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 32 Functional annotation of livestock genomes: chromatin structure and regulation of gene expression

2019 ◽  
Vol 97 (Supplement_2) ◽  
pp. 15-16
Author(s):  
Sylvain Foissac ◽  
Sarah Djebali ◽  
Kylie Munyard ◽  
Nathalie Vialaneix ◽  
Andrea Rau ◽  
...  
Keyword(s):  
Gene Expression ◽  
Functional Annotation ◽  
Regulation Of Gene Expression ◽  
Cell Types ◽  
Chromatin Accessibility ◽  
Rna Seq ◽  
Chromosome Conformation ◽  
Accessible Chromatin ◽  
Animal Genomes

Abstract Improving the functional annotation of animal genomes is a key challenge in bridging the gap between genotype and phenotype, thus enabling predictive biology. Regarding livestock production, major outcomes are expected from a better understanding of the genetic architecture underlying quantitative traits. As part of the Functional Annotation of ANimal Genomes action (FAANG: www.faang.org), the FR-AgENCODE project generated omics data to improve the reference annotation of the cattle, pig, goat and chicken genome. High-throughput molecular assays have been performed on tissues/cells relevant to immune and metabolic traits. From two males and two females per species (pig, cattle, goat, chicken), strand-oriented RNA-seq gene expression and ATAC-seq chromatin accessibility assays were performed on liver and two PBMC-sorted T-cell types (CD4+ and CD8+). Chromosome Conformation Capture (in situ Hi-C) was also carried out on liver samples. About 4,000 samples have been collected at the INRA biorepository and registered at the EBI BioSamples registry. More than 80% of the planned experiments could be completed, generating ~11.5 billions of sequencing reads over the 3 assays. While most (50–80%) RNA-seq reads mapped to annotated exons, thousands of novel transcripts were found, with ~60K mRNAs and ~22K lncRNAs in cattle. Differentially expressed genes between cell types were enriched for immunity- or metabolism-related terms, and differentially accessible chromatin regions were identified as potential regulatory sites. Interestingly, correlations between gene expression and promoter accessibility across samples were skewed towards both positive and negative values, suggesting distinct regulatory mechanisms of gene expression. These patterns have been further investigated using human data from the Epigenome Roadmap Mapping Consortium. Altogether, this study illustrates the interest of a coordinated effort to tackle the genome-to-phenome challenge and provides a useful resource to the community. Availability: www.fragencode.org.

Functional Annotation of Animal Genomes (FAANG): Current Achievements and Roadmap

2019 ◽  
Vol 7 (1) ◽  
pp. 65-88 ◽  
Author(s):  
Elisabetta Giuffra ◽  
Christopher K. Tuggle ◽  
Keyword(s):  
Functional Annotation ◽  
Chromatin Modification ◽  
Chromatin Accessibility ◽  
Genomic Research ◽  
Data Sets ◽  
Genome Wide ◽  
Data Collection And Analysis ◽  
Genome Wide Data ◽  
Animal Genomics ◽  
Animal Genomes

Functional annotation of genomes is a prerequisite for contemporary basic and applied genomic research, yet farmed animal genomics is deficient in such annotation. To address this, the FAANG (Functional Annotation of Animal Genomes) Consortium is producing genome-wide data sets on RNA expression, DNA methylation, and chromatin modification, as well as chromatin accessibility and interactions. In addition to informing our understanding of genome function, including comparative approaches to elucidate constrained sequence or epigenetic elements, these annotation maps will improve the precision and sensitivity of genomic selection for animal improvement. A scientific community–driven effort has already created a coordinated data collection and analysis enterprise crucial for the success of this global effort. Although it is early in this continuing process, functional data have already been produced and application to genetic improvement reported. The functional annotation delivered by the FAANG initiative will add value and utility to the greatly improved genome sequences being established for domesticated animal 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 Systematic clustering algorithm for chromatin accessibility data and its application to hematopoietic cells

2020 ◽  
Vol 16 (11) ◽  
pp. e1008422
Author(s):  
Azusa Tanaka ◽  
Yasuhiro Ishitsuka ◽  
Hiroki Ohta ◽  
Akihiro Fujimoto ◽  
Jun-ichirou Yasunaga ◽  
...  
Keyword(s):  
Data Reduction ◽  
Clustering Algorithm ◽  
High Throughput Sequencing ◽  
Hematopoietic Cells ◽  
Cell Types ◽  
Chromatin Accessibility ◽  
Open Chromatin ◽  
Genome Wide ◽  
Data Reduction Method ◽  
Effective Analysis

The huge amount of data acquired by high-throughput sequencing requires data reduction for effective analysis. Here we give a clustering algorithm for genome-wide open chromatin data using a new data reduction method. This method regards the genome as a string of 1s and 0s based on a set of peaks and calculates the Hamming distances between the strings. This algorithm with the systematically optimized set of peaks enables us to quantitatively evaluate differences between samples of hematopoietic cells and classify cell types, potentially leading to a better understanding of leukemia pathogenesis.

