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https://www.readbyqxmd.com/read/29671394/higher-order-partial-least-squares-for-predicting-gene-expression-levels-from-chromatin-states
#1
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/29670199/evolutionary-convergence-and-divergence-in-archaeal-chromosomal-proteins-and-chromo-like-domains-from-bacteria-and-eukaryotes
#2
Gurmeet Kaur, Lakshminarayan M Iyer, Srikrishna Subramanian, L Aravind
SH3-fold-β-barrel domains of the chromo-like superfamily recognize epigenetic marks in eukaryotic proteins. Their provenance has been placed either in archaea, based on apparent structural similarity to chromatin-compacting Sul7d and Cren7 proteins, or in bacteria based on the presence of sequence homologs. Using sequence and structural evidence we establish that the archaeal Cren7/Sul7 proteins emerged from a zinc ribbon (ZnR) ancestor. Further, we show that the ancestral eukaryotic chromo-like domains evolved from bacterial versions, likely acquired from early endosymbioses, which already possessed an aromatic cage for recognition of modified amino-groups...
April 18, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29670067/cpg-methylation-changes-g-quadruplex-structures-derived-from-gene-promoters-and-interaction-with-vegf-and-sp1
#3
Kaori Tsukakoshi, Shiori Saito, Wataru Yoshida, Shinichi Goto, Kazunori Ikebukuro
G-quadruplex (G4) is a DNA/RNA conformation that consists of two or more G-tetrads resulting from four-guanine bases connected by Hoogsteen-type hydrogen bonds, which is often found in the telomeres of chromatin, as well as in the promoter regions of genes. The function of G4 in the genomic DNA is being elucidated and some G4-protein interactions have been reported; these are believed to play a role in vital cellular functions. In this study, we focused on CpG methylation, a well-known epigenetic modification of the genomic DNA, especially found in the promoter regions...
April 18, 2018: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/29669339/upregulation-of-lncdq-is-associated-with-poor-prognosis-and-promotes-tumor-progression-via-epigenetic-regulation-of-the-emt-pathway-in-hcc
#4
Bing Zeng, Zewei Lin, Huilin Ye, Di Cheng, Guangtao Zhang, Jindu Zhou, Zhifeng Huang, Meng Wang, Canfeng Cai, Jun Zeng, Chaoming Tang, Jikui Liu
BACKGROUND/AIMS: Long noncoding RNAs (lncRNAs) are key regulators of cancer initiation and progression. In this study, we investigated the clinical value and functional role of LncRNA DQ786243 (LncDQ) in the pathogenesis of hepatocellular carcinoma (HCC). METHODS: To investigate the expression level of LncDQ in HCC, we performed quantitative real-time PCR using total RNA extracted from HCC tumor tissues and their matched non-neoplastic counterparts, as well as from the serum of HCC patients and healthy volunteers...
April 13, 2018: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/29669261/chrebp-deficiency-leads-to-diarrhea-predominant-irritable-bowel-syndrome
#5
Ah-Reum Oh, Seonyong Sohn, Junghoon Lee, Jong-Min Park, Ki Taek Nam, Ki-Baik Hahm, Young-Bum Kim, Ho-Jae Lee, Ji-Young Cha
OBJECTIVE: Fructose malabsorption is a common digestive disorder in which absorption of fructose in the small intestine is impaired. An abnormality of the main intestinal fructose transporter proteins has been proposed as a cause for fructose malabsorption. However the underlying molecular mechanism for this remains unclear. In this study, we investigated whether carbohydrate response element-binding protein (ChREBP) plays a role in intestinal fructose absorption through the regulation of genes involved in fructose transport and metabolism and ion transport...
April 15, 2018: Metabolism: Clinical and Experimental
https://www.readbyqxmd.com/read/29669022/dna-mediated-dimerization-on-a-compact-sequence-signature-controls-enhancer-engagement-and-regulation-by-foxa1
#6
Xuecong Wang, Yogesh Srivastava, Aleksander Jankowski, Vikas Malik, Yuanjie Wei, Ricardo C H Del Rosario, Vlad Cojocaru, Shyam Prabhakar, Ralf Jauch
FOXA1 is a transcription factor capable to bind silenced chromatin to direct context-dependent cell fate conversion. Here, we demonstrate that a compact palindromic DNA element (termed 'DIV' for its diverging half-sites) induces the homodimerization of FOXA1 with strongly positive cooperativity. Alternative structural models are consistent with either an indirect DNA-mediated cooperativity or a direct protein-protein interaction. The cooperative homodimer formation is strictly constrained by precise half-site spacing...
