scholarly journals ATACgraph: Profiling Genome-Wide Chromatin Accessibility From ATAC-seq

2021 ◽  
Vol 11 ◽  
Author(s):  
Rita Jui-Hsien Lu ◽  
Yen-Ting Liu ◽  
Chih Wei Huang ◽  
Ming-Ren Yen ◽  
Chung-Yen Lin ◽  
...  
Keyword(s):  
Chromatin Accessibility ◽  
Specific Information ◽  
Sequencing Data ◽  
Genome Wide ◽  
Bioinformatics Software ◽  
The Galaxy ◽  
Chromatin Immunoprecipitation Sequencing ◽  
Cloud Users ◽  
Accessible Chromatin ◽  
Analyze Data

Assay for transposase-accessible chromatin using sequencing data (ATAC-seq) is an efficient and precise method for revealing chromatin accessibility across the genome. Most of the current ATAC-seq tools follow chromatin immunoprecipitation sequencing (ChIP-seq) strategies that do not consider ATAC-seq-specific properties. To incorporate specific ATAC-seq quality control and the underlying biology of chromatin accessibility, we developed a bioinformatics software named ATACgraph for analyzing and visualizing ATAC-seq data. ATACgraph profiles accessible chromatin regions and provides ATAC-seq-specific information including definitions of nucleosome-free regions (NFRs) and nucleosome-occupied regions. ATACgraph also allows identification of differentially accessible regions between two ATAC-seq datasets. ATACgraph incorporates the docker image with the Galaxy platform to provide an intuitive user experience via the graphical interface. Without tedious installation processes on a local machine or cloud, users can analyze data through activated websites using pre-designed workflows or customized pipelines composed of ATACgraph modules. Overall, ATACgraph is an effective tool designed for ATAC-seq for biologists with minimal bioinformatics knowledge to analyze chromatin accessibility. ATACgraph can be run on any ATAC-seq data with no limit to specific genomes. As validation, we demonstrated ATACgraph on human genome to showcase its functions for ATAC-seq interpretation. This software is publicly accessible and can be downloaded at https://github.com/RitataLU/ATACgraph.

scholarly journals Predicting transcription factor binding in single cells through deep learning

2020 ◽  
Vol 6 (51) ◽  
pp. eaba9031
Author(s):  
Laiyi Fu ◽  
Lihua Zhang ◽  
Emmanuel Dollinger ◽  
Qinke Peng ◽  
Qing Nie ◽  
...  
Keyword(s):  
Deep Learning ◽  
Single Cell ◽  
Single Cells ◽  
Cell Types ◽  
Chromatin Accessibility ◽  
Sequence Motifs ◽  
Genome Wide ◽  
Chromatin Immunoprecipitation Sequencing ◽  
Deep Learning Model ◽  
Accessible Chromatin

Characterizing genome-wide binding profiles of transcription factors (TFs) is essential for understanding biological processes. Although techniques have been developed to assess binding profiles within a population of cells, determining them at a single-cell level remains elusive. Here, we report scFAN (single-cell factor analysis network), a deep learning model that predicts genome-wide TF binding profiles in individual cells. scFAN is pretrained on genome-wide bulk assay for transposase-accessible chromatin sequencing (ATAC-seq), DNA sequence, and chromatin immunoprecipitation sequencing (ChIP-seq) data and uses single-cell ATAC-seq to predict TF binding in individual cells. We demonstrate the efficacy of scFAN by both studying sequence motifs enriched within predicted binding peaks and using predicted TFs for discovering cell types. We develop a new metric “TF activity score” to characterize each cell and show that activity scores can reliably capture cell identities. scFAN allows us to discover and study cellular identities and heterogeneity based on chromatin accessibility profiles.

scholarly journals Enhancement and Imputation of Peak Signal Enables Accurate Cell-Type Classification in scATAC-seq

2021 ◽  
Vol 12 ◽  
Author(s):  
Zhe Cui ◽  
Ya Cui ◽  
Yan Gao ◽  
Tao Jiang ◽  
Tianyi Zang ◽  
...  
Keyword(s):  
Single Cell ◽  
Mononuclear Cells ◽  
Cell Types ◽  
Chromatin Accessibility ◽  
Support Vector ◽  
Cell Type ◽  
Peripheral Blood Mononuclear ◽  
Copy Numbers ◽  
Genome Wide ◽  
Accessible Chromatin

Single-cell Assay Transposase Accessible Chromatin sequencing (scATAC-seq) has been widely used in profiling genome-wide chromatin accessibility in thousands of individual cells. However, compared with single-cell RNA-seq, the peaks of scATAC-seq are much sparser due to the lower copy numbers (diploid in humans) and the inherent missing signals, which makes it more challenging to classify cell type based on specific expressed gene or other canonical markers. Here, we present svmATAC, a support vector machine (SVM)-based method for accurately identifying cell types in scATAC-seq datasets by enhancing peak signal strength and imputing signals through patterns of co-accessibility. We applied svmATAC to several scATAC-seq data from human immune cells, human hematopoietic system cells, and peripheral blood mononuclear cells. The benchmark results showed that svmATAC is free of literature-based markers and robust across datasets in different libraries and platforms. The source code of svmATAC is available at https://github.com/mrcuizhe/svmATAC under the MIT license.

