keyword
MENU ▼
Read by QxMD icon Read
search

Dnase-seq

keyword
https://www.readbyqxmd.com/read/29772251/advances-of-dnase-seq-for-mapping-active-gene-regulatory-elements-across-the-genome-in-animals
#1
REVIEW
Ailing Chen, Daozhen Chen, Ying Chen
Expression of the eukaryotic genome is a highly complex and tightly regulated process, and its regulation depends on interactions among cis-acting elements and transcription factors. Identification of active gene regulatory elements is key to understanding transcriptional control of biological processes including differentiation, development, proliferation, cell-type specificity, and responses to the environment. DNase I hypersensitive sites (DHSs) are markers of open chromatin that provide a very effective method of targeting all types of cis-regulatory elements (CREs) including enhancers, promoters, insulators, silencers, and locus control regions...
May 14, 2018: Gene
https://www.readbyqxmd.com/read/29715506/similar-bowtie-structures-and-distinct-largest-strong-components-are-identified-in-the-transcriptional-regulatory-networks-of-arabidopsis-thaliana-during-photomorphogenesis-and-heat-shock
#2
Shitao Luo, Fengming Zhang, Yingfei Ruan, Jie Li, Zheng Zhang, Yan Sun, Shixiong Deng, Rui Peng
Photomorphogenesis and heat shock are critical biological processes of plants. A recent research constructed the transcriptional regulatory networks (TRNs) of Arabidopsis thaliana during these processes using DNase-seq. In this study, by strong decomposition, we revealed that each of these TRNs can be represented as a similar bowtie structure with only one non-trivial and distinct strong component. We further identified distinct patterns of variation of a few light-related genes in these bowtie structures during photomorphogenesis...
April 28, 2018: Bio Systems
https://www.readbyqxmd.com/read/29617930/impact-of-car-agonist-ligand-tcpobop-on-mouse-liver-chromatin-accessibility
#3
Nicholas J Lodato, Andy Rampersaud, David J Waxman
Activation of the nuclear receptor and transcription factor CAR (Nr1i3) by its specific agonist ligand TCPOBOP (1,4-bis[2-(3,5-dichloropyridyloxy)]benzene) dysregulates hundreds of genes in mouse liver and is linked to male-biased hepatocarcinogenesis. To elucidate the genomic organization of CAR-induced gene responses, we investigated the distribution of TCPOBOP-responsive RefSeq coding and long non-coding RNA (lncRNA) genes across the megabase-scale topologically associating domains (TADs) that segment the genome, and which provide a structural framework that functionally constrains enhancer-promoter interactions...
April 2, 2018: Toxicological Sciences: An Official Journal of the Society of Toxicology
https://www.readbyqxmd.com/read/29608722/comparative-serum-challenges-show-divergent-patterns-of-gene-expression-and-open-chromatin-in-human-and-chimpanzee
#4
Jason Pizzollo, William J Nielsen, Yoichiro Shibata, Alexias Safi, Gregory E Crawford, Gregory A Wray, Courtney C Babbitt
Humans experience higher rates of age-associated diseases than our closest living evolutionary relatives, chimpanzees. Environmental factors can explain many of these increases in disease risk, but species-specific genetic changes can also play a role. Alleles that confer increased disease susceptibility later in life can persist in a population in the absence of selective pressure if those changes confer positive adaptation early in life. One age-associated disease that disproportionately affects humans compared with chimpanzees is epithelial cancer...
March 1, 2018: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29558892/global-analysis-of-primary-mesenchyme-cell-cis-regulatory-modules-by-chromatin-accessibility-profiling
#5
Tanvi Shashikant, Jian Ming Khor, Charles A Ettensohn
BACKGROUND: The developmental gene regulatory network (GRN) that underlies skeletogenesis in sea urchins and other echinoderms is a paradigm of GRN structure, function, and evolution. This transcriptional network is deployed selectively in skeleton-forming primary mesenchyme cells (PMCs) of the early embryo. To advance our understanding of this model developmental GRN, we used genome-wide chromatin accessibility profiling to identify and characterize PMC cis-regulatory modules (CRMs)...