April 14, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29667342/middle-down-characterization-of-the-cell-cycle-dependence-of-histone-h4-post-translational-modifications-and-proteoforms
#7
Tingting Jiang, Michael E Hoover, Matthew V Holt, Michael A Freitas, Alan G Marshall, Nicolas L Young
Post-translational modifications (PTMs) of histones are important epigenetic regulatory mechanisms that are often dysregulated in cancer. We employ middle-down proteomics to investigate the PTMs and proteoforms of histone H4 during cell cycle progression. We use pH gradient weak cation exchange-hydrophilic interaction liquid chromatography (WCX-HILIC) for on-line liquid chromatography-mass spectrometry analysis to separate and analyze the proteoforms of histone H4. This provides enhanced separation of proteoforms, including positional isomers, and simplifies downstream data analysis...
April 17, 2018: Proteomics
https://www.readbyqxmd.com/read/29667321/the-ethanol-extraction-of-prepared-psoralea-corylifolia-induces-apoptosis-and-autophagy-and-alteres-genes-expression-assayed-by-cdna-microarray-in-human-prostate-cancer-pc-3-cells
#8
Chia-Hsin Lin, Shinji Funayama, Shu-Fen Peng, Chao-Lin Kuo, Jing-Gung Chung
Prostate cancer is the most common male reproductive system cancer. The prevalence of prostate cancer in Europe and the United States is higher than that in the Asian region. However, the treatment of prostate cancer remains unsatisfactory. Psoralea corylifolia has been used to cure this disease as Chinese medicine in the Asian region. In this study, we analyzed the components of ethanol extraction of unprepared and prepared P. corylifolia by HPLC. Psoralen and isopsoralen content from the prepared P. corylifolia is twofold higher than that from unprepared, so we use the prepared extraction in this study...
April 18, 2018: Environmental Toxicology
https://www.readbyqxmd.com/read/29667247/the-nuclear-factor-constans-complex-antagonizes-polycomb-repression-to-de-repress-flowering-locus-t-expression-in-response-to-inductive-long-days-in-arabidopsis
#9
Xiao Luo, Zheng Gao, Yizhong Wang, Zhijuan Chen, Wenju Zhang, Jirong Huang, Hao Yu, Yuehui He
Many plants sense the seasonal cues, day length or photoperiod changes, to align the timing of the developmental transition to flowering with changing seasons for reproductive success. Inductive day lengths through the photoperiod pathway induces the expression of FLOWERING LOCUS T (FT) or FT relatives that encode a major mobile florigen to promote flowering. In Arabidopsis thaliana, under inductive long days the photoperiod pathway output CONSTANS (CO) accumulates toward the end of the day and associates with the B and C subunits of Nuclear Factor Y (NF-Y) to form the NF-CO complex that acts to promote FT expression near dusk, whereas Polycomb group (PcG) proteins function to silence FT expression...
April 18, 2018: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/29666907/three-dimensional-analysis-of-nuclear-heterochromatin-distribution-during-early-development-in-the-rabbit
#10
Amélie Bonnet-Garnier, Kiên Kiêu, Tiphaine Aguirre-Lavin, Krisztina Tar, Pierre Flores, Zichuan Liu, Nathalie Peynot, Martine Chebrout, András Dinnyés, Véronique Duranthon, Nathalie Beaujean
Changes to the spatial organization of specific chromatin domains such as constitutive heterochromatin have been studied extensively in somatic cells. During early embryonic development, drastic epigenetic reprogramming of both the maternal and paternal genomes, followed by chromatin remodeling at the time of embryonic genome activation (EGA), have been observed in the mouse. Very few studies have been performed in other mammalian species (human, bovine, or rabbit) and the data are far from complete. During this work, we studied the three-dimensional organization of pericentromeric regions during the preimplantation period in the rabbit using specific techniques (3D-FISH) and tools (semi-automated image analysis)...
April 18, 2018: Chromosoma
https://www.readbyqxmd.com/read/29666116/critical-influences-on-the-pathogenesis-of-follicular-lymphoma
#11
Ralf Küppers, Freda K Stevenson
The development of follicular lymphoma (FL) from a founder B cell with an upregulation of BCL2, via the t(14;18) translocation, to a proliferating clone, poised to undergo further transformation to an aggressive lymphoma, illustrates the opportunistic Darwinian process of tumorigenesis. Protection against apoptosis allows an innocent cell to persist and divide, with dangerous accumulation of further mutational changes, commonly involving inactivation of chromatin-modifying genes. But this is not all. FL cells reflect normal B cells in relying on expression of surface Ig...
