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Yao Q, Zhu L, Shi Z, Banerjee S, Chen C. Topoisomerase-modulated genome-wide DNA supercoiling domains colocalize with nuclear compartments and regulate human gene expression. Nat Struct Mol Biol 2024:10.1038/s41594-024-01377-5. [PMID: 39152238 DOI: 10.1038/s41594-024-01377-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 07/24/2024] [Indexed: 08/19/2024]
Abstract
DNA supercoiling is a biophysical feature of the double helix with a pivotal role in biological processes. However, understanding of DNA supercoiling in the chromatin remains limited. Here, we developed azide-trimethylpsoralen sequencing (ATMP-seq), a DNA supercoiling assay offering quantitative accuracy while minimizing genomic bias and background noise. Using ATMP-seq, we directly visualized transcription-dependent negative and positive twin-supercoiled domains around genes and mapped kilobase-resolution DNA supercoiling throughout the human genome. Remarkably, we discovered megabase-scale supercoiling domains (SDs) across all chromosomes that are modulated mainly by topoisomerases I and IIβ. Transcription activities, but not the consequent supercoiling accumulation in the local region, contribute to SD formation, indicating the long-range propagation of transcription-generated supercoiling. Genome-wide SDs colocalize with A/B compartments in both human and Drosophila cells but are distinct from topologically associating domains (TADs), with negative supercoiling accumulation at TAD boundaries. Furthermore, genome-wide DNA supercoiling varies between cell states and types and regulates human gene expression, underscoring the importance of supercoiling dynamics in chromatin regulation and function.
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Affiliation(s)
- Qian Yao
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Linying Zhu
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Zhen Shi
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Subhadra Banerjee
- Laboratory of Genome Integrity, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Chongyi Chen
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
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2
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Salignon J, Millan-Ariño L, Garcia MU, Riedel CG. Cactus: A user-friendly and reproducible ATAC-Seq and mRNA-Seq analysis pipeline for data preprocessing, differential analysis, and enrichment analysis. Genomics 2024; 116:110858. [PMID: 38735595 DOI: 10.1016/j.ygeno.2024.110858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 05/06/2024] [Accepted: 05/09/2024] [Indexed: 05/14/2024]
Abstract
The ever decreasing cost of Next-Generation Sequencing coupled with the emergence of efficient and reproducible analysis pipelines has rendered genomic methods more accessible. However, downstream analyses are basic or missing in most workflows, creating a significant barrier for non-bioinformaticians. To help close this gap, we developed Cactus, an end-to-end pipeline for analyzing ATAC-Seq and mRNA-Seq data, either separately or jointly. Its Nextflow-, container-, and virtual environment-based architecture ensures efficient and reproducible analyses. Cactus preprocesses raw reads, conducts differential analyses between conditions, and performs enrichment analyses in various databases, including DNA-binding motifs, ChIP-Seq binding sites, chromatin states, and ontologies. We demonstrate the utility of Cactus in a multi-modal and multi-species case study as well as by showcasing its unique capabilities as compared to other ATAC-Seq pipelines. In conclusion, Cactus can assist researchers in gaining comprehensive insights from chromatin accessibility and gene expression data in a quick, user-friendly, and reproducible manner.
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Affiliation(s)
- Jérôme Salignon
- Department of Bioscience and Nutrition, Karolinska Institute, Blickagången 16, Huddinge SE-141 83, Sweden.
| | - Lluís Millan-Ariño
- Department of Bioscience and Nutrition, Karolinska Institute, Blickagången 16, Huddinge SE-141 83, Sweden
| | - Maxime U Garcia
- National Genomics Infrastructure, Science for Life Laboratory, Tomtebodavägen 23A, Solna SE-171 65, Sweden; Department of Oncology-Pathology, Karolinska Institute, Visionsgatan 4, Solna SE-171 64, Sweden
| | - Christian G Riedel
- Department of Bioscience and Nutrition, Karolinska Institute, Blickagången 16, Huddinge SE-141 83, Sweden.
