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https://www.readbyqxmd.com/read/28931929/a-resource-of-large-scale-molecular-markers-for-monitoring-agropyron-cristatum-chromatin-introgression-in-wheat-background-based-on-transcriptome-sequences
#1
Jinpeng Zhang, Weihua Liu, Yuqing Lu, Qunxing Liu, Xinming Yang, Xiuquan Li, Lihui Li
Agropyron cristatum is a wild grass of the tribe Triticeae and serves as a gene donor for wheat improvement. However, very few markers can be used to monitor A. cristatum chromatin introgressions in wheat. Here, we reported a resource of large-scale molecular markers for tracking alien introgressions in wheat based on transcriptome sequences. By aligning A. cristatum unigenes with the Chinese Spring reference genome sequences, we designed 9602 A. cristatum expressed sequence tag-sequence-tagged site (EST-STS) markers for PCR amplification and experimental screening...
September 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28910411/molecular-population-genetics-of-the-polycomb-genes-in-drosophila-subobscura
#2
Juan M Calvo-Martín, Montserrat Papaceit, Carmen Segarra
Polycomb group (PcG) proteins are important regulatory factors that modulate the chromatin state. They form protein complexes that repress gene expression by the introduction of posttranslational histone modifications. The study of PcG proteins divergence in Drosophila revealed signals of coevolution among them and an acceleration of the nonsynonymous evolutionary rate in the lineage ancestral to the obscura group species, mainly in subunits of the Pcl-PRC2 complex. Herein, we have studied the nucleotide polymorphism of PcG genes in a natural population of D...
2017: PloS One
https://www.readbyqxmd.com/read/28892201/two-brm-promoter-polymorphisms-predict-poor-survival-in-patients-with-hepatocellular-carcinoma
#3
Ivan Pasic, Kit Man Wong, Jonghun John Lee, Osvaldo Espin-Garcia, Yonathan Brhane, Dangxiao Cheng, Zhuo Chen, Devalben Patel, Catherine Brown, Roxana Bucur, David Reisman, Jennifer J Knox, Wei Xu, Rayjean J Hung, Geoffrey Guo, Sean P Cleary
BACKGROUND: Polymorphisms in the promoter of the BRM gene, a critical subunit of the chromatin remodeling SWI/SNF complex, have previously been implicated in risk and prognosis in Caucasian-predominant lung, head and neck, esophageal, and pancreatic cancers, and in hepatocellular cancers in Asians. We investigated the role of these polymorphisms in hepatocellular carcinoma (HCC) risk and prognosis. METHODS: HCC cases were recruited in a comprehensive cancer centre while the matched controls were recruited from family practice units from the same catchment area...
September 11, 2017: Molecular Carcinogenesis
https://www.readbyqxmd.com/read/28879201/wnt-%C3%AE-catenin-pathway-and-epigenetic-mechanisms-regulate-the-pitt-hopkins-syndrome-and-schizophrenia-risk-gene-tcf4
#4
Krista M Hennig, Daniel M Fass, Wen-Ning Zhao, Steven D Sheridan, Ting Fu, Serkan Erdin, Alexei Stortchevoi, Diane Lucente, Jannine D Cody, David Sweetser, James F Gusella, Michael E Talkowski, Stephen J Haggarty
Genetic variation within the transcription factor TCF4 locus can cause the intellectual disability and developmental disorder Pitt-Hopkins syndrome (PTHS), whereas single-nucleotide polymorphisms within noncoding regions are associated with schizophrenia. These genetic findings position TCF4 as a link between transcription and cognition; however, the neurobiology of TCF4 remains poorly understood. Here, we quantitated multiple distinct TCF4 transcript levels in human induced pluripotent stem cell-derived neural progenitors and differentiated neurons, and PTHS patient fibroblasts...
July 2017: Molecular Neuropsychiatry
https://www.readbyqxmd.com/read/28877499/h4-tails-potentially-produce-the-diversity-in-the-orientation-of-two-nucleosomes
#5
Hisashi Ishida, Hidetoshi Kono
Histone tails play an important role in internucleosomal interaction and chromatin compaction. To understand how the H4 tails are involved in the internucleosomal interaction, an adaptively biased molecular dynamics simulation of 63 models of two stacked nucleosomes, each with the H4 tails in different locations, was carried out. This simulation generated a variety of orientations of the separated nucleosomes depending on the formation of the H4 tail bridge between the H4 tails and the DNA of the neighboring nucleosomes...