April 17, 2018: Blood
https://www.readbyqxmd.com/read/29665352/epigenetic-and-non-epigenetic-functions-of-the-rybp-protein-in-development-and-disease-short-title-the-rybp-drybp-protein
#12
REVIEW
Carolina J Simoes da Silva, Rocío Simón, Ana Busturia
Over the last decades significant advances have been made in our understanding of the molecular mechanisms controlling organismal development. Among these mechanisms the knowledge gained on the roles played by epigenetic regulation of gene expression is extensive. Epigenetic control of transcription requires the function of protein complexes whose specific biochemical activities, such as histone mono-ubiquitylation, affect chromatin compaction and, consequently activation or repression of gene expression. Complexes composed of Polycomb Group (PcG) proteins promote transcriptional silencing while those containing trithorax group (trxG) proteins promote transcriptional activation...
April 14, 2018: Mechanisms of Ageing and Development
https://www.readbyqxmd.com/read/29664021/a-tlr-akt-foxo3-immune-tolerance-like-pathway-disrupts-the-repair-capacity-of-oligodendrocyte-progenitors
#13
Taasin Srivastava, Parham Diba, Justin M Dean, Fatima Banine, Daniel Shaver, Matthew Hagen, Xi Gong, Weiping Su, Ben Emery, Daniel L Marks, Edward N Harris, Bruce Baggenstoss, Paul H Weigel, Larry S Sherman, Stephen A Back
Cerebral white matter injury (WMI) persistently disrupts myelin regeneration by oligodendrocyte progenitor cells (OPCs). We identified a specific bioactive hyaluronan fragment (bHAf) that downregulates myelin gene expression and chronically blocks OPC maturation and myelination via a tolerance-like mechanism that dysregulates pro-myelination signaling via AKT. Desensitization of AKT occurs via TLR4 but not TLR2 or CD44. OPC differentiation was selectively blocked by bHAf in a maturation-dependent fashion at the late OPC (preOL) stage by a noncanonical TLR4/TRIF pathway that induced persistent activation of the FoxO3 transcription factor downstream of AKT...
April 16, 2018: Journal of Clinical Investigation
https://www.readbyqxmd.com/read/29662614/transcriptional-orchestration-of-mitochondrial-homeostasis-in-a-cellular-model-of-pgc-1-related-coactivator-dependent-thyroid-tumor
#14
Solenne Dumont, Soazig Le Pennec, Audrey Donnart, Raluca Teusan, Marja Steenman, Catherine Chevalier, Rémi Houlgatte, Frédérique Savagner
The PGC-1 (Peroxisome proliferator-activated receptor Gamma Coactivator-1) family of coactivators (PGC-1α, PGC-1β, and PRC) plays a central role in the transcriptional control of mitochondrial biogenesis and oxidative phosphorylation (OXPHOS) processes. These coactivators integrate mitochondrial energy production into cell metabolism using complementary pathways. The XTC.UC1 cell line is a mitochondria-rich model of thyroid tumors whose biogenesis is almost exclusively dependent on PRC. Here we aim to propose an integrative view of the cellular pathways regulated by PRC through integration of cDNA and miRNA microarray data and chromatin immunoprecipitation results obtained from XTC...
March 23, 2018: Oncotarget
https://www.readbyqxmd.com/read/29662163/polymer-physics-predicts-the-effects-of-structural-variants-on-chromatin-architecture
#15
Simona Bianco, Darío G Lupiáñez, Andrea M Chiariello, Carlo Annunziatella, Katerina Kraft, Robert Schöpflin, Lars Wittler, Guillaume Andrey, Martin Vingron, Ana Pombo, Stefan Mundlos, Mario Nicodemi
Structural variants (SVs) can result in changes in gene expression due to abnormal chromatin folding and cause disease. However, the prediction of such effects remains a challenge. Here we present a polymer-physics-based approach (PRISMR) to model 3D chromatin folding and to predict enhancer-promoter contacts. PRISMR predicts higher-order chromatin structure from genome-wide chromosome conformation capture (Hi-C) data. Using the EPHA4 locus as a model, the effects of pathogenic SVs are predicted in silico and compared to Hi-C data generated from mouse limb buds and patient-derived fibroblasts...
