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 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 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 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 Terminal selectors organize postmitotic chromatin accessibility for acquisition of serotonergic identity

2021 ◽  
Author(s):  
Xinrui L Zhang ◽  
William C Spencer ◽  
Nobuko Tabuchi ◽  
Evan S Deneris
Keyword(s):  
Single Cell ◽  
Chromatin Accessibility ◽  
Open Chromatin ◽  
Regulatory Sequences ◽  
Early Maturation ◽  
Accessible Chromatin

Assembly of transcriptomes encoding unique neuronal identities requires selective accessibility of regulatory inputs to cis-regulatory sequences in nucleosome-embedded chromatin. Yet the mechanisms involved in shaping postmitotic neuronal chromatin are poorly understood. Here we used ATAC-seq, ChIPmentation, and single-cell analyses to show that unique distal enhancers and super-enhancers define the Pet1 neuron lineage that generates serotonin (5-HT) neurons. Heterogeneous single cell chromatin landscapes are established early in postmitotic Pet1 neurons and reveal the regulatory programs driving Pet1 neuron subtype identities. Terminal selectors, Pet1 and Lmx1b, control chromatin accessibility in Pet1 neurons to select enhancers for 5-HT neurotransmission and synaptogenesis. In addition, these factors are required to maintain chromatin accessibility during early maturation suggesting that postmitotic open chromatin is unstable and requires continuous terminal selector input. Together our findings reveal a previously unrecognized function of terminal selectors in organizing postmitotic accessible chromatin for the development of specialized neuronal identities.

scholarly journals Multi-omics analysis for potential inflammation-related genes involved in tumor immune evasion via extended application of epigenetic data

2021 ◽  
Author(s):  
Chenshen Huang ◽  
Ning Wang ◽  
Na Zhang ◽  
Zhizhan Ni ◽  
Xiaohong Liu ◽  
...  
Keyword(s):  
Immune Evasion ◽  
Chromatin Accessibility ◽  
Open Chromatin ◽  
Tumor Immune Evasion ◽  
Omics Analysis ◽  
Extended Application ◽  
Open Chromatin Region ◽  
Chromatin Immunoprecipitation Sequencing ◽  
Accessible Chromatin

Background: Accumulating evidence suggests that inflammation-related genes may play key roles in tumor immune evasion. Programmed cell death ligand 1 (PD-L1) is an important immune checkpoint involved in mediating antitumor immunity. We performed multi-omics analysis to explore key inflammation-related genes affecting the transcriptional regulation of PD-L1 expression. Methods: The open chromatin region of the PD-L1 promoter was mapped using the assay for transposase-accessible chromatin using sequencing (ATAC-seq) profiles. Correlation analysis of epigenetic data (ATAC-seq) and transcriptome data (RNA-seq) were performed to identify inflammation-related transcription factors whose expression levels were correlated with the chromatin accessibility of the PD-L1 promoter. Chromatin immunoprecipitation sequencing (ChIP-seq) profiles were used to confirm the physical binding of the TF STAT2 and the predicted binding regions. We also confirmed the results of the bioinformatics analysis with cell experiments. Results: We identified chr9:5449463-5449962 and chr9:5450250-5450749 as reproducible open chromatin regions in the PD-L1 promoter. Moreover, we observed a correlation between STAT2 expression and the accessibility of the aforementioned regions. Furthermore, we confirmed its physical binding through ChIP-seq profiles and demonstrated the regulation of PD-L1 by STAT2 overexpression in vitro. Multiple databases were also used for the validation of the results. Conclusion: Our study identified STAT2 as a direct upstream TF regulating PD-L1 expression. The interaction of STAT2 and PD-L1 might be associated with tumor immune evasion in cancers, suggesting the potential value for tumor treatment.

scholarly journals Chromatin accessibility profiling in Neurospora crassa reveals molecular features associated with accessible and inaccessible chromatin

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Aileen R. Ferraro ◽  
Abigail J. Ameri ◽  
Zefu Lu ◽  
Masayuki Kamei ◽  
Robert J. Schmitz ◽  
...  
Keyword(s):  
Neurospora Crassa ◽  
Filamentous Fungi ◽  
Chromatin Accessibility ◽  
Open Chromatin ◽  
Turnover Rates ◽  
Promoter Regions ◽  
H3k36 Methylation ◽  
Molecular Features ◽  
A Genome ◽  
Accessible Chromatin

