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Polymorphism chromatin

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https://www.readbyqxmd.com/read/29761399/chromatin-immunoprecipitation-in-macrophages
#1
Germain Rousselet
Macrophages are highly polymorphic depending upon their cellular origin and their tissue environment. The different forms that a macrophage can adopt fundamentally reflect different transcription patterns. In addition, macrophages are exquisitely sensitive to a wide variety of signals coming from either infectious agents or damaged tissues. Most of the responses to these signals involve rapid and massive modifications of transcription. The control of transcription relies on the one hand on the posttranslational modification of histones, and on the other hand on the binding on the chromatin of multiple protein complexes...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29748466/detecting-differential-transcription-factor-activity-from-atac-seq-data
#2
Ignacio J Tripodi, Mary A Allen, Robin D Dowell
Transcription factors are managers of the cellular factory, and key components to many diseases. Many non-coding single nucleotide polymorphisms affect transcription factors, either by directly altering the protein or its functional activity at individual binding sites. Here we first briefly summarize high-throughput approaches to studying transcription factor activity. We then demonstrate, using published chromatin accessibility data (specifically ATAC-seq), that the genome-wide profile of TF recognition motifs relative to regions of open chromatin can determine the key transcription factor altered by a perturbation...
May 10, 2018: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/29735606/allele-specific-control-of-replication-timing-and-genome-organization-during-development
#3
Juan Carlos Rivera-Mulia, Andrew Dimond, Daniel Vera, Claudia Trevilla-Garcia, Takayo Sasaki, Jared Zimmerman, Catherine Dupont, Joost Gribnau, Peter Fraser, David M Gilbert
DNA replication occurs in a defined temporal order known as the replication-timing (RT) program. RT is regulated during development in discrete chromosomal units, coordinated with transcriptional activity and 3D genome organization. Here, we derived distinct cell types from F1 hybrid musculus X castaneus mouse crosses and exploited the high single nucleotide polymorphism (SNP) density to characterize allelic differences in RT (Repli-seq), genome organization (Hi-C and promoter-capture Hi-C), gene expression (total nuclear RNA-seq) and chromatin accessibility (ATAC-seq)...
May 7, 2018: Genome Research
https://www.readbyqxmd.com/read/29718103/a-powerful-approach-reveals-numerous-expression-quantitative-trait-haplotypes-in-multiple-tissues
#4
Dingge Ying, Mulin Jun Li, Pak Chung Sham, Miaoxin Li
Motivation: Recently many studies showed single nucleotide polymorphisms (SNPs) affect gene expression and contribute to development of complex traits/diseases in a tissue context-dependent manner. However, little is known about haplotype's influence on gene expression and complex traits, which reflects the interaction effect between SNPs. Results: In the present study, we firstly proposed a regulatory region guided eQTL haplotype association analysis approach, and then systematically investigate the expression quantitative trait loci (eQTL) haplotypes in 20 different tissues by the approach...
April 26, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29672586/selection-on-the-regulation-of-sympathetic-nervous-activity-in-humans-and-chimpanzees
#5
Kang Seon Lee, Paramita Chatterjee, Eun-Young Choi, Min Kyung Sung, Jaeho Oh, Hyejung Won, Seong-Min Park, Youn-Jae Kim, Soojin V Yi, Jung Kyoon Choi
Adrenergic α2C receptor (ADRA2C) is an inhibitory modulator of the sympathetic nervous system. Knockout mice for this gene show physiological and behavioural alterations that are associated with the fight-or-flight response. There is evidence of positive selection on the regulation of this gene during chicken domestication. Here, we find that the neuronal expression of ADRA2C is lower in human and chimpanzee than in other primates. On the basis of three-dimensional chromatin structure, we identified a cis-regulatory region whose DNA sequences have been significantly accelerated in human and chimpanzee...
April 2018: PLoS Genetics
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/29667924/telomerase-may-paradoxically-accelerate-aging-of-the-dna-methylome
#7
Andrew R Mendelsohn, James W Larrick
DNA methylation (DNAm) clocks such as the Horvath DNAm clock provide the most accurate biological determination of biological age relative to chronological age available today. However, there is little correlation between DNAm clocks, telomere-based aging clocks, and transcriptomic-based aging clocks. Recently, a genome-wide association study identified single-nucleotide polymorphism variants of TERT, the gene that encodes telomerase, as accelerating intrinsic aging in the Horvath DNAm clock. These same variants have been previously associated with long telomeres in leukocytes, suggesting that TERT acts paradoxically on telomere-associated aging and DNAm-associated aging...
April 2018: Rejuvenation Research
https://www.readbyqxmd.com/read/29667298/distinct-chromatin-structures-at-the-monoamine-oxidase-a-maoa-promoter-correlate-with-allele-specific-expression-in-sh-sy5y-cells
#8
M Manca, V Pessoa, P Myers, A Pickles, J Hill, H Sharp, C Murgatroyd, V J Bubb, J P Quinn
Monoamine oxidase-A (MAOA) metabolises monoamines and is implicated in the pathophysiology of psychiatric disorders. A polymorphic repetitive DNA domain, termed the uVNTR (upstream variable number tandem repeat), located at the promoter of the MAOA gene is a risk factor for many of these disorders. MAOA is on the X chromosome suggesting gender could play a role in regulation. We analysed MAOA regulation in the human female cell line, SH-SY5Y, which is polymorphic for the uVNTR. This heterozygosity allowed us to correlate allele specific gene expression with allele specific transcription factor binding and epigenetic marks for MAOA...
