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https://www.readbyqxmd.com/read/28087897/fgfr1-analyses-in-four-patients-with-hypogonadotropic-hypogonadism-with-split-hand-foot-malformation-implications-for-the-promoter-region
#1
Kohnosuke Ohtaka, Yasuko Fujisawa, Fumio Takada, Yukihiro Hasegawa, Tatsuya Miyoshi, Tomonobu Hasegawa, Hideaki Miyoshi, Hiraku Kameda, Misuzu Kurokawa Seo, Maki Fukami, Tsutomu Ogata
Heterozygous loss-of-function mutations of FGFR1 cause various disorders including hypogonadotropic hypogonadism with split-hand/foot malformation (HH-SHFM). We examined FGFR1 in four Japanese patients with HH-SHFM (cases 1-4) and the mother of case 4 with HH only. Cases 1 and 2 had heterozygous loss-of-function mutations with no dominant negative effect [c.289G>A, p.(G97S); and c.2231G>C, p.(R744T)], and case 3 had a splice donor site mutation [c.1663+1G>T]. Notably, case 4 had a maternally inherited 8,312 bp microdeletion that involved non-coding exon 1U and impaired FGFR1 expression...
January 13, 2017: Human Mutation
https://www.readbyqxmd.com/read/28077316/chromatin-dynamics-regulate-mesenchymal-stem-cell-lineage-specification-and-differentiation-to-osteogenesis
#2
Hai Wu, Jonathan A R Gordon, Troy W Whitfield, Phillip W L Tai, Andre J van Wijnen, Janet L Stein, Gary S Stein, Jane B Lian
Multipotent mesenchymal stromal cells (MSCs) are critical for regeneration of multiple tissues. Epigenetic mechanisms are fundamental regulators of lineage specification and cell fate, and as such, we addressed the question of which epigenetic modifications characterize the transition of nascent MSCs to a tissue specific MSC-derived phenotype. By profiling the temporal changes of seven histone marks correlated to gene expression during proliferation, early commitment, matrix deposition, and mineralization stages, we identified distinct epigenetic mechanisms that regulate transcriptional programs necessary for tissue-specific phenotype development...
January 8, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28053168/ccnet-database-of-co-expression-networks-with-functional-modules-for-diploid-and-polyploid-gossypium
#3
Qi You, Wenying Xu, Kang Zhang, Liwei Zhang, Xin Yi, Dongxia Yao, Chunchao Wang, Xueyan Zhang, Xinhua Zhao, Nicholas J Provart, Fuguang Li, Zhen Su
Plant genera with both diploid and polyploid species are a common evolutionary occurrence. Polyploids, especially allopolyploids such as cotton and wheat, are a great model system for heterosis research. Here, we have integrated genome sequences and transcriptome data of Gossypium species to construct co-expression networks and identified functional modules from different cotton species, including 1155 and 1884 modules in G. arboreum and G. hirsutum, respectively. We overlayed the gene expression results onto the co-expression network...
January 4, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28041684/ash1l-suppresses-matrix-metalloproteinase-through-mitogen-activated-protein-kinase-signaling-pathway-in-pulpitis
#4
Yin Bei, Hui Tianqian, Yu Fanyuan, Luo Haiyun, Liao Xueyang, Yang Jing, Wang Chenglin, Ye Ling
INTRODUCTION: Pulpitis is an inflammation of dental pulp produced by a response to external stimuli. The response entails substantial cellular and molecular activities. Both genetic and epigenetic regulators contribute to the occurrence of pulpitis. However, the epigenetic mechanisms are still poorly understood. In this research, we studied the role of the absent, small, or homeotic-like (ASH1L) gene in the process of pulpitis. METHODS: Human dental pulp cells (HDPCs) were stimulated with proinflammatory cytokine tumor necrosis factor alpha (TNF-α)...
December 29, 2016: Journal of Endodontics
https://www.readbyqxmd.com/read/28032247/a-systemic-identification-approach-for-primary-transcription-start-site-of-arabidopsis-mirnas-from-multidimensional-omics-data
#5
Qi You, Hengyu Yan, Yue Liu, Xin Yi, Kang Zhang, Wenying Xu, Zhen Su
The 22-nucleotide non-coding microRNAs (miRNAs) are mostly transcribed by RNA polymerase II and are similar to protein-coding genes. Unlike the clear process from stem-loop precursors to mature miRNAs, the primary transcriptional regulation of miRNA, especially in plants, still needs to be further clarified, including the original transcription start site, functional cis-elements and primary transcript structures. Due to several well-characterized transcription signals in the promoter region, we proposed a systemic approach integrating multidimensional "omics" (including genomics, transcriptomics, and epigenomics) data to improve the genome-wide identification of primary miRNA transcripts...
