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https://www.readbyqxmd.com/read/29244146/ezh2-mutations-found-in-the-weaver-overgrowth-syndrome-cause-a-partial-loss-of-h3k27-histone-methyltransferase-activity
#1
Julian C Lui, Kevin M Barnes, Lijin Dong, Shanna Yue, Evan Graber, Robert Rapaport, Andrew Dauber, Ola Nilsson, Jeffrey Baron
Context: Weaver syndrome is characterized by tall stature, advanced bone age, characteristic facies, and variable intellectual disability. It is caused by heterozygous mutations in EZH2, a histone methyltransferase responsible for H3K27 trimethylation. However, no early truncating mutations have been identified, suggesting that null mutations do not cause Weaver syndrome. Objective: To test alternative hypotheses that EZH2 variants found in Weaver syndrome either cause a gain of function or a partial loss of function...
December 13, 2017: Journal of Clinical Endocrinology and Metabolism
https://www.readbyqxmd.com/read/29243324/validation-of-histone-deacetylase-3-as-a-therapeutic-target-in-castration-resistant-prostate-cancer
#2
Abigail B McLeod, James P Stice, Suzanne E Wardell, Holly M Alley, Ching-Yi Chang, Donald P McDonnell
BACKGROUND: Whereas the androgen receptor (AR) signaling axis remains a therapeutic target in castration-resistant prostate cancer (CRPC), the emergence of AR mutations and splice variants as mechanisms underlying resistance to contemporary inhibitors of this pathway highlights the need for new therapeutic approaches to target this disease. Of significance in this regard is the considerable preclinical data, indicating that histone deacetylase (HDAC) inhibitors may have utility in the treatment of CRPC...
December 15, 2017: Prostate
https://www.readbyqxmd.com/read/29242288/a-role-for-mono-methylation-of-histone-h3-k27-in-gene-activity-in-drosophila
#3
Liangjun Wang, Preeti Joshi, Ellen L Miller, LeeAnn Higgins, Matthew Slattery, Jeffrey A Simon
Polycomb repressive complex 2 (PRC2) is a conserved chromatin-modifying enzyme that methylates histone H3 on lysine-27 (K27).  PRC2 can add one, two, or three methyl groups and the fully methylated product, H3-K27me3, is a hallmark of Polycomb-silenced chromatin.  Less is known about functions of K27me1 and K27me2 and the dynamics of flux through these states.  These modifications could serve mainly as intermediates to produce K27me3 or they could each convey distinct epigenetic information.  To investigate this, we engineered a variant of Drosophila melanogaster PRC2 which is converted into a mono-methyltransferase...
December 14, 2017: Genetics
https://www.readbyqxmd.com/read/29241742/diagnostic-utility-of-histone-h3-3g34-w-g34r-and-g34-v-mutant-specific-antibodies-for-giant-cell-tumors-of-bone
#4
Hidetaka Yamamoto, Takeshi Iwasaki, Yuichi Yamada, Yoshihiro Matsumoto, Hiroshi Otsuka, Masato Yoshimoto, Kenichi Kohashi, Kenichi Taguchi, Ryohei Yokoyama, Yasuharu Nakashima, Yoshinao Oda
Giant cell tumors of bone (GCTBs) are characterized by mononuclear stromal cells and osteoclast-like giant cells; up to 95% have H3F3A gene mutation. The RANKL inhibitor denosumab, when used for the treatment of GCTB, leads to histological changes such as new bone formation and giant cell depletion. Here we assessed the diagnostic utility of immunohistochemical staining with the antibodies against histone H3.3G34 W, G34R and G34 V mutant proteins for GCTB and other histologically similar bone and joint lesions...
December 11, 2017: Human Pathology
https://www.readbyqxmd.com/read/29232016/characterization-of-h3-3-and-hira-expression-and-function-in-bovine-early-embryos
#5
Kun Zhang, Han Wang, Sandeep K Rajput, Joseph K Folger, George W Smith
Histone variant H3.3 is encoded by two distinct genes, H3F3A and H3F3B, that are closely associated with actively transcribed genes. H3.3 replacement is continuous and essential for maintaining correct chromatin structure during mouse oogenesis. Upon fertilization, H3.3 is incorporated to parental chromatin, and is required for blastocyst formation in mice. The H3.3 exchange process is facilitated by the chaperone HIRA, particularly during zygote development. We previously demonstrated that H3.3 is required for bovine early embryonic development; here, we explored the mechanisms of its functional requirement...