April 18, 2018: Genes, Brain, and Behavior
https://www.readbyqxmd.com/read/29626084/genetic-loci-governing-androgenic-capacity-in-perennial-ryegrass-lolium-perenne-l
#9
Rachel F Begheyn, Steven A Yates, Timothy Sykes, Bruno Studer
Immature pollen can be induced to switch developmental pathways from gametogenesis to embryogenesis and subsequently regenerate into homozygous, diploid plants. Such androgenic production of doubled haploids is particularly useful for species where inbreeding is hampered by effective self-incompatibility systems. Therefore, increasing the generally low androgenic capacity of perennial ryegrass ( Lolium perenne L.) germplasm would enable the efficient production of homozygous plant material, so that a more effective exploitation of heterosis through hybrid breeding schemes can be realized...
April 6, 2018: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29599440/genome-wide-analysis-of-replication-timing-by-next-generation-sequencing-with-e-l-repli-seq
#10
Claire Marchal, Takayo Sasaki, Daniel Vera, Korey Wilson, Jiao Sima, Juan Carlos Rivera-Mulia, Claudia Trevilla-García, Coralin Nogues, Ebtesam Nafie, David M Gilbert
This protocol is an extension to: Nat. Protoc. 6, 870-895 (2014); doi:10.1038/nprot.2011.328; published online 02 June 2011Cycling cells duplicate their DNA content during S phase, following a defined program called replication timing (RT). Early- and late-replicating regions differ in terms of mutation rates, transcriptional activity, chromatin marks and subnuclear position. Moreover, RT is regulated during development and is altered in diseases. Here, we describe E/L Repli-seq, an extension of our Repli-chip protocol...
May 2018: Nature Protocols
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
#11
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/29593729/genomic-effects-of-the-vitamin-d-receptor-potentially-the-link-between-vitamin-d-immune-cells-and-multiple-sclerosis
#12
REVIEW
Ming Lu, Bruce V Taylor, Heinrich Körner
Vitamin D has a plethora of functions that are important for the maintenance of general health and in particular, the functional integrity of the immune system, such as promoting an anti-inflammatory cytokine profile and reducing the Treg/Th17 ratio. Multiple sclerosis (MS) is a chronic, inflammatory, and neurodegenerative central nervous system (CNS) disorder of probable autoimmune origin. MS is characterized by recurring or progressive demyelination and degeneration of the CNS due in part to a misguided immune response to as yet undefined (CNS) antigens, potentially including myelin basic protein and proteolipid protein...
2018: Frontiers in Immunology
https://www.readbyqxmd.com/read/29588580/a-functional-snp-upstream-of-the-adrb2-gene-is-associated-with-copd
#13
Jin-Xiu Li, Wei-Ping Fu, Jing Zhang, Xiao-Hua Zhang, Chang Sun, Lu-Ming Dai, Li Zhong, Li Yu, Ya-Ping Zhang
Background: Previous studies have suggested that β2 -adrenergic receptor ( ADRB2 ) is associated with COPD. However, the role of genetic polymorphisms in ADRB2 on COPD has not been evaluated yet. Methods: In this study, SNaPshot genotyping, luciferase assay, chromatin immunoprecipitation and real-time polymerase chain reaction were adopted to investigate the association between ADRB2 genetic polymorphisms and COPD, comprehensively. Results: One single nucleotide polymorphism (rs12654778), located upstream of ADRB2 , showed a significant association with COPD by the logistic regression analysis after adjusting for age, sex and smoking history ( p =0...
2018: International Journal of Chronic Obstructive Pulmonary Disease
https://www.readbyqxmd.com/read/29566053/the-development-of-functional-mapping-by-three-sex-related-loci-on-the-third-whorl-of-different-sex-types-of-carica-papaya-l
#14
Chen-Yu Lee, Hui-Jun Lin, Kotapati Kasi Viswanath, Chih-Peng Lin, Bill Chia-Han Chang, Pei-Hsun Chiu, Chan-Tai Chiu, Ren-Huang Wang, Shih-Wen Chin, Fure-Chyi Chen
Carica papaya L. is an important economic crop worldwide and is used as a model plant for sex-determination research. To study the different flower sex types, we screened sex-related genes using alternative splicing sequences (AS-seqs) from a transcriptome database of the three flower sex types, i.e., males, females, and hermaphrodites, established at 28 days before flowering using 15 bacterial artificial chromosomes (BACs) of C. papaya L. After screening, the cDNA regions of the three sex-related loci, including short vegetative phase-like (CpSVPL), the chromatin assembly factor 1 subunit A-like (CpCAF1AL), and the somatic embryogenesis receptor kinase (CpSERK), which contained eight sex-related single-nucleotide polymorphisms (SNPs) from the different sex types of C...