December 28, 2016: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28031467/maternal-sall4-is-indispensable-for-epigenetic-maturation-of-mouse-oocytes
#6
Kai Xu, Xia Chen, Hui Yang, Yiwen Xu, Yuanlin He, Chenfei Wang, Hua Huang, Baodong Liu, Wenqiang Liu, Jingyi Li, Xiaochen Kou, Yanhong Zhao, Kun Zhao, Linfeng Zhang, Zhenzhen Hou, Hong Wang, Hailin Wang, Jing Li, Hengyu Fan, Fengchao Wang, Yawei Gao, Yong Zhang, Jiayu Chen, Shaorong Gao
Splat-like 4 (Sall4) plays important roles in maintaining pluripotency of embryonic stem cells and in various developmental processes. Here, we find that Sall4 is highly expressed in oocytes and early embryos. To investigate the roles of SALL4 in oogenesis, we generated Sall4 maternal specific knockout mice by using CRISPR/Cas9 system. And we find that the maternal deletion of Sall4 causes developmental arrest of oocytes at germinal vesicle stage with non-surrounded nucleus and the subsequent meiosis resumption is prohibited...
December 28, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28028175/the-transcriptional-corepressor-sin3-directly-regulates-genes-involved-in-methionine-catabolism-and-affects-histone-methylation-linking-epigenetics-and-metabolism
#7
Mengying Liu, Lori A Pile
Chromatin modification and cellular metabolism are tightly connected. Chromatin modifiers regulate the expression of genes involved in metabolism and, in turn, the levels of metabolites. The generated metabolites are utilized by chromatin modifiers to affect epigenetic modification. The mechanism for this cross-talk, however, remains incompletely understood. The corepressor SIN3 controls histone acetylation through association with the histone deacetylase RPD3. The SIN3 complex is known to regulate genes involved in a number of metabolic processes...
December 27, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28007739/ischemic-preconditioning-confers-epigenetic-repression-of-mtor-and-induction-of-autophagy-through-g9a-dependent-h3k9-dimethylation
#8
Olof Gidlöf, Andrea L Johnstone, Kerstin Bader, Bohdan B Khomtchouk, Jiaqi J O'Reilly, Selvi Celik, Derek J Van Booven, Claes Wahlestedt, Bernhard Metzler, David Erlinge
BACKGROUND: Ischemic preconditioning (IPC) protects the heart from prolonged ischemic insult and reperfusion injury through a poorly understood mechanism. Post-translational modifications of histone residues can confer rapid and drastic switches in gene expression in response to various stimuli, including ischemia. The aim of this study was to investigate the effect of histone methylation in the response to cardiac ischemic preconditioning. METHODS AND RESULTS: We used cardiac biopsies from mice subjected to IPC to quantify global levels of 3 of the most well-studied histone methylation marks (H3K9me2, H3K27me3, and H3K4me3) with Western blot and found that H3K9me2 levels were significantly increased in the area at risk compared to remote myocardium...
December 22, 2016: Journal of the American Heart Association
https://www.readbyqxmd.com/read/28004446/is-h3k4me3-instructive-for-transcription-activation
#9
Françoise S Howe, Harry Fischl, Struan C Murray, Jane Mellor
Tri-methylation of lysine 4 on histone H3 (H3K4me3) is a near-universal chromatin modification at the transcription start site of active genes in eukaryotes from yeast to man and its levels reflect the amount of transcription. Because of this association, H3K4me3 is often described as an 'activating' histone modification and assumed to have an instructive role in the transcription of genes, but the field is lacking a conserved mechanism to support this view. The overwhelming finding from genome-wide studies is that actually very little transcription changes upon removal of most H3K4me3 under steady-state or dynamically changing conditions, including at mammalian CpG island promoters...
January 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/27999180/a-ketogenic-diet-rescues-hippocampal-memory-defects-in-a-mouse-model-of-kabuki-syndrome
#10
Joel S Benjamin, Genay O Pilarowski, Giovanni A Carosso, Li Zhang, David L Huso, Loyal A Goff, Hilary J Vernon, Kasper D Hansen, Hans T Bjornsson
Kabuki syndrome is a Mendelian intellectual disability syndrome caused by mutations in either of two genes (KMT2D and KDM6A) involved in chromatin accessibility. We previously showed that an agent that promotes chromatin opening, the histone deacetylase inhibitor (HDACi) AR-42, ameliorates the deficiency of adult neurogenesis in the granule cell layer of the dentate gyrus and rescues hippocampal memory defects in a mouse model of Kabuki syndrome (Kmt2d(+/βGeo)). Unlike a drug, a dietary intervention could be quickly transitioned to the clinic...