September 5, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28838355/sixteen-years-of-meiotic-silencing-by-unpaired-dna
#6
T M Hammond
The filamentous fungus Neurospora crassa possesses a process called meiotic silencing by unpaired DNA (MSUD). MSUD has a remarkable ability to scan homologous chromosomes for unpaired DNA during meiosis. After unpaired DNA is identified, MSUD silences all RNA from the unpaired DNA along with any RNA transcribed from homologous sequences at other locations in the genome, regardless of their pairing state. The mechanism by which unpaired DNA is detected is unknown. Unpaired DNA segments can be as short as 1.3kb, if not shorter, and DNA sequences with only a small level of polymorphism (6%) can be considered unpaired by MSUD...
2017: Advances in Genetics
https://www.readbyqxmd.com/read/28817232/crystal-structure-of-the-melampsora-lini-effector-avrp-reveals-insights-into-a-possible-nuclear-function-and-recognition-by-the-flax-disease-resistance-protein-p
#7
Xiaoxiao Zhang, Nadya Farah, Laura Rolston, Daniel J Ericsson, Ann-Maree Catanzariti, Maud Bernoux, Thomas Ve, Katerina Bendak, Chunhong Chen, Joel P Mackay, Gregory J Lawrence, Adrienne Hardham, Jeffrey G Ellis, Simon J Williams, Peter N Dodds, David A Jones, Bostjan Kobe
The effector protein AvrP is secreted by the flax rust fungal pathogen (Melampsora lini) and recognized specifically by the flax (Linum usitatissimum) P disease resistance protein, leading to effector-triggered immunity. To investigate the biological function of this effector and mechanisms of specific recognition by the P resistance protein, we determined the crystal structure of AvrP. The structure reveals an elongated zinc-finger-like structure with a novel interleaved zinc-binding topology. The residues responsible for zinc binding are conserved in AvrP effector variants and mutations of these motifs result in loss of P-mediated recognition...
August 17, 2017: Molecular Plant Pathology
https://www.readbyqxmd.com/read/28801681/nrf1-and-zscan10-bind-to-the-promoter-region-of-the-six1-gene-and-their-effects-body-measurements-in-qinchuan-cattle
#8
Da-Wei Wei, Lin-Sheng Gui, Sayed Haidar Abbas Raza, Song Zhang, Rajwali Khan, Li Wang, Hong-Fang Guo, Lin-Sen Zan
The SIX1 homeobox gene belongs to the six homeodomain family and is widely thought to play a principal role in mediating of skeletal muscle development. In the present study, we determined that the bovine SIX1 gene was highly expressed in the longissimus thoracis and physiologically immature individuals. DNA sequencing of 428 individual Qinchuan cattle identified nine single nucleotide polymorphisms (SNPs) in the promoter region of the SIX1 gene. Using a series of 5' deletion promoter plasmid luciferase reporter assays and 5'-rapid amplification of cDNA end analysis (RACE), two of these SNPs were found to be located in the proximal minimal promoter region -216/-28 relative to the transcriptional start site (TSS)...
August 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28794385/association-between-a-ccl17-genetic-variant-and-risk-of-coronary-artery-disease-in-a-chinese-han-population
#9
Yicong Ye, Xinglin Yang, Bo Long, Haiyu Pang, Yicheng Zhu, Shuyang Zhang
BACKGROUND: In the present study we investigated the effects of genetic variations in the C-C motif chemokine ligand 17 (CCL17) gene on serum CCL17 levels and risk of coronary artery disease (CAD).Methods and Results:A case-control study was conducted to determine causal inferences amongCCL17single-nucleotide polymorphisms (SNPs), serum CCL17 levels, and risk of CAD. Luciferase assays, electrophoretic mobility shift assays (EMSA), and allele-specific quantitative chromatin immunoprecipitation (ChIP) assays were used to assess the function of the SNPs...
August 8, 2017: Circulation Journal: Official Journal of the Japanese Circulation Society
https://www.readbyqxmd.com/read/28755661/association-of-alpha-a-crystallin-polymorphisms-with-susceptibility-to-nuclear-age-related-cataract-in-a-han-chinese-population
#10
Zhennan Zhao, Qi Fan, Peng Zhou, HongFei Ye, Lei Cai, Yi Lu
BACKGROUND: Alpha A-crystallin (CRYAA) is considered critical for the maintenance of lens transparency and is related to the pathogenesis of age-related cataracts (ARCs), especially the nuclear subtype. As the 5' untranslated region (5' UTR) modulates gene expression, the purpose of current study was to investigate whether single nucleotide polymorphisms (SNPs) in the 5' UTR of CRYAA were associated with susceptibility to ARC in a Han Chinese population and to clarify the mechanism of this association...
