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https://www.readbyqxmd.com/read/28105934/charm-discovery-of-combinatorial-chromatin-modification-patterns-in-hepatitis-b-virus-x-transformed-mouse-liver-cancer-using-association-rule-mining
#1
Sung Hee Park, Sun-Min Lee, Young-Joon Kim, Sangsoo Kim
BACKGROUND: Various chromatin modifications, identified in large-scale epigenomic analyses, are associated with distinct phenotypes of different cells and disease phases. To improve our understanding of these variations, many computational methods have been developed to discover novel sites and cell-specific chromatin modifications. Despite the availability of existing methods, there is still room for further improvement when they are applied to resolve the histone code hypothesis. Hence, we aim to investigate the development of a computational method to provide new insights into de novo combinatorial pattern discovery of chromatin modifications to characterize epigenetic variations in distinct phenotypes of different cells...
December 13, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/28105224/suppression-of-pdcd4-mediated-by-the-long-non-coding-rna-hotair-inhibits-the-proliferation-and-invasion-of-glioma-cells
#2
Yong'An Chen, Yusong Bian, Shanpeng Zhao, Fanqiang Kong, Xin'Gang Li
Programmed cell death protein 4 (PDCD4) has recently been demonstrated to be implicated in translation and transcription, and the regulation of cell growth. However, the mechanisms underlying PDCD4 function in glioma cells remain to be elucidated. The current study investigated the function and regulation of PDCD4 and the results demonstrated that the expression of PDCD4 was significantly reduced in glioma cells compared with normal cells. When PDCD4 was overexpressed in glioma cells, the proliferation rate and invasive capability of the cells greatly decreased, suggesting that PDCD4 functions as a tumor suppressor in this cell type...
December 2016: Oncology Letters
https://www.readbyqxmd.com/read/28103771/structure-based-study-of-natural-products-with-anti-schistosoma-activity
#3
Ibezim Akachukwu, Olujide Oludayo Olubiyi, Ata Kosisochukwu, Mbah Chika John, Nwodo Ngozi Justina
: Background Schistosomiasis is a parasitic protozoal disease caused by flatworms of the genus Schistosoma. Although the disease threatens millions of lives, it is still at the top list of neglected tropical diseases and praziquantel, the only common schistosocidal drug in use, has records of decreasing efficiency and cases of resistance. Also, reports revealed that people in the rural areas, who are most affected, rely mostly on traditional herbal medicines because of limited access to modern healthcare...
January 19, 2017: Current Computer-aided Drug Design
https://www.readbyqxmd.com/read/28102705/the-acetyl-code-in-rheumatoid-arthritis-and-other-rheumatic-diseases
#4
Chiara Angiolilli, Dominique L Baeten, Timothy R Radstake, Kris A Reedquist
Growing evidence supports the idea that aberrancies in epigenetic processes contribute to the onset and progression of human immune-mediated inflammatory diseases, such as rheumatoid arthritis (RA). Epigenetic regulators of histone tail modifications play a role in chromatin accessibility and transcriptional responses to inflammatory stimuli. Among these, histone deacetylases (HDACs) regulate the acetylation status of histones and nonhistone proteins, essential for immune responses. Broad-spectrum HDAC inhibitors are well-known anti-inflammatory agents and reduce disease severity in animal models of arthritis; however, selective HDAC inhibitors remain poorly studied...
January 19, 2017: Epigenomics
https://www.readbyqxmd.com/read/28101820/insulin-insulin-like-growth-factor-1-signalling-iis-based-regulation-of-lifespan-across-species
#5
REVIEW
Rebecca Mathew, Manika Pal Bhadra, Utpal Bhadra
An organism's well-being is facilitated by numerous molecular and biochemical pathways that ensure homeostasis within cells and tissues. Aging causes a gradual let-down in the maintenance of homeostasis due to various endogenous and environmental challenges, leading to amassing of damages, functional deterioration of different tissues and vulnerability to ailments. Nutrient sensing pathways that maintain glucose homeostasis in body are involved in regulation of aging. Insulin/insulin-like growth factor-1 (IGF-1) signalling (IIS) pathway was the first nutrient sensing pathway discovered to affect the aging process...