March 20, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29472540/exploiting-genetic-variation-to-uncover-rules-of-transcription-factor-binding-and-chromatin-accessibility
#6
Vivek Behera, Perry Evans, Carolyne J Face, Nicole Hamagami, Laavanya Sankaranarayanan, Cheryl A Keller, Belinda Giardine, Kai Tan, Ross C Hardison, Junwei Shi, Gerd A Blobel
Single-nucleotide variants that underlie phenotypic variation can affect chromatin occupancy of transcription factors (TFs). To delineate determinants of in vivo TF binding and chromatin accessibility, we introduce an approach that compares ChIP-seq and DNase-seq data sets from genetically divergent murine erythroid cell lines. The impact of discriminatory single-nucleotide variants on TF ChIP signal enables definition at single base resolution of in vivo binding characteristics of nuclear factors GATA1, TAL1, and CTCF...
February 22, 2018: Nature Communications
https://www.readbyqxmd.com/read/29463772/proliferation-of-regulatory-dna-elements-derived-from-transposable-elements-in-the-maize-genome
#7
Hainan Zhao, Wenli Zhang, Lifen Chen, Lei Wang, Alexandre P Marand, Yufeng Wu, Jiming Jiang
Genomic regions free of nucleosomes, which are hypersensitive to DNase I digestion, are known as DNase I hypersensitive sites (DHSs) and frequently contain cis-regulatory DNA elements. To investigate their prevalence and characteristics in maize ( Zea mays ), we developed high-resolution genome-wide DHS maps using a modified DNase-seq technique. Maize DHSs exhibit depletion of nucleosomes and low levels of DNA methylation and are enriched with conserved noncoding sequences (CNSs). We developed a protoplast-based transient transformation assay to assess the potential gene expression enhancer and/or promoter functions associated with DHSs, which showed that more than 80% of DHSs overlapping with CNSs showed an enhancer function...
April 2018: Plant Physiology
https://www.readbyqxmd.com/read/29459038/molecular-characterization-of-gene-regulatory-networks-in-primary-human-tracheal-and-bronchial-epithelial-cells
#8
Austin E Gillen, Rui Yang, Calvin U Cotton, Aura Perez, Scott H Randell, Shih-Hsing Leir, Ann Harris
BACKGROUND: Robust methods to culture primary airway epithelial cells were developed several decades ago and these cells provide the model of choice to investigate many diseases of the human lung. However, the molecular signature of cells from different regions of the airway epithelium has not been well characterized. METHODS: We utilize DNase-seq and RNA-seq to examine the molecular signatures of primary cells derived from human tracheal and bronchial tissues, as well as healthy and diseased (cystic fibrosis (CF)) donor lung tissue...
February 17, 2018: Journal of Cystic Fibrosis: Official Journal of the European Cystic Fibrosis Society
https://www.readbyqxmd.com/read/29420797/octopus-toolkit-a-workflow-to-automate-mining-of-public-epigenomic-and-transcriptomic-next-generation-sequencing-data
#9
Taemook Kim, Hogyu David Seo, Lothar Hennighausen, Daeyoup Lee, Keunsoo Kang
Octopus-toolkit is a stand-alone application for retrieving and processing large sets of next-generation sequencing (NGS) data with a single step. Octopus-toolkit is an automated set-up-and-analysis pipeline utilizing the Aspera, SRA Toolkit, FastQC, Trimmomatic, HISAT2, STAR, Samtools, and HOMER applications. All the applications are installed on the user's computer when the program starts. Upon the installation, it can automatically retrieve original files of various epigenomic and transcriptomic data sets, including ChIP-seq, ATAC-seq, DNase-seq, MeDIP-seq, MNase-seq and RNA-seq, from the gene expression omnibus data repository...
February 6, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29322784/bioinformatic-analysis-of-changes-in-rna-polymerase-ii-transcription-stimulated-by-estradiol-in-mcf7-cells
#10
J Wu, Y Cai, G Zhao
Estradiol (E2) is the most potent estrogen and RNA polymerase II (Pol II) regulates a great mass of gene expression. This study was designed to illustrate the mechanisms of estrogen-dependent human breast cancer (BC) through Pol II. ChIP-seq data, DNase-seq data and other sequencing data of human BC MCF-7 cells were downloaded from Gene Expression Omnibus database. Each of these datasets included one control and one E2 treated sample. Sequence alignment was performed and Pol II factor binding signal was determined...
