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https://www.readbyqxmd.com/read/29052193/identification-of-open-chromatin-regions-in-plant-genomes-using-atac-seq
#1
Marko Bajic, Kelsey A Maher, Roger B Deal
Identifying and characterizing highly accessible chromatin regions assists in determining the location of genomic regulatory elements and understanding transcriptional regulation. In this chapter, we describe an approach to map accessible chromatin features in plants using the Assay for Transposase-Accessible Chromatin, combined with high-throughput sequencing (ATAC-seq), which was originally developed for cultured animal cells. This technique utilizes a hyperactive Tn5 transposase to cause DNA cleavage and simultaneous insertion of sequencing adapters into open chromatin regions of the input nuclei...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29046480/epigenetic-mechanisms-underlying-maternal-diabetes-associated-risk-of-congenital-heart-disease
#2
Madhumita Basu, Jun-Yi Zhu, Stephanie LaHaye, Uddalak Majumdar, Kai Jiao, Zhe Han, Vidu Garg
Birth defects are the leading cause of infant mortality, and they are caused by a combination of genetic and environmental factors. Environmental risk factors may contribute to birth defects in genetically susceptible infants by altering critical molecular pathways during embryogenesis, but experimental evidence for gene-environment interactions is limited. Fetal hyperglycemia associated with maternal diabetes results in a 5-fold increased risk of congenital heart disease (CHD), but the molecular basis for this correlation is unknown...
October 19, 2017: JCI Insight
https://www.readbyqxmd.com/read/29038474/a-shared-runx1-bound-zbtb16-enhancer-directs-innate-and-innate-like-lymphoid-lineage-development
#3
Ai-Ping Mao, Isabel E Ishizuka, Darshan N Kasal, Malay Mandal, Albert Bendelac
Zbtb16-encoded PLZF is a signature transcription factor (TF) that directs the acquisition of T-helper effector programs during the development of multiple innate lymphocyte lineages, including natural killer T cell, innate lymphoid cell, mucosal-associated invariant T cell and γδ lineages. PLZF is also essential in osteoblast and spermatogonial development. How Zbtb16 itself is regulated in different lineages is incompletely understood. Here, by systematic CRISPR/Cas9-assisted deletions of chromatin accessible regions within the Zbtb16 locus in mouse, we identify a critical enhancer controlling PLZF expression exclusively in innate lymphoid lineages...
October 16, 2017: Nature Communications
https://www.readbyqxmd.com/read/29030848/profiling-open-chromatin-structure-in-the%C3%A2-ovarian-somatic-cells-using-atac-seq
#4
Kensaku Murano, Yuka W Iwasaki, Haruhiko Siomi
The assay for transposase-accessible chromatin using sequencing (ATAC-seq) was recently established as a method to profile open chromatin, which overcomes the sample size limitations of the alternative methods DNase/MNase-seq. To investigate the role of Piwi in heterochromatin formation around transposable element loci, we have used ATAC-seq to examine chromatin accessibility at target transposable elements in a Drosophila cultured cell line, ovarian somatic cells (OSCs). In this chapter, we describe our method to profile open chromatin structure in OSCs using ATAC-seq...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29023442/environmental-perturbations-lead-to-extensive-directional-shifts-in-rna-processing
#5
Allison L Richards, Donovan Watza, Anthony Findley, Adnan Alazizi, Xiaoquan Wen, Athma A Pai, Roger Pique-Regi, Francesca Luca
Environmental perturbations have large effects on both organismal and cellular traits, including gene expression, but the extent to which the environment affects RNA processing remains largely uncharacterized. Recent studies have identified a large number of genetic variants associated with variation in RNA processing that also have an important role in complex traits; yet we do not know in which contexts the different underlying isoforms are used. Here, we comprehensively characterized changes in RNA processing events across 89 environments in five human cell types and identified 15,300 event shifts (FDR = 15%) comprised of eight event types in over 4,000 genes...
October 12, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/29020802/recent-advances-in-the-systems-biology-of-aging
#6
Daniel Edward Lee Promislow, Mark A McCormick
<b><i>Significance</i></b>: Reductionist studies have contributed greatly to our understanding of the basic biology of aging in recent years but we still do not understand fundamental mechanisms for many identified drugs and pathways. Use of systems approaches will help us move forward in our understanding of aging. <b><i>Recent Advances</i></b>: Recent work described here has illustrated the power of systems biology to inform our understanding of aging through the study of 1) diet restriction; 2) neurodegenerative disease; and 3) biomarkers of aging...