December 12, 2017: Molecular Reproduction and Development
https://www.readbyqxmd.com/read/29228394/the-psychiatric-risk-gene-transcription-factor-4-tcf4-regulates-neurodevelopmental-pathways-associated-with-schizophrenia-autism-and-intellectual-disability
#6
Marc P Forrest, Matthew J Hill, David H Kavanagh, Katherine E Tansey, Adrian J Waite, Derek J Blake
Background: Common genetic variants in and around the gene encoding transcription factor 4 (TCF4) are associated with an increased risk of schizophrenia. Conversely, rare damaging TCF4 mutations cause Pitt-Hopkins syndrome and have also been found in individuals with intellectual disability (ID) and autism spectrum disorder (ASD). Methods: Chromatin immunoprecipitation and next generation sequencing were used to identify the genomic targets of TCF4. These data were integrated with expression, epigenetic and disease gene sets using a range of computational tools...
December 8, 2017: Schizophrenia Bulletin
https://www.readbyqxmd.com/read/29224150/bisulphite-sequencing-of-chromatin-immunoprecipitated-dna-bischip-seq
#7
Clare Stirzaker, Jenny Z Song, Aaron L Statham, Susan J Clark
Epigenetic regulation plays a critical role in gene expression, cellular differentiation, and disease. There is a complex interplay between the different layers of epigenetic information, including DNA methylation, nucleosome positions, histone modifications, histone variants, and other important epigenetic regulators. The different modifications do not act independently of each other and their relationship plays an important role in governing the regulation of the epigenome. Of these, DNA methylation is the best-studied epigenetic modification in mammals...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29221109/protein-phosphatase-4-regulatory-subunit-2-ppp4r2-is-recurrently-deleted-in-acute-myeloid-leukemia-and-required-for-efficient-dna-double-strand-break-repair
#8
Julia K Herzig, Lars Bullinger, Alpaslan Tasdogan, Philipp Zimmermann, Martin Schlegel, Veronica Teleanu, Daniela Weber, Frank G Rücker, Peter Paschka, Anna Dolnik, Edith Schneider, Florian Kuchenbauer, Florian H Heidel, Christian Buske, Hartmut Döhner, Konstanze Döhner, Verena I Gaidzik
We have previously identified a recurrent deletion at chromosomal band 3p14.1-p13 in patients with acute myeloid leukemia (AML). Among eight protein-coding genes, this microdeletion affects the protein phosphatase 4 regulatory subunit 2 (PPP4R2), which plays an important role in DNA damage response (DDR). Investigation of mRNA expression during murine myelopoiesis determined that Ppp4r2 is higher expressed in more primitive hematopoietic cells. PPP4R2 expression in primary AML samples compared to healthy bone marrow was significantly lower, particularly in patients with 3p microdeletion or complex karyotype...
November 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/29218910/pan-cancer-analysis-of-expressed-somatic-nucleotide-variants-in-long-intergenic-non-coding-rna
#9
Travers Ching, Lana X Garmire
Long intergenic non-coding RNAs have been shown to play important roles in cancer. However, because lincRNAs are a relatively new class of RNAs compared to protein-coding mRNAs, the mutational landscape of lincRNAs has not been as extensively studied. Here we characterize expressed somatic nucleotide variants within lincRNAs using 12 cancer RNA-Seq datasets in TCGA. We build machine-learning models to discriminate somatic variants from germline variants within lincRNA regions (AUC 0.987). We build another model to differentiate lincRNA somatic mutations from background regions (AUC 0...
2018: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/29212814/structural-basis-for-assembly-of-the-cbf3-kinetochore-complex
#10
Vera Leber, Andrea Nans, Martin R Singleton
Eukaryotic chromosomes contain a specialised region known as the centromere, which forms the platform for kinetochore assembly and microtubule attachment. The centromere is distinguished by the presence of nucleosomes containing the histone H3 variant, CENP-A. In budding yeast, centromere establishment begins with the recognition of a specific DNA sequence by the CBF3 complex. This in turn facilitates CENP-ACse4 nucleosome deposition and kinetochore assembly. Here, we describe a 3.6 Å single-particle cryo-EM reconstruction of the core CBF3 complex, incorporating the sequence-specific DNA-binding protein Cep3 together with regulatory subunits Ctf13 and Skp1...
