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https://www.readbyqxmd.com/read/28934504/accumulation-of-histone-variant-h3-3-with-age-is-associated-with-profound-changes-in-the-histone-methylation-landscape
#1
Andrey Tvardovskiy, Veit Schwämmle, Stefan J Kempf, Adelina Rogowska-Wrzesinska, Ole N Jensen
Deposition of replication-independent histone variant H3.3 into chromatin is essential for many biological processes, including development and reproduction. Unlike replication-dependent H3.1/2 isoforms, H3.3 is expressed throughout the cell cycle and becomes enriched in postmitotic cells with age. However, lifelong dynamics of H3 variant replacement and the impact of this process on chromatin organization remain largely undefined. Using quantitative middle-down proteomics we demonstrate that H3.3 accumulates to near saturation levels in the chromatin of various mouse somatic tissues by late adulthood...
September 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28934481/automatic-identification-of-informative-regions-with-epigenomic-changes-associated-to-hematopoiesis
#2
Enrique Carrillo-de-Santa-Pau, David Juan, Vera Pancaldi, Felipe Were, Ignacio Martin-Subero, Daniel Rico, Alfonso Valencia
Hematopoiesis is one of the best characterized biological systems but the connection between chromatin changes and lineage differentiation is not yet well understood. We have developed a bioinformatic workflow to generate a chromatin space that allows to classify 42 human healthy blood epigenomes from the BLUEPRINT, NIH ROADMAP and ENCODE consortia by their cell type. This approach let us to distinguish different cells types based on their epigenomic profiles, thus recapitulating important aspects of human hematopoiesis...
September 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28934465/regulation-of-chromatin-folding-by-conformational-variations-of-nucleosome-linker-dna
#3
Jenna M Buckwalter, Davood Norouzi, Anna Harutyunyan, Victor B Zhurkin, Sergei A Grigoryev
Linker DNA conformational variability has been proposed to direct nucleosome array folding into more or less compact chromatin fibers but direct experimental evidence for such models are lacking. Here, we tested this hypothesis by designing nucleosome arrays with A-tracts at specific locations in the nucleosome linkers to induce inward (AT-IN) and outward (AT-OUT) bending of the linker DNA. Using electron microscopy and analytical centrifugation techniques, we observed spontaneous folding of AT-IN nucleosome arrays into highly compact structures, comparable to those induced by linker histone H1...
September 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28934222/endogenous-rgs14-is-a-cytoplasmic-nuclear-shuttling-protein-that-localizes-to-juxtanuclear-membranes-and-chromatin-rich-regions-of-the-nucleus
#4
Mary Rose Branch, John R Hepler
Regulator of G protein signaling 14 (RGS14) is a multifunctional scaffolding protein that integrates G protein and H-Ras/MAPkinase signaling pathways to regulate synaptic plasticity important for hippocampal learning and memory. However, to date, little is known about the subcellular distribution and roles of endogenous RGS14 in a neuronal cell line. Most of what is known about RGS14 cellular behavior is based on studies of tagged, recombinant RGS14 ectopically overexpressed in unnatural host cells. Here, we report for the first time a comprehensive assessment of the subcellular distribution and dynamic localization of endogenous RGS14 in rat B35 neuroblastoma cells...
2017: PloS One
https://www.readbyqxmd.com/read/28933695/cooperative-interactions-enable-singular-olfactory-receptor-expression-in-mouse-olfactory-neurons
#5
Kevin Monahan, Ira Schieren, Jonah Cheung, Alice Mumbey-Wafula, Edwin S Monuki, Stavros Lomvardas
The monogenic and monoallelic expression of only one out of >1000 mouse olfactory receptor (ORs) genes requires the formation of large heterochromatic chromatin domains that sequester the OR gene clusters. Within these domains, intergenic transcriptional enhancers evade heterochromatic silencing and converge into interchromosomal hubs that assemble over the transcriptionally active OR. The significance of this nuclear organization in OR choice remains elusive. Here, we show that transcription factors Lhx2 and Ebf specify OR enhancers by binding in a functionally cooperative fashion to stereotypically spaced motifs that defy heterochromatin...