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.

scholarly journals Genome-wide identification of accessible chromatin regions in bumblebee (Bombus terrestris) by ATAC-seq

2019 ◽  
Author(s):  
Xiaomeng Zhao ◽  
Weilin Xu ◽  
Sarah Schaack ◽  
Cheng Sun
Keyword(s):  
Crop Production ◽  
High Throughput Sequencing ◽  
Developmental Stages ◽  
Bombus Terrestris ◽  
Regulatory Elements ◽  
Natural Ecosystem ◽  
Protein Coding ◽  
Genome Wide ◽  
Pollinating Insects ◽  
Accessible Chromatin

AbstractBumblebees (Hymenoptera: Apidae) are important pollinating insects that play pivotal roles in crop production and natural ecosystem services. To date, while the protein-coding sequences of bumblebees have been extensively annotated, regulatory elements, such as promoters and enhancers, have been poorly annotated in the bumblebee genome. To achieve a comprehensive profile of accessible chromatin regions and provide clues for all possible regulatory elements in the bumblebee genome, we did ATAC-seq (Assay for Transposase-Accessible Chromatin with high-throughput sequencing) for B. terrestris samples derived from its four developmental stages: egg, larva, pupa, and adult, respectively. The sequencing reads of ATAC-seq were mapped to B. terrestris reference genome, and the accessible chromatin regions of bumblebee were identified and characterized by using bioinformatic methods. Our study will provide important resources not only for uncovering regulatory elements in the bumblebee genome, but also for expanding our understanding of bumblebee biology. The ATAC-seq data generated in this study has been deposited in NCBI GEO (accession#: GSE131063).

scholarly journals 29 Introduction to functional annotation of animal genomes consortium

2019 ◽  
Vol 97 (Supplement_2) ◽  
pp. 17-17
Author(s):  
Christopher K Tuggle ◽  
Elisabetta Giuffra
Keyword(s):  
Functional Annotation ◽  
Animal Species ◽  
Chromatin Modification ◽  
Chromatin Accessibility ◽  
Genomic Research ◽  
Chromatin Interactions ◽  
Knowledge Deficit ◽  
Animal Genomics ◽  
Functional Components ◽  
Animal Genomes

Abstract The annotation of the functional components of genomes is required for both basic and applied genomic research, yet farmed animal genomics are deficient in such annotation. This talk will introduce the Functional Annotation of ANimal Genomes (FAANG) consortium, which was initiated in 2014 to address this knowledge deficit. An overarching theme of early FAANG efforts is the collaborative approach required for such comprehensive research, thus another emphasis of this talk will be our community efforts to develop the environment for successful FAANG research. FAANG scientists have created a coordinated data collection and analysis enterprise crucial for success of this global effort, and funding of ~$20 million has been secured for current projects in several species, with an anticipated doubling of this support during 2019. Member FAANG consortium labs are producing genome-wide datasets on RNA expression, DNA methylation, chromatin modification, chromatin accessibility, and chromatin interactions for many agriculturally relevant animal species. The goal of a first-generation global chromatin state map for cattle, chicken, pig, and potentially other species is projected for completion in the next 3–5 years. These data will be used both to better understand animal genome function at the epigenetic level, as well as improve the precision and sensitivity of genomic selection for animal improvement. The functional annotation delivered by the FAANG initiative will add value and utility to the greatly improved genome sequences being established for domesticated animal species.

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 The landscape of accessible chromatin in quiescent and post-myocardial infarction cardiac fibroblasts

2021 ◽  
Author(s):  
Chaoyang Li ◽  
Jiangwen Sun ◽  
Qianglin Liu ◽  
Sanjeeva Dodlapati ◽  
Hao Ming ◽  
...  
Keyword(s):  
Gene Expression ◽  
Myocardial Infarction ◽  
High Throughput Sequencing ◽  
Cardiac Fibroblasts ◽  
Expression Profiles ◽  
Integrated Analysis ◽  
Matrix Remodeling ◽  
Rna Seq ◽  
Genome Wide ◽  
Accessible Chromatin

AbstractAfter myocardial infarction, quiescent cardiac fibroblasts are activated and undergo multiple proliferation and differentiation events, which contribute to the extracellular matrix remodeling of the infarcted myocardium. We recently found that cardiac fibroblasts of different differentiation states had distinct expression profiles closely related to their functions. Gene expression is directly regulated by chromatin state. However, the role of chromatin reorganization in the drastic gene expression changes during post-MI differentiation of cardiac fibroblast has not been revealed. In this study, the gene expression profiling and genome-wide mapping of accessible chromatin in mouse cardiac fibroblasts isolated from uninjured hearts and the infarcts at different time points were performed by RNA sequencing (RNA-seq) and the assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq), respectively. ATAC-seq peaks were highly enriched in the promoter area and distal areas where enhancers might be located. A positive correlation was identified between the transcription level and promoter accessibility for many dynamically expressed genes. In addition, it was found that DNA methylation may contribute to the post-MI chromatin remodeling and gene expression in cardiac fibroblasts. Integrated analysis of ATAC-seq and RNA-seq datasets also identified transcription factors that possibly contributed to the differential gene expression between cardiac fibroblasts of different states.

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.

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