Genomic and epigenomic active vitamin Dresponses in human colonic organoids

2021 ◽  
Author(s):  
Jinchao Li ◽  
David Witonsky ◽  
Emily Sprague ◽  
Dereck Alleyne ◽  
Margaret C Bielski ◽  
...  
Keyword(s):  
Gene Expression ◽  
Vitamin D ◽  
Differentially Expressed Genes ◽  
Chromatin Accessibility ◽  
Differentially Expressed ◽  
Active Vitamin ◽  
Host Environment ◽  
Genome Wide ◽  
Ideal System ◽  
Accessible Chromatin

Background & Aims: Active vitamin D, 1α,25(OH)2D3, is a nuclear hormone with roles in colonic homeostasis and carcinogenesis; yet, mechanisms underlying these effects are incompletely understood. Organoids are an ideal system to study genomic and epigenomic host-environment interactions. We utilize colonic organoids to measure 1α,25(OH)2D3 responses on genome-wide gene expression and chromatin accessibility over time. Methods: Human colonic organoids were treated in triplicate with 100nM 1α,25(OH)2D3 or vehicle control for 4 and 18 hours (h) for chromatin accessibility, and 6 and 24h for gene expression. ATAC- and RNA-sequencing were performed. Differentially accessible peaks were analyzed using DiffBind and EdgeR; differentially expressed genes were analyzed using DESeq2. Motif enrichment was determined using HOMER. Results: At 6h and 24h, 2870 and 2721 differentially expressed genes, respectively (false discovery rate, FDR<5%) were identified with overall stronger responses with 1α,25(OH)2D3. Vitamin D treatment led to stronger chromatin accessibility especially at 4h. The vitamin D receptor (VDR) motif was strongly enriched among accessible chromatin peaks with 1α,25(OH)2D3 treatment accounting for 30.5% and 11% of target sequences at 4h and 18h, respectively (FDR<1%). Genes such as CYP24A1, FGF19, MYC, FOS and TGFBR2 showed significant transcriptional and chromatin accessibility responses to 1α,25(OH)2D3 treatment with accessible chromatin located distant from promoters for some gene regions. Conclusions: Assessment of chromatin accessibility and transcriptional responses to 1α,25(OH)2D3 yielded new observations about vitamin D genome-wide effects in the colon facilitated by application of human colonic organoids. This framework can be applied to study host-environment interactions between individuals and populations in future.

scholarly journals A pooling-based approach to mapping genetic variants associated with DNA methylation

2015 ◽  
Author(s):  
Irene Miriam Kaplow ◽  
Julia L MacIsaac ◽  
Sarah M Mah ◽  
Lisa M McEwen ◽  
Michael S Kobor ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Genetic Variants ◽  
Statistical Power ◽  
Epigenetic Modification ◽  
Chromatin Accessibility ◽  
Ctcf Binding ◽  
Sequencing Data ◽  
Individual Level ◽  
Novel Approach ◽  
Genome Wide

DNA methylation is an epigenetic modification that plays a key role in gene regulation. Previous studies have investigated its genetic basis by mapping genetic variants that are associated with DNA methylation at specific sites, but these have been limited to microarrays that cover less than 2% of the genome and cannot account for allele-specific methylation (ASM). Other studies have performed whole-genome bisulfite sequencing on a few individuals, but these lack statistical power to identify variants associated with DNA methylation. We present a novel approach in which bisulfite-treated DNA from many individuals is sequenced together in a single pool, resulting in a truly genome-wide map of DNA methylation. Compared to methods that do not account for ASM, our approach increases statistical power to detect associations while sharply reducing cost, effort, and experimental variability. As a proof of concept, we generated deep sequencing data from a pool of 60 human cell lines; we evaluated almost twice as many CpGs as the largest microarray studies and identified over 2,000 genetic variants associated with DNA methylation. We found that these variants are highly enriched for associations with chromatin accessibility and CTCF binding but are less likely to be associated with traits indirectly linked to DNA, such as gene expression and disease phenotypes. In summary, our approach allows genome-wide mapping of genetic variants associated with DNA methylation in any tissue of any species, without the need for individual-level genotype or methylation data.