January 3, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27994035/arabidopsis-swi-snf-chromatin-remodeling-complex-binds-both-promoters-and-terminators-to-regulate-gene-expression
#11
Rafal Archacki, Ruslan Yatusevich, Daniel Buszewicz, Katarzyna Krzyczmonik, Jacek Patryn, Roksana Iwanicka-Nowicka, Przemyslaw Biecek, Bartek Wilczynski, Marta Koblowska, Andrzej Jerzmanowski, Szymon Swiezewski
ATP-dependent chromatin remodeling complexes are important regulators of gene expression in Eukaryotes. In plants, SWI/SNF-type complexes have been shown critical for transcriptional control of key developmental processes, growth and stress responses. To gain insight into mechanisms underlying these roles, we performed whole genome mapping of the SWI/SNF catalytic subunit BRM in Arabidopsis thaliana, combined with transcript profiling experiments. Our data show that BRM occupies thousands of sites in Arabidopsis genome, most of which located within or close to genes...
December 19, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27993776/fccac-functional-canonical-correlation-analysis-to-evaluate-covariance-between-nucleic-acid-sequencing-datasets
#12
Pedro Madrigal
: : Computational evaluation of variability across DNA or RNA sequencing datasets is a crucial step in genomic science, as it allows both to evaluate reproducibility of biological or technical replicates, and to compare different datasets to identify their potential correlations. Here we present fCCAC, an application of functional canonical correlation analysis to assess covariance of nucleic acid sequencing datasets such as chromatin immunoprecipitation followed by deep sequencing (ChIP-seq)...
December 19, 2016: Bioinformatics
https://www.readbyqxmd.com/read/27993679/epigenetic-activation-of-sin1-promotes-nsclc-cell-proliferation-and-metastasis-by-affecting-the-epithelial-mesenchymal-transition
#13
Zhongwu Hu, Yaqin Wang, Yuemei Wang, Bao Zang, Hongxia Hui, Zhenbing You, Xiaowei Wang
Stress-activated protein kinase (SAPK) interacting protein 1 (SIN1) is an essential component of mTORC2. Previous studies have shown that SIN1 is a key regulator of Akt pathway which plays an important role in various pathological conditions including cancer. While its effects and mechanisms on the progression of NSCLC remain unknown. In this study, we report that SIN1 is able to promote the growth and migration of NSCLC cells both in vitro and in vivo. Overexpression of SIN1 promoted A549 and H1299 cells proliferation by both MTT and colony formation assays...
December 18, 2016: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/27992400/the-histone-demethylase-utx-regulates-the-lineage-specific-epigenetic-program-of-invariant-natural-killer-t-cells
#14
Semir Beyaz, Ji Hyung Kim, Luca Pinello, Michael E Xifaras, Yu Hu, Jialiang Huang, Marc A Kerenyi, Partha P Das, R Anthony Barnitz, Aurelie Herault, Rizkullah Dogum, W Nicholas Haining, Ömer H Yilmaz, Emmanuelle Passegue, Guo-Cheng Yuan, Stuart H Orkin, Florian Winau
Invariant natural killer T cells (iNKT cells) are innate-like lymphocytes that protect against infection, autoimmune disease and cancer. However, little is known about the epigenetic regulation of iNKT cell development. Here we found that the H3K27me3 histone demethylase UTX was an essential cell-intrinsic factor that controlled an iNKT-cell lineage-specific gene-expression program and epigenetic landscape in a demethylase-activity-dependent manner. UTX-deficient iNKT cells exhibited impaired expression of iNKT cell signature genes due to a decrease in activation-associated H3K4me3 marks and an increase in repressive H3K27me3 marks within the promoters occupied by UTX...
December 19, 2016: Nature Immunology
https://www.readbyqxmd.com/read/27984043/myeloid-leukemia-factor-acts-in-a-chaperone-complex-to-regulate-transcription-factor-stability-and-gene-expression
#15
Jamie O Dyer, Arnob Dutta, Madelaine Gogol, Vikki M Weake, George Dialynas, Xilan Wu, Christopher Seidel, Ying Zhang, Laurence Florens, Michael P Washburn, Susan M Abmayr, Jerry L Workman
Mutations that affect Myeloid Leukemia Factor (MLF) proteins are associated with leukemia and several other cancers. However, with no strong homology to other proteins of known function, the role of MLF proteins in the cell has remained elusive. Here we describe a proteomics approach that identifies MLF as a member of a nuclear chaperone complex containing a DnaJ protein, BAG2 and Hsc70. This complex associates with chromatin and regulates expression of target genes. The MLF complex is bound to sites of nucleosome depletion and sites containing active chromatin marks (e...
