scholarly journals Assessing chromatin accessibility in maize using ATAC-seq

2019 ◽  
Author(s):  
Yi-Jing Lee ◽  
Pearl Chang ◽  
Jui-Hsien Lu ◽  
Pao-Yang Chen ◽  
Chung-Ju Rachel Wang
Keyword(s):  
Cell Sorting ◽  
High Throughput Sequencing ◽  
Crop Improvement ◽  
Practical Method ◽  
Chromatin Accessibility ◽  
Crop Species ◽  
Chromatin Profiling ◽  
Key Steps ◽  
Accessible Chromatin ◽  
Complex Genome

Background: Maize is an important crop that has a complex genome. A better understanding of maize chromatin architecture provides great opportunities for crop improvement, because chromatin accessibility influences gene expression, thereby affecting agricultural traits. The newly developed method for chromatin profiling, Assay for Transposase Accessible Chromatin with high-throughput sequencing (ATAC-seq), has been developed to investigate chromatin accessibility. Result: We adapt this method by testing parameters of several key steps and generate the first ATAC-seq protocol for maize. We demonstrate that purification of maize nuclei to eliminate organelles can be achieved without the need for cell sorting, and that only a standard bench-top centrifuge is required for sample preparation. Finally, our sequence analyses confirm that our protocol of ATAC-seq can be successfully used to assess the chromatin landscape in maize. Conclusion: The ATAC-seq provides a useful technique to study the chromatin accessibility. Given the parameters tested in our study, it can be a simple and practical method for maize and may be a foundation for similar studies in other crop species.

scholarly journals ATAC-seq with unique molecular identifiers improves quantification and footprinting

2020 ◽  
Vol 3 (1) ◽  
Author(s):  
Tao Zhu ◽  
Keyan Liao ◽  
Rongfang Zhou ◽  
Chunjiao Xia ◽  
Weibo Xie
Keyword(s):  
Transcription Factor ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Pcr Amplification ◽  
Chromatin Accessibility ◽  
Link Type ◽  
Pcr Duplicates ◽  
Identify Transcription Factor ◽  
Accessible Chromatin ◽  
Accurate Quantification

AbstractATAC-seq (Assay for Transposase-Accessible Chromatin with high-throughput sequencing) provides an efficient way to analyze nucleosome-free regions and has been applied widely to identify transcription factor footprints. Both applications rely on the accurate quantification of insertion events of the hyperactive transposase Tn5. However, due to the presence of the PCR amplification, it is impossible to accurately distinguish independently generated identical Tn5 insertion events from PCR duplicates using the standard ATAC-seq technique. Removing PCR duplicates based on mapping coordinates introduces increasing bias towards highly accessible chromatin regions. To overcome this limitation, we establish a UMI-ATAC-seq technique by incorporating unique molecular identifiers (UMIs) into standard ATAC-seq procedures. UMI-ATAC-seq can rescue about 20% of reads that are mistaken as PCR duplicates in standard ATAC-seq in our study. We demonstrate that UMI-ATAC-seq could more accurately quantify chromatin accessibility and significantly improve the sensitivity of identifying transcription factor footprints. An analytic pipeline is developed to facilitate the application of UMI-ATAC-seq, and it is available at https://github.com/tzhu-bio/UMI-ATAC-seq.

scholarly journals One-pot universal NicE-seq: all enzymatic downstream processing of 4% formaldehyde crosslinked cells for chromatin accessibility genomics

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Udayakumar S. Vishnu ◽  
Pierre-Olivier Estève ◽  
Hang Gyeong Chin ◽  
Sriharsa Pradhan
Keyword(s):  
Mammalian Cells ◽  
Molecular Subtypes ◽  
Downstream Processing ◽  
Chromatin Accessibility ◽  
One Pot ◽  
Tn5 Transposon ◽  
Chromatin Profiling ◽  
Nicking Enzyme ◽  
Accessible Chromatin ◽  
Enzymatic Fragmentation

