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https://www.readbyqxmd.com/read/29148792/proteomic-markers-of-the-functional-sperm-population-in-bovines-1-comparison-of-low-and-high-density-spermatozoa-following-cryopreservation
#1
Olivier D'Amours, Gilles Frenette, Sylvie Bourassa, Ezequiel Calvo, Patrick Blondin, Robert Sullivan
Mammalian semen contains a heterogeneous population of sperm cells. This heterogeneity results from variability in the complex processes of cell differentiation in the testis, biochemical modifications undergone by spermatozoa during transit along the male reproductive tract, interactions with secretions from accessory sex glands at ejaculation, and, in the context of reproductive technologies, in the ability of ejaculated spermatozoa to resist damage associated with freeze-thaw procedures. When submitted to density gradient centrifugation, ejaculated spermatozoa distribute themselves into two distinct populations: a low-density population characterized by low motility parameters, and a high-density population with high motility characteristics...
November 17, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/29114019/native-elongating-transcript-sequencing-reveals-global-anti-correlation-between-sense-and-antisense-nascent-transcription-in-fission-yeast
#2
Maxime Wery, Camille Gautier, Marc Descrimes, Mayuko Yoda, Hervé Vennin-Rendos, Valérie Migeot, Daniel Gautheret, Damien Hermand, Antonin Morillon
Antisense transcription can regulate sense gene expression. However, previous annotations of antisense transcription units have been based on detection of mature antisense long non-coding (aslnc)RNAs by RNA-Seq and/or micro-arrays, only giving a partial view of the antisense transcription landscape and incomplete molecular bases for antisense-mediated regulation. Here, we used Native Elongating Transcript sequencing to map genome-wide nascent antisense transcription in fission yeast. Strikingly, antisense transcription was detected for most protein-coding genes, correlating with low sense transcription, especially when overlapping the mRNA start site...
November 7, 2017: RNA
https://www.readbyqxmd.com/read/29106411/extrachromosomal-telomere-repeat-dna-is-linked-to-alt-development-via-cgas-sting-dna-sensing-pathway
#3
Yi-An Chen, Yi-Ling Shen, Hsuan-Yu Hsia, Yee-Peng Tiang, Tzu-Ling Sung, Liuh-Yow Chen
Extrachromosomal telomere repeat (ECTR) DNA is unique to cancer cells that maintain telomeres through the alternative lengthening of telomeres (ALT) pathway, but the role of ECTRs in ALT development remains elusive. We found that induction of ECTRs in normal human fibroblasts activated the cGAS-STING-TBK1-IRF3 signaling axis to trigger IFNβ production and a type I interferon response, resulting in cell-proliferation defects. In contrast, ALT cancer cells are commonly defective in sensing cytosolic DNA. We found that STING expression was inhibited in ALT cancer cell lines and transformed ALT cells...
November 6, 2017: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/29104064/a-chemical-proteomics-approach-to-reveal-direct-protein-protein-interactions-in-living-cells
#4
Ralph E Kleiner, Lisa E Hang, Kelly R Molloy, Brian T Chait, Tarun M Kapoor
Protein-protein interactions mediate essential cellular processes, however the detection of native interactions is challenging since they are often low affinity and context dependent. Here, we develop a chemical proteomics approach in vivo CLASPI [iCLASPI] (in vivo crosslinking-assisted and stable isotope labeling by amino acids in cell culture [SILAC]-based protein identification) relying upon photo-crosslinking, amber suppression, and SILAC-based quantitative proteomics to profile context-dependent protein-protein interactions in living cells...
October 25, 2017: Cell Chemical Biology
https://www.readbyqxmd.com/read/29053954/spt6-gets-in-the-way-of-polycomb-to-promote-esc-pluripotency
#5
François Robert
Despite expressing high levels of Polycomb group proteins, embryonic stem cells (ESCs) are refractory to H3K27 trimethylation, notably at super-enhancers regulating key pluripotency genes. In this issue of Molecular Cell, Wang et al. (2017) report that the histone chaperone Spt6 prevents H3K27 trimethylation of key ESC super-enhancers.