October 27, 2016: Journal of Molecular Biology
https://www.readbyqxmd.com/read/27979968/rag-recombinase-as-a-selective-pressure-for-genome-evolution
#16
D Passagem-Santos, M Bonnet, D Sobral, I Trancoso, J G Silva, V M Barreto, A Athanasiadis, J Demengeot, J B Pereira-Leal
The RAG recombinase is a domesticated transposable element co-opted in jawed vertebrates to drive the process of the so-called V(D)J recombination, which is the hallmark of the adaptive immune system to produce antigen receptors. RAG targets, namely, the Recombination Signal Sequences (RSS), are rather long and degenerated sequences, which highlights the ability of the recombinase to interact with a wide range of target sequences, including outside of antigen receptor loci. The recognition of such cryptic targets by the recombinase threatens genome integrity by promoting aberrant DNA recombination, as observed in lymphoid malignancies...
December 14, 2016: Genome Biology and Evolution
https://www.readbyqxmd.com/read/27979589/in-vitro-hydroquinone-induced-instauration-of-histone-bivalent-mark-on-human-retroelements-line-1-in-hl60-cells
#17
Monica Mancini, Martina Mandruzzato, Alba C Garzia, Nora Sahnane, Elena Magnani, Filippo Macchi, Mustapha Oulad-Abdelghani, Pierre Oudet, Valentina Bollati, Silvia Fustinoni, Daniela Furlan, Ian M Bonapace
Benzene is extensively used in industry despite its leukemogenic activity, representing a significant occupational hazard. We investigated if long-term treatment with low-doses hydroquinone (HQ), a benzene metabolite, might be sufficient to alter in vitro the epigenetic signature underlining LINE-1 sequences, a poorly explored step in health risks associated with benzene exposure. In HL-60 cell line, exploring the epigenetic events occurring in chromatin, we found the transient instauration of the distinctive signature combining the repressive H3Lys27 tri-methylation mark and the activating H3Lys4 tri-methylation mark (H3K27me3/H3K4me3), indicating a tendency toward a poised chromatin conformation...
December 13, 2016: Toxicology in Vitro: An International Journal Published in Association with BIBRA
https://www.readbyqxmd.com/read/27942458/single-nucleotide-level-mapping-of-dna-double-strand-breaks-in-human-hek293t-cells
#18
Bernard J Pope, Khalid Mahmood, Chol-Hee Jung, Peter Georgeson, Daniel J Park
Constitutional biological processes involve the generation of DNA double-strand breaks (DSBs). The production of such breaks and their subsequent resolution are also highly relevant to neurodegenerative diseases and cancer, in which extensive DNA fragmentation has been described Stephens et al. (2011), Blondet et al. (2001). Tchurikov et al. Tchurikov et al. (2011, 2013) have reported previously that frequent sites of DSBs occur in chromosomal domains involved in the co-ordinated expression of genes. This group report that hot spots of DSBs in human HEK293T cells often coincide with H3K4me3 marks, associated with active transcription Kravatsky et al...
March 2017: Genomics Data
https://www.readbyqxmd.com/read/27939396/a-role-for-peroxisome-proliferator-activated-receptor-gamma-coactivator-1%C3%AE-in-nucleus-accumbens-neuron-subtypes-in-cocaine-action
#19
Ramesh Chandra, Michel Engeln, T Chase Francis, Prasad Konkalmatt, Dipal Patel, Mary Kay Lobo
BACKGROUND: Molecules critically involved in cocaine behavioral plasticity are known to regulate and interact with peroxisome proliferator-activated receptor gamma coactivator-1α (PGC-1α). In addition, the PGC-1α promoter has binding sites for early growth response 3 (Egr3), which plays a dynamic role in cocaine action in nucleus accumbens (NAc) medium spiny neuron (MSN) subtypes, those enriched in dopamine receptor D1 (D1-MSN) versus D2 (D2-MSN). However, the role of PGC-1α in NAc in cocaine action is unknown...
October 28, 2016: Biological Psychiatry
https://www.readbyqxmd.com/read/27934912/bix01294-an-inhibitor-of-histone-methyltransferase-induces-autophagy-dependent-differentiation-of-glioma-stem-like-cells
#20
Iwona Anna Ciechomska, Piotr Przanowski, Judyta Jackl, Bartosz Wojtas, Bozena Kaminska
Glioblastoma (GBM) contains rare glioma stem-like cells (GSCs) with capacities of self-renewal, multi-lineage differentiation, and resistance to conventional therapy. Drug-induced differentiation of GSCs is recognized as a promising approach of anti-glioma therapy. Accumulating evidence suggests that unique properties of stem cells depend on autophagy. Here we demonstrate that BIX01294, an inhibitor of a G9a histone methyltransferase (introducing H3K9me2 and H3K27me3 repressive marks) triggers autophagy in human glioma cells...
December 9, 2016: Scientific Reports
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