Abstract Background Accessible chromatin landscape allows binding of transcription factors, and remodeling of promoter and enhancer elements during development. Chromatin accessibility along with integrated multiomics approaches have been used for determining molecular subtypes of cancer in patient samples. Results One-pot Universal NicE-seq (One-pot UniNicE-seq) is an improved accessible chromatin profiling method that negate DNA purification and incorporate sonication free enzymatic fragmentation before library preparation and is suited to a variety of mammalian cells. One-pot UniNicE-seq is versatile, capable of profiling 4% formaldehyde fixed chromatin in as low as 25 fixed cells. Accessible chromatin profile is more efficient on formaldehyde-fixed cells using one-pot UniNicE-seq compared to Tn5 transposon mediated methods, demonstrating its versatility. Conclusion One-pot UniNicE-seq allows the entire process of accessible chromatin labeling and enrichment in one pot at 4% formaldehyde cross-linking conditions. It doesn’t require enzyme titration, compared to other technologies, since accessible chromatin is labelled with 5mC incorporation and deter degradation by nicking enzyme, thus opening the possibility for automation.

scholarly journals I-ATAC: interactive pipeline for the management and pre-processing of ATAC-seq samples

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e4040 ◽  
Author(s):  
Zeeshan Ahmed ◽  
Duygu Ucar
Keyword(s):  
Chromatin Accessibility ◽  
Clinical Samples ◽  
Open Chromatin ◽  
Data Generation ◽  
Desktop Application ◽  
Feature Based ◽  
Cross Platform ◽  
Chromatin Profiling ◽  
User Friendly ◽  
Accessible Chromatin

Assay for Transposase Accessible Chromatin (ATAC-seq) is an open chromatin profiling assay that is adapted to interrogate chromatin accessibility from small cell numbers. ATAC-seq surmounted a major technical barrier and enabled epigenome profiling of clinical samples. With this advancement in technology, we are now accumulating ATAC-seq samples from clinical samples at an unprecedented rate. These epigenomic profiles hold the key to uncovering how transcriptional programs are established in diverse human cells and are disrupted by genetic or environmental factors. Thus, the barrier to deriving important clinical insights from clinical epigenomic samples is no longer one of data generation but of data analysis. Specifically, we are still missing easy-to-use software tools that will enable non-computational scientists to analyze their own ATAC-seq samples. To facilitate systematic pre-processing and management of ATAC-seq samples, we developed an interactive, cross-platform, user-friendly and customized desktop application: interactive-ATAC (I-ATAC). I-ATAC integrates command-line data processing tools (FASTQC, Trimmomatic, BWA, Picard, ATAC_BAM_shiftrt_gappedAlign.pl, Bedtools and Macs2) into an easy-to-use platform with user interface to automatically pre-process ATAC-seq samples with parallelized and customizable pipelines. Its performance has been tested using public ATAC-seq datasets in GM12878 and CD4+T cells and a feature-based comparison is performed with some available interactive LIMS (Galaxy, SMITH, SeqBench, Wasp, NG6, openBIS). I-ATAC is designed to empower non-computational scientists to process their own datasets and to break to exclusivity of data analyses to computational scientists. Additionally, I-ATAC is capable of processing WGS and ChIP-seq samples, and can be customized by the user for one-independent or multiple-sequential operations.

scholarly journals The accessible promoter–mediated supplementary effect of ACE2 provides new insight into the tissue tropism of SARS-CoV-2

2020 ◽  
Author(s):  
Qi Jiang ◽  
Guifang Du ◽  
Junting Wang ◽  
XiaoHan Tang ◽  
Xuejun wang ◽  
...  
Keyword(s):  
Cell Lines ◽  
High Throughput Sequencing ◽  
Chromatin Accessibility ◽  
Tissue Tropism ◽  
Open Chromatin ◽  
Converting Enzyme ◽  
Angiotensin Converting Enzyme 2 ◽  
Novel Coronavirus ◽  
Accessible Chromatin ◽  
Insight Into