September 21, 2017: ELife
https://www.readbyqxmd.com/read/28933587/the-pro-apoptotic-bax-protein-influences-cell-growth-and-differentiation-from-the-nucleus-in-healthy-interphasic-cells
#6
Stéphanie Brayer, Audrey Joannes, Madeleine Jaillet, Elisa Gregianin, Souhir Mahmoudi, Joëlle Marchal Sommé, Aurélie Fabre, Pierre Mordant, Aurélie Cazes, Bruno Crestani, Arnaud A Mailleux
It has become more and more evident that the BCL-2 family proteins mediate a wide range of non-apoptotic functions. The pro-apoptotic BAX protein has been reported in interphasic nuclei. Whether the nuclear form of BAX could be involved in non-apoptotic function is still unknown. Our study showed for the first time that BAX was associated with chromatin in vitro. Next, we used gain and loss of function approaches to decipher the potential role of nuclear BAX in non-apoptotic cells. In vitro, nuclear BAX promoted cell proliferation in lung epithelial cells and primary human lung fibroblasts by modulating CDKN1A expression...
September 21, 2017: Cell Cycle
https://www.readbyqxmd.com/read/28932910/a-histone-deacetylase-gene-slhda3-acts-as-a-negative-regulator-of-fruit-ripening-and-carotenoid-accumulation
#7
Jun-E Guo, Zongli Hu, Xiaohui Yu, Anzhou Li, Fenfen Li, Yunshu Wang, Shibing Tian, Guoping Chen
SlHDA3 functions as an inhibitor and regulates tomato fruit ripening and carotenoid accumulation. Post-translational modifications, including histones acetylation, play a pivotal role in the changes of chromatin structure dynamic modulation and gene activity. The regulation of histone acetylation is achieved by the action of histone acetyltransferases and deacetylases, which play crucial roles in the regulation of transcription activation. There is an increasing research focus on histone deacetylation in crops, but the role of histone deacetylase genes (HDACs) in tomato has not been elucidated...
September 20, 2017: Plant Cell Reports
https://www.readbyqxmd.com/read/28932635/colony-stimulating-factor-1-induced-aif1-expression-in-tumor-associated-macrophages-enhances-the-progression-of-hepatocellular-carcinoma
#8
Hao Cai, Xiao-Dong Zhu, Jian-Yang Ao, Bo-Gen Ye, Yuan-Yuan Zhang, Zong-Tao Chai, Cheng-Hao Wang, Wen-Kai Shi, Man-Qing Cao, Xiao-Long Li, Hui-Chuan Sun
M2-polarized (alternatively activated) macrophages play an important role in the progression of hepatocellular carcinoma (HCC). Allograft inflammatory factor 1 (AIF1) is overexpressed in M2-polarized macrophages. This study explored the role of AIF1 in tumor-associated macrophages in HCC. Macrophages were stimulated with colony-stimulating factor 1 (CSF1) to characterize the regulatory pathway of AIF1 in macrophages. The chromatin immunoprecipitation and luciferase reporter gene assay were conducted to examine transcription factors associated with AIF1 expression...
2017: Oncoimmunology
https://www.readbyqxmd.com/read/28932035/epigenetics-in-oral-squamous-cell-carcinoma
#9
REVIEW
K N Hema, T Smitha, H S Sheethal, S Angeline Mirnalini
Oral squamous cell carcinoma (OSCC) is the most common type of oral neoplasm, accounting for over 90% of all oral malignancies and 38% of head and neck tumors. Worldwide, OSCC is the eighth most common human cancer, with more than 500,000 new cases being diagnosed every year with a fairly onerous prognosis, encouraging further research on factors that might modify disease outcome. Genetic and/or environmental risk factors associated with the development of oral cancer have been sufficiently understood (smoking, alcohol, betel, diet, living habits, etc...
May 2017: Journal of Oral and Maxillofacial Pathology: JOMFP
https://www.readbyqxmd.com/read/28931929/a-resource-of-large-scale-molecular-markers-for-monitoring-agropyron-cristatum-chromatin-introgression-in-wheat-background-based-on-transcriptome-sequences
#10
Jinpeng Zhang, Weihua Liu, Yuqing Lu, Qunxing Liu, Xinming Yang, Xiuquan Li, Lihui Li
Agropyron cristatum is a wild grass of the tribe Triticeae and serves as a gene donor for wheat improvement. However, very few markers can be used to monitor A. cristatum chromatin introgressions in wheat. Here, we reported a resource of large-scale molecular markers for tracking alien introgressions in wheat based on transcriptome sequences. By aligning A. cristatum unigenes with the Chinese Spring reference genome sequences, we designed 9602 A. cristatum expressed sequence tag-sequence-tagged site (EST-STS) markers for PCR amplification and experimental screening...