October 19, 2017: Molecular Cell
https://www.readbyqxmd.com/read/29036702/a-hyperdynamic-h3-3-nucleosome-marks-promoter-regions-in-pluripotent-embryonic-stem-cells
#6
Sharon Schlesinger, Binyamin Kaffe, Shai Melcer, Jose D Aguilera, Divya M Sivaraman, Tommy Kaplan, Eran Meshorer
Histone variants and their chaperones are key regulators of eukaryotic transcription, and are critical for normal development. The histone variant H3.3 has been shown to play important roles in pluripotency and differentiation, and although its genome-wide patterns have been investigated, little is known about the role of its dynamic turnover in transcriptional regulation. To elucidate the role of H3.3 dynamics in embryonic stem cell (ESC) biology, we generated mouse ESC lines carrying a single copy of a doxycycline (Dox)-inducible HA-tagged version of H3...
September 25, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29033324/the-elongation-factor-spt6-maintains-esc-pluripotency-by-controlling-super-enhancers-and-counteracting-polycomb-proteins
#7
A Hongjun Wang, Aster H Juan, Kyung Dae Ko, Pei-Fang Tsai, Hossein Zare, Stefania Dell'Orso, Vittorio Sartorelli
Spt6 coordinates nucleosome dis- and re-assembly, transcriptional elongation, and mRNA processing. Here, we report that depleting Spt6 in embryonic stem cells (ESCs) reduced expression of pluripotency factors, increased expression of cell-lineage-affiliated developmental regulators, and induced cell morphological and biochemical changes indicative of ESC differentiation. Selective downregulation of pluripotency factors upon Spt6 depletion may be mechanistically explained by its enrichment at ESC super-enhancers, where Spt6 controls histone H3K27 acetylation and methylation and super-enhancer RNA transcription...
October 19, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28983190/ion-mobility-mass-spectrometry-reveals-evidence-of-specific-complex-formation-between-human-histone-deacetylase-8-and-poly-r-c-binding-protein-1
#8
Shuai Niu, Byung Chul Kim, Carol A Fierke, Brandon T Ruotolo
Histone deacetylase 8, part of a broad class of proteins responsible for regulating transcription and many other cellular processes and directly linked to a host of human disease through its mis-function, has been canonically described as a zinc-based mettalo-enzyme for many years. Recent evidence, however, has linked this protein to iron incorporation, loaded through transient interactions with the poly r(C)-binding protein 1, a metallo-chaperone and storage protein. In this report, we construct and deploy an electrospray-mass spectrometry based assay aimed at quantifying the interaction strength between these two weakly-associated proteins, as well as the zinc and iron associated form of the histone deacetylase...
September 2017: International Journal of Mass Spectrometry
https://www.readbyqxmd.com/read/28982979/a-simple-and-versatile-system-for-the-atp-dependent-assembly-of-chromatin
#9
Mai T Khuong, Jia Fei, Grisel Cruz-Becerra, James T Kadonaga
Chromatin is the natural form of DNA in the eukaryotic nucleus, and is the substrate for diverse biological phenomena. The functional analysis of these processes would ideally be carried out with nucleosomal templates that are assembled with customized core histones, DNA sequences, and chromosomal proteins. Here we report a simple, reliable, and versatile method for the ATP-dependent assembly of evenly-spaced nucleosome arrays. This minimal chromatin assembly system comprises the Drosophila nucleoplasmin-like protein (dNLP) histone chaperone, the imitation switch (ISWI) ATP-driven motor protein, core histones, template DNA, and ATP...
October 5, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28981850/histone-chaperone-hira-deposits-histone-h3-3-onto-foreign-viral-dna-and-contributes-to-anti-viral-intrinsic-immunity
#10
Taranjit Singh Rai, Mandy Glass, John J Cole, Mohammad I Rather, Morgan Marsden, Matthew Neilson, Claire Brock, Ian R Humphreys, Roger D Everett, Peter D Adams
The HIRA histone chaperone complex deposits histone H3.3 into nucleosomes in a DNA replication- and sequence-independent manner. As herpesvirus genomes enter the nucleus as naked DNA, we asked whether the HIRA chaperone complex affects herpesvirus infection. After infection of primary cells with HSV or CMV, or transient transfection with naked plasmid DNA, HIRA re-localizes to PML bodies, sites of cellular anti-viral activity. HIRA co-localizes with viral genomes, binds to incoming viral and plasmid DNAs and deposits histone H3...
