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https://www.readbyqxmd.com/read/28090596/extracellular-vesicle-associated-long-non-coding-rnas-functionally-enhance-cell-viability
#1
Chris Hewson, David Capraro, Jon Burdach, Noel Whitaker, Kevin V Morris
Cells communicate with one another to create microenvironments and share resources. One avenue by which cells communicate is through the action of exosomes. Exosomes are extracellular vesicles that are released by one cell and taken up by neighbouring cells. But how exosomes instigate communication between cells has remained largely unknown. We present evidence here that particular long non-coding RNA molecules are preferentially packaged into exosomes. We also find that a specific class of these exosome associated non-coding RNAs functionally modulate cell viability by direct interactions with L-lactate dehydrogenase B (LDHB), high-mobility group protein 17 (HMG-17), and CSF2RB, proteins involved in metabolism, nucleosomal architecture and cell signalling respectively...
October 2016: Noncoding RNA Res
https://www.readbyqxmd.com/read/28089519/role-of-nhp6-and-hmo1-in-swi-snf-occupancy-and-nucleosome-landscape-at-gene-regulatory-regions
#2
Matias I Hepp, Michaela Smolle, Cristian Gidi, Roberto Amigo, Nicole Valenzuela, Axel Arriagada, Alejandro Maureira, Madelaine M Gogol, Marcela Torrejón, Jerry L Workman, José L Gutiérrez
Diverse chromatin modifiers are involved in regulation of gene expression at the level of transcriptional regulation. Among these modifiers are ATP-dependent chromatin remodelers, where the SWI/SNF complex is the founding member. It has been observed that High Mobility Group (HMG) proteins can influence the activity of a number of these chromatin remodelers. In this context, we have previously demonstrated that the yeast HMG proteins Nhp6 and Hmo1 can stimulate SWI/SNF activity. Here, we studied the genome-wide binding patterns of Nhp6, Hmo1 and the SWI/SNF complex, finding that most of gene promoters presenting high occupancy of this complex also display high enrichment of these HMG proteins...
January 9, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28088556/regulation-of-docetaxel-sensitivity-in-prostate-cancer-cells-by-hsa-mir-125a-3p-via-modulation-of-mta1-signaling
#3
Jian-Zhou Liu, Feng-Yan Yin, Chang-You Yan, Hui Wang, Xiao-Hui Luo
OBJECTIVE: To identify the potential down-stream targets of hsa-miR-125a-3p, a mature form of miR-125a, during the pathogenesis of chemoresistance in prostate cancer (PCa). METHODS: Expression levels of hsa-miR-125a-3p was assessed in chemoresistant PCa tissues and experimentally-established chemoresistant cells using quantitative RT-PCR (qRT-PCR). The effect of hsa-miR-125a-3p knockdown or hsa-miR-125a-3p overexpression on the Dox-induced cell death was evaluated using apoptosis ELISA in chemosensitive PC-3 cells or in chemoresistant PC-3 cells (PC-3R)...
January 11, 2017: Urology
https://www.readbyqxmd.com/read/28081156/generation-of-a-stable-transgenic-swine-model-expressing-a-porcine-histone-2b-egfp-fusion-protein-for-cell-tracking-and-chromosome-dynamics-studies
#4
Renan B Sper, Sehwon Koh, Xia Zhang, Sean Simpson, Bruce Collins, Jeff Sommer, Robert M Petters, Ignacio Caballero, Jeff L Platt, Jorge A Piedrahita
Transgenic pigs have become an attractive research model in the field of translational research, regenerative medicine, and stem cell therapy due to their anatomic, genetic and physiological similarities with humans. The development of fluorescent proteins as molecular tags has allowed investigators to track cell migration and engraftment levels after transplantation. Here we describe the development of two transgenic pig models via SCNT expressing a fusion protein composed of eGFP and porcine Histone 2B (pH2B)...