December 6, 2017: EMBO Journal
https://www.readbyqxmd.com/read/29208640/shaping-chromatin-in-the-nucleus-the-bricks-and-the-architects
#11
David Sitbon, Katrina Podsypanina, Tejas Yadav, Geneviève Almouzni
Chromatin organization in the nucleus provides a vast repertoire of information in addition to that encoded genetically. Understanding how this organization impacts genome stability and influences cell fate and tumorigenesis is an area of rapid progress. Considering the nucleosome, the fundamental unit of chromatin structure, the study of histone variants (the bricks) and their selective loading by histone chaperones (the architects) is particularly informative. Here, we report recent advances in understanding how relationships between histone variants and their chaperones contribute to tumorigenesis using cell lines and Xenopus development as model systems...
December 5, 2017: Cold Spring Harbor Symposia on Quantitative Biology
https://www.readbyqxmd.com/read/29206173/histone-macroh2a1-a-chromatin-point-of-intersection-between-fasting-senescence-and-cellular-regeneration
#12
REVIEW
Oriana Lo Re, Manlio Vinciguerra
Histone variants confer chromatin unique properties. They have specific genomic distribution, regulated by specific deposition and removal machineries. Histone variants, mostly of canonical histones H2A, H2B and H3, have important roles in early embryonic development, in lineage commitment of stem cells, in the converse process of somatic cell reprogramming to pluripotency and, in some cases, in the modulation of animal aging and life span. MacroH2A1 is a variant of histone H2A, present in two alternatively exon-spliced isoforms macroH2A1...
December 5, 2017: Genes
https://www.readbyqxmd.com/read/29203834/molecular-and-cellular-issues-of-kmt2a-variants-involved-in-wiedemann-steiner-syndrome
#13
Nicolas Lebrun, Irina Giurgea, Alice Goldenberg, Anne Dieux, Alexandra Afenjar, Jamal Ghoumid, Bertrand Diebold, Léo Mietton, Audrey Briand-Suleau, Pierre Billuart, Thierry Bienvenu
Variants in KMT2A, encoding the histone methyltransferase KMT2A, are a growing cause of intellectual disability (ID). Up to now, the majority of KMT2A variants are non-sense and frameshift variants causing a typical form of Wiedemann-Steiner syndrome. We studied KMT2A gene in a cohort of 200 patients with unexplained syndromic and non-syndromic ID and identified four novel variants, one splice and three missense variants, possibly deleterious. We used primary cells from the patients and molecular approaches to determine the deleterious effects of those variants on KMT2A expression and function...
December 4, 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/29203539/novel-and-shared-neoantigen-derived-from-histone-3-variant-h3-3k27m-mutation-for-glioma-t-cell-therapy
#14
Zinal S Chheda, Gary Kohanbash, Kaori Okada, Naznin Jahan, John Sidney, Matteo Pecoraro, Xinbo Yang, Diego A Carrera, Kira M Downey, Shruti Shrivastav, Shuming Liu, Yi Lin, Chetana Lagisetti, Pavlina Chuntova, Payal B Watchmaker, Sabine Mueller, Ian F Pollack, Raja Rajalingam, Angel M Carcaboso, Matthias Mann, Alessandro Sette, K Christopher Garcia, Yafei Hou, Hideho Okada
The median overall survival for children with diffuse intrinsic pontine glioma (DIPG) is less than one year. The majority of diffuse midline gliomas, including more than 70% of DIPGs, harbor an amino acid substitution from lysine (K) to methionine (M) at position 27 of histone 3 variant 3 (H3.3). From a CD8+ T cell clone established by stimulation of HLA-A2+ CD8+ T cells with synthetic peptide encompassing the H3.3K27M mutation, complementary DNA for T cell receptor (TCR) α- and β-chains were cloned into a retroviral vector...
December 4, 2017: Journal of Experimental Medicine
https://www.readbyqxmd.com/read/29198523/resetting-the-yeast-epigenome-with-human-nucleosomes
#15
David M Truong, Jef D Boeke
Humans and yeast are separated by a billion years of evolution, yet their conserved histones retain central roles in gene regulation. Here, we "reset" yeast to use core human nucleosomes in lieu of their own (a rare event taking 20 days), which initially only worked with variant H3.1. The cells adapt by acquiring suppressor mutations in cell-division genes or by acquiring certain aneuploid states. Converting five histone residues to their yeast counterparts restored robust growth. We reveal that humanized nucleosomes are positioned according to endogenous yeast DNA sequence and chromatin-remodeling network, as judged by a yeast-like nucleosome repeat length...