July 29, 2017: BMC Ophthalmology
https://www.readbyqxmd.com/read/28747224/regions-of-common-inter-individual-dna-methylation-differences-in-human-monocytes-genetic-basis-and-potential-function
#11
Christopher Schröder, Elsa Leitão, Stefan Wallner, Gerd Schmitz, Ludger Klein-Hitpass, Anupam Sinha, Karl-Heinz Jöckel, Stefanie Heilmann-Heimbach, Per Hoffmann, Markus M Nöthen, Michael Steffens, Peter Ebert, Sven Rahmann, Bernhard Horsthemke
BACKGROUND: There is increasing evidence for inter-individual methylation differences at CpG dinucleotides in the human genome, but the regional extent and function of these differences have not yet been studied in detail. For identifying regions of common methylation differences, we used whole genome bisulfite sequencing data of monocytes from five donors and a novel bioinformatic strategy. RESULTS: We identified 157 differentially methylated regions (DMRs) with four or more CpGs, almost none of which has been described before...
July 26, 2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/28722347/foxo3-longevity-interactome-on-chromosome-6
#12
Timothy A Donlon, Brian J Morris, Randi Chen, Kamal H Masaki, Richard C Allsopp, D Craig Willcox, Ayako Elliott, Bradley J Willcox
FOXO3 has been implicated in longevity in multiple populations. By DNA sequencing in long-lived individuals, we identified all single nucleotide polymorphisms (SNPs) in FOXO3 and showed 41 were associated with longevity. Thirteen of these had predicted alterations in transcription factor binding sites. Those SNPs appeared to be in physical contact, via RNA polymerase II binding chromatin looping, with sites in the FOXO3 promoter, and likely function together as a cis-regulatory unit. The SNPs exhibited a high degree of LD in the Asian population, in which they define a specific longevity haplotype that is relatively common...
October 2017: Aging Cell
https://www.readbyqxmd.com/read/28722229/a-transposon-directed-epigenetic-change-in-zmcct-underlies-quantitative-resistance-to-gibberella-stalk-rot-in-maize
#13
Chao Wang, Qin Yang, Weixiang Wang, Yipu Li, Yanling Guo, Dongfeng Zhang, Xuena Ma, Wei Song, Jiuran Zhao, Mingliang Xu
A major resistance quantitative trait locus, qRfg1, significantly enhances maize resistance to Gibberella stalk rot, a devastating disease caused by Fusarium graminearum. However, the underlying molecular mechanism remains unknown. We adopted a map-based cloning approach to identify the resistance gene at qRfg1 and examined the dynamic epigenetic changes during qRfg1-mediated maize resistance to the disease. A CCT domain-containing gene, ZmCCT, is the causal gene at the qRfg1 locus and a polymorphic CACTA-like transposable element (TE1) c...
September 2017: New Phytologist
https://www.readbyqxmd.com/read/28715484/multiple-renal-cancer-susceptibility-polymorphisms-modulate-the-hif-pathway
#14
Steffen Grampp, Virginia Schmid, Rafik Salama, Victoria Lauer, Franziska Kranz, James L Platt, James Smythies, Hani Choudhry, Margarete Goppelt-Struebe, Peter J Ratcliffe, David R Mole, Johannes Schödel
Un-physiological activation of hypoxia inducible factor (HIF) is an early event in most renal cell cancers (RCC) following inactivation of the von Hippel-Lindau tumor suppressor. Despite intense study, how this impinges on cancer development is incompletely understood. To test for the impact of genetic signals on this pathway, we aligned human RCC-susceptibility polymorphisms with genome-wide assays of HIF-binding and observed highly significant overlap. Allele-specific assays of HIF binding, chromatin conformation and gene expression together with eQTL analyses in human tumors were applied to mechanistic analysis of one such overlapping site at chromosome 12p12...
July 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28693387/the-flc-locus-a-platform-for-discoveries-in-epigenetics-and-adaptation
#15
Charles Whittaker, Caroline Dean
Our understanding of the detailed molecular mechanisms underpinning adaptation is still poor. One example for which mechanistic understanding of regulation has converged with studies of life history variation is Arabidopsis thaliana FLOWERING LOCUS C (FLC). FLC determines the need for plants to overwinter and their ability to respond to prolonged cold in a process termed vernalization. This review highlights how molecular analysis of vernalization pathways has revealed important insight into antisense-mediated chromatin silencing mechanisms that regulate FLC...