September 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28931593/active-ran-regulates-anillin-function-during-cytokinesis
#11
Daniel Beaudet, Tara Akhshi, Julia Phillipp, Christopher Law, Alisa Piekny
Cytokinesis cleaves a cell into two daughters at the end of mitosis, and must be spatially coordinated with chromosome segregation to prevent aneuploidy. The dogma is that the mitotic spindle governs the assembly and constriction of an actomyosin ring. Here, we reveal a function for active Ran in spatially restricting the ring. Our model is that during anaphase, 'free' importins, whose gradient inversely correlates with active Ran and chromatin position, function as a molecular ruler for the recruitment and localization of anillin, a contractile protein and crucial regulator of cytokinesis...
September 20, 2017: Molecular Biology of the Cell
https://www.readbyqxmd.com/read/28931573/chd7-collaborates-with-sox2-to-regulate-activation-of-oligodendrocyte-precursor-cells-after-spinal-cord-injury
#12
Toru Doi, Toru Ogata, Junji Yamauchi, Yasuhiro Sawada, Sakae Tanaka, Motoshi Nagao
Oligodendrocyte precursor cells (OPCs) act as a reservoir of new oligodendrocytes (OLs) in homeostatic and pathological conditions. OPCs are activated in response to injury, to generate myelinating OLs; however, the underlying mechanisms remain poorly understood. Here we show that Chd7 regulates OPC activation after spinal cord injury (SCI). Chd7 is expressed in OPCs in the adult spinal cord and its expression is upregulated with a concomitant increase in Sox2 expression following SCI. OPC-specific ablation of Chd7 in the injured mice leads to reduced OPC proliferation, the loss of OPC identity, and impaired OPC differentiation...
September 20, 2017: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/28931559/variation-in-position-effect-variegation-within-a-natural-population
#13
Keegan J P Kelsey, Andrew G Clark
Changes in chromatin state may drive changes in gene expression, and it is of growing interest to understand the population genetic forces that drive differences in chromatin state. Here, we use the phenomenon of position effect variegation (PEV), a well-studied proxy for chromatin state, to survey variation in PEV among a naturally derived population. Further, we explore the genetic architecture of natural variation in factors that modify PEV. While previous mutation screens have identified over 150 suppressors and enhancers of PEV, it remains unknown to what extent allelic variation in these modifiers mediate inter-individual variation in PEV...
September 20, 2017: Genetics
https://www.readbyqxmd.com/read/28931432/hypomethylated-domain-enriched-dna-motifs-prepattern-the-accessible-nucleosome-organization-in-teleosts
#14
Ryohei Nakamura, Ayako Uno, Masahiko Kumagai, Shinichi Morishita, Hiroyuki Takeda
BACKGROUND: Gene promoters in vertebrate genomes show distinct chromatin features such as stably positioned nucleosome array and DNA hypomethylation. The nucleosomes are known to have certain sequence preferences, and the prediction of nucleosome positioning from DNA sequence has been successful in some organisms such as yeast. However, at gene promoters where nucleosomes are much more stably positioned than in other regions, the sequence-based model has failed to work well, and sequence-independent mechanisms have been proposed...
September 20, 2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/28931413/topological-organization-and-dynamic-regulation-of-human-trna-genes-during-macrophage-differentiation
#15
Kevin Van Bortle, Douglas H Phanstiel, Michael P Snyder
BACKGROUND: The human genome is hierarchically organized into local and long-range structures that help shape cell-type-specific transcription patterns. Transfer RNA (tRNA) genes (tDNAs), which are transcribed by RNA polymerase III (RNAPIII) and encode RNA molecules responsible for translation, are dispersed throughout the genome and, in many cases, linearly organized into genomic clusters with other tDNAs. Whether the location and three-dimensional organization of tDNAs contribute to the activity of these genes has remained difficult to address, due in part to unique challenges related to tRNA sequencing...
September 20, 2017: Genome Biology
https://www.readbyqxmd.com/read/28930672/histone-h3-methylated-at-arginine-17-is-essential-for-reprogramming-the-paternal-genome-in-zygotes
#16
Yuki Hatanaka, Takeshi Tsusaka, Natsumi Shimizu, Kohtaro Morita, Takehiro Suzuki, Shinichi Machida, Manabu Satoh, Arata Honda, Michiko Hirose, Satoshi Kamimura, Narumi Ogonuki, Toshinobu Nakamura, Kimiko Inoue, Yoshihiko Hosoi, Naoshi Dohmae, Toru Nakano, Hitoshi Kurumizaka, Kazuya Matsumoto, Yoichi Shinkai, Atsuo Ogura
At fertilization, the paternal genome undergoes extensive reprogramming through protamine-histone exchange and active DNA demethylation, but only a few maternal factors have been defined in these processes. We identified maternal Mettl23 as a protein arginine methyltransferase (PRMT), which most likely catalyzes the asymmetric dimethylation of histone H3R17 (H3R17me2a), as indicated by in vitro assays and treatment with TBBD, an H3R17 PRMT inhibitor. Maternal histone H3.3, which is essential for paternal nucleosomal assembly, is unable to be incorporated into the male pronucleus when it lacks R17me2a...