October 12, 2017: Antioxidants & Redox Signaling
https://www.readbyqxmd.com/read/28986717/synthesis-and-spectroscopic-studies-of-phenanthroimidazole-imine-derivatives-and-evaluation-of-their-antioxidant-activity
#7
Sibel Gülle, Seçil Çelik Erbaş, Ataç Uzel
The phenanthroimidazole derivatives are used in the drug industry in large scale. In this study four new phenanthroimidazole-imine derivatives were synthesized and their spectroscopic studies as well as their antioxidant behaviors were examined. Structural analyses were made by FT-IR, (1)H-NMR, (13)C-NMR, LC-MS spectroscopy techniques. UV-vis absorption and emission spectroscopy techniques have been used to determine the photophysical characteristics of four newly synthesized phenanthroimidazoles. The maximum absorption and emission wavelengths, molar extinction coefficients (ε), singlet energy levels (Es), Stokes' shift values (Δλ) of phenanthroimidazole-imine derivatives are given...
October 7, 2017: Journal of Fluorescence
https://www.readbyqxmd.com/read/28986391/altered-hydroxymethylation-is-seen-at-regulatory-regions-in-pancreatic-cancer-and-regulates-oncogenic-pathways
#8
Sanchari Bhattacharyya, Kith Pradhan, Nathaniel Campbell, Jozef Mazdo, Aparna Vasantkumar, Shahina Maqbool, Tushar D Bhagat, Sonal Gupta, Masako Suzuki, Yiting Yu, John M Greally, Ulrich Steidl, James Bradner, Meelad Dawlaty, Lucy Godley, Anirban Maitra, Amit Verma
Transcriptional deregulation of oncogenic pathways is a hallmark of cancer and can be due to epigenetic alterations. 5-Hydroxymethylcytosine (5-hmC) is an epigenetic modification that has not been studied in pancreatic cancer. Genome-wide analysis of 5-hmC-enriched loci with hmC-seal was conducted in a cohort of low-passage pancreatic cancer cell lines, primary patient-derived xenografts, and pancreatic controls and revealed strikingly altered patterns in neoplastic tissues. Differentially hydroxymethylated regions preferentially affected known regulatory regions of the genome, specifically overlapping with known H3K4me1 enhancers...
October 6, 2017: Genome Research
https://www.readbyqxmd.com/read/28985528/chromatin-and-single-cell-rna-seq-profiling-reveal-dynamic-signaling-and-metabolic-transitions-during-human-spermatogonial-stem-cell-development
#9
Jingtao Guo, Edward J Grow, Chongil Yi, Hana Mlcochova, Geoffrey J Maher, Cecilia Lindskog, Patrick J Murphy, Candice L Wike, Douglas T Carrell, Anne Goriely, James M Hotaling, Bradley R Cairns
Human adult spermatogonial stem cells (hSSCs) must balance self-renewal and differentiation. To understand how this is achieved, we profiled DNA methylation and open chromatin (ATAC-seq) in SSEA4(+) hSSCs, analyzed bulk and single-cell RNA transcriptomes (RNA-seq) in SSEA4(+) hSSCs and differentiating c-KIT(+) spermatogonia, and performed validation studies via immunofluorescence. First, DNA hypomethylation at embryonic developmental genes supports their epigenetic "poising" in hSSCs for future/embryonic expression, while core pluripotency genes (OCT4 and NANOG) were transcriptionally and epigenetically repressed...
October 5, 2017: Cell Stem Cell
https://www.readbyqxmd.com/read/28973438/p53-regulates-enhancer-accessibility-and-activity-in-response-to-dna-damage
#10
Scott T Younger, John L Rinn
The tumor suppressor p53 is a well-characterized transcription factor that can bind gene promoters and regulate target gene transcription in response to DNA damage. Recent studies, however, have revealed that p53 binding events occur predominantly within regulatory enhancer elements. The effect of p53 binding on enhancer function has not been systematically evaluated. Here, we perform a genome-scale analysis of enhancer activity from p53-bound sequences using a series of massively parallel reporter assays (MPRAs) coupled with the assay for transposase-accessible chromatin (ATAC-Seq)...
