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https://www.readbyqxmd.com/read/29748466/detecting-differential-transcription-factor-activity-from-atac-seq-data
#1
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
#2
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/29727464/patterns-of-chromatin-accessibility-along-the-anterior-posterior-axis-in-the-early-drosophila-embryo
#3
Jenna E Haines, Michael B Eisen
As the Drosophila embryo transitions from the use of maternal RNAs to zygotic transcription, domains of open chromatin, with relatively low nucleosome density and specific histone marks, are established at promoters and enhancers involved in patterned embryonic transcription. However it remains unclear how regions of activity are established during early embryogenesis, and if they are the product of spatially restricted or ubiquitous processes. To shed light on this question, we probed chromatin accessibility across the anterior-posterior axis (A-P) of early Drosophila melanogaster embryos by applying a transposon based assay for chromatin accessibility (ATAC-seq) to anterior and posterior halves of hand-dissected, cellular blastoderm embryos...
May 4, 2018: PLoS Genetics
https://www.readbyqxmd.com/read/29722874/rsat-2018-regulatory-sequence-analysis-tools-20th-anniversary
#4
Nga Thi Thuy Nguyen, Bruno Contreras-Moreira, Jaime A Castro-Mondragon, Walter Santana-Garcia, Raul Ossio, Carla Daniela Robles-Espinoza, Mathieu Bahin, Samuel Collombet, Pierre Vincens, Denis Thieffry, Jacques van Helden, Alejandra Medina-Rivera, Morgane Thomas-Chollier
RSAT (Regulatory Sequence Analysis Tools) is a suite of modular tools for the detection and the analysis of cis-regulatory elements in genome sequences. Its main applications are (i) motif discovery, including from genome-wide datasets like ChIP-seq/ATAC-seq, (ii) motif scanning, (iii) motif analysis (quality assessment, comparisons and clustering), (iv) analysis of regulatory variations, (v) comparative genomics. Six public servers jointly support 10 000 genomes from all kingdoms. Six novel or refactored programs have been added since the 2015 NAR Web Software Issue, including updated programs to analyse regulatory variants (retrieve-variation-seq, variation-scan, convert-variations), along with tools to extract sequences from a list of coordinates (retrieve-seq-bed), to select motifs from motif collections (retrieve-matrix), and to extract orthologs based on Ensembl Compara (get-orthologs-compara)...
May 2, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29720659/chromatin-analysis-in-human-early-development-reveals-epigenetic-transition-during-zga
#5
Jingyi Wu, Jiawei Xu, Bofeng Liu, Guidong Yao, Peizhe Wang, Zili Lin, Bo Huang, Xuepeng Wang, Tong Li, Senlin Shi, Nan Zhang, Fuyu Duan, Jia Ming, Xiangyang Zhang, Wenbin Niu, Wenyan Song, Haixia Jin, Yihong Guo, Shanjun Dai, Linli Hu, Lanlan Fang, Qiujun Wang, Yuanyuan Li, Wei Li, Jie Na, Wei Xie, Yingpu Sun
Upon fertilization, drastic chromatin reorganization occurs during preimplantation development 1 . However, the global chromatin landscape and its molecular dynamics in this period remain largely unexplored in humans. Here we investigate chromatin states in human preimplantation development using an improved assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) 2 . We find widespread accessible chromatin regions in early human embryos that overlap extensively with putative cis-regulatory sequences and transposable elements...
May 2, 2018: Nature
https://www.readbyqxmd.com/read/29703886/plasma-cell-differentiation-is-controlled-by-multiple-cell-division-coupled-epigenetic-programs
#6
Christopher D Scharer, Benjamin G Barwick, Muyao Guo, Alexander P R Bally, Jeremy M Boss
The genomic loci associated with B cell differentiation that are subject to transcriptional and epigenetic regulation in vivo are not well defined, leaving a gap in our understanding of the development of humoral immune responses. Here, using an in vivo T cell independent B cell differentiation model, we define a cellular division-dependent cis-regulatory element road map using ATAC-seq. Chromatin accessibility changes correlate with gene expression and reveal the reprogramming of transcriptional networks and the genes they regulate at specific cell divisions...
