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https://www.readbyqxmd.com/read/28730681/histone-variants-expression-in-peripheral-blood-mononuclear-cells-of-patients-with-rheumatoid-arthritis
#1
Maryam Asadipour, Vahideh Hassan-Zadeh, Naheed Aryaeian, Farhad Shahram, Mahdi Mahmoudi
AIM: The purpose of the present study was to analyze the expression of four histone variants, implicated in the regulation of gene expression, in peripheral blood mononuclear cell (PBMC) samples of patients with rheumatoid arthritis and healthy controls. METHOD: We analyzed the expression of three genes encoding histone variants H3.3, H2A.Z, macroH2A1.1 and macroH2A1.2 in PBMC samples of 50 patients with RA, diagnosed according to American College of Rheumatology (ACR) criteria, and 51 matched healthy controls using SYBR green real-time polymerase chain reaction...
July 21, 2017: International Journal of Rheumatic Diseases
https://www.readbyqxmd.com/read/28727848/the-nuclear-proteome-of-trypanosoma-brucei
#2
Carina Goos, Mario Dejung, Christian J Janzen, Falk Butter, Susanne Kramer
Trypanosoma brucei is a protozoan flagellate that is transmitted by tsetse flies into the mammalian bloodstream. The parasite has a huge impact on human health both directly by causing African sleeping sickness and indirectly, by infecting domestic cattle. The biology of trypanosomes involves some highly unusual, nuclear-localised processes. These include polycistronic transcription without classical promoters initiated from regions defined by histone variants, trans-splicing of all transcripts to the exon of a spliced leader RNA, transcription of some very abundant proteins by RNA polymerase I and antigenic variation, a switch in expression of the cell surface protein variants that allows the parasite to resist the immune system of its mammalian host...
2017: PloS One
https://www.readbyqxmd.com/read/28720323/rapid-divergence-of-histones-in-hydrozoa-cnidaria-and-evolution-of-a-novel-histone-involved-in-dna-damage-response-in-hydra
#3
Puli Chandramouli Reddy, Suyog Ubhe, Neha Sirwani, Rasika Lohokare, Sanjeev Galande
Histones are fundamental components of chromatin in all eukaryotes. Hydra, an emerging model system belonging to the basal metazoan phylum Cnidaria, provides an ideal platform to understand the evolution of core histone components at the base of eumetazoan phyla. Hydra exhibits peculiar properties such as tremendous regenerative capacity, lack of organismal senescence and rarity of malignancy. In light of the role of histone modifications and histone variants in these processes it is important to understand the nature of histones themselves and their variants in hydra...
June 15, 2017: Zoology: Analysis of Complex Systems, ZACS
https://www.readbyqxmd.com/read/28718505/immunogenomic-approaches-to-understand-the-function-of-immune-disease-variants
#4
REVIEW
Dafni Anna Glinos, Blagoje Soskic, Gosia Trynka
Mapping hundreds of genetic variants through genome wide association studies provided an opportunity to gain insights into the pathobiology of immune mediated diseases. However, since most of the disease variants fall outside the gene coding sequences, thereby implicating gene expression regulation as the causal mechanism, the functional interpretation of the exact role of the associated variants remains to be determined. Despite these challenges, integration of disease associated variants with large scale genomic maps of cell type specific gene regulation both at chromatin and transcript levels deliver examples of functionally prioritised causal variants and genes...
July 17, 2017: Immunology
https://www.readbyqxmd.com/read/28706522/expressed-centromere-specific-histone-3-cenh3-variants-in-cultivated-triploid-and-wild-diploid-bananas-musa-spp
#5
Kariuki S Muiruri, Anne Britt, Nelson O Amugune, Edward K Nguu, Simon Chan, Leena Tripathi
Centromeres are specified by a centromere specific histone 3 (CENH3) protein, which exists in a complex environment, interacting with conserved proteins and rapidly evolving satellite DNA sequences. The interactions may become more challenging if multiple CENH3 versions are introduced into the zygote as this can affect post-zygotic mitosis and ultimately sexual reproduction. Here, we characterize CENH3 variant transcripts expressed in cultivated triploid and wild diploid progenitor bananas. We describe both splice- and allelic-[Single Nucleotide Polymorphisms (SNP)] variants and their effects on the predicted secondary structures of protein...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28701485/gt-rich-promoters-can-drive-rna-pol-ii-transcription-and-deposition-of-h2a-z-in-african-trypanosomes
#6
Carolin Wedel, Konrad U Förstner, Ramona Derr, T Nicolai Siegel
Genome-wide transcription studies are revealing an increasing number of "dispersed promoters" that, unlike "focused promoters", lack well-conserved sequence motifs and tight regulation. Dispersed promoters are nevertheless marked by well-defined chromatin structures, suggesting that specific sequence elements must exist in these unregulated promoters. Here, we have analyzed regions of transcription initiation in the eukaryotic parasite Trypanosoma brucei, in which RNA polymerase II transcription initiation occurs over broad regions without distinct promoter motifs and lacks regulation...