January 18, 2017: Biogerontology
https://www.readbyqxmd.com/read/28097824/mechanisms-of-metabolic-memory-and-renal-hypoxia-as-a-therapeutic-target-in-diabetic-kidney-disease
#6
REVIEW
Yosuke Hirakawa, Tetsuhiro Tanaka, Masaomi Nangaku
Diabetic kidney disease (DKD) is a worldwide public health problem. The definition of DKD is being under discussion. Although the term DKD was originally defined as "kidney disease specific to diabetes", DKD frequently means chronic kidney disease (CKD) with diabetes mellitus and includes not only classical diabetic nephropathy, but also kidney dysfunction due to nephrosclerosis and other causes. Metabolic memory plays a crucial role in the progression of various complications of diabetes, including DKD. The mechanisms of metabolic memory in DKD are supposed to include advanced glycation end products, DNA methylation, histone modifications, and non-coding RNA including microRNA...
January 17, 2017: Journal of Diabetes Investigation
https://www.readbyqxmd.com/read/28093893/arabidopsis-thaliana-glutathione-s-transferase-theta-2-interacts-with-rsi1-fld-to-activate-systemic-acquired-resistance
#7
Zeeshan Zahoor Banday, Ashis Kumar Nandi
A partly infected plant develops systemic acquired resistance (SAR) and shows heightened resistance during subsequent infections. The infected parts generate certain mobile signals that travel to the distal tissues and help in activation of SAR. SAR is associated with epigenetic modifications of several defense-related genes. However, the mechanisms by which mobile signals contribute to epigenetic changes are little known. Previously we had shown that the Arabidopsis REDUCED SYSTEMIC IMMUNITY 1 (RSI1, alias FLOWERING LOCUS D; FLD), which codes for a putative histone demethylase is required for the activation of SAR...
January 17, 2017: Molecular Plant Pathology
https://www.readbyqxmd.com/read/28091569/epigenetic-regulation-of-plasmodium-falciparum-clonally-variant-gene-expression-during-development-in-anopheles-gambiae
#8
Elena Gómez-Díaz, Rakiswendé S Yerbanga, Thierry Lefèvre, Anna Cohuet, M Jordan Rowley, Jean Bosco Ouedraogo, Victor G Corces
P. falciparum phenotypic plasticity is linked to the variant expression of clonal multigene families such as the var genes. We have examined changes in transcription and histone modifications that occur during sporogonic development of P. falciparum in the mosquito host. All var genes are silenced or transcribed at low levels in blood stages (gametocyte/ring) of the parasite in the human host. After infection of mosquitoes, a single var gene is selected for expression in the oocyst, and transcription of this gene increases dramatically in the sporozoite...
January 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28089111/the-molecular-landscape-of-colitis-associated-carcinogenesis
#9
Deborah Saraggi, Matteo Fassan, Claudia Mescoli, Marco Scarpa, Nicola Valeri, Andrea Michielan, Renata D'Incá, Massimo Rugge
In spite of the well-established histopathological phenotyping of IBD-associated preneoplastic and neoplastic lesions, their molecular landscape remains to be fully elucidated. Several studies have pinpointed the initiating role of longstanding/relapsing inflammatory insult on the intestinal mucosa, with the activation of different pro-inflammatory cytokines (TNF-α, IL-6, IL-10, IFN-γ), chemokines and metabolites of arachidonic acid resulting in the activation of key transcription factors such as NF-κB. Longstanding inflammation may also modify the intestinal microbiota, prompting the overgrowth of genotoxic microorganisms, which may act as further cancer promoters...
December 21, 2016: Digestive and Liver Disease
https://www.readbyqxmd.com/read/28087897/fgfr1-analyses-in-four-patients-with-hypogonadotropic-hypogonadism-with-split-hand-foot-malformation-implications-for-the-promoter-region
#10
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/28087289/clinical-utility-and-functional-analysis-of-variants-in-atrial-fibrillation-associated-locus-4q25
#11
Yusuke Ebana, Kouichi Ozaki, Lian Liu, Hitoshi Hachiya, Kenzo Hirao, Mitsuaki Isobe, Michiaki Kubo, Toshihiro Tanaka, Tetsushi Furukawa
BACKGROUND: Chromosome 4q25 has been repeatedly identified as atrial fibrillation (AF)-sensitive locus in multiple genome-wide association studies (GWAS) and is considered to hold some clues to AF pathogenesis. We aimed to investigate the clinical utilities in Japanese and to unveil the function of the 4q25 locus in affecting transcription of adjacent genes. METHODS: We conducted AF GWAS in Japanese population (1382 AF cases and 1478 controls) and the replication panel (1666 AF cases and 1229 controls) with detailed clinical information which showed the acceleration of AF onset...
