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H3K4me3

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https://www.readbyqxmd.com/read/29672864/menin-regulates-the-serine-biosynthetic-pathway-in-ewing-sarcoma
#1
Laurie K Svoboda, Selina Shiqing K Teh, Sudha Sud, Samuel Kerk, Aaron Zebolsky, Sydney Treichel, Dafydd Thomas, Christopher J Halbrook, Ho-Joon Lee, Daniel Kremer, Li Zhang, Szymon Klossowski, Armand R Bankhead, Brian Magnuson, Mats Ljungman, Tomasz Cierpicki, Jolanta Grembecka, Costas A Lyssiotis, Elizabeth R Lawlor
Developmental transcription programs are epigenetically regulated by multi-protein complexes, including the menin- and MLL-containing trithorax (TrxG) complexes, which promote gene transcription by depositing the H3K4me3 activating mark at target gene promoters. We recently reported that in Ewing sarcoma, MLL1 (lysine methyltransferase 2A, KMT2A) and menin are overexpressed and function as oncogenes. Small molecule inhibition of the menin-MLL interaction leads to loss of menin and MLL1 protein expression and to inhibition of growth and tumorigenicity...
April 19, 2018: Journal of Pathology
https://www.readbyqxmd.com/read/29671394/higher-order-partial-least-squares-for-predicting-gene-expression-levels-from-chromatin-states
#2
Shiquan Sun, Xifang Sun, Yan Zheng
BACKGROUND: Extensive studies have shown that gene expression levels are strongly affected by chromatin mark combinations via at least two mechanisms, i.e., activation or repression. But their combinatorial patterns are still unclear. To further understand the relationship between histone modifications and gene expression levels, here in this paper, we introduce a purely geometric higher-order representation, tensor (also called multidimensional array), which might borrow more unknown interactions in chromatin states to predicting gene expression levels...
April 11, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/29666467/ascorbic-acid-induces-global-epigenetic-reprogramming-to-promote-meiotic-maturation-and-developmental-competence-of-porcine-oocytes
#3
Xiao-Xia Yu, Yun-Hua Liu, Xiao-Man Liu, Pei-Chao Wang, Shuai Liu, Jia-Kun Miao, Zhi-Qiang Du, Cai-Xia Yang
L-ascorbic acid (Vitamin C) can enhance the meiotic maturation and developmental competence of porcine oocytes, but the underlying molecular mechanism remains obscure. Here we show the role of ascorbic acid in regulating epigenetic status of both nucleic acids and chromatin to promote oocyte maturation and development in pigs. Supplementation of 250 μM L-ascorbic acid 2-phosphate sesquimagnesium salt hydrate (AA2P) during in vitro maturation significantly enhanced the nuclear maturation (as indicated by higher rate of first polar body extrusion and increased Bmp15 mRNA level), reduced level of reactive oxygen species, and promoted developmental potency (higher cleavage and blastocyst rates of parthenotes, and decreased Bax and Caspase3 mRNA levels in blastocysts) of pig oocytes...
April 17, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29665055/s6k1-controls-epigenetic-plasticity-for-the-expression-of-pancreatic-%C3%AE-%C3%AE-cell-marker-genes
#4
Sang Ah Yi, Jieun Lee, Jong Woo Park, Jihoon Han, Min Gyu Lee, Ki Hong Nam, Jee Hun Park, Hwamok Oh, Sung Jin Ahn, Saetbyul Kim, So Hee Kwon, Dong-Gyu Jo, Jeung-Whan Han
The failure of insulin production by pancreatic β cells is a common hallmark of type 1 diabetes mellitus (T1DM). Because administration of exogenous insulin is associated with diabetes-derived complications, endogenous α to β cell transition can be an attractive alternative. Although decreased β cell size and hypoinsulinaemia have been observed in S6K1-deficient mice, the molecular mechanism underlying the involvement of S6K1 in the transcriptional regulation of insulin remains elusive. Here, we show that the hypoinsulinaemic phenotype of S6K1-deficient mice stems from the dysregulated transcription of a set of genes required for insulin and glucagon production...