Abstract Background：Angiotensin-converting enzyme 2 (ACE2) has been confirmed to be a receptor for the newly discovered severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, cell surface ACE2 expression is reported to be inconsistent with clinical tissue tropism of SARS-CoV-2, which complicates understanding of the pathogenesis of 2019 novel coronavirus disease (COVID-19). The consumption of ACE2 by internalization and shedding processes may explain this discordance. Results：To understand the discordance between ACE2 expression and the tissue tropism of SARS-CoV-2, we examined the chromatin accessibility of ACE2 promoter in hundreds of tissues and cell lines using public DNase-seq and assay for transposase-accessible chromatin with high throughput sequencing (ATAC-seq) data. We find that ACE2 promoter is only accessible in three tissues including lung, large intestine and placenta. Also, we examined tumors tissues and ACE2 promoter is observed accessible in five tumors with reported SARS-CoV-2 susceptibility. We confirmed the susceptibility by performing SARS-CoV-2 pseudovirus infection in several cell lines. Conclusions：We propose that open chromatin at the promoter mediates the ACE2 supplementary effect and ensures the entry of SARS-CoV-2. This hypothesis provides a new view and potential clues for further investigation of COVID-19 pathogenesis.

scholarly journals Successful ATAC-Seq From Snap-Frozen Equine Tissues

2021 ◽  
Vol 12 ◽  
Author(s):  
Sichong Peng ◽  
Rebecca Bellone ◽  
Jessica L. Petersen ◽  
Theodore S. Kalbfleisch ◽  
Carrie J. Finno
Keyword(s):  
Functional Annotation ◽  
High Throughput Sequencing ◽  
Chromatin Accessibility ◽  
Tissue Type ◽  
Tissue Samples ◽  
Genome Wide ◽  
Frozen Tissue ◽  
And Storage ◽  
Accessible Chromatin ◽  
Animal Genomes

An assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) has become an increasingly popular method to assess genome-wide chromatin accessibility in isolated nuclei from fresh tissues. However, many biobanks contain only snap-frozen tissue samples. While ATAC-seq has been applied to frozen brain tissues in human, its applicability in a wide variety of tissues in horse remains unclear. The Functional Annotation of Animal Genome (FAANG) project is an international collaboration aimed to provide high quality functional annotation of animal genomes. The equine FAANG initiative has generated a biobank of over 80 tissues from two reference female animals and experiments to begin to characterize tissue specificity of genome function for prioritized tissues have been performed. Due to the logistics of tissue collection and storage, extracting nuclei from a large number of tissues for ATAC-seq at the time of collection is not always practical. To assess the feasibility of using stored frozen tissues for ATAC-seq and to provide a guideline for the equine FAANG project, we compared ATAC-seq results from nuclei isolated from frozen tissue to cryopreserved nuclei (CN) isolated at the time of tissue harvest in liver, a highly cellular homogenous tissue, and lamina, a relatively acellular tissue unique to the horse. We identified 20,000–33,000 accessible chromatin regions in lamina and 22–61,000 in liver, with consistently more peaks identified using CN isolated at time of tissue collection. Our results suggest that frozen tissues are an acceptable substitute when CN are not available. For more challenging tissues such as lamina, nuclei extraction at the time of tissue collection is still preferred for optimal results. Therefore, tissue type and accessibility to intact nuclei should be considered when designing ATAC-seq experiments.

scholarly journals ATAC-seq with unique molecular identifiers improves quantification and footprinting

2020 ◽  
Author(s):  
Tao Zhu ◽  
Keyan Liao ◽  
Rongfang Zhou ◽  
Chunjiao Xia ◽  
Weibo Xie
Keyword(s):  
Transcription Factor ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Pcr Amplification ◽  
Chromatin Accessibility ◽  
Link Type ◽  
Pcr Duplicates ◽  
Identify Transcription Factor ◽  
Accessible Chromatin ◽  
Accurate Quantification