2018: Neoplasma
https://www.readbyqxmd.com/read/29284001/dnase-capture-reveals-differential-transcription-factor-binding-modalities
#11
Daniel Kang, Richard Sherwood, Amira Barkal, Tatsunori Hashimoto, Logan Engstrom, David Gifford
We describe DNase-capture, an assay that increases the analytical resolution of DNase-seq by focusing its sequencing phase on selected genomic regions. We introduce a new method to compensate for capture bias called BaseNormal that allows for accurate recovery of transcription factor protection profiles from DNase-capture data. We show that these normalized data allow for nuanced detection of transcription factor binding heterogeneity with as few as dozens of sites.
2017: PloS One
https://www.readbyqxmd.com/read/29155775/mapping-genome-wide-accessible-chromatin-in-primary-human-t-lymphocytes-by-atac-seq
#12
Ivana Grbesa, Miriam Tannenbaum, Avital Sarusi-Portuguez, Michal Schwartz, Ofir Hakim
Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq) is a method used for the identification of open (accessible) regions of chromatin. These regions represent regulatory DNA elements (e.g., promoters, enhancers, locus control regions, insulators) to which transcription factors bind. Mapping the accessible chromatin landscape is a powerful approach for uncovering active regulatory elements across the genome. This information serves as an unbiased approach for discovering the network of relevant transcription factors and mechanisms of chromatin structure that govern gene expression programs...
November 13, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29126307/universal-correction-of-enzymatic-sequence-bias-reveals-molecular-signatures-of-protein-dna-interactions
#13
André L Martins, Ninad M Walavalkar, Warren D Anderson, Chongzhi Zang, Michael J Guertin
Coupling molecular biology to high-throughput sequencing has revolutionized the study of biology. Molecular genomics techniques are continually refined to provide higher resolution mapping of nucleic acid interactions and structure. Sequence preferences of enzymes can interfere with the accurate interpretation of these data. We developed seqOutBias to characterize enzymatic sequence bias from experimental data and scale individual sequence reads to correct intrinsic enzymatic sequence biases. SeqOutBias efficiently corrects DNase-seq, TACh-seq, ATAC-seq, MNase-seq and PRO-seq data...
January 25, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29074739/genome-wide-discovery-of-active-regulatory-elements-and-transcription-factor-footprints-in-caenorhabditis-elegans-using-dnase-seq
#14
Margaret C W Ho, Porfirio Quintero-Cadena, Paul W Sternberg
Deep sequencing of size-selected DNase I-treated chromatin (DNase-seq) allows high-resolution measurement of chromatin accessibility to DNase I cleavage, permitting identification of de novo active cis -regulatory modules (CRMs) and individual transcription factor (TF) binding sites. We adapted DNase-seq to nuclei isolated from C. elegans embryos and L1 arrest larvae to generate high-resolution maps of TF binding. Over half of embryonic DNase I hypersensitive sites (DHSs) were annotated as noncoding, with 24% in intergenic, 12% in promoters, and 28% in introns, with similar statistics observed in L1 arrest larvae...
December 2017: Genome Research
https://www.readbyqxmd.com/read/29069282/chromatin-accessibility-prediction-via-a-hybrid-deep-convolutional-neural-network
#15
Qiao Liu, Fei Xia, Qijin Yin, Rui Jiang
Motivation: A majority of known genetic variants associated with human-inherited diseases lie in non-coding regions that lack adequate interpretation, making it indispensable to systematically discover functional sites at the whole genome level and precisely decipher their implications in a comprehensive manner. Although computational approaches have been complementing high-throughput biological experiments towards the annotation of the human genome, it still remains a big challenge to accurately annotate regulatory elements in the context of a specific cell type via automatic learning of the DNA sequence code from large-scale sequencing data...