April 27, 2018: Nature Communications
https://www.readbyqxmd.com/read/29695788/tfap2c-regulates-transcription-in-human-naive-pluripotency-by-opening-enhancers
#7
William A Pastor, Wanlu Liu, Di Chen, Jamie Ho, Rachel Kim, Timothy J Hunt, Anastasia Lukianchikov, Xiaodong Liu, Jose M Polo, Steven E Jacobsen, Amander T Clark
Naive and primed pluripotent human embryonic stem cells bear transcriptional similarity to pre- and post-implantation epiblast and thus constitute a developmental model for understanding the pluripotent stages in human embryo development. To identify new transcription factors that differentially regulate the unique pluripotent stages, we mapped open chromatin using ATAC-seq and found enrichment of the activator protein-2 (AP2) transcription factor binding motif at naive-specific open chromatin. We determined that the AP2 family member TFAP2C is upregulated during primed to naive reversion and becomes widespread at naive-specific enhancers...
May 2018: Nature Cell Biology
https://www.readbyqxmd.com/read/29686798/computational-methods-for-assessing-chromatin-hierarchy
#8
REVIEW
Pearl Chang, Moloya Gohain, Ming-Ren Yen, Pao-Yang Chen
The hierarchical organization of chromatin is known to associate with diverse cellular functions; however, the precise mechanisms and the 3D structure remain to be determined. With recent advances in high-throughput next generation sequencing (NGS) techniques, genome-wide profiling of chromatin structures is made possible. Here, we provide a comprehensive overview of NGS-based methods for profiling "higher-order" and "primary-order" chromatin structures from both experimental and computational aspects...
2018: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/29686426/transcript-indexed-atac-seq-for-precision-immune-profiling
#9
Ansuman T Satpathy, Naresha Saligrama, Jason D Buenrostro, Yuning Wei, Beijing Wu, Adam J Rubin, Jeffrey M Granja, Caleb A Lareau, Rui Li, Yanyan Qi, Kevin R Parker, Maxwell R Mumbach, William S Serratelli, David G Gennert, Alicia N Schep, M Ryan Corces, Michael S Khodadoust, Youn H Kim, Paul A Khavari, William J Greenleaf, Mark M Davis, Howard Y Chang
T cells create vast amounts of diversity in the genes that encode their T cell receptors (TCRs), which enables individual clones to recognize specific peptide-major histocompatibility complex (MHC) ligands. Here we combined sequencing of the TCR-encoding genes with assay for transposase-accessible chromatin with sequencing (ATAC-seq) analysis at the single-cell level to provide information on the TCR specificity and epigenomic state of individual T cells. By using this approach, termed transcript-indexed ATAC-seq (T-ATAC-seq), we identified epigenomic signatures in immortalized leukemic T cells, primary human T cells from healthy volunteers and primary leukemic T cells from patient samples...
April 23, 2018: Nature Medicine
https://www.readbyqxmd.com/read/29649445/chromatin-accessibility-based-characterization-of-the-gene-regulatory-network-underlying-plasmodium-falciparum-blood-stage-development
#10
Christa Geeke Toenhake, Sabine Anne-Kristin Fraschka, Mahalingam Shanmugiah Vijayabaskar, David Robert Westhead, Simon Jan van Heeringen, Richárd Bártfai
Underlying the development of malaria parasites within erythrocytes and the resulting pathogenicity is a hardwired program that secures proper timing of gene transcription and production of functionally relevant proteins. How stage-specific gene expression is orchestrated in vivo remains unclear. Here, using the assay for transposase accessible chromatin sequencing (ATAC-seq), we identified ∼4,000 regulatory regions in P. falciparum intraerythrocytic stages. The vast majority of these sites are located within 2 kb upstream of transcribed genes and their chromatin accessibility pattern correlates positively with abundance of the respective mRNA transcript...