AbstractATAC-seq (Assay for Transposase-Accessible Chromatin with high-throughput sequencing) provides an efficient way to analyze nucleosome-free regions and has been applied widely to identify transcription factor footprints. Both applications rely on the accurate quantification of insertion events of the hyperactive transposase Tn5. However, due to the presence of the PCR amplification, it is impossible to accurately distinguish independently generated identical Tn5 insertion events from PCR duplicates using the standard ATAC-seq technique. Removing PCR duplicates based on mapping coordinates introduces an increasing bias towards highly accessible chromatin regions. To overcome this limitation, we establish a UMI-ATAC-seq technique by incorporating unique molecular identifiers (UMIs) into standard ATAC-seq procedures. In our study, UMI-ATAC-seq can rescue about 20% of reads that are mistaken as PCR duplicates in standard ATAC-seq, which helps identify an additional 50% or more of footprints. We demonstrate that UMI-ATAC-seq could more accurately quantify chromatin accessibility and significantly improve the sensitivity of identifying transcription factor footprints. An analytic pipeline is developed to facilitate the application of UMI-ATAC-seq, and it is available at https://github.com/tzhu-bio/UMI-ATAC-seq.

scholarly journals A standalone software platform for the interactive management and pre-processing of ATAC-seq samples

2017 ◽  
Author(s):  
Zeeshan Ahmed ◽  
Duygu Ucar
Keyword(s):  
Chromatin Accessibility ◽  
Clinical Samples ◽  
Open Chromatin ◽  
Data Generation ◽  
Desktop Application ◽  
Interactive Management ◽  
Cross Platform ◽  
Chromatin Profiling ◽  
User Friendly ◽  
Accessible Chromatin

Assay for Transposase Accessible Chromatin (ATAC-seq) is an open chromatin profiling assay that is adapted to interrogate chromatin accessibility from small cell numbers. ATAC-seq surmounted a major technical barrier and enabled epigenome profiling of clinical samples. With this advancement in technology we are now accumulating ATAC-seq samples from clinical samples at an unprecedented rate. These epigenomic profiles hold the key to uncover how transcriptional programs are established in diverse human cells and are disrupted by genetic or environmental factors. Thus, the barrier to deriving important clinical insights from clinical epigenomic samples is no longer one of data generation, but of data analysis. Specifically, we are still missing easy-to-use software tools that will enable non-computational scientists to analyze their own ATAC-seq samples. To facilitate systematic pre-processing and management of ATAC-seq samples, we developed an interactive, cross platform, user-friendly desktop application: interactive-ATAC (I-ATAC). I-ATAC integrates command-line data processing tools (e.g., FASTQC for quality checking) into an easy-to-use platform with user interface to automatically pre-process ATAC-seq samples with parallelized and customizable pipelines. Its performance has been tested using public ATAC-seq datasets in GM12878 and CD4+ T cells. I-ATAC is designed to empower non-computational scientists to process their own datasets and to break to exclusivity of data analyses to computational scientists.

scholarly journals Dynamic chromatin accessibility landscape changes following interleukin-1 stimulation

2020 ◽  
Author(s):  
Matt J. Barter ◽  
Kathleen Cheung ◽  
Julia Falk ◽  
Andreas C. Panagiotopoulos ◽  
Caitlin Cosimini ◽  
...  
Keyword(s):  
Gene Expression ◽  
High Throughput Sequencing ◽  
Regulatory Element ◽  
Interleukin 1 ◽  
Chromatin Modification ◽  
Chromatin Accessibility ◽  
Open Chromatin ◽  
Enhancer Activity ◽  
Cytokine Stimulation ◽  
Accessible Chromatin