September 19, 2017: Cell Reports
https://www.readbyqxmd.com/read/28930671/cohesin-can-remain-associated-with-chromosomes-during-dna-replication
#17
James D P Rhodes, Judith H I Haarhuis, Jonathan B Grimm, Benjamin D Rowland, Luke D Lavis, Kim A Nasmyth
To ensure disjunction to opposite poles during anaphase, sister chromatids must be held together following DNA replication. This is mediated by cohesin, which is thought to entrap sister DNAs inside a tripartite ring composed of its Smc and kleisin (Scc1) subunits. How such structures are created during S phase is poorly understood, in particular whether they are derived from complexes that had entrapped DNAs prior to replication. To address this, we used selective photobleaching to determine whether cohesin associated with chromatin in G1 persists in situ after replication...
September 19, 2017: Cell Reports
https://www.readbyqxmd.com/read/28930659/group-1-innate-lymphoid-cell-lineage-identity-is-determined-by-a-cis-regulatory-element-marked-by-a-long-non-coding-rna
#18
Walter K Mowel, Sam J McCright, Jonathan J Kotzin, Magalie A Collet, Asli Uyar, Xin Chen, Alexandra DeLaney, Sean P Spencer, Anthony T Virtue, EnJun Yang, Alejandro Villarino, Makoto Kurachi, Margaret C Dunagin, Gretchen Harms Pritchard, Judith Stein, Cynthia Hughes, Diogo Fonseca-Pereira, Henrique Veiga-Fernandes, Arjun Raj, Taku Kambayashi, Igor E Brodsky, John J O'Shea, E John Wherry, Loyal A Goff, John L Rinn, Adam Williams, Richard A Flavell, Jorge Henao-Mejia
Commitment to the innate lymphoid cell (ILC) lineage is determined by Id2, a transcriptional regulator that antagonizes T and B cell-specific gene expression programs. Yet how Id2 expression is regulated in each ILC subset remains poorly understood. We identified a cis-regulatory element demarcated by a long non-coding RNA (lncRNA) that controls the function and lineage identity of group 1 ILCs, while being dispensable for early ILC development and homeostasis of ILC2s and ILC3s. The locus encoding this lncRNA, which we termed Rroid, directly interacted with the promoter of its neighboring gene, Id2, in group 1 ILCs...
September 19, 2017: Immunity
https://www.readbyqxmd.com/read/28930559/histone-deacetylase-a-potential-therapeutic-target-for-ovarian-dysfunction
#19
Sunita Sunita, Pankaj Kumar Singh, Suneel Kumar Onteru, Dheer Singh
Post-partum uterine disorders and reproductive tract infections cause ovarian dysfunction and infertility. Histone deacetylases (HDACs) prevent the relaxation of chromatin, and positively or negatively regulate transcription. Hence, HDACs play a pivotal role in altering the gene expression that impact different signalling pathways underling ovarian dysfunction. Thus, HDAC inhibitors (HDACi) may act as potential therapeutic targets in the treatment of an array of disorders impacting ovarian function.
January 1, 2018: Frontiers in Bioscience (Landmark Edition)
https://www.readbyqxmd.com/read/28930539/transcriptional-regulation-of-p57-kip2-expression-during-development-differentiation-and-disease
#20
Marianna N Rossi, Oriella Andresini, Francesca Matteini, Rossella Maione
p57(kip2) is the most complex member of the CIP/KIP family of cyclin-dependent kinase inhibitors and plays a fundamental role in regulating cell cycle and differentiation during mammalian development. Consistently with a key role for p57(kip2) in the spatial and temporal control of cell proliferation, its expression is fine-tuned by multiple regulatory mechanisms, resulting in a tissue-, developmental phase- and cell type-specific pattern. Moreover, p57(kip2) is an imprinted gene, further supporting the importance of its proper expression dosage...
January 1, 2018: Frontiers in Bioscience (Landmark Edition)
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