2018: PloS One
https://www.readbyqxmd.com/read/29562725/genetic-and-epigenetic-regulation-in-nonalcoholic-fatty-liver-disease-nafld
#15
REVIEW
José A Del Campo, Rocío Gallego-Durán, Paloma Gallego, Lourdes Grande
Genetics and epigenetics play a key role in the development of several diseases, including nonalcoholic fatty liver disease (NAFLD). Family studies demonstrate that first degree relatives of patients with NAFLD are at a much higher risk of the disease than the general population. The development of the Genome Wide Association Study (GWAS) technology has allowed the identification of numerous genetic polymorphisms involved in the evolution of diseases (e.g., PNPLA3 , MBOAT7 ). On the other hand, epigenetic changes interact with inherited risk factors to determine an individual's susceptibility to NAFLD...
March 19, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29537884/current-status-of-sperm-functional-genomics-and-its-diagnostic-potential-of-fertility-in-bovine-bos-taurus
#16
Sellappan Selvaraju, Sivashanmugam Parthipan, Lakshminarayana Somashekar, B Krishnan Binsila, Atul P Kolte, Arunachalam Arangasamy, Janivara Parameshwaraiah Ravindra, Stephen A Krawetz
With artificial insemination (AI) and other precision dependent assisted reproductive technologies (ART) being followed in large scale in human and animal reproduction, assessing semen quality and fertilizability is under continuous scrutiny. Various tests have been developed to predict semen quality, but so far no single, highly reliable test is available. In this regard, transcriptomic profiling of spermatozoa assumes significance as it carries the information about spermatogenesis, sperm function, and paternal roles in post-fertilization events...
March 14, 2018: Systems Biology in Reproductive Medicine
https://www.readbyqxmd.com/read/29531791/evidence-for-a-second-ankylosing-spondylitis-associated-runx3-regulatory-polymorphism
#17
Matteo Vecellio, Adrian Cortes, Amity R Roberts, Jonathan Ellis, Carla Jayne Cohen, Julian C Knight, Matthew A Brown, Paul Bowness, Bryan Paul Wordsworth
Objectives: To explore the functions of RUNX3 single nucleotide polymorphisms (SNPs) associated with ankylosing spondylitis (AS). Methods: Individual SNP associations were evaluated in 4230 UK cases. Their effects on transcription factor (TF) binding, transcription regulation, chromatin modifications, gene expression and gene interactions were tested by database interrogation, luciferase reporter assays, electrophoretic mobility gel shifts, chromatin immunoprecipitation and real-time PCR...
2018: RMD Open
https://www.readbyqxmd.com/read/29530928/nucleosomes-and-dna-methylation-shape-meiotic-dsb-frequency-in-arabidopsis-thaliana-transposons-and-gene-regulatory-regions
#18
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...
April 2018: Genome Research
https://www.readbyqxmd.com/read/29528523/multiple-functional-variants-at-13q14-risk-locus-for-osteoporosis-regulate-rankl-expression-through-long-range-super-enhancer
#19
Dong-Li Zhu, Xiao-Feng Chen, Wei-Xin Hu, Shan-Shan Dong, Bing-Jie Lu, Yu Rong, Yi-Xiao Chen, Hao Chen, Hlaing Nwe Thynn, Nai-Ning Wang, Yan Guo, Tie-Lin Yang
RANKL is a key regulator involved in bone metabolism, and a drug target for osteoporosis. The clinical diagnosis and assessment of osteoporosis are mainly based on bone mineral density (BMD). Previous powerful genomewide association studies (GWASs) have identified multiple intergenic single-nucleotide polymorphisms (SNPs) located over 100 kb upstream of RANKL and 65 kb downstream of AKAP11 at 13q14.11 for osteoporosis. Whether these SNPs exert their roles on osteoporosis through RANKL is unknown. In this study, we conducted integrative analyses combining expression quantitative trait locus (eQTL), genomic chromatin interaction (high-throughput chromosome conformation capture [Hi-C]), epigenetic annotation, and a series of functional assays...
March 12, 2018: Journal of Bone and Mineral Research: the Official Journal of the American Society for Bone and Mineral Research
https://www.readbyqxmd.com/read/29491472/integrative-functional-analysis-of-super-enhancer-snps-for-coronary-artery-disease
#20
Juexiao Gong, Chuan Qiu, Dan Huang, Yiyan Zhang, Shengyong Yu, Chunping Zeng
Clinical research in coronary artery disease (CAD) primarily focused on genetic variants located in protein-coding regions. Recently, mutations fall within non-coding regions have been suggested to be essential to the pathogenesis of human complex disease. Super enhancer is a densely spaced cluster of transcriptional enhancers located in non-coding regions, which is critical for regulating cell-type specific gene expression. However, the underlying mechanism of the super enhancer single-nucleotide polymorphisms (SNPs) affecting the risk of CAD remains unclear...
May 2018: Journal of Human Genetics
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