AbstractGenome-wide methods for examining chromatin modification provide detailed information on regulatory regions of the genome. Dynamic modifications of chromatin allow rapid access of the gene regulatory machinery to condensed genomic regions facilitating subsequent gene expression. Inflammatory cytokine stimulation of cells can cause rapid gene expression changes through direct signalling pathway-mediated transcription factor activation and regulatory element binding.Here we used the Assay for Transposase Accessible Chromatin with high-throughput sequencing (ATAC-seq) to assess regions of the genome that are differentially accessible following treatment of cells with interleukin-1 (IL-1). We identified 126,483 open chromatin regions, with 241 regions significantly differentially accessible following stimulation, with 64 and 177 more or less accessible, respectively. These differentially accessible regions predominantly correspond to regions of the genome marked as enhancers. Motif searching identified an overrepresentation of a number of transcription factors, most notably RelA in the regions becoming more accessible, with analysis of ChIP-seq data confirmed RelA binding to these regions. A significant correlation in differential chromatin accessibility and gene expression was also observed.Functionality in regulating gene expression was confirmed using CRISPR/Cas9 genome-editing to delete regions for that became more accessible following stimulation in the genes MMP13, IKBKE and C1QTNF1. These same regions were also accessible for activation using a dCas9-transcriptional activator and showed enhancer activity in a cellular model.Together, these data describe and functionally validate a number of dynamically accessible chromatin regions involved in inflammatory signalling.

scholarly journals Impact of the gut microbiota on enhancer accessibility in gut intraepithelial lymphocytes

2016 ◽  
Vol 113 (51) ◽  
pp. 14805-14810 ◽  
Author(s):  
Nicholas P. Semenkovich ◽  
Joseph D. Planer ◽  
Philip P. Ahern ◽  
Nicholas W. Griffin ◽  
Charles Y. Lin ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
High Throughput Sequencing ◽  
Immune Cell ◽  
Intraepithelial Lymphocytes ◽  
Chromatin Accessibility ◽  
Functional Variation ◽  
Germ Free ◽  
The Face ◽  
Functional Features ◽  
Accessible Chromatin

The gut microbiota impacts many aspects of host biology including immune function. One hypothesis is that microbial communities induce epigenetic changes with accompanying alterations in chromatin accessibility, providing a mechanism that allows a community to have sustained host effects even in the face of its structural or functional variation. We used Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq) to define chromatin accessibility in predicted enhancer regions of intestinal αβ+and γδ+intraepithelial lymphocytes purified from germ-free mice, their conventionally raised (CONV-R) counterparts, and mice reared germ free and then colonized with CONV-R gut microbiota at the end of the suckling–weaning transition. Characterizing genes adjacent to traditional enhancers and super-enhancers revealed signaling networks, metabolic pathways, and enhancer-associated transcription factors affected by the microbiota. Our results support the notion that epigenetic modifications help define microbial community-affiliated functional features of host immune cell lineages.

scholarly journals Organizational properties of a functional mammalian cis-regulome

2019 ◽  
Author(s):  
Virendra K. Chaudhri ◽  
Krista Dienger-Stambaugh ◽  
Zhiguo Wu ◽  
Mahesh Shrestha ◽  
Harinder Singh
Keyword(s):  
Transcription Factor ◽  
B Cells ◽  
Dna Binding ◽  
Chromatin Accessibility ◽  
Motif Analysis ◽  
Transcription Profiles ◽  
Genomic Analyses ◽  
Enhancer Function ◽  
Chromatin Profiling ◽  
Accessible Chromatin

AbstractMammalian genomic states are distinguished by their chromatin and transcription profiles. Most genomic analyses rely on chromatin profiling to infer cis-regulomes controlling distinctive cellular states. By coupling FAIRE-seq with STARR-seq and integrating Hi-C we assemble a functional cis-regulome for activated murine B-cells. Within 55,130 accessible chromatin regions we delineate 9,989 active enhancers communicating with 7,530 promoters. The cis-regulome is dominated by long range enhancer-promoter interactions (>100kb) and complex combinatorics, implying rapid evolvability. Genes with multiple enhancers display higher rates of transcription and multi-genic enhancers manifest graded levels of H3K4me1 and H3K27ac in poised and activated states, respectively. Motif analysis of pathway-specific enhancers reveals diverse transcription factor (TF) codes controlling discrete processes. The cis-regulome strikingly enriches for combinatorial DNA binding regions of lineage determining TFs. Their genomic binding patterns reveal that onset of chromatin accessibility is associated with binding of simpler combinations whereas enhancer function requires greater complexity.

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