April 17, 2018: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/29659013/dietary-fat-and-fiber-interact-to-uniquely-modify-global-histone-post-translational-epigenetic-programming-in-a-rat-colon-cancer-progression-model
#5
Karen Triff, Mathew W McLean, Evelyn Callaway, Jennifer Goldsby, Ivan Ivanov, Robert S Chapkin
Dietary fermentable fiber generates short-chain fatty acids (SCFA), e.g., butyrate, in the colonic lumen which serves as a chemoprotective histone deacetylase inhibitor and/or as an acetylation substrate for histone acetylases. In addition, n-3 polyunsaturated fatty acids (n-3 PUFA) in fish oil can affect the chromatin landscape by acting as ligands for tumor suppressive nuclear receptors. In an effort to gain insight into the global dimension of post-translational modification of histones (including H3K4me3 and H3K9ac) and clarify the chemoprotective impact of dietary bioactive compounds on transcriptional control in a preclinical model of colon cancer, we generated high-resolution genome-wide RNA (RNA-Seq) and "chromatin-state" (H3K4me3-seq and H3K9ac-seq) maps for intestinal (epithelial colonocytes) crypts in rats treated with a colon carcinogen and fed diets containing bioactive (i) fish oil, (ii) fermentable fiber (a rich source of SCFA), (iii) a combination of fish oil plus pectin or (iv) control, devoid of fish oil or pectin...
April 16, 2018: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/29649476/h2a-z-containing-nucleosomes-are-evicted-to-activate-atmyb44-transcription-in-response-to-salt-stress
#6
Nguyen Hoai Nguyen, Jong-Joo Cheong
Transcripts of the Arabidopsis transcription factor gene, AtMYB44, accumulate rapidly to mediate a tolerance mechanism in response to salt stress. The AtMYB44 promoter is activated by salt stress, as illustrated in AtMYB44pro::GUS transgenic plants. Chromatin immunoprecipitation (ChIP) assays revealed that RNA polymerases were enriched on the AtMYB44 gene, especially on TSS-proximal regions, and nucleosome density was markedly reduced in the AtMYB44 gene-body region in response to salt stress. In addition, H2A...
April 9, 2018: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29649410/sca1-lin-cd117-mouse-bone-marrow-derived-mesenchymal-stem-cells-regulate-immature-dendritic-cell-maturation-by-inhibiting-tlr4-irf8-signaling-via-the-notch-rbp-j-pathway
#7
Xingxia Liu, ShaoDa Ren, Chaozhuo Ge, Kai Cheng, Xiaojing Li, Robert Chunhua Zhao
Mesenchymal stem cells (MSCs) have a superior immunomodulatory capacity compared to other cells of the immune system, and they hold great promise for treating various immune disorders. However, their regulatory effects on the maturation of immature dendritic cells (imDCs) are not fully understood. Here, we show that Sca-1+Lin-CD117-MSCs restrain the LPS-stimulated maturation transition of imDCs co-cultured without exogenous cytokines. The Notch signaling pathway plays a critical role in the process by controlling IRF8 expression in an RBP-J-dependent manner...
March 13, 2018: Stem Cells and Development
https://www.readbyqxmd.com/read/29643185/expression-of-mutant-asxl1-perturbs-hematopoiesis-and-promotes-susceptibility-to-leukemic-transformation
#8
Reina Nagase, Daichi Inoue, Alessandro Pastore, Takeshi Fujino, Hsin-An Hou, Norimasa Yamasaki, Susumu Goyama, Makoto Saika, Akinori Kanai, Yasuyuki Sera, Sayuri Horikawa, Yasunori Ota, Shuhei Asada, Yasutaka Hayashi, Kimihito Cojin Kawabata, Reina Takeda, Hwei-Fang Tien, Hiroaki Honda, Omar Abdel-Wahab, Toshio Kitamura
Additional sex combs like 1 ( ASXL1 ) is frequently mutated in myeloid malignancies and clonal hematopoiesis of indeterminate potential (CHIP). Although loss of ASXL1 promotes hematopoietic transformation, there is growing evidence that ASXL1 mutations might confer an alteration of function. In this study, we identify that physiological expression of a C-terminal truncated Asxl1 mutant in vivo using conditional knock-in (KI) results in myeloid skewing, age-dependent anemia, thrombocytosis, and morphological dysplasia...