January 10, 2017: Journal of Cardiology
https://www.readbyqxmd.com/read/28076955/post-translational-modifications-of-trypanosoma-cruzi-canonical-and-variant-histones
#12
Gisele F A Picchi, Vanessa Zulkievicz, Marco Aurelio Krieger, Nilson T Zanchin, Samuel Goldenberg, Lyris M F de Godoy
Chagas disease, caused by Trypanosoma cruzi, still affects millions of people around the world. No vaccines neither treatment for chronic Chagas disease are available, and chemotherapy for the acute phase is hindered by limited efficacy and severe side effects. The processes by which the parasite acquires infectivity and survives in different hosts involve tight regulation of gene expression, mainly post-transcriptionally. Nevertheless, chromatin structure/organization of trypanosomatids is similar to other eukaryotes, including histone variants and post-translational modifications...
January 11, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28064387/the-role-of-histone-modifications-and-telomere-alterations-in-the-pathogenesis-of-diffuse-gliomas-in-adults-and-children
#13
REVIEW
Julieann Lee, D A Solomon, Tarik Tihan
Genetic profiling is an increasingly useful tool for sub-classification of gliomas in adults and children. Specific gene mutations, structural rearrangements, DNA methylation patterns, and gene expression profiles are now recognized to define molecular subgroups of gliomas that arise in distinct anatomic locations and patient age groups, and also provide a better prediction of clinical outcomes for glioma patients compared to histologic assessment alone. Understanding the role of these distinctive genetic alterations in gliomagenesis is also important for the development of potential targeted therapeutic interventions...
January 7, 2017: Journal of Neuro-oncology
https://www.readbyqxmd.com/read/28064188/upset-the-drosophila-homologue-of-set3-is-required-for-viability-and-the-proper-balance-of-active-and-repressive-chromatin-marks
#14
Kyle A McElroy, Youngsook Lucy Jung, Barry M Zee, Charlotte I Wang, Peter J Park, Mitzi I Kuroda
Chromatin plays a critical role in faithful implementation of gene expression programs. Different post-translational modifications of histone proteins reflect the underlying state of gene activity, and many chromatin proteins write, erase, bind, or are repelled by these histone marks. One such protein is UpSET, the Drosophila homolog of yeast Set3 and mammalian KMT2E (MLL5). Here we show that UpSET is necessary for the proper balance between active and repressed states. Using CRISPR/Cas-9 editing, we generated S2 cells which are mutant for upset We found that loss of UpSET is tolerated in S2 cells, but that heterochromatin is misregulated, as evidenced by a strong decrease in H3K9me2 levels assessed by bulk histone post-translational modification quantification...
January 6, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28057213/a-new-molecular-mechanism-underlying-the-antitumor-effect-of-dna-methylation-inhibitors-via-an-antiviral-immune-response
#15
Y Saito, T Nakaoka, H Saito
Chromatin remodeling mediated by DNA methylation and histone modifications play critical roles in the transcriptional regulation of protein-coding genes, noncoding RNAs such as microRNAs, and endogenous retroviruses (ERVs). Many studies have shown that aberrant DNA methylation and histone modifications are associated with the initiation and progression of various malignancies. Epigenetic silencing of tumor suppressor genes in cancer is generally mediated by DNA hypermethylation of CpG island promoters and histone modifications such as histone deacetylation, methylation of histone H3 lysine 9 (H3K9), and trimethylation of H3K27...
2017: Advances in Protein Chemistry and Structural Biology
https://www.readbyqxmd.com/read/28054407/from-genetics-to-epigenetics-new-insights-into-keloid-scarring
#16
REVIEW
Yongjing He, Zhenjun Deng, Mansour Alghamdi, Lechun Lu, Mark W Fear, Li He
Keloid scarring is a dermal fibroproliferative response characterized by excessive and progressive deposition of collagen; aetiology and molecular pathology underlying keloid formation and progression remain unclear. Genetic predisposition is important in the pathogenic processes of keloid formation, however, environmental factors and epigenetic mechanisms may also play pivotal roles. Epigenetic modification is a recent area of investigation in understanding the molecular pathogenesis of keloid scarring and there is increasing evidence that epigenetic changes may play a role in induction and persistent activation of fibroblasts in keloid scars...