2017: PloS One
https://www.readbyqxmd.com/read/28079247/dynamic-location-changes-of-bub1-phosphorylated-h2athr133-with-cenh3-nucleosome-in-maize-centromeric-regions
#5
Handong Su, Yalin Liu, Qianhua Dong, Chao Feng, Jing Zhang, Yang Liu, James A Birchler, Fangpu Han
The genomic stability of all organisms requires precise cell division with proper chromosome orientation. The Bub1-H2Aph-Sgo1 pathway and spindle assembly checkpoint (SAC) components have been identified in yeast and mammals that are important for sister centromere orientation and chromosome segregation. However, their roles in plants are not clear. Maize meiotic mutants and minichromosomes were used to study the role of H2AThr133 phosphorylation and SAC components in sister centromere orientation and chromosome segregation...
January 12, 2017: New Phytologist
https://www.readbyqxmd.com/read/28077840/novel-gatad2b-loss-of-function-mutations-cause-intellectual-disability-in-two-unrelated-cases
#6
Xiaomei Luo, Yongyi Zou, Bo Tan, Yue Zhang, Jing Guo, Lanlan Zeng, Rui Zhang, Hu Tan, Xianda Wei, Yiqiao Hu, Yu Zheng, Desheng Liang, Lingqian Wu
GATA zinc finger domain-containing 2B (GATAD2B) is a subunit of the methyl-CpG-binding protein-1 complex (MECP1), which deacetylates methylated nucleosomes and regresses transcriptional activity. Recently, GATAD2B has been elucidated as a candidate gene in patients with intellectual disability (ID). In this study, we identified two novel heterozygous frameshift mutations of GATAD2B in two unrelated ID cases through next-generation sequencing (NGS). Both of the mutations c.80_81insGATGT and c.552_555delGAAA cause truncated proteins that might be detrimental to neurodevelopment...
January 12, 2017: Journal of Human Genetics
https://www.readbyqxmd.com/read/28075351/circulating-nucleosomes-and-nucleosome-modifications-as-biomarkers-in-cancer
#7
REVIEW
Peter McAnena, James A L Brown, Michael J Kerin
Traditionally the stratification of many cancers involves combining tumour and clinicopathological features (e.g., patient age; tumour size, grade, receptor status and location) to inform treatment options and predict recurrence risk and survival. However, current biomarkers often require invasive excision of the tumour for profiling, do not allow monitoring of the response to treatment and stratify patients into broad heterogeneous groups leading to inconsistent treatment responses. Here we explore and describe the benefits of using circulating biomarkers (nucleosomes and/or modifications to nucleosomes) as a non-invasive method for detecting cancer and monitoring response to treatment...
January 8, 2017: Cancers
https://www.readbyqxmd.com/read/28070131/dna-nanotechnology-a-nucleosome-clamp
#8
Chiara Pastore
No abstract text is available yet for this article.
January 10, 2017: Nature Nanotechnology
https://www.readbyqxmd.com/read/28069585/expression-of-hmgb2-indicates-worse-survival-of-patients-and-is-required-for-the-maintenance-of-warburg-effect-in-pancreatic-cancer
#9
Xin Cai, Hongjian Ding, Yanxia Liu, Gaofeng Pan, Qingguo Li, Zhen Yang, Weiyan Liu
High mobility group proteins (HMGs) are the second most abundant chromatin proteins and exert global genomic functions in the establishment of active or inactive chromatin domains. Through interaction with nucleosomes, transcription factors, nucleosome-remodeling machines and histones, the HMGs family proteins contribute to the fine tuning of transcription in response to rapid environmental changes. Mammalian high mobility group Bs (HMGBs) are characterized by two tandem HMG box domains followed by a long acidic tail...
January 9, 2017: Acta Biochimica et Biophysica Sinica
https://www.readbyqxmd.com/read/28069312/centromeres-drive-a-hard-bargain
#10
REVIEW
Leah F Rosin, Barbara G Mellone
Centromeres are essential chromosomal structures that mediate the accurate distribution of genetic material during meiotic and mitotic cell divisions. In most organisms, centromeres are epigenetically specified and propagated by nucleosomes containing the centromere-specific H3 variant, centromere protein A (CENP-A). Although centromeres perform a critical and conserved function, CENP-A and the underlying centromeric DNA are rapidly evolving. This paradox has been explained by the centromere drive hypothesis, which proposes that CENP-A is undergoing an evolutionary tug-of-war with selfish centromeric DNA...