July 12, 2017: EMBO Journal
https://www.readbyqxmd.com/read/28697848/roles-of-rnase-p-and-its-subunits
#7
REVIEW
Nayef Jarrous
Recent studies show that nuclear RNase P is linked to chromatin structure and function. Thus, variants of this ribonucleoprotein (RNP) complex bind to chromatin of small noncoding RNA genes; integrate into initiation complexes of RNA polymerase (Pol) III; repress histone H3.3 nucleosome deposition; control tRNA and PIWI-interacting RNA (piRNA) gene clusters for genome defense; and respond to Werner syndrome helicase (WRN)-related replication stress and DNA double-strand breaks (DSBs). Likewise, the related RNase MRP and RMRP-TERT (telomerase reverse transcriptase) are implicated in RNA-dependent RNA polymerization for chromatin silencing, whereas the telomerase carries out RNA-dependent DNA polymerization for telomere lengthening...
July 8, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28687524/pierpont-syndrome-associated-with-the-p-tyr446cys-missense-mutation-in-tbl1xr1
#8
Anne Slavotinek, Heather Pua, Ugur Hodoglugil, Jude Abadie, Joseph Shieh, Jessica Van Ziffle, Mark Kvale, Hane Lee, Pui-Yan Kwok, Neil Risch, Marta Sabbadini
We present a 7-year old male with severe delays, hypotonia and dysmorphic features who had striking, deep palmar and plantar creases and pillowing of the soft tissues of the palms and soles. His facial features included a high anterior hairline, small eyes with narrowed palpebral fissures, a bulbous nasal tip with a short columella, and a large mouth with a thin upper vermilion, and small chin. He had a submucous cleft palate, bilateral cryptorchidism and hydronephrosis. Cranial imaging demonstrated an Arnold Chiari malformation that was also present in his maternal uncle by report...
July 4, 2017: European Journal of Medical Genetics
https://www.readbyqxmd.com/read/28684426/arabidopsis-atrx-modulates-h3-3-occupancy-and-fine-tunes-gene-expression
#9
Céline Duc, Matthias Benoit, Gwénaëlle Détourné, Lauriane Simon, Axel Poulet, Matthieu Jung, Alaguraj Veluchamy, David Latrasse, Samuel Le Goff, Sylviane Cotterell, Christophe Tatout, Moussa Benhamed, Aline V Probst
Histones are essential components of the nucleosome, the major chromatin subunit that structures linear DNA molecules and regulates access of other proteins to DNA. Specific histone chaperone complexes control the correct deposition of canonical histones and their variants to modulate nucleosome structure and stability. In this study, we characterize the Arabidopsis Alpha Thalassemia-mental Retardation X-linked (ATRX) ortholog and show that ATRX is involved in histone H3 deposition. Arabidopsis ATRX mutant alleles are viable, but show developmental defects and reduced fertility...
July 6, 2017: Plant Cell
https://www.readbyqxmd.com/read/28683716/putative-enhancer-sites-in-the-bovine-genome-are-enriched-with-variants-affecting-complex-traits
#10
Min Wang, Timothy P Hancock, Iona M MacLeod, Jennie E Pryce, Benjamin G Cocks, Benjamin J Hayes
BACKGROUND: Enhancers are non-coding DNA sequences, which when they are bound by specific proteins increase the level of gene transcription. Enhancers activate unique gene expression patterns within cells of different types or under different conditions. Enhancers are key contributors to gene regulation, and causative variants that affect quantitative traits in humans and mice have been located in enhancer regions. However, in the bovine genome, enhancers as well as other regulatory elements are not yet well defined...