March 1, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29059382/dreambase-dna-modification-rna-regulation-and-protein-binding-of-expressed-pseudogenes-in-human-health-and-disease
#16
Ling-Ling Zheng, Ke-Ren Zhou, Shun Liu, Ding-Yao Zhang, Ze-Lin Wang, Zhi-Rong Chen, Jian-Hua Yang, Liang-Hu Qu
Although thousands of pseudogenes have been annotated in the human genome, their transcriptional regulation, expression profiles and functional mechanisms are largely unknown. In this study, we developed dreamBase (http://rna.sysu.edu.cn/dreamBase) to facilitate the investigation of DNA modification, RNA regulation and protein binding of potential expressed pseudogenes from multidimensional high-throughput sequencing data. Based on ∼5500 ChIP-seq and DNase-seq datasets, we identified genome-wide binding profiles of various transcription-associated factors around pseudogene loci...
January 4, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/28904015/sasquatch-predicting-the-impact-of-regulatory-snps-on-transcription-factor-binding-from-cell-and-tissue-specific-dnase-footprints
#17
Ron Schwessinger, Maria C Suciu, Simon J McGowan, Jelena Telenius, Stephen Taylor, Doug R Higgs, Jim R Hughes
In the era of genome-wide association studies (GWAS) and personalized medicine, predicting the impact of single nucleotide polymorphisms (SNPs) in regulatory elements is an important goal. Current approaches to determine the potential of regulatory SNPs depend on inadequate knowledge of cell-specific DNA binding motifs. Here, we present Sasquatch, a new computational approach that uses DNase footprint data to estimate and visualize the effects of noncoding variants on transcription factor binding. Sasquatch performs a comprehensive k -mer-based analysis of DNase footprints to determine any k -mer's potential for protein binding in a specific cell type and how this may be changed by sequence variants...
October 2017: Genome Research
https://www.readbyqxmd.com/read/28789639/cipher-a-flexible-and-extensive-workflow-platform-for-integrative-next-generation-sequencing-data-analysis-and-genomic-regulatory-element-prediction
#18
Carlos Guzman, Iván D'Orso
BACKGROUND: Next-generation sequencing (NGS) approaches are commonly used to identify key regulatory networks that drive transcriptional programs. Although these technologies are frequently used in biological studies, NGS data analysis remains a challenging, time-consuming, and often irreproducible process. Therefore, there is a need for a comprehensive and flexible workflow platform that can accelerate data processing and analysis so more time can be spent on functional studies. RESULTS: We have developed an integrative, stand-alone workflow platform, named CIPHER, for the systematic analysis of several commonly used NGS datasets including ChIP-seq, RNA-seq, MNase-seq, DNase-seq, GRO-seq, and ATAC-seq data...
August 8, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28764645/correcting-nucleotide-specific-biases-in-high-throughput-sequencing-data
#19
Jeremy R Wang, Bryan Quach, Terrence S Furey
BACKGROUND: High-throughput sequence (HTS) data exhibit position-specific nucleotide biases that obscure the intended signal and reduce the effectiveness of these data for downstream analyses. These biases are particularly evident in HTS assays for identifying regulatory regions in DNA (DNase-seq, ChIP-seq, FAIRE-seq, ATAC-seq). Biases may result from many experiment-specific factors, including selectivity of DNA restriction enzymes and fragmentation method, as well as sequencing technology-specific factors, such as choice of adapters/primers and sample amplification methods...
August 1, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28704389/differential-chromatin-profiles-partially-determine-transcription-factor-binding
#20
Rujian Chen, David K Gifford
We characterize how genomic variants that alter chromatin accessibility influence regulatory factor binding with a new method called DeltaBind that predicts condition specific factor binding more accurately than other methods based on DNase-seq data. Using DeltaBind and DNase-seq experiments we predicted the differential binding of 18 factors in K562 and GM12878 cells with an average precision of 28% at 10% recall, with the prediction of individual factors ranging from 5% to 65% precision. We further found that genome variants that alter chromatin accessibility are not necessarily predictive of altering proximal factor binding...
2017: PloS One
keyword
keyword
97520
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"