November 8, 2017: Cell
https://www.readbyqxmd.com/read/29198113/characterization-of-chlamydomonas-reinhardtii-core-histones-by-top-down-mass-spectrometry-reveals-unique-algae-specific-variants-and-post-translational-modifications
#16
Aliyya Khan, Carlo K Eikani, Hana Khan, Anthony T Iavarone, James J Pesavento
The unicellular microalga Chlamydomonas reinhardtii has played an instrumental role in the development of many new fields (bio-products, biofuels, etc.) as well as the advancement of basic science (photosynthetic apparati, flagellar function, etc.). Chlamydomonas' versatility ultimately derives from the genes encoded in its genome and the way that the expression of these genes is regulated, which is largely influenced by a family of DNA binding proteins called histones. In this study, we characterize C. reinhardtii core histones, both variants and their post-translational modifications, by chromatographic separation followed by top-down mass spectrometry (TDMS)...
December 3, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/29197353/histone-profiling-reveals-the-h1-3-histone-variant-as-a-prognostic-biomarker-for-pancreatic-ductal-adenocarcinoma
#17
Monika Bauden, Theresa Kristl, Agata Sasor, Bodil Andersson, György Marko-Varga, Roland Andersson, Daniel Ansari
BACKGROUND: Epigenetic alterations have been recognized as important contributors to the pathogenesis of PDAC. However, the role of histone variants in pancreatic tumor progression is still not completely understood. The aim of this study was to explore the expression and prognostic significance of histone protein variants in PDAC patients. METHODS: Liquid chromatography-tandem mass spectrometry (LC-MS/MS) was employed for qualitative analysis of histone variants and histone related post-translational modifications (PTMs) in PDAC and normal pancreatic tissues...
December 2, 2017: BMC Cancer
https://www.readbyqxmd.com/read/29196559/remarkable-evolutionary-plasticity-of-centromeric-chromatin
#18
Steven Henikoff, Jitendra Thakur, Sivakanthan Kasinathan, Paul B Talbert
Centromeres were familiar to cell biologists in the late 19th century, but for most eukaryotes the basis for centromere specification has remained enigmatic. Much attention has been focused on the cenH3 (CENP-A) histone variant, which forms the foundation of the centromere. To investigate the DNA sequence requirements for centromere specification, we applied a variety of epigenomic approaches, which have revealed surprising diversity in centromeric chromatin properties. Whereas each point centromere of budding yeast is occupied by a single precisely positioned tetrameric nucleosome with one cenH3 molecule, the "regional" centromeres of fission yeast contain unphased presumably octameric nucleosomes with two cenH3s...
December 1, 2017: Cold Spring Harbor Symposia on Quantitative Biology
https://www.readbyqxmd.com/read/29194511/prolyl-isomerization-of-the-cenp-a-n-terminus-regulates-centromeric-integrity-in-fission-yeast
#19
Hwei Ling Tan, Kim Kiat Lim, Qiaoyun Yang, Jing-Song Fan, Ahmed Mahmoud Mohammed Sayed, Liy Sim Low, Bingbing Ren, Teck Kwang Lim, Qingsong Lin, Yu-Keung Mok, Yih-Cherng Liou, Ee Sin Chen
Centromeric identity and chromosome segregation are determined by the precise centromeric targeting of CENP-A, the centromere-specific histone H3 variant. The significance of the amino-terminal domain (NTD) of CENP-A in this process remains unclear. Here, we assessed the functional significance of each residue within the NTD of CENP-A from Schizosaccharomyces pombe (SpCENP-A) and identified a proline-rich 'GRANT' (Genomic stability-Regulating site within CENP-A N-Terminus) motif that is important for CENP-A function...
November 29, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29186682/control-of-gene-expression-in-senescence-through-transcriptional-read-through-of-convergent-protein-coding-genes
#20
Lisa Muniz, Maharshi Krishna Deb, Marion Aguirrebengoa, Sandra Lazorthes, Didier Trouche, Estelle Nicolas
Antisense RNAs are non-coding RNAs that can regulate their corresponding sense RNAs and are generally produced from specific promoters. We uncover here a family of antisense RNAs, named START RNAs, produced during cellular senescence by transcriptional read-through at convergent protein-coding genes. Importantly, START RNAs repress the expression of their corresponding sense RNAs. In proliferative cells, we found that the Pol II elongation rate is limited downstream of TTS at START loci, allowing transcription termination to occur before Pol II reaches the convergent genes, thus preventing antisense RNA production and interference with the expression of the convergent genes...
November 28, 2017: Cell Reports
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