July 6, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28682228/-genetics-and-epigenetics-of-schizophrenia-and-other-psychoses
#11
Boris Chaumette, Oussama Kebir, Marie-Odile Krebs
Schizophrenia and other psychoses are categorical psychiatric diagnoses corresponding to frequent and heterogeneous disorders. Their physiopathology still remains largely unknown despite numerous recent advances. In particular, the last decade has identified different types of genetic variants, thanks to emergence of high-throughput methods. These methods allow both the identification of rare variants with a large effect such as punctual mutations or copy-number variants and the identification of frequent variants with a limited effect such as polymorphisms...
2017: Biologie Aujourd'hui
https://www.readbyqxmd.com/read/28677724/tnfr2-promotes-adriamycin-resistance-in-breast-cancer-cells-by-repairing-dna-damage
#12
Fuqian Yang, Nana Zhao, Nan Wu
In recent years, tumor necrosis factor receptor 2 (TNFR2) has attracted increasing attention for its important roles in promoting proliferation, migration and angiogenesis in several types of cancer. However, its role in drug resistance remain unclear. In the present study, TNFR2 expression levels in MDA‑MB‑231 and MCF‑7 breast cancer cells were demonstrated to be associated with Adriamycin (ADM) resistance. Silencing of TNFR2 in MCF‑7 cells significantly inhibited ADM resistance, while overexpression of TNFR2 in MDA‑MB‑231 cells significantly enhanced ADM resistance...
June 30, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28669576/histone-h2a-monoubiquitination-in-neurodevelopmental-disorders
#13
REVIEW
Anshika Srivastava, Brian McGrath, Stephanie L Bielas
Covalent histone modifications play an essential role in gene regulation and cellular specification required for multicellular organism development. Monoubiquitination of histone H2A (H2AUb1) is a reversible transcriptionally repressive mark. Exchange of histone H2A monoubiquitination and deubiquitination reflects the succession of transcriptional profiles during development required to produce cellular diversity from pluripotent cells. Germ-line pathogenic variants in components of the H2AUb1 regulatory axis are being identified as the genetic basis of congenital neurodevelopmental disorders...
June 29, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28663935/differential-gene-expression-analysis-by-rna-seq-reveals-the-importance-of-actin-cytoskeletal-proteins-in-erythroleukemia-cells
#14
Vanessa Fernández-Calleja, Pablo Hernández, Jorge B Schvartzman, Mario García de Lacoba, Dora B Krimer
Development of drug resistance limits the effectiveness of anticancer treatments. Understanding the molecular mechanisms triggering this event in tumor cells may lead to improved therapeutic strategies. Here we used RNA-seq to compare the transcriptomes of a murine erythroleukemia cell line (MEL) and a derived cell line with induced resistance to differentiation (MEL-R). RNA-seq analysis identified a total of 596 genes (Benjamini-Hochberg adjusted p-value < 0.05) that were differentially expressed by more than two-fold, of which 81...
2017: PeerJ
https://www.readbyqxmd.com/read/28655778/six-rowed-spike-3-vrs3-is-a-histone-demethylase-that-controls-lateral-spikelet-development-in-barley
#15
G Wilma van Esse, Agatha Walla, Andreas Finke, Maarten Koornneef, Ales Pecinka, Maria von Korff
The complex nature of crop genomes has long prohibited the efficient isolation of agronomically relevant genes. However, recent advances in next-generation sequencing (NGS) technologies provide new ways to accelerate fine-mapping and gene isolation in crops. We used RNA-sequencing of allelic six-rowed spike 3 (vrs3) mutants with altered spikelet development for gene identification and functional analysis in barley (Hordeum vulgare). Variant calling in two allelic vrs3 mutants revealed that VRS3 encodes a putative histone lysine demethylase with a conserved zinc finger, Jumonji C and N domain...
June 27, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28654055/chromatin-immunoprecipitation-chip-in-mouse-t-cell-lines
#16
Benedetto Daniele Giaimo, Francesca Ferrante, Tilman Borggrefe
Signaling pathways regulate gene expression programs via the modulation of the chromatin structure at different levels, such as by post-translational modifications (PTMs) of histone tails, the exchange of canonical histones with histone variants, and nucleosome eviction. Such regulation requires the binding of signal-sensitive transcription factors (TFs) that recruit chromatin-modifying enzymes at regulatory elements defined as enhancers. Understanding how signaling cascades regulate enhancer activity requires a comprehensive analysis of the binding of TFs, chromatin modifying enzymes, and the occupancy of specific histone marks and histone variants...