April 11, 2018: Cell Host & Microbe
https://www.readbyqxmd.com/read/29625068/chromatin-accessibility-dynamics-during-chemical-induction-of-pluripotency
#11
Shangtao Cao, Shengyong Yu, Dongwei Li, Jing Ye, Xuejie Yang, Chen Li, Xiaoshan Wang, Yuanbang Mai, Yue Qin, Jian Wu, Jiangping He, Chunhua Zhou, He Liu, Bentian Zhao, Xiaodong Shu, Chuman Wu, Ruiping Chen, Waiyee Chan, Guangjin Pan, Jiekai Chen, Jing Liu, Duanqing Pei
Despite its exciting potential, chemical induction of pluripotency (CIP) efficiency remains low and the mechanisms are poorly understood. We report the development of an efficient two-step serum- and replating-free CIP protocol and the associated chromatin accessibility dynamics (CAD) by assay for transposase-accessible chromatin (ATAC)-seq. CIP reorganizes the somatic genome to an intermediate state that is resolved under 2iL condition by re-closing previously opened loci prior to pluripotency acquisition with gradual opening of loci enriched with motifs for the OCT/SOX/KLF families...
April 5, 2018: Cell Stem Cell
https://www.readbyqxmd.com/read/29618724/global-dynamics-of-stage-specific-transcription-factor-binding-during-thymocyte-development
#12
Tomonori Hosoya, Ricardo D'Oliveira Albanus, John Hensley, Greggory Myers, Yasuhiro Kyono, Jacob Kitzman, Stephen C J Parker, James Douglas Engel
In vertebrates, multiple transcription factors (TFs) bind to gene regulatory elements (promoters, enhancers, and silencers) to execute developmental expression changes. ChIP experiments are often used to identify where TFs bind to regulatory elements in the genome, but the requirement of TF-specific antibodies hampers analyses of tens of TFs at multiple loci. Here we tested whether TF binding predictions using ATAC-seq can be used to infer the identity of TFs that bind to functionally validated enhancers of the Cd4, Cd8, and Gata3 genes in thymocytes...
April 4, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29610331/evolutionary-emergence-of-the-rac3b-rfng-sgca-regulatory-cluster-refined-mechanisms-for-hindbrain-boundaries-formation
#13
Joaquín Letelier, Javier Terriente, Ivan Belzunce, Adria Voltes, Cristian Alberto Undurraga, Rocio Polvillo, Lucie Devos, Juan J Tena, Ignacio Maeso, Sylvie Retaux, José Luis Gomez-Skarmeta, Juan R Martínez-Morales, Cristina Pujades
Developmental programs often rely on parallel morphogenetic mechanisms that guarantee precise tissue architecture. While redundancy constitutes an obvious selective advantage, little is known on how novel morphogenetic mechanisms emerge during evolution. In zebrafish, rhombomeric boundaries behave as an elastic barrier, preventing cell intermingling between adjacent compartments. Here, we identify the fundamental role of the small-GTPase Rac3b in actomyosin cable assembly at hindbrain boundaries. We show that the novel rac3b / rfng / sgca regulatory cluster, which is specifically expressed at the boundaries, emerged in the Ostariophysi superorder by chromosomal rearrangement that generated new cis -regulatory interactions...
April 2, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29605854/assay-for-transposase-accessible-chromatin-atac-seq-to-chart-the-open-chromatin-landscape-of-human-pancreatic-islets
#14
Helena Raurell-Vila, Mireia Ramos-Rodríguez, Lorenzo Pasquali
The regulatory mechanisms that ensure an accurate control of gene transcription are central to cellular function, development and disease. Such mechanisms rely largely on noncoding regulatory sequences that allow the establishment and maintenance of cell identity and tissue-specific cellular functions.The study of chromatin structure and nucleosome positioning allowed revealing transcription factor accessible genomic sites with regulatory potential, facilitating the comprehension of tissue-specific cis-regulatory networks...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29603380/identification-of-chromatin-accessible-domains-in-non-alcoholic-steatohepatitis-derived-hepatocellular-carcinoma
#15
Mekonnen Lemma Dechassa, Volodymyr Tryndyak, Aline de Conti, Wenming Xiao, Frederick A Beland, Igor P Pogribny
Non-alcoholic steatohepatitis (NASH) is becoming one of the major causes of hepatocellular carcinoma (HCC) in the United States and Western countries; however, the molecular mechanisms associated with NASH-related liver carcinogenesis are not well understood. In the present study, we investigated cancer-associated chromatin alterations using a model that resembles the development of NASH-related HCC in humans. An assay for transposase-accessible chromatin with high throughput sequencing (ATAC-seq) identified 1,677 tumor-specific chromatin-accessible regions in NASH-derived HCC tissue samples...