April 11, 2018: Journal of Experimental Medicine
https://www.readbyqxmd.com/read/29624717/sirt3-restricts-hbv-transcription-and-replication-via-epigenetic-regulation-of-cccdna-involving-suv39h1-and-setd1a-histone-methyltransferases
#9
Ji-Hua Ren, Jie-Li Hu, Sheng-Tao Cheng, Hai-Bo Yu, Vincent Kam Wai Wong, Betty Yuen Kwan Law, Yong-Feng Yang, Ying Huang, Yi Liu, Wei-Xian Chen, Xue-Fei Cai, Hua Tang, Yuan Hu, Wen-Lu Zhang, Xiang Liu, Quan-Xin Long, Li Zhou, Na-Na Tao, Hong-Zhong Zhou, Qiu-Xia Yang, Fang Ren, Lin He, Rui Gong, Ai-Long Huang, Juan Chen
Hepatitis B virus (HBV) infection remains a major health problem worldwide. Maintenance of the covalently closed circular DNA (cccDNA) which serves as a template for HBV RNA transcription is responsible for the failure of eradicating chronic HBV during current antiviral therapy. cccDNA is assembled with cellular histone proteins into chromatin, but little is known about the regulation of HBV chromatin by histone posttranslational modifications. In this study, we identified SIRT3 as a host factor restricting HBV transcription and replication by screening seven members of Sirtuin family which is the class III histone deacetylase...
April 6, 2018: Hepatology: Official Journal of the American Association for the Study of Liver Diseases
https://www.readbyqxmd.com/read/29616070/the-rice-rolled-fine-striped-rfs-chd3-mi-2-chromatin-remodeling-factor-epigenetically-regulates-genes-involved-in-oxidative-stress-responses-during-leaf-development
#10
Sung-Hwan Cho, Chung-Hee Lee, Eunji Gi, Yehyun Yim, Hee-Jong Koh, Kiyoon Kang, Nam-Chon Paek
In rice ( Oryza sativa ), moderate leaf rolling increases photosynthetic competence and raises grain yield; therefore, this important agronomic trait has attracted much attention from plant biologists and breeders. However, the relevant molecular mechanism remains unclear. Here, we isolated and characterized Rolled Fine Striped ( RFS ), a key gene affecting rice leaf rolling, chloroplast development, and reactive oxygen species (ROS) scavenging. The rfs-1 gamma-ray allele and the rfs-2 T-DNA insertion allele of RFS failed to complement each other and their mutants had similar phenotypes, producing extremely incurved leaves due to defective development of vascular cells on the adaxial side...
2018: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29611871/sip1-participates-in-regulation-of-flowering-time-in-rice-by-recruiting-ostrx1-to-ehd1
#11
Pengfei Jiang, Shiliang Wang, Han Zheng, Hao Li, Fei Zhang, Yanhua Su, Zuntao Xu, Haiyan Lin, Qian Qian, Yong Ding
Flowering time (heading date) in rice (Oryza sativa) is an important agronomic trait that determines yield. The levels of histone H3 lysine 4 trimethylation (H3K4me3) modulated by TRITHORAX-like proteins regulate gene transcription, flowering time and environmental stress responses. However, plant TRITHORAX-like proteins have no known DNA-binding domain, and therefore the mechanism that gives sequence specificity to these proteins remains unclear. Here, we show that the rice TRITHORAX-like protein OsTrx1 is recruited to its target, Early heading date 1 (Ehd1), by the C2H2 zinc finger protein SDG723/OsTrx1/OsSET33 Interaction Protein 1 (SIP1)...
