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 Chromatin Accessibility Landscapes of Acute Lymphoblastic Leukemia

Blood ◽  
2021 ◽  
Vol 138 (Supplement 1) ◽  
pp. 2215-2215
Author(s):  
Kelly R. Barnett ◽  
Jonathan D. Diedrich ◽  
Brennan P. Bergeron ◽  
Wenjian Yang ◽  
Kristine R. Crews ◽  
...  
Keyword(s):  
Acute Lymphoblastic Leukemia ◽  
Board Of Directors ◽  
Molecular Subtypes ◽  
Lymphoblastic Leukemia ◽  
Transcriptional Profiling ◽  
Data Monitoring Committee ◽  
Chromatin Accessibility ◽  
Advisory Committees ◽  
Gene Regulatory ◽  
Accessible Chromatin

Abstract Acute lymphoblastic leukemia (ALL) is the most common malignancy in pediatric patients spanning both B- and T-cell lineages. ALL also occurs less commonly in adults but with cure rates of only around 30%. Past work has characterized ALL into molecular subtypes spanning a range of aberrant chromosomal rearrangements and oncogene chimeric fusions driving malignancy. While transcriptional profiling of these subtypes has been extensively examined, the accompanying chromatin accessibility landscape and corresponding gene regulatory repertoire is not well characterized for many subtypes. To better profile the ALL epigenomic and gene regulatory repertoire we examined chromatin accessibility of 12 distinct molecular subtypes (BCR-ABL1, ETV6-RUNX1, Hyperdiploid, Hypodiploid, KMT2A rearranged, Ph-Like, PAX5, DUX4/ERG, TCF3-PBX1, T-ALL, Early T Precursor and B-other) across 189 primary patient samples of pediatric ALL (n = 106) and adult ALL (n = 83) origin using ATAC-seq. To our knowledge, this represents the largest collection of chromatin accessibility data in primary ALL samples spanning multiple molecular subtypes to date. Collectively, we identified over 600,000 accessible chromatin sites in the ALL genome with over 50,000 regions of differentially accessible chromatin encompassing both common and subtype-specific modalities. Further, transcription factor (TF) footprint profiling of ATAC-seq yielded tens of thousands of candidate TF binding events and identified key TF drivers within distinct molecular subtypes. We additionally performed H3K27ac ChIP-seq in a subset of 12 primary ALL patient samples, with integration of these histone data for select patient samples allowing inferences about candidate super-enhancer drivers of ALL molecular subtypes. Overall, these analyses and data offer a window into the gene regulatory and epigenetic landscape of ALL, and further highlight the complexity and heterogeneity of accessible chromatin landscapes among distinct molecular subtypes of ALL. Disclosures Stock: Pfizer: Consultancy, Honoraria, Research Funding; amgen: Honoraria; agios: Honoraria; jazz: Honoraria; kura: Honoraria; kite: Honoraria; morphosys: Honoraria; servier: Honoraria; syndax: Consultancy, Honoraria; Pluristeem: Consultancy, Honoraria. Pui: Adaptive Biotechnologies: Membership on an entity's Board of Directors or advisory committees; Novartis: Other: Data Monitoring Committee. Evans: Princess Máxima Center for Pediatric Oncology, Scientific Advisory Board, Chair: Membership on an entity's Board of Directors or advisory committees; St. Jude Children's Research Hospital, Emeritus Member (began Jan 2021): Ended employment in the past 24 months; BioSkryb, Inc.: Membership on an entity's Board of Directors or advisory committees.

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 Visualization and sequencing of accessible chromatin reveals cell cycle and post romidepsin treatment dynamics

2020 ◽  
Author(s):  
Pierre-Olivier Estève ◽  
Udayakumar S. Vishnu ◽  
Hang Gyeong Chin ◽  
Sriharsa Pradhan
Keyword(s):  
Gene Expression ◽  
Cell Cycle ◽  
Histone Deacetylases ◽  
Mammalian Cells ◽  
Chromatin Accessibility ◽  
Cell Type Specificity ◽  
Myc Oncogene ◽  
Genome Wide ◽  
A Cell ◽  
Accessible Chromatin

AbstractChromatin accessibility is a predictor of gene expression, cell division and cell type specificity. NicE-viewSeq (Nicking Enzyme assisted viewing and Sequencing) allows accessible chromatin visualization and sequencing with overall lower mitochondrial DNA and duplicated sequences interference relative to ATAC-see. Using NicE-viewSeq, we interrogated the accessibility of chromatin in a cell cycle (G1, S and G2/M) - specific manner using mammalian cells. Despite DNA replication and subsequent condensation of chromatin to chromosomes, chromatin accessibility remained generally preserved with minimal subtle alterations. Genome-wide alteration of chromatin accessibility within TSS and enhancer elements gradually decreased as cells progressed from G1 to G2M, with distinct differential accessibility near consensus transcription factors sites. Inhibition of histone deacetylases promoted accessible chromatin within gene bodies, correlating with apoptotic gene expression. In addition, reduced chromatin accessibility for the MYC oncogene pathway correlated with down regulation of pertinent genes. Surprisingly, repetitive RNA loci expression remained unaltered following histone acetylation-mediated increased accessibility. Therefore, we suggest that subtle changes in chromatin accessibility is a prerequisite during cell cycle and histone deacetylase inhibitor mediated therapeutics.