January 5, 2017: Cell Proliferation
https://www.readbyqxmd.com/read/28053115/cytosine-methylation-at-cpcpg-sites-triggers-accumulation-of-non-cpg-methylation-in-gene-bodies
#17
Nicolae Radu Zabet, Marco Catoni, Filippo Prischi, Jerzy Paszkowski
Methylation of cytosine is an epigenetic mark involved in the regulation of transcription, usually associated with transcriptional repression. In mammals, methylated cytosines are found predominantly in CpGs but in plants non-CpG methylation (in the CpHpG or CpHpH contexts, where H is A, C or T) is also present and is associated with the transcriptional silencing of transposable elements. In addition, CpG methylation is found in coding regions of active genes. In the absence of the demethylase of lysine 9 of histone 3 (IBM1), a subset of body-methylated genes acquires non-CpG methylation...
January 3, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28052964/whole-genome-bisulfite-sequencing-of-human-pancreatic-islets-reveals-novel-differentially-methylated-regions-in-type-2-diabetes-pathogenesis
#18
Petr Volkov, Karl Bacos, Jones K Ofori, Jonathan Lou S Esguerra, Lena Eliasson, Tina Rönn, Charlotte Ling
Current knowledge about the role of epigenetics in type 2 diabetes (T2D) remains limited. Only a few studies have investigated DNA methylation of selected candidate genes or a very small fraction of genomic CpG sites in human pancreatic islets, the tissue of primary pathogenic importance for diabetes. Our aim was to characterize the whole-genome DNA methylation landscape in human pancreatic islets, to identify differentially methylated regions (DMRs) in diabetic islets, and to investigate the function of DMRs in islet biology...
January 4, 2017: Diabetes
https://www.readbyqxmd.com/read/28052439/an-hdac-inhibitor-entinostat-ms-275-partially-prevents-delayed-cranial-suture-closure-in-heterozygous-runx2-null-mice
#19
H S Bae, W J Yoon, Y D Cho, R Islam, H R Shin, B S Kim, J M Lim, M S Seo, S A Cho, K Y Choi, S H Baek, H G Kim, K M Woo, J H Baek, Y S Lee, H M Ryoo
Cleidocranial dysplasia (CCD) is an autosomal dominant skeletal disorder caused by mutations in RUNX2, coding a key transcription factor of early osteogenesis. CCD patients suffer from the developmental defects in cranial bones. Despite numerous investigations and clinical approaches, no therapeutic strategy has been suggested to prevent CCD. Here, we show that fetal administration of Entinostat/MS-275, a class I histone deacetylase (HDAC)-specific inhibitor, partially prevents delayed closure of cranial sutures in Runx2(+/-) mice strain of C57BL/6J by two mechanisms: (1) post-translational acetylation of Runx2 protein, which stabilized the protein and activated its transcriptional activity; and (2) epigenetic regulation of Runx2 and other bone marker genes...
January 4, 2017: Journal of Bone and Mineral Research: the Official Journal of the American Society for Bone and Mineral Research
https://www.readbyqxmd.com/read/28034318/sensitive-and-precise-characterization-of-combinatorial-histone-modifications-by-selective-derivatization-coupled-with-rplc-ethcd-ms-ms
#20
Rijing Liao, Dan Zheng, Aiying Nie, Shaolian Zhou, Haibing Deng, Yuan Gao, Pengyuan Yang, Yanyan Yu, Lin Tan, Wei Qi, Jiaxi Wu, En Li, Wei Yi
Deciphering the combinatorial histone codes has been a long-standing interest in the epigenetics field, which requires the reliable and robust characterization of the post-translational modifications (PTMs) coexisting on histones. To this end, weak cation exchange hydrophilic interaction liquid chromatography is commonly used in middle-down liquid chromatography-mass spectrometry approaches for online separation of variously modified histone peptides. Here we provide a novel strategy that combines the selective histone peptide derivatization using N-hydroxysuccinimide propionate ester with reversed-phase liquid chromatography (RPLC) for the robust, sensitive, and reliable characterization of combinatorial histone PTMs...
January 11, 2017: Journal of Proteome Research
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