June 17, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28647357/biophysical-characterization-of-histone-h3-3-k27m-point-mutation
#17
Szabolcs Hetey, Beáta Boros-Oláh, Tímea Kuik-Rózsa, Qiuzhen Li, Zsolt Karányi, Zoltán Szabó, Jason Roszik, Nikoletta Szalóki, György Vámosi, Katalin Tóth, Lóránt Székvölgyi
Lysine 27 to methionine (K27 M) mutation of the histone variant H3.3 drives the formation of an aggressive glioblastoma multiforme tumor in infants. Here we analyzed how the methionine substitution alters the stability of H3.3 nucleosomes in vitro and modifies its kinetic properties in live cells. We also determined whether the presence of mutant nucleosomes perturbed the mobility of the PRC2 subunit Ezh2 (enhancer-of-zeste homolog 2). We found that K27 M nucleosomes maintained the wild-type molecular architecture both at the level of bulk histones and single nucleosomes and followed similar diffusion kinetics to wild-type histones in live cells...
June 21, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28645917/multivalent-binding-of-pwwp2a-to-h2a-z-regulates-mitosis-and-neural-crest-differentiation
#18
Sebastian Pünzeler, Stephanie Link, Gabriele Wagner, Eva C Keilhauer, Nina Kronbeck, Ramona Mm Spitzer, Susanne Leidescher, Yolanda Markaki, Edith Mentele, Catherine Regnard, Katrin Schneider, Daisuke Takahashi, Masayuki Kusakabe, Chiara Vardabasso, Lisa M Zink, Tobias Straub, Emily Bernstein, Masahiko Harata, Heinrich Leonhardt, Matthias Mann, Ralph Aw Rupp, Sandra B Hake
Replacement of canonical histones with specialized histone variants promotes altering of chromatin structure and function. The essential histone variant H2A.Z affects various DNA-based processes via poorly understood mechanisms. Here, we determine the comprehensive interactome of H2A.Z and identify PWWP2A as a novel H2A.Z-nucleosome binder. PWWP2A is a functionally uncharacterized, vertebrate-specific protein that binds very tightly to chromatin through a concerted multivalent binding mode. Two internal protein regions mediate H2A...
June 23, 2017: EMBO Journal
https://www.readbyqxmd.com/read/28623522/h3-k27m-mutations-are-extremely-rare-in-posterior-fossa-group-a-ependymoma
#19
Scott Ryall, Miguel Guzman, Samer K Elbabaa, Betty Luu, Stephen C Mack, Michal Zapotocky, Michael D Taylor, Cynthia Hawkins, Vijay Ramaswamy
BACKGROUND: Mutations in the tail of histone H3 (K27M) are frequently found in pediatric midline high-grade glioma's but have rarely been reported in other malignancies. Recently, recurrent somatic nucleotide variants in histone H3 (H3 K27M) have been reported in group A posterior fossa ependymoma (EPN_PFA), an entity previously described to have no recurrent mutations. However, the true incidence of H3 K27M mutations in EPN_PFA is unknown. METHODS: In order to discern the frequency of K27M mutations in histone H3 in EPN_PFA, we analyzed 151 EPN_PFA previously profiled with genome-wide methylation arrays using a validated droplet digital PCR assay...
July 2017: Child's Nervous System: ChNS: Official Journal of the International Society for Pediatric Neurosurgery
https://www.readbyqxmd.com/read/28617799/p53-and-tap63-participate-in-the-recombination-dependent-pachytene-arrest-in-mouse-spermatocytes
#20
Marina Marcet-Ortega, Sarai Pacheco, Ana Martínez-Marchal, Helena Castillo, Elsa Flores, Maria Jasin, Scott Keeney, Ignasi Roig
To protect germ cells from genomic instability, surveillance mechanisms ensure meiosis occurs properly. In mammals, spermatocytes that display recombination defects experience a so-called recombination-dependent arrest at the pachytene stage, which relies on the MRE11 complex-ATM-CHK2 pathway responding to unrepaired DNA double-strand breaks (DSBs). Here, we asked if p53 family members-targets of ATM and CHK2-participate in this arrest. We bred double-mutant mice combining a mutation of a member of the p53 family (p53, TAp63, or p73) with a Trip13 mutation...
June 2017: PLoS Genetics
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