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 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 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 Chromatin accessibility of circulating CD8+ T cells predicts treatment response to PD-1 blockade in patients with gastric cancer

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Hyun Mu Shin ◽  
Gwanghun Kim ◽  
Sangjib Kim ◽  
Ji Hyun Sim ◽  
Jiyeob Choi ◽  
...  
Keyword(s):  
Gastric Cancer ◽  
T Cells ◽  
Cd8 T Cells ◽  
Peripheral Blood ◽  
Clinical Benefit ◽  
Chromatin Accessibility ◽  
Genomic Profiling ◽  
Genome Wide ◽  
Tumor Sequencing ◽  
Accessible Chromatin

AbstractAlthough tumor genomic profiling has identified small subsets of gastric cancer (GC) patients with clinical benefit from anti-PD-1 treatment, not all responses can be explained by tumor sequencing alone. We investigate epigenetic elements responsible for the differential response to anti-PD-1 therapy by quantitatively assessing the genome-wide chromatin accessibility of circulating CD8+ T cells in patients’ peripheral blood. Using an assay for transposase-accessible chromatin using sequencing (ATAC-seq), we identify unique open regions of chromatin that significantly distinguish anti-PD-1 therapy responders from non-responders. GC patients with high chromatin openness of circulating CD8+ T cells are significantly enriched in the responder group. Concordantly, patients with high chromatin openness at specific genomic positions of their circulating CD8+ T cells demonstrate significantly better survival than those with closed chromatin. Here we reveal that epigenetic characteristics of baseline CD8+ T cells can be used to identify metastatic GC patients who may benefit from anti-PD-1 therapy.

scholarly journals TNF-induced inflammatory genes escape repression in fibroblast-like synoviocytes: transcriptomic and epigenomic analysis

2019 ◽  
Vol 78 (9) ◽  
pp. 1205-1214 ◽  
Author(s):  
Christopher Loh ◽  
Sung-ho Park ◽  
Angela Lee ◽  
Ruoxi Yuan ◽  
Lionel B Ivashkiv ◽  
...  
Keyword(s):  
Transcriptional Repression ◽  
High Throughput Sequencing ◽  
Human Monocyte ◽  
Regulatory Elements ◽  
Chromatin Accessibility ◽  
Genome Wide ◽  
Healthy Donors ◽  
Chromatin Activation ◽  
Chromatin Immunoprecipitation Sequencing ◽  
Fibroblast Like Synoviocytes

ObjectiveWe investigated genome-wide changes in gene expression and chromatin remodelling induced by tumour necrosis factor (TNF) in fibroblast-like synoviocytes (FLS) and macrophages to better understand the contribution of FLS to the pathogenesis of rheumatoid arthritis (RA).MethodsFLS were purified from patients with RA and CD14+ human monocyte-derived macrophages were obtained from healthy donors. RNA-sequencing, histone 3 lysine 27 acetylation (H3K27ac), chromatin immunoprecipitation-sequencing (ChIP-seq) and assay for transposable accessible chromatin by high throughput sequencing (ATAC-seq) were performed in control and TNF-stimulated cells.ResultsWe discovered 280 TNF-inducible arthritogenic genes which are transiently expressed and subsequently repressed in macrophages, but in RA, FLS are expressed with prolonged kinetics that parallel the unremitting kinetics of RA synovitis. 80 out of these 280 fibroblast-sustained genes (FSGs) that escape repression in FLS relative to macrophages were desensitised (tolerised) in macrophages. Epigenomic analysis revealed persistent H3K27 acetylation and increased chromatin accessibility in regulatory elements associated with FSGs in TNF-stimulated FLS. The accessible regulatory elements of FSGs were enriched in binding motifs for nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB), interferon-regulatory factors (IRFs) and activating protein-1 (AP-1). Inhibition of bromodomain and extra-terminal motif (BET) proteins, which interact with histone acetylation, suppressed sustained induction of FSGs by TNF.ConclusionOur genome-wide analysis has identified the escape of genes from transcriptional repression in FLS as a novel mechanism potentially contributing to the chronic unremitting synovitis observed in RA. Our finding that TNF induces sustained chromatin activation in regulatory elements of the genes that escape repression in RA FLS suggests that altering or targeting chromatin states in FLS (eg, with inhibitors of BET proteins) is an attractive therapeutic strategy.

scholarly journals Concentration Dependent Chromatin States Induced by the Bicoid Morphogen Gradient

2017 ◽  
Author(s):  
Colleen E. Hannon ◽  
Shelby A. Blythe ◽  
Eric F. Wieschaus
Keyword(s):  
Target Genes ◽  
Positional Information ◽  
Chromatin Accessibility ◽  
Open Chromatin ◽  
Genome Wide ◽  
Low Concentrations ◽  
High Concentrations ◽  
Accessible Chromatin ◽  
Anterior Posterior

ABSTRACTIn 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. Bcd drives an open chromatin state at a subset its targets. Our data support a model where Bcd influences chromatin structure to gain access to concentration-sensitive targets at high concentrations, while concentration-insensitive targets are found in more accessible chromatin and are bound at low concentrations.

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