Abstract Background Regulation of chromatin accessibility and transcription are tightly coordinated processes. Studies in yeast and higher eukaryotes have described accessible chromatin regions, but little work has been done in filamentous fungi. Results Here we present a genome-scale characterization of accessible chromatin regions in Neurospora crassa, which revealed characteristic molecular features of accessible and inaccessible chromatin. We present experimental evidence of inaccessibility within heterochromatin regions in Neurospora, and we examine features of both accessible and inaccessible chromatin, including the presence of histone modifications, types of transcription, transcription factor binding, and relative nucleosome turnover rates. Chromatin accessibility is not strictly correlated with expression level. Accessible chromatin regions in the model filamentous fungus Neurospora are characterized the presence of H3K27 acetylation and commonly associated with pervasive non-coding transcription. Conversely, methylation of H3 lysine-36 catalyzed by ASH1 is correlated with inaccessible chromatin within promoter regions. Conclusions: In N. crassa, H3K27 acetylation is the most predictive histone modification for open chromatin. Conversely, our data show that H3K36 methylation is a key marker of inaccessible chromatin in gene-rich regions of the genome. Our data are consistent with an expanded role for H3K36 methylation in intergenic regions of filamentous fungi compared to the model yeasts, S. cerevisiae and S. pombe, which lack homologs of the ASH1 methyltransferase.

scholarly journals ShinyArchR.UiO: User-friendly, integrative and open-source tool for visualisation of single-cell ATAC-seq data using ArchR

2021 ◽  
Author(s):  
Ankush Sharma ◽  
Akshay Akshay ◽  
Marie Rogne ◽  
Ragnhild Eskeland
Keyword(s):  
Single Cell ◽  
Open Source ◽  
Cell Fate ◽  
Single Cells ◽  
Chromatin Accessibility ◽  
Data Accessibility ◽  
Shiny App ◽  
User Friendly ◽  
Collaborative Efforts ◽  
Accessible Chromatin

Motivation: Mapping of chromatin accessibility landscapes in single-cells and the integration with gene expression enables a better understanding of gene regulatory mechanisms defining cell identities and cell-fate determination in development and disease. Generally, raw data generated from single-cell Assay for Transposase-Accessible Chromatin sequencing (scATAC-seq) are deposited in reposito-ries that are inaccessible due to lack of in-depth knowledge of computational programming. Results: We have developed ShinyArchR.UiO, an R-based shiny app, that facilitates scATAC-seq data accessibility and visualisation in a user-friendly, interactive, and open-source web interface. ShinyArchR.UiO is a tool that can streamline collaborative efforts for interpretation of massive chro-matin accessible data and promotes open access data sharing for wider audiences.

scholarly journals Single-Cell RNA Sequencing and Assay for Transposase-Accessible Chromatin Using Sequencing Reveals Cellular and Molecular Dynamics of Aortic Aging in Mice

2021 ◽  
Author(s):  
Wenhui Xie ◽  
Yilang Ke ◽  
Qinyi You ◽  
Jing Li ◽  
Lu Chen ◽  
...  
Keyword(s):  
Endothelial Cells ◽  
Single Cell ◽  
Rna Sequencing ◽  
Chromatin Accessibility ◽  
Open Chromatin ◽  
Vascular Aging ◽  
Chromatin States ◽  
Single Cell Rna Sequencing ◽  
The Impact ◽  
Accessible Chromatin

Objective: The impact of vascular aging on cardiovascular diseases has been extensively studied; however, little is known regarding the cellular and molecular mechanisms underlying age-related vascular aging in aortic cellular subpopulations. Approach and Results: Transcriptomes and transposase-accessible chromatin profiles from the aortas of 4-, 26-, and 86-week-old C57/BL6J mice were analyzed using single-cell RNA sequencing and assay for transposase-accessible chromatin sequencing. By integrating the heterogeneous transcriptome and chromatin accessibility data, we identified cell-specific TF (transcription factor) regulatory networks and open chromatin states. We also determined that aortic aging affects cell interactions, inflammation, cell type composition, dysregulation of transcriptional control, and chromatin accessibility. Endothelial cells 1 have higher gene set activity related to cellular senescence and aging than do endothelial cells 2. Moreover, construction of senescence trajectories shows that endothelial cell 1 and fibroblast senescence is associated with distinct TF open chromatin states and an mRNA expression model. Conclusions: Our data provide a system-wide model for transcriptional and epigenetic regulation during aortic aging at single-cell resolution.

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 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.

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