January 6, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28069134/the-multifaceted-contributions-of-chromatin-to-hiv-1-integration-transcription-and-latency
#11
E De Crignis, T Mahmoudi
The capacity of the human immunodeficiency virus (HIV-1) to establish latent infections constitutes a major barrier to the development of a cure for HIV-1. In latent infection, replication competent HIV-1 provirus is integrated within the host genome but remains silent, masking the infected cells from the activity of the host immune response. Despite the progress in elucidating the molecular players that regulate HIV-1 gene expression, the mechanisms driving the establishment and maintenance of latency are still not fully understood...
2017: International Review of Cell and Molecular Biology
https://www.readbyqxmd.com/read/28067915/histone-degradation-in-response-to-dna-damage-enhances-chromatin-dynamics-and-recombination-rates
#12
Michael H Hauer, Andrew Seeber, Vijender Singh, Raphael Thierry, Ragna Sack, Assaf Amitai, Mariya Kryzhanovska, Jan Eglinger, David Holcman, Tom Owen-Hughes, Susan M Gasser
Nucleosomes are essential for proper chromatin organization and the maintenance of genome integrity. Histones are post-translationally modified and often evicted at sites of DNA breaks, facilitating the recruitment of repair factors. Whether such chromatin changes are localized or genome-wide is debated. Here we show that cellular levels of histones drop 20-40% in response to DNA damage. This histone loss occurs from chromatin, is proteasome-mediated and requires both the DNA damage checkpoint and the INO80 nucleosome remodeler...
January 9, 2017: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/28067802/stabilization-of-nucleosomes-by-histone-tails-and-by-fact-revealed-by-spfret-microscopy
#13
Maria E Valieva, Nadezhda S Gerasimova, Kseniya S Kudryashova, Anastasia L Kozlova, Mikhail P Kirpichnikov, Qi Hu, Maria Victoria Botuyan, Georges Mer, Alexey V Feofanov, Vasily M Studitsky
A correct chromatin structure is important for cell viability and is tightly regulated by numerous factors. Human protein complex FACT (facilitates chromatin transcription) is an essential factor involved in chromatin transcription and cancer development. Here FACT-dependent changes in the structure of single nucleosomes were studied with single-particle Förster resonance energy transfer (spFRET) microscopy using nucleosomes labeled with a donor-acceptor pair of fluorophores, which were attached to the adjacent gyres of DNA near the contact between H2A-H2B dimers...
January 6, 2017: Cancers
https://www.readbyqxmd.com/read/28065669/the-role-of-chromatin-structure-in-gene-regulation-of-the-human-malaria-parasite
#14
REVIEW
Gayani Batugedara, Xueqing M Lu, Evelien M Bunnik, Karine G Le Roch
The human malaria parasite, Plasmodium falciparum, depends on a coordinated regulation of gene expression for development and propagation within the human host. Recent developments suggest that gene regulation in the parasite is largely controlled by epigenetic mechanisms. Here, we discuss recent advancements contributing to our understanding of the mechanisms controlling gene regulation in the parasite, including nucleosome landscape, histone modifications, and nuclear architecture. In addition, various processes involved in regulation of parasite-specific genes and gene families are examined...
January 5, 2017: Trends in Parasitology
https://www.readbyqxmd.com/read/28064308/-structural-studies-of-chromatin-remodeling-factors
#15
O I Volokh, N I Derkacheva, V M Studitsky, O S Sokolova
Changes of chromatin structure require participation of chromatin remodeling factors (CRFs), which are ATP-dependent multisubunit complexes that change the structure of the nucleosome without covalently modifying its components. CRFs act together with other protein factors to regulate the extent of chromatin condensation. Four CRF families are currently distinguished based on their structural and biochemical characteristics: SWI/SNF, ISWI, Mi-2/CHD, and SWR/INO80. X-ray diffraction analysis and electron microscopy are the main methods to obtain structural information about macromolecules...