July 10, 2017: Annual Review of Cell and Developmental Biology
https://www.readbyqxmd.com/read/28671686/the-methyltransferase-setdb1-regulates-a-large-neuron-specific-topological-chromatin-domain
#16
Yan Jiang, Yong-Hwee Eddie Loh, Prashanth Rajarajan, Teruyoshi Hirayama, Will Liao, Bibi S Kassim, Behnam Javidfar, Brigham J Hartley, Lisa Kleofas, Royce B Park, Benoit Labonte, Seok-Man Ho, Sandhya Chandrasekaran, Catherine Do, Brianna R Ramirez, Cyril J Peter, Julia T C W, Brian M Safaie, Hirofumi Morishita, Panos Roussos, Eric J Nestler, Anne Schaefer, Benjamin Tycko, Kristen J Brennand, Takeshi Yagi, Li Shen, Schahram Akbarian
We report locus-specific disintegration of megabase-scale chromosomal conformations in brain after neuronal ablation of Setdb1 (also known as Kmt1e; encodes a histone H3 lysine 9 methyltransferase), including a large topologically associated 1.2-Mb domain conserved in humans and mice that encompasses >70 genes at the clustered protocadherin locus (hereafter referred to as cPcdh). The cPcdh topologically associated domain (TAD(cPcdh)) in neurons from mutant mice showed abnormal accumulation of the transcriptional regulator and three-dimensional (3D) genome organizer CTCF at cryptic binding sites, in conjunction with DNA cytosine hypomethylation, histone hyperacetylation and upregulated expression...
August 2017: Nature Genetics
https://www.readbyqxmd.com/read/28659708/specific-correlation-between-the-major-chromosome-10q26-haplotype-conferring-risk-for-age-related-macular-degeneration-and-the-expression-of-htra1
#17
Sha-Mei Liao, Wei Zheng, Jiang Zhu, Casey A Lewis, Omar Delgado, Maura A Crowley, Natasha M Buchanan, Bruce D Jaffee, Thaddeus P Dryja
PURPOSE: A region within chromosome 10q26 has a set of single nucleotide polymorphisms (SNPs) that define a haplotype that confers high risk for age-related macular degeneration (AMD). We used a bioinformatics approach to search for genes in this region that may be responsible for risk for AMD by assessing levels of gene expression in individuals carrying different haplotypes and by searching for open chromatin regions in the retinal pigment epithelium (RPE) that might include one or more of the SNPs...
2017: Molecular Vision
https://www.readbyqxmd.com/read/28615534/functional-dissection-of-breast-cancer-risk-associated-tert-promoter-variants
#18
Sonja Helbig, Leesa Wockner, Annick Bouendeu, Ursula Hille-Betz, Karen McCue, Juliet D French, Stacey L Edwards, Hilda A Pickett, Roger R Reddel, Georgia Chenevix-Trench, Thilo Dörk, Jonathan Beesley
The multi-cancer susceptibility locus at 5p15.33 includes TERT, encoding the telomerase catalytic subunit. Genome-wide association studies (GWAS) have identified six single nucleotide polymorphisms (SNPs) in the TERT promoter associated with decreased breast cancer risk, although the precise causal variants and their mechanisms of action have remained elusive. Luciferase reporter assays indicated that the protective haplotype reduced TERT promoter activity in human mammary epithelial and cancer cells in an estrogen-independent manner...
May 26, 2017: Oncotarget
https://www.readbyqxmd.com/read/28592555/genetic-dissection-of-morphometric-traits-reveals-that-phytochrome-b-affects-nucleus-size-and-heterochromatin-organization-in-arabidopsis-thaliana
#19
Basten L Snoek, Penka Pavlova, Federico Tessadori, Anton J M Peeters, Clara Bourbousse, Fredy Barneche, Hans de Jong, Paul F Fransz, Martijn van Zanten
Microscopically visible chromatin is partitioned into two major components in Arabidopsis thaliana nuclei. On one hand, chromocenters are conspicuous foci of highly condensed "heterochromatic" domains that contain mostly repeated sequences. On the other hand, less condensed and gene-rich "euchromatin" emanates from these chromocenters. This differentiation, together with the dynamic nature of chromatin compaction in response to developmental and environmental stimuli, makes Arabidopsis a powerful system for studying chromatin organization and dynamics...
August 7, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28555645/a-promoter-proximal-transcript-targeted-by-genetic-polymorphism-controls-e-cadherin-silencing-in-human-cancers
#20
Giuseppina Pisignano, Sara Napoli, Marco Magistri, Sarah N Mapelli, Chiara Pastori, Stefano Di Marco, Gianluca Civenni, Domenico Albino, Claudia Enriquez, Sara Allegrini, Abhishek Mitra, Gioacchino D'Ambrosio, Maurizia Mello-Grand, Giovanna Chiorino, Ramon Garcia-Escudero, Gabriele Varani, Giuseppina M Carbone, Carlo V Catapano
Long noncoding RNAs are emerging players in the epigenetic machinery with key roles in development and diseases. Here we uncover a complex network comprising a promoter-associated noncoding RNA (paRNA), microRNA and epigenetic regulators that controls transcription of the tumour suppressor E-cadherin in epithelial cancers. E-cadherin silencing relies on the formation of a complex between the paRNA and microRNA-guided Argonaute 1 that, together, recruit SUV39H1 and induce repressive chromatin modifications in the gene promoter...
May 30, 2017: Nature Communications
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