April 16, 2018: Nature Genetics
https://www.readbyqxmd.com/read/29661843/functional-analysis-of-hif1-histone-chaperone-in-saccharomyces-cerevisiae
#16
Nora S Dannah, Syed Nabeel-Shah, Christoph F Kurat, Sarah A Sabatinos, Jeffrey Fillingham
The Hif1 protein in the yeast Saccharomyces cerevisie is an evolutionarily conserved H3/H4-specific chaperone and a subunit of the nuclear Hat1 complex that catalyzes the acetylation of newly synthesized histone H4. Hif1, as well as its human homolog NASP, has been implicated in an array of chromatin-related processes including histone H3/H4 transport, chromatin assembly and DNA repair. In this study, we elucidate the functional aspects of Hif1. Initially we establish the wide distribution of Hif1 homologs with an evolutionarily conserved pattern of four tetratricopeptide repeats (TPR) motifs throughout the major fungal lineages and beyond...
April 16, 2018: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29660381/arid1a-ablation-leads-to-multiple-drug-resistance-in-ovarian-cancer-via-transcriptional-activation-of-mrp2
#17
Qingyu Luo, Xiaowei Wu, Yiping Zhang, Tong Shu, Fang Ding, Hongyan Chen, Pengfei Zhao, Wan Chang, Xiaolin Zhu, Zhihua Liu
Multiple Drug Resistance (MDR) of ovarian cancer is a severe trouble for clinical treatment and always attributes to a bad prognosis. AT-rich interaction domain 1 A (ARID1A) has been recognized as a bona fide tumor suppressor gene in recent years, with the highest mutation rate in ovarian cancer. Previous study illustrated that ARID1A expression is negatively correlated with chemoresistance of ovarian cancer cases. However, the specific role of ARID1A in chemoresistance of ovarian cancer remains elusive. In this study, we showed that ARID1A knockdown in ovarian cancer cells significantly reduced their apoptosis rate and led to MDR, while ectopic expression of ARID1A showed opposite effects...
April 13, 2018: Cancer Letters
https://www.readbyqxmd.com/read/29660196/genome-wide-hi-c-analysis-reveals-extensive-hierarchical-chromatin-interactions-in-rice
#18
Qianli Dong, Ning Li, Xiaochong Li, Zan Yuan, Dejian Xie, Xiaofei Wang, Jianing Li, Yanan Yu, Jinbin Wang, Baoxu Ding, Zhibin Zhang, Changping Li, Yao Bian, Ai Zhang, Ying Wu, Bao Liu, Lei Gong
The non-random spatial packing of chromosomes in the nucleus plays critical roles in orchestrating gene expression and genome function. Here, we present a Hi-C analysis of the chromatin interaction patterns in rice (Oryza sativa L.) at hierarchical architectural levels. We confirm that rice chromosomes occupy their own territories with certain preferential inter-chromosomal associations. Moderate compartment delimitation and extensive TADs (Topologically Associated Domains) were determined to be associated with heterogeneous genomic compositions and epigenetic marks in the rice genome...
April 16, 2018: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/29660180/a-chromatin-loop-represses-wuschel-expression-in-arabidopsis
#19
Lin Guo, Xiuwei Cao, Yuhao Liu, Jun Li, Yongpeng Li, Dongming Li, Ke Zhang, Caixia Gao, Aiwu Dong, Xigang Liu
WUSCHEL (WUS) is critical for plant meristem maintenance and determinacy in Arabidopsis, and the regulation of its spatiotemporal expression patterns is complex. We previously found that AGAMOUS (AG), a key MADS-domain transcription factor in floral organ identity and floral meristem determinacy, can directly suppress WUS expression through the recruitment of the Polycomb group (PcG) protein TERMINAL FLOWER2 (TFL2, also known as LIKE HETEROCHROMATIN PROTEIN1, LHP1) at the WUS locus. However, the mechanism by which WUS is repressed remains unclear...
April 16, 2018: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/29659982/transcription-start-site-analysis-reveals-widespread-divergent-transcription-in-d-melanogaster-and-core-promoter-encoded-enhancer-activities
#20
Sarah Rennie, Maria Dalby, Marta Lloret-Llinares, Stylianos Bakoulis, Christian Dalager Vaagensø, Torben Heick Jensen, Robin Andersson
Mammalian gene promoters and enhancers share many properties. They are composed of a unified promoter architecture of divergent transcripton initiation and gene promoters may exhibit enhancer function. However, it is currently unclear how expression strength of a regulatory element relates to its enhancer strength and if the unifying architecture is conserved across Metazoa. Here we investigate the transcription initiation landscape and its associated RNA decay in Drosophila melanogaster. We find that the majority of active gene-distal enhancers and a considerable fraction of gene promoters are divergently transcribed...
April 6, 2018: Nucleic Acids Research
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