainly characterized by increased carcinogenesis in the skin. The function of NER factors, including xeroderma pigmentosum group C (XPC), can be regulated by post-translational modifications such as ubiquitination. However, the role of phosphorylation in XPC function remains unknown...
April 6, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29659982/transcription-start-site-analysis-reveals-widespread-divergent-transcription-in-d-melanogaster-and-core-promoter-encoded-enhancer-activities
#10
Sarah Rennie, Maria Dalby, Marta Lloret-Llinares, Stylianos Bakoulis, Christian Dalager Vaagensø, Torben Heick Jensen, Robin Andersson
Mammalian gene promoters and enhancers share many properties. They are composed of a unified promoter architecture of divergent transcripton initiation and gene promoters may exhibit enhancer function. However, it is currently unclear how expression strength of a regulatory element relates to its enhancer strength and if the unifying architecture is conserved across Metazoa. Here we investigate the transcription initiation landscape and its associated RNA decay in Drosophila melanogaster. We find that the majority of active gene-distal enhancers and a considerable fraction of gene promoters are divergently transcribed...
April 6, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29659013/dietary-fat-and-fiber-interact-to-uniquely-modify-global-histone-post-translational-epigenetic-programming-in-a-rat-colon-cancer-progression-model
#11
Karen Triff, Mathew W McLean, Evelyn Callaway, Jennifer Goldsby, Ivan Ivanov, Robert S Chapkin
Dietary fermentable fiber generates short-chain fatty acids (SCFA), e.g., butyrate, in the colonic lumen which serves as a chemoprotective histone deacetylase inhibitor and/or as an acetylation substrate for histone acetylases. In addition, n-3 polyunsaturated fatty acids (n-3 PUFA) in fish oil can affect the chromatin landscape by acting as ligands for tumor suppressive nuclear receptors. In an effort to gain insight into the global dimension of post-translational modification of histones (including H3K4me3 and H3K9ac) and clarify the chemoprotective impact of dietary bioactive compounds on transcriptional control in a preclinical model of colon cancer, we generated high-resolution genome-wide RNA (RNA-Seq) and "chromatin-state" (H3K4me3-seq and H3K9ac-seq) maps for intestinal (epithelial colonocytes) crypts in rats treated with a colon carcinogen and fed diets containing bioactive (i) fish oil, (ii) fermentable fiber (a rich source of SCFA), (iii) a combination of fish oil plus pectin or (iv) control, devoid of fish oil or pectin...
April 16, 2018: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/29651103/versatile-and-efficient-chromatin-pull-down-methodology-based-on-dna-triple-helix-formation
#12
Asako Isogawa, Robert P Fuchs, Shingo Fujii
The goal of present paper is to develop a reliable DNA-based method for isolation of protein complexes bound to DNA (Isolation of DNA Associated Proteins: IDAP). We describe a robust and versatile procedure to pull-down chromatinized DNA sequences-of-interest by formation of a triple helix between a sequence tag present in the DNA and a complementary triple helix forming oligonucleotide (TFO) coupled to a desthiobiotin residue. Following optimization to insure efficient recovery of native plasmids via TFO probe in vitro, the procedure is shown to work under various experimental situations...
April 12, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29651053/targeted-in-situ-genome-wide-profiling-with-high-efficiency-for-low-cell-numbers
#13
Peter J Skene, Jorja G Henikoff, Steven Henikoff
Cleavage under targets and release using nuclease (CUT&RUN) is an epigenomic profiling strategy in which antibody-targeted controlled cleavage by micrococcal nuclease releases specific protein-DNA complexes into the supernatant for paired-end DNA sequencing. As only the targeted fragments enter into solution, and the vast majority of DNA is left behind, CUT&RUN has exceptionally low background levels. CUT&RUN outperforms the most widely used chromatin immunoprecipitation (ChIP) protocols in resolution, signal-to-noise ratio and depth of sequencing required...
May 2018: Nature Protocols
https://www.readbyqxmd.com/read/29649476/h2a-z-containing-nucleosomes-are-evicted-to-activate-atmyb44-transcription-in-response-to-salt-stress
#14
Nguyen Hoai Nguyen, Jong-Joo Cheong
Transcripts of the Arabidopsis transcription factor gene, AtMYB44, accumulate rapidly to mediate a tolerance mechanism in response to salt stress. The AtMYB44 promoter is activated by salt stress, as illustrated in AtMYB44pro::GUS transgenic plants. Chromatin immunoprecipitation (ChIP) assays revealed that RNA polymerases were enriched on the AtMYB44 gene, especially on TSS-proximal regions, and nucleosome density was markedly reduced in the AtMYB44 gene-body region in response to salt stress. In addition, H2A...