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 Universal NicE-seq for high resolution accessible chromatin profiling for formaldehyde fixed and FFPE tissues

2020 ◽  
Author(s):  
Hang Gyeong Chin ◽  
Zhiyi Sun ◽  
Udayakumar S. Vishnu ◽  
Christina Hao ◽  
Paloma Cejas ◽  
...  
Keyword(s):  
High Resolution ◽  
Mammalian Cells ◽  
Signal To Noise Ratio ◽  
Genomic Feature ◽  
Tissue Sections ◽  
Ffpe Tissues ◽  
Chromatin Profiling ◽  
Limited Digestion ◽  
Ffpe Tissue Section ◽  
Accessible Chromatin

AbstractAccessible chromatin plays a central role in gene expression and chromatin architecture. Current accessible chromatin approaches depend on limited digestion/cutting and pasting adaptors at the accessible DNA, thus requiring additional materials and time for optimization. Universal NicE-seq (UniNicE-seq) is an improved accessible chromatin profiling method that negate the optimization step and is suited to a variety of mammalian cells and tissues. Addition of 5-methyldeoxycytidine triphosphate during accessible chromatin labeling and an on-bead library making step substantially improved the signal to noise ratio while protecting the accessible regions from repeated nicking in cell lines, mouse T cells, mouse kidney, and human frozen tissue sections. We also demonstrate one tube UniNicE-seq for FFPE tissue section for direct NGS library preparation without sonication and DNA purification steps. These refinements allowed reliable mapping of accessible chromatin for high resolution genomic feature studies.

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.

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 Universal NicE-seq for high-resolution accessible chromatin profiling for formaldehyde-fixed and FFPE tissues

2020 ◽  
Vol 12 (1) ◽  
Author(s):  
Hang Gyeong Chin ◽  
Zhiyi Sun ◽  
Udayakumar S. Vishnu ◽  
Pengying Hao ◽  
Paloma Cejas ◽  
...  
Keyword(s):  
High Resolution ◽  
Mammalian Cells ◽  
Signal To Noise Ratio ◽  
Genomic Feature ◽  
Tissue Sections ◽  
Ffpe Tissues ◽  
Chromatin Profiling ◽  
Limited Digestion ◽  
Ffpe Tissue Section ◽  
Accessible Chromatin

Abstract Accessible chromatin plays a central role in gene expression and chromatin architecture. Current accessible chromatin approaches depend on limited digestion/cutting and pasting adaptors at the accessible DNA, thus requiring additional materials and time for optimization. Universal NicE-seq (UniNicE-seq) is an improved accessible chromatin profiling method that negates the optimization step and is suited to a variety of mammalian cells and tissues. Addition of 5-methyldeoxycytidine triphosphate during accessible chromatin labeling and an on-bead library making step substantially improved the signal to noise ratio while protecting the accessible regions from repeated nicking in cell lines, mouse T cells, mouse kidney, and human frozen tissue sections. We also demonstrate one tube UniNicE-seq for the FFPE tissue section for direct NGS library preparation without sonication and DNA purification steps. These refinements allowed reliable mapping of accessible chromatin for high-resolution genomic feature studies.

scholarly journals Scalable, multimodal profiling of chromatin accessibility and protein levels in single cells

2020 ◽  
Author(s):  
Eleni P. Mimitou ◽  
Caleb A. Lareau ◽  
Kelvin Y. Chen ◽  
Andre L. Zorzetto-Fernandes ◽  
Yusuke Takeshima ◽  
...  
Keyword(s):  
Single Cells ◽  
Chromatin Accessibility ◽  
Surface Proteins ◽  
Protein Markers ◽  
Peripheral Blood Mononuclear ◽  
Robust Detection ◽  
Protein Levels ◽  
Technological Advances ◽  
Chromatin Profiling ◽  
Accessible Chromatin

ABSTRACTRecent technological advances have enabled massively parallel chromatin profiling with single-cell Assay for Transposase Accessible Chromatin by sequencing (scATAC-seq) in thousands of individual cells. Here, we extend these approaches and present ATAC with Select Antigen Profiling by sequencing, ASAP-seq, a tool to simultaneously profile accessible chromatin and protein levels in thousands of single cells. Our approach pairs sparse scATAC-seq data with robust detection of hundreds of cell surface and intracellular protein markers and optional capture of mitochondrial DNA (mtDNA) for clonal tracking, thus concomitantly capturing three distinct modalities in single cells. Importantly, ASAP-seq uses a novel bridging approach that repurposes antibody:oligo conjugates designed for existing technologies that pair protein measurements with single cell RNA-seq. We demonstrate the utility of ASAP-seq by revealing coordinated and distinct changes in chromatin, RNA, and surface proteins during native hematopoietic differentiation, peripheral blood mononuclear cell stimulation, and as a combinatorial decoder and reporter of multiplexed perturbations in primary T cells.

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