November 16, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28978835/effect-of-mutation-on-diagnosis-risk-stratification-and-treatment-decisions-in-philadelphia-negative-myeloproliferative-neoplasms
#11
Keita Kirito
Since the discovery of the activating mutation of JAK2, known as JAK2V617F, our understanding of mutation profiles, and the biological significance of this mutation in Philadelphia-negative (Ph-) MPNs has drastically changed over the last decade. Mutations of the thrombopoietin receptor MPL and chaperone protein calreticulin gene also induce aberrant activation of JAK and downstream molecules, including STAT proteins, and contribute to the development of MPNs. Mutations of the genes JAK2, MPL, and calreticulin are referred to as "driver mutations" for MPNs...
2017: [Rinshō Ketsueki] the Japanese Journal of Clinical Hematology
https://www.readbyqxmd.com/read/28973436/dual-function-of-swc5-in-swr-remodeling-atpase-activation-and-histone-h2a-eviction
#12
Lu Sun, Ed Luk
The chromatin remodeler SWR deposits histone H2A.Z at promoters and other regulatory sites via an ATP-driven histone exchange reaction that replaces nucleosomal H2A with H2A.Z. Simultaneous binding of SWR to both H2A nucleosome and free H2A.Z induces SWR ATPase activity and engages the histone exchange mechanism. Swc5 is a conserved subunit of the 14-polypeptide SWR complex that is required for the histone exchange reaction, but its molecular role is unknown. We found that Swc5, although not required for substrate binding, is required for SWR ATPase stimulation, suggesting that Swc5 is required to couple substrate recognition to ATPase activation...
September 29, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28966044/hdac6-suppresses-age-dependent-ectopic-fat-accumulation-by-maintaining-the-proteostasis-of-plin2-in-drosophila
#13
Yan Yan, Hao Wang, Minling Hu, Lifen Jiang, Yang Wang, Pingsheng Liu, Xuehong Liang, Jiyong Liu, Changqing Li, Anya Lindström-Battle, Sin Man Lam, Guanghou Shui, Wu-Min Deng, Renjie Jiao
Age-dependent ectopic fat accumulation (EFA) in animals contributes to the progression of tissue aging and diseases such as obesity, diabetes, and cancer. However, the primary causes of age-dependent EFA remain largely elusive. Here, we characterize the occurrence of age-dependent EFA in Drosophila and identify HDAC6, a cytosolic histone deacetylase, as a suppressor of EFA. Loss of HDAC6 leads to significant age-dependent EFA, lipid composition imbalance, and reduced animal longevity on a high-fat diet. The EFA and longevity phenotypes are ameliorated by a reduction of the lipid-droplet-resident protein PLIN2...
October 9, 2017: Developmental Cell
https://www.readbyqxmd.com/read/28943310/asf1a-promotes-non-homologous-end-joining-repair-by-facilitating-phosphorylation-of-mdc1-by-atm-at-double-strand-breaks
#14
Kyung Yong Lee, Jun-Sub Im, Etsuko Shibata, Anindya Dutta
Double-strand breaks (DSBs) of DNA in eukaryotic cells are predominantly repaired by non-homologous end joining (NHEJ). The histone chaperone anti-silencing factor 1a (ASF1a) interacts with MDC1 and is recruited to sites of DSBs to facilitate the interaction of phospho-ATM with MDC1 and phosphorylation of MDC1, which are required for the recruitment of RNF8/RNF168 histone ubiquitin ligases. Thus, ASF1a deficiency reduces histone ubiquitination at DSBs, decreasing the recruitment of 53BP1, and decreases NHEJ, rendering cells more sensitive to DSBs...
October 5, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28934510/caf-1-induced-oligomerization-of-histones-h3-h4-and-mutually-exclusive-interactions-with-asf1-guide-h3-h4-transitions-among-histone-chaperones-and-dna
#15
Wallace H Liu, Sarah C Roemer, Alex M Port, Mair E A Churchill
No abstract text is available yet for this article.