April 3, 2018: New Phytologist
https://www.readbyqxmd.com/read/29593737/overall-downregulation-of-mrnas-and-enrichment-of-h3k4me3-change-near-genome-wide-association-study-signals-in-systemic-lupus-erythematosus-cell-specific-effects
#12
Zhe Zhang, Lihua Shi, Li Song, Kelly Maurer, Michele A Petri, Kathleen E Sullivan
This study was designed to define gene expression and H3K4me3 histone modifications in T cells, B cells, and monocytes in systemic lupus erythematosus (SLE). Array studies of total peripheral blood mononuclear cells have demonstrated gene expression signatures related to neutrophils, interferon, and other inflammatory pathways. It is not clear how consistent these effects are across different cell types. In this study, RNA-seq and chromatin immunoprecipitation-seq were utilized to identify gene expression patterns and H3K4me3 histone modifications related to promoter activation in SLE...
2018: Frontiers in Immunology
https://www.readbyqxmd.com/read/29592776/epigenetic-dynamics-of-hoxa10-gene-in-infertile-women-with-endometriosis
#13
Yasaman Samadieh, Raha Favaedi, Fariba Ramezanali, Parvaneh Afsharian, Reza Aflatoonian, Maryam Shahhoseini
Endometriosis, which has been considered an epigenetic disease, is a prevalent gynecological disorder worldwide. With an emphasis on changes in the HOXA10 gene expression of the endometrium of women with endometriosis, the aim of this study was to investigate HOXA10 gene expression and its correlation with the epigenetic characteristics of the specific promoter region of the gene in the eutopic and ectopic endometrium of women with endometriosis. Thirty-six patients and 21 healthy fertile women were recruited as participants of this study...
January 1, 2018: Reproductive Sciences
https://www.readbyqxmd.com/read/29581424/a-comprehensive-map-coupling-histone-modifications-with-gene-regulation-in-adult-dopaminergic-and-serotonergic-neurons
#14
Erik Södersten, Konstantinos Toskas, Vilma Rraklli, Katarina Tiklova, Åsa K Björklund, Markus Ringnér, Thomas Perlmann, Johan Holmberg
The brain is composed of hundreds of different neuronal subtypes, which largely retain their identity throughout the lifespan of the organism. The mechanisms governing this stability are not fully understood, partly due to the diversity and limited size of clinically relevant neuronal populations, which constitute a technical challenge for analysis. Here, using a strategy that allows for ChIP-seq combined with RNA-seq in small neuronal populations in vivo, we present a comparative analysis of permissive and repressive histone modifications in adult midbrain dopaminergic neurons, raphe nuclei serotonergic neurons, and embryonic neural progenitors...
March 26, 2018: Nature Communications
https://www.readbyqxmd.com/read/29579310/transcriptional-and-epigenetic-adaptation-of-maize-chromosomes-in-oat-maize-addition-lines
#15
Zhaobin Dong, Juan Yu, Hui Li, Wei Huang, Ling Xu, Yue Zhao, Tao Zhang, Wenying Xu, Jiming Jiang, Zhen Su, Weiwei Jin
By putting heterologous genomic regulatory systems into contact, chromosome addition lines derived from interspecific or intergeneric crosses allow the investigation of transcriptional regulation in new genomic environments. Here, we report the transcriptional and epigenetic adaptation of stably inherited alien maize chromosomes in two oat-maize addition (OMA) lines. We found that the majority of maize genes displayed maize-specific transcription in the oat genomic environment. Nevertheless, a quarter of the expressed genes encoded by the two maize chromosomes were differentially expressed genes (DEGs)...
March 20, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29576547/expression-specificity-and-compensation-effect-of-ash2l-1-ash2l-2-in-mouse-embryonic-stem-cells
#16
Jing Xie, Chen Fan, Jing-Long Zhang, Shi-Qiang Zhang
H3K4me3 is an important epigenetic modification that plays a critical role in maintaining self-renewal of mouse embryonic stem cells (mESCs). H3K4me3 is catalyzed mainly by the mixed lineage leukemia (MLL) methyl-transferase complex. ASH2L, a core subunit of the MLL complex, participates in regulating the open state of chromatin in mESCs. There are two isoforms of the ASH2L protein: ASH2L-1 (80 kDa), which only exists in mouse embryonic fibroblasts and ASH2L-2 (65 kDa), which is the predominant isoform in mESCs...