September 29, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28967863/chromatin-accessibility-underlies-synthetic-lethality-of-swi-snf-subunits-in-arid1a-mutant-cancers
#11
Timothy W R Kelso, Devin K Porter, Maria Luisa Amaral, Maxim N Shokhirev, Christopher Benner, Diana C Hargreaves
ARID1A, a subunit of the SWI/SNF chromatin remodeling complex, is frequently mutated in cancer. Deficiency in its homolog ARID1B is synthetically lethal with ARID1A mutation. However, the functional relationship between these homologs has not been explored. Here, we use ATAC-seq, genome-wide histone modification mapping, and expression analysis to examine colorectal cancer cells lacking one or both ARID proteins. We find that ARID1A has a dominant role in maintaining chromatin accessibility at enhancers, while the contribution of ARID1B is evident only in the context of ARID1A mutation...
October 2, 2017: ELife
https://www.readbyqxmd.com/read/28931935/alpha-tc1-and-beta-tc-6-genomic-profiling-uncovers-both-shared-and-distinct-transcriptional-regulatory-features-with-their-primary-islet-counterparts
#12
Nathan Lawlor, Ahrim Youn, Romy Kursawe, Duygu Ucar, Michael L Stitzel
Alpha TC1 (αTC1) and Beta-TC-6 (βTC6) mouse islet cell lines are cellular models of islet (dys)function and type 2 diabetes (T2D). However, genomic characteristics of these cells, and their similarities to primary islet alpha and beta cells, are undefined. Here, we report the epigenomic (ATAC-seq) and transcriptomic (RNA-seq) landscapes of αTC1 and βTC6 cells. Each cell type exhibits hallmarks of its primary islet cell counterpart including cell-specific expression of beta (e.g., Pdx1) and alpha (e.g., Arx) cell transcription factors (TFs), and enrichment of binding motifs for these TFs in αTC1/βTC6 cis-regulatory elements...
September 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28917157/density-of-calcium-in-the-ascending-thoracic-aorta-and-risk-of-incident-cardiovascular-disease-events
#13
Isac C Thomas, Robyn L McClelland, Erin D Michos, Matthew A Allison, Nketi I Forbang, W T Longstreth, Wendy S Post, Nathan D Wong, Matthew J Budoff, Michael H Criqui
BACKGROUND AND AIMS: The volume and density of coronary artery calcium (CAC) both independently predict cardiovascular disease (CVD) beyond standard risk factors, with CAC density inversely associated with incident CVD after accounting for CAC volume. We tested the hypothesis that ascending thoracic aorta calcium (ATAC) volume and density predict incident CVD events independently of CAC. METHODS: The Multi-Ethnic Study of Atherosclerosis (MESA) is a prospective cohort study of participants without clinical CVD at baseline...
October 2017: Atherosclerosis
https://www.readbyqxmd.com/read/28906531/red-cell-distribution-width-is-correlated-with-extensive-coronary-artery-disease-in-patients-with-diabetes-mellitus
#14
Atac Celik, Metin Karayakali, Fatih Altunkas, Kayihan Karaman, Arif Arisoy, Koksal Ceyhan, Hasan Kadi, Fatih Koc
INTRODUCTION: Previous studies have predicted an independent relationship between red cell distribution width (RDW) and the risk of death and cardiovascular events in patients with coronary artery disease (CAD). The aim of this study was to investigate the relationship between RDW and extensiveness of CAD in patients with diabetes mellitus (DM). METHODS: Two hundred and thirty-three diabetic patients who underwent coronary angiographies at our centre in 2010 were included in the study...
August 23, 2017: Cardiovascular Journal of Africa
https://www.readbyqxmd.com/read/28891464/concentration-dependent-chromatin-states-induced-by-the-bicoid-morphogen-gradient
#15
Colleen E Hannon, Shelby A Blythe, Eric F Wieschaus
In Drosophila, graded expression of the maternal transcription factor Bicoid (Bcd) provides positional information to activate target genes at different positions along the anterior-posterior axis. We have measured the genome-wide binding profile of Bcd using ChIP-seq in embryos expressing single, uniform levels of Bcd protein, and grouped Bcd-bound targets into four classes based on occupancy at different concentrations. By measuring the biochemical affinity of target enhancers in these classes in vitro and genome-wide chromatin accessibility by ATAC-seq, we found that the occupancy of target sequences by Bcd is not primarily determined by Bcd binding sites, but by chromatin context...