September 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28915577/vorinostat-suppresses-hypoxia-signaling-by-modulating-nuclear-translocation-of-hypoxia-inducible-factor-1-alpha
#16
Chao Zhang, Chunzhang Yang, Michael J Feldman, Herui Wang, Ying Pang, Dominic M Maggio, Dongwang Zhu, Cody L Nesvick, Pauline Dmitriev, Petra Bullova, Prashant Chittiboina, Roscoe O Brady, Karel Pacak, Zhengping Zhuang
Histone deacetylase inhibitors (HDACis) are a potent class of tumor-suppressive agents traditionally believed to exert their effects through loosening tightly-wound chromatin resulting in de-inhibition of various tumor suppressive genes. Recent literature however has shown altered intratumoral hypoxia signaling with HDACi administration not attributable to changes in chromatin structure. We sought to determine the precise mechanism of HDACi-mediated hypoxia signaling attenuation using vorinostat (SAHA), an FDA-approved class I/IIb/IV HDACi...
August 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/28910138/hsp90-inhibition-and-cellular-stress-elicits-phenotypic-plasticity-in-hematopoietic-differentiation
#17
Abdalla A Lawag, Jennifer M Napper, Caroline A Hunter, Nickolas A Bacon, Seth Deskins, Manaf El-Hamdani, Sarah-Leigh Govender, Emine C Koc, Vincent E Sollars
Cancer cells exist in a state of Darwinian selection using mechanisms that produce changes in gene expression through genetic and epigenetic alteration to facilitate their survival. Cellular plasticity, or the ability to alter cellular phenotype, can assist in survival of premalignant cells as they progress to full malignancy by providing another mechanism of adaptation. The connection between cellular stress and the progression of cancer has been established, although the details of the mechanisms have yet to be fully elucidated...
October 2017: Cellular Reprogramming
https://www.readbyqxmd.com/read/28883625/redundant-functions-for-nap1-and-chz1-in-h2a-z-deposition
#18
Raghuvar Dronamraju, Srinivas Ramachandran, Deepak K Jha, Alexander T Adams, Julia V DiFiore, Michael A Parra, Nikolay V Dokholyan, Brian D Strahl
H2A.Z is a histone H2A variant that contributes to transcriptional regulation, DNA damage response and limits heterochromatin spreading. In Saccharomyces cerevisiae, H2A.Z is deposited by the SWR-C complex, which relies on several histone chaperones including Nap1 and Chz1 to deliver H2A.Z-H2B dimers to SWR-C. However, the mechanisms by which Nap1 and Chz1 cooperate to bind H2A.Z and their contribution to H2A.Z deposition in chromatin is not well understood. Using structural modeling and molecular dynamics simulations, we identify a series of H2A...
September 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28856239/histone-hypervariants-h2a-z-1-and-h2a-z-2-play-independent-and-context-specific-roles-in-neuronal-activity-induced-transcription-of-arc-arg3-1-and-other-immediate-early-genes
#19
Carissa J Dunn, Pushpita Sarkar, Emma R Bailey, Shannon Farris, Meilan Zhao, James M Ward, Serena M Dudek, Ramendra N Saha
The histone variant H2A.Z is an essential and conserved regulator of eukaryotic gene transcription. However, the exact role of this histone in the transcriptional process remains perplexing. In vertebrates, H2A.Z has two hypervariants, H2A.Z.1 and H2A.Z.2, that have almost identical sequences except for three amino acid residues. Due to such similarity, functional specificity of these hypervariants in neurobiological processes, if any, remain largely unknown. In this study with dissociated rat cortical neurons, we asked if H2A...
July 2017: ENeuro
https://www.readbyqxmd.com/read/28840237/orchestrating-the-specific-assembly-of-centromeric-nucleosomes
#20
Ewelina Zasadzińska, Daniel R Foltz
Centromeres are chromosomal loci that are defined epigenetically in most eukaryotes by incorporation of a centromere-specific nucleosome in which the canonical histone H3 variant is replaced by Centromere Protein A (CENP-A). Therefore, the assembly and propagation of centromeric nucleosomes are critical for maintaining centromere identify and ensuring genomic stability. Centromeres direct chromosome segregation (during mitosis and meiosis) by recruiting the constitutive centromere-associated network of proteins throughout the cell cycle that in turn recruits the kinetochore during mitosis...
2017: Progress in Molecular and Subcellular Biology
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