March 20, 2018: Yi Chuan, Hereditas
https://www.readbyqxmd.com/read/29565495/down-regulation-of-jarid1b-expression-inhibits-cell-proliferation-induces-apoptosis-and-blocks-cell-cycle-in-human-acute-lymphoblastic-leukemia-cells
#17
Y-Q Huang, Y Zou, R-J Zheng, X-D Ma
OBJECTIVE: Acute lymphocytic leukemia (ALL) is a multi-factorial blood disease with unknown pathogenesis. Histone H3K4 methylation was significantly reduced in ALL patients, whereas jumonji AT-rich interactive domain 1B (JARID1B) was the specific demethylase of H3K4me. This study explores the expression level of JARID1B in ALL patients and down-regulated JARID1B expression in ALL cells to explore the function of JARID1B in ALL. PATIENTS AND METHODS: JARID1B mRNA expression level in ALL patients was detected by Real-time PCR...
March 2018: European Review for Medical and Pharmacological Sciences
https://www.readbyqxmd.com/read/29556340/the-role-of-ptrf-cavin1-as-a-biomarker-in-both-glioma-and-serum-exosomes
#18
Kai Huang, Chuan Fang, Kaikai Yi, Xing Liu, Hongzhao Qi, Yanli Tan, Junhu Zhou, Ying Li, Mingyang Liu, Yuqing Zhang, Jingxuan Yang, Jianning Zhang, Min Li, Chunsheng Kang
Exosomes play critical roles in intercellular communication in both nearby and distant cells in individuals and organs. Polymerase I and transcript release factor (PTRF), also known as Cavin1, has previously been described as a critical factor in caveola formation, and aberrant PTRF expression has been reported in various malignancies. However, the function of PTRF in tumor progression remains controversial, and its role in glioma is poorly understood. In this study, we report that PTRF is associated with malignancy grade and poor prognosis in glioma patients...
2018: Theranostics
https://www.readbyqxmd.com/read/29531162/-lnc-chop-promotes-immunosuppressive-function-of-myeloid-derived-suppressor-cells-in-tumor-and-inflammatory-environments
#19
Yunhuan Gao, Tiantian Wang, Yuanyuan Li, Yuan Zhang, Rongcun Yang
Myeloid-derived suppressor cells (MDSCs) are major regulators of immune responses in cancer. Both C/EBP homologous protein (CHOP) and C/EBPβ play a critical role in regulating immunosuppressive function of MDSCs. In this study, we identified a novel long noncoding RNA termed as lnc-chop in MDSCs, which may interact with CHOP and the C/EBPβ isoform liver-enriched inhibitory protein. The binding of lnc-chop with both CHOP and the C/EBPβ isoform liver-enriched inhibitory protein promoted the activation of C/EBPβ and upregulated the expression of arginase-1, NO synthase 2, NADPH oxidase 2, and cyclooxygenase-2, which are related to the immunosuppressive function of MDSCs in inflammatory and tumor environments...
March 12, 2018: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/29530928/nucleosomes-and-dna-methylation-shape-meiotic-dsb-frequency-in-arabidopsis-thaliana-transposons-and-gene-regulatory-regions
#20
Kyuha Choi, Xiaohui Zhao, Andrew J Tock, Christophe Lambing, Charles J Underwood, Thomas J Hardcastle, Heïdi Serra, Juhyun Kim, Hyun Seob Cho, Jaeil Kim, Piotr A Ziolkowski, Nataliya E Yelina, Ildoo Hwang, Robert A Martienssen, Ian R Henderson
Meiotic recombination initiates from DNA double-strand breaks (DSBs) generated by SPO11 topoisomerase-like complexes. Meiotic DSB frequency varies extensively along eukaryotic chromosomes, with hotspots controlled by chromatin and DNA sequence. To map meiotic DSBs throughout a plant genome, we purified and sequenced Arabidopsis thaliana SPO11-1-oligonucleotides. SPO11-1-oligos are elevated in gene promoters, terminators, and introns, which is driven by AT-sequence richness that excludes nucleosomes and allows SPO11-1 access...
March 12, 2018: Genome Research
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