April 9, 2018: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29648537/the-conformation-of-the-histone-h3-tail-inhibits-association-of-the-bptf-phd-finger-with-the-nucleosome
#15
Emma A Morrison, Samuel Bowerman, Kelli L Sylvers, Jeff Wereszczynski, Catherine A Musselman
Histone tails harbor a plethora of post-translational modifications that direct the function of chromatin regulators, which recognize them through effector domains. Effector domain/histone interactions have been broadly studied, but largely using peptide fragments of histone tails. Here, we extend these studies into the nucleosome context and find that the conformation adopted by the histone H3 tails is inhibitory to BPTF PHD finger binding. Using NMR spectroscopy and MD simulations, we show that the H3 tails interact robustly but dynamically with nucleosomal DNA, substantially reducing PHD finger association...
April 12, 2018: ELife
https://www.readbyqxmd.com/read/29643390/functional-crosstalk-between-histone-h2b-ubiquitylation-and-h2a-modifications-and-variants
#16
Felix Wojcik, Geoffrey P Dann, Leslie Y Beh, Galia T Debelouchina, Raphael Hofmann, Tom W Muir
Ubiquitylation of histone H2B at lysine residue 120 (H2BK120ub) is a prominent histone posttranslational modification (PTM) associated with the actively transcribed genome. Although H2BK120ub triggers several critical downstream histone modification pathways and changes in chromatin structure, less is known about the regulation of the ubiquitylation reaction itself, in particular with respect to the modification status of the chromatin substrate. Here we employ an unbiased library screening approach to profile the impact of pre-existing chromatin modifications on de novo ubiquitylation of H2BK120 by the cognate human E2:E3 ligase pair, UBE2A:RNF20/40...
April 11, 2018: Nature Communications
https://www.readbyqxmd.com/read/29642537/epigenetic-mechanisms-impacting-aging-a-focus-on-histone-levels-and-telomeres
#17
REVIEW
Shufei Song, F Brad Johnson
Aging and age-related diseases pose some of the most significant and difficult challenges to modern society as well as to the scientific and medical communities. Biological aging is a complex, and, under normal circumstances, seemingly irreversible collection of processes that involves numerous underlying mechanisms. Among these, chromatin-based processes have emerged as major regulators of cellular and organismal aging. These include DNA methylation, histone modifications, nucleosome positioning, and telomere regulation, including how these are influenced by environmental factors such as diet...
April 9, 2018: Genes
https://www.readbyqxmd.com/read/29626928/protein-protein-interactions-in-dna-base-excision-repair
#18
REVIEW
N A Moor, O I Lavrik
The system of base excision repair (BER) ensures correction of the most abundant DNA damages in mammalian cells and plays an important role in maintaining genome stability. Enzymes and protein factors participate in the multistage BER in a coordinated fashion, which ensures repair efficiency. The suggested coordination mechanisms are based on formation of protein complexes stabilized via either direct or indirect DNA-mediated interactions. The results of investigation of direct interactions of the proteins participating in BER with each other and with other proteins are outlined in this review...
April 2018: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/29625185/epigenetic-modifications-in-the-embryonic-and-induced-pluripotent-stem-cells
#19
Rasoul Godini, Haider Yabr Lafta, Hossein Fallahi
Epigenetic modifications are involved in global reprogramming of the cell transcriptome. Therefore, synchronized major shifts in the expression of many genes could be achieved through epigenetic changes. The regulation of gene expression could be implemented by different epigenetic events including histone modifications, DNA methylation and chromatin remodelling. Interestingly, it has been documented that reprogramming of somatic cells to induced pluripotent stem (iPS) cells is also a typical example of epigenetic modifications...
April 4, 2018: Gene Expression Patterns: GEP
https://www.readbyqxmd.com/read/29624717/sirt3-restricts-hbv-transcription-and-replication-via-epigenetic-regulation-of-cccdna-involving-suv39h1-and-setd1a-histone-methyltransferases
#20
Ji-Hua Ren, Jie-Li Hu, Sheng-Tao Cheng, Hai-Bo Yu, Vincent Kam Wai Wong, Betty Yuen Kwan Law, Yong-Feng Yang, Ying Huang, Yi Liu, Wei-Xian Chen, Xue-Fei Cai, Hua Tang, Yuan Hu, Wen-Lu Zhang, Xiang Liu, Quan-Xin Long, Li Zhou, Na-Na Tao, Hong-Zhong Zhou, Qiu-Xia Yang, Fang Ren, Lin He, Rui Gong, Ai-Long Huang, Juan Chen
Hepatitis B virus (HBV) infection remains a major health problem worldwide. Maintenance of the covalently closed circular DNA (cccDNA) which serves as a template for HBV RNA transcription is responsible for the failure of eradicating chronic HBV during current antiviral therapy. cccDNA is assembled with cellular histone proteins into chromatin, but little is known about the regulation of HBV chromatin by histone posttranslational modifications. In this study, we identified SIRT3 as a host factor restricting HBV transcription and replication by screening seven members of Sirtuin family which is the class III histone deacetylase...
April 6, 2018: Hepatology: Official Journal of the American Association for the Study of Liver Diseases
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