September 11, 2017: ELife
https://www.readbyqxmd.com/read/28859074/open-chromatin-profiling-identifies-ap1-as-a-transcriptional-regulator-in-oesophageal-adenocarcinoma
#16
Edward Britton, Connor Rogerson, Shaveta Mehta, Yaoyong Li, Xiaodun Li, Rebecca C Fitzgerald, Yeng S Ang, Andrew D Sharrocks
Oesophageal adenocarcinoma (OAC) is one of the ten most prevalent forms of cancer and is showing a rapid increase in incidence and yet exhibits poor survival rates. Compared to many other common cancers, the molecular changes that occur in this disease are relatively poorly understood. However, genes encoding chromatin remodeling enzymes are frequently mutated in OAC. This is consistent with the emerging concept that cancer cells exhibit reprogramming of their chromatin environment which leads to subsequent changes in their transcriptional profile...
August 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28846090/an-improved-atac-seq-protocol-reduces-background-and-enables-interrogation-of-frozen-tissues
#17
M Ryan Corces, Alexandro E Trevino, Emily G Hamilton, Peyton G Greenside, Nicholas A Sinnott-Armstrong, Sam Vesuna, Ansuman T Satpathy, Adam J Rubin, Kathleen S Montine, Beijing Wu, Arwa Kathiria, Seung Woo Cho, Maxwell R Mumbach, Ava C Carter, Maya Kasowski, Lisa A Orloff, Viviana I Risca, Anshul Kundaje, Paul A Khavari, Thomas J Montine, William J Greenleaf, Howard Y Chang
We present Omni-ATAC, an improved ATAC-seq protocol for chromatin accessibility profiling that works across multiple applications with substantial improvement of signal-to-background ratio and information content. The Omni-ATAC protocol generates chromatin accessibility profiles from archival frozen tissue samples and 50-μm sections, revealing the activities of disease-associated DNA elements in distinct human brain structures. The Omni-ATAC protocol enables the interrogation of personal regulomes in tissue context and translational studies...
October 2017: Nature Methods
https://www.readbyqxmd.com/read/28844864/the-short-isoform-of-brd4-promotes-hiv-1-latency-by-engaging-repressive-swi-snf-chromatin-remodeling-complexes
#18
Ryan J Conrad, Parinaz Fozouni, Sean Thomas, Hendrik Sy, Qiang Zhang, Ming-Ming Zhou, Melanie Ott
BET proteins commonly activate cellular gene expression, yet inhibiting their recruitment paradoxically reactivates latent HIV-1 transcription. Here we identify the short isoform of BET family member BRD4 (BRD4S) as a corepressor of HIV-1 transcription. We found that BRD4S was enriched in chromatin fractions of latently infected T cells, and it was more rapidly displaced from chromatin upon BET inhibition than the long isoform. BET inhibition induced marked nucleosome remodeling at the latent HIV-1 promoter, which was dependent on the activity of BRG1-associated factors (BAF), an SWI/SNF chromatin-remodeling complex with known repressive functions in HIV-1 transcription...
September 21, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28825706/chromvar-inferring-transcription-factor-associated-accessibility-from-single-cell-epigenomic-data
#19
Alicia N Schep, Beijing Wu, Jason D Buenrostro, William J Greenleaf
Single-cell ATAC-seq (scATAC) yields sparse data that make conventional analysis challenging. We developed chromVAR (http://www.github.com/GreenleafLab/chromVAR), an R package for analyzing sparse chromatin-accessibility data by estimating gain or loss of accessibility within peaks sharing the same motif or annotation while controlling for technical biases. chromVAR enables accurate clustering of scATAC-seq profiles and characterization of known and de novo sequence motifs associated with variation in chromatin accessibility...
October 2017: Nature Methods
https://www.readbyqxmd.com/read/28809012/comparative-genomics-as-a-foundation-for-evo-devo-studies-in-birds
#20
Phil Grayson, Simon Y W Sin, Timothy B Sackton, Scott V Edwards
Developmental genomics is a rapidly growing field, and high-quality genomes are a useful foundation for comparative developmental studies. A high-quality genome forms an essential reference onto which the data from numerous assays and experiments, including ChIP-seq, ATAC-seq, and RNA-seq, can be mapped. A genome also streamlines and simplifies the development of primers used to amplify putative regulatory regions for enhancer screens, cDNA probes for in situ hybridization, microRNAs (miRNAs) or short hairpin RNAs (shRNA) for RNA interference (RNAi) knockdowns, mRNAs for misexpression studies, and even guide RNAs (gRNAs) for CRISPR knockouts...
2017: Methods in Molecular Biology
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