November 2016: Molekuliarnaia Biologiia
https://www.readbyqxmd.com/read/28063255/targeting-of-the-fun30-nucleosome-remodeller-by-the-dpb11-scaffold-facilitates-cell-cycle-regulated-dna-end-resection
#16
Susanne Cs Bantele, Pedro Ferreira, Dalia Gritenaite, Dominik Boos, Boris Pfander
DNA double strand breaks (DSBs) can be repaired by either recombination-based or direct ligation-based mechanisms. Pathway choice is made at the level of DNA end resection, a nucleolytic processing step, which primes DSBs for repair by recombination. Resection is thus under cell cycle control, but additionally regulated by chromatin and nucleosome remodellers. Here we show that both layers of control converge in the regulation of resection by the evolutionarily conserved Fun30/SMARCAD1 remodeller. Yeast Fun30 and human SMARCAD1 are cell cycle-regulated by interaction with the DSB-localized scaffold proteins Dpb11 and TOPBP1, respectively...
January 7, 2017: ELife
https://www.readbyqxmd.com/read/28062749/targeting-of-a-thaliana-knl2-to-centromeres-depends-on-the-conserved-cenpc-k-motif-in-its-c-terminus
#17
Michael Sandmann, Paul Talbert, Dmitri Demidov, Markus Kuhlmann, Twan Rutten, Udo Conrad, Inna Lermontova
KNL2 (KINETOCHORE NULL 2) is involved in recognition of centromeres and in centromeric localization of the centromere-specific histone cenH3. Our study revealed a cenH3 nucleosome-binding CENPC-k motif at the C-terminus of Arabidopsis thaliana KNL2, which is conserved among a wide spectrum of eukaryotes. Centromeric localization of KNL2 is abolished by deletion of the CENPC-k motif and by mutating single conserved amino acids, but can be restored by insertion of the corresponding motif of A. thaliana CENP-C...
January 6, 2017: Plant Cell
https://www.readbyqxmd.com/read/28060558/the-connection-between-brg1-ctcf-and-topoisomerases-at-tad-boundaries
#18
A Rasim Barutcu, Jane B Lian, Janet L Stein, Gary S Stein, Anthony N Imbalzano
The eukaryotic genome is partitioned into topologically associating domains (TADs). Despite recent advances characterizing TADs and TAD boundaries, the organization of these structures is an important dimension of genome architecture and function that is not well understood. Recently, we demonstrated that knockdown of BRG1, an ATPase driving the chromatin remodeling activity of mammalian SWI/SNF enzymes, globally alters long-range genomic interactions and results in a reduction of TAD boundary strength. We provided evidence suggesting that this effect may be due to BRG1 affecting nucleosome occupancy around CTCF sites present at TAD boundaries...
January 6, 2017: Nucleus
https://www.readbyqxmd.com/read/28059759/a-global-view-of-meiotic-double-strand-break-end-resection
#19
Eleni P Mimitou, Shintaro Yamada, Scott Keeney
DNA double-strand breaks that initiate meiotic recombination are exonucleolytically processed. This 5'→3' resection is a central, conserved feature of recombination but remains poorly understood. To address this lack, we mapped resection endpoints genome-wide at high resolution in Saccharomyces cerevisiae Full-length resection requires Exo1 exonuclease and the DSB-responsive kinase Tel1, but not Sgs1 helicase. Tel1 also promotes efficient and timely resection initiation. Resection endpoints display pronounced heterogeneity between genomic loci that reflects a tendency for nucleosomes to block Exo1, yet Exo1 also appears to digest chromatin with high processivity and at rates similar to naked DNA in vitro...
January 6, 2017: Science
https://www.readbyqxmd.com/read/28057215/the-role-of-epigenetic-regulation-in-transcriptional-memory-in-the-immune-system
#20
A M Woodworth, A F Holloway
The immune system is exquisitely poised to identify, respond to, and eradicate pathogens from the body, as well as to produce a more rapid and augmented response to a subsequent encounter with the pathogen. These cellular responses rely on the highly coordinated and rapid activation of gene expression programs as well as the ability of the cell to retain a memory of the initial gene response. It is clear that chromatin structure and epigenetic mechanisms play a crucial role in determining these gene responses, and in fact the immune system has proved an instructive model for investigating the multifaceted mechanisms through which the chromatin landscape contributes to gene expression programs...
2017: Advances in Protein Chemistry and Structural Biology
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