March 30, 2018: Molecular Carcinogenesis
https://www.readbyqxmd.com/read/29579120/hsv-1-induced-disruption-of-transcription-termination-resembles-a-cellular-stress-response-but-selectively-increases-chromatin-accessibility-downstream-of-genes
#16
Thomas Hennig, Marco Michalski, Andrzej J Rutkowski, Lara Djakovic, Adam W Whisnant, Marie-Sophie Friedl, Bhaskar Anand Jha, Marisa A P Baptista, Anne L'Hernault, Florian Erhard, Lars Dölken, Caroline C Friedel
Lytic herpes simplex virus 1 (HSV-1) infection triggers disruption of transcription termination (DoTT) of most cellular genes, resulting in extensive intergenic transcription. Similarly, cellular stress responses lead to gene-specific transcription downstream of genes (DoG). In this study, we performed a detailed comparison of DoTT/DoG transcription between HSV-1 infection, salt and heat stress in primary human fibroblasts using 4sU-seq and ATAC-seq. Although DoTT at late times of HSV-1 infection was substantially more prominent than DoG transcription in salt and heat stress, poly(A) read-through due to DoTT/DoG transcription and affected genes were significantly correlated between all three conditions, in particular at earlier times of infection...
March 26, 2018: PLoS Pathogens
https://www.readbyqxmd.com/read/29572403/genome-wide-mapping-of-dna-accessibility-and-binding-sites-for-creb-and-c-ebp-%C3%AE-in-vasopressin-sensitive-collecting-duct-cells
#17
Hyun Jun Jung, Viswanathan Raghuram, Jae Wook Lee, Mark A Knepper
Background Renal water excretion is controlled by vasopressin, in part through regulation of the transcription of the aquaporin-2 gene ( Aqp2 ). Methods To identify enhancer regions likely to be involved in the regulation of Aqp2 and other principal cell-specific genes, we used several next generation DNA-sequencing techniques in a well characterized cultured cell model of collecting duct principal cells (mpkCCD). To locate enhancers, we performed the assay for transposase-accessible chromatin using sequencing (ATAC-Seq) to identify accessible regions of DNA and integrated the data with data generated by chromatin immunoprecipitation followed by next generation DNA-sequencing (ChIP-Seq) for CCCTC binding factor (CTCF) binding, histone H3 lysine-27 acetylation, and RNA polymerase II...
May 2018: Journal of the American Society of Nephrology: JASN
https://www.readbyqxmd.com/read/29561703/chromium-disrupts-chromatin-organization-and-ctcf-access-to-its-cognate-sites-in-promoters-of-differentially-expressed-genes
#18
Andrew VonHandorf, Francisco Javier Sánchez-Martín, Jacek Biesiada, Hongxia Zhang, Xiang Zhang, Mario Medvedovic, Alvaro Puga
Hexavalent chromium compounds are well-established respiratory carcinogens used in industrial processes. While inhalation exposure constitutes an occupational risk affecting mostly chromium workers, environmental exposure from drinking water is a widespread gastrointestinal cancer risk, affecting millions of people throughout the world. Cr(VI) is genotoxic, forming protein-Cr-DNA adducts and silencing tumor suppressor genes, but its mechanism of action at the molecular level is poorly understood. Our prior work using FAIRE showed that Cr(VI) disrupted the binding of transcription factors CTCF and AP-1 to their cognate chromatin sites...
March 21, 2018: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/29558892/global-analysis-of-primary-mesenchyme-cell-cis-regulatory-modules-by-chromatin-accessibility-profiling
#19
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/29545397/molecular-transitions-in-early-progenitors-during-human-cord-blood-hematopoiesis
#20
Shiwei Zheng, Efthymia Papalexi, Andrew Butler, William Stephenson, Rahul Satija
Hematopoietic stem cells (HSCs) give rise to diverse cell types in the blood system, yet our molecular understanding of the early trajectories that generate this enormous diversity in humans remains incomplete. Here, we leverage Drop-seq, a massively parallel single-cell RNA sequencing (scRNA-seq) approach, to individually profile 20,000 progenitor cells from human cord blood, without prior enrichment or depletion for individual lineages based on surface markers. Our data reveal a transcriptional compendium of progenitor states in human cord blood, representing four committed lineages downstream from HSC, alongside the transcriptional dynamics underlying fate commitment...
March 15, 2018: Molecular Systems Biology
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