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3
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Hsieh JWA, Lin PY, Wang CT, Lee YJ, Chang P, Lu RJH, Chen PY, Wang CJR. Establishing an optimized ATAC-seq protocol for the maize. FRONTIERS IN PLANT SCIENCE 2024; 15:1370618. [PMID: 38863553 PMCID: PMC11165127 DOI: 10.3389/fpls.2024.1370618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 05/07/2024] [Indexed: 06/13/2024]
Abstract
The advent of next-generation sequencing in crop improvement offers unprecedented insights into the chromatin landscape closely linked to gene activity governing key traits in plant development and adaptation. Particularly in maize, its dynamic chromatin structure is found to collaborate with massive transcriptional variations across tissues and developmental stages, implying intricate regulatory mechanisms, which highlights the importance of integrating chromatin information into breeding strategies for precise gene controls. The depiction of maize chromatin architecture using Assay for Transposase Accessible Chromatin with high-throughput sequencing (ATAC-seq) provides great opportunities to investigate cis-regulatory elements, which is crucial for crop improvement. In this context, we developed an easy-to-implement ATAC-seq protocol for maize with fewer nuclei and simple equipment. We demonstrate a streamlined ATAC-seq protocol with four key steps for maize in which nuclei purification can be achieved without cell sorting and using only a standard bench-top centrifuge. Our protocol, coupled with the bioinformatic analysis, including validation by read length periodicity, key metrics, and correlation with transcript abundance, provides a precise and efficient assessment of the maize chromatin landscape. Beyond its application to maize, our testing design holds the potential to be applied to other crops or other tissues, especially for those with limited size and amount, establishing a robust foundation for chromatin structure studies in diverse crop species.
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Affiliation(s)
- Jo-Wei Allison Hsieh
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
- Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei, Taiwan
| | - Pei-Yu Lin
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Chi-Ting Wang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Yi-Jing Lee
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Pearl Chang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
- Department of Tropical Agriculture and International Cooperation/Department of Biological Science and Technology, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Rita Jui-Hsien Lu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Pao-Yang Chen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
- Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei, Taiwan
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4
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Miao Z, Kim J. Uniform quantification of single-nucleus ATAC-seq data with Paired-Insertion Counting (PIC) and a model-based insertion rate estimator. Nat Methods 2024; 21:32-36. [PMID: 38049698 PMCID: PMC10776405 DOI: 10.1038/s41592-023-02103-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 10/25/2023] [Indexed: 12/06/2023]
Abstract
Existing approaches to scoring single-nucleus assay for transposase-accessible chromatin with sequencing (snATAC-seq) feature matrices from sequencing reads are inconsistent, affecting downstream analyses and displaying artifacts. We show that, even with sparse single-cell data, quantitative counts are informative for estimating the regulatory state of a cell, which calls for a consistent treatment. We propose Paired-Insertion Counting as a uniform method for snATAC-seq feature characterization and provide a probability model for inferring latent insertion dynamics from snATAC-seq count matrices.
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Affiliation(s)
- Zhen Miao
- Graduate Group in Genomics and Computational Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Junhyong Kim
- Graduate Group in Genomics and Computational Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA.
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Satam H, Joshi K, Mangrolia U, Waghoo S, Zaidi G, Rawool S, Thakare RP, Banday S, Mishra AK, Das G, Malonia SK. Next-Generation Sequencing Technology: Current Trends and Advancements. BIOLOGY 2023; 12:997. [PMID: 37508427 PMCID: PMC10376292 DOI: 10.3390/biology12070997] [Citation(s) in RCA: 82] [Impact Index Per Article: 82.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 07/09/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023]
Abstract
The advent of next-generation sequencing (NGS) has brought about a paradigm shift in genomics research, offering unparalleled capabilities for analyzing DNA and RNA molecules in a high-throughput and cost-effective manner. This transformative technology has swiftly propelled genomics advancements across diverse domains. NGS allows for the rapid sequencing of millions of DNA fragments simultaneously, providing comprehensive insights into genome structure, genetic variations, gene expression profiles, and epigenetic modifications. The versatility of NGS platforms has expanded the scope of genomics research, facilitating studies on rare genetic diseases, cancer genomics, microbiome analysis, infectious diseases, and population genetics. Moreover, NGS has enabled the development of targeted therapies, precision medicine approaches, and improved diagnostic methods. This review provides an insightful overview of the current trends and recent advancements in NGS technology, highlighting its potential impact on diverse areas of genomic research. Moreover, the review delves into the challenges encountered and future directions of NGS technology, including endeavors to enhance the accuracy and sensitivity of sequencing data, the development of novel algorithms for data analysis, and the pursuit of more efficient, scalable, and cost-effective solutions that lie ahead.
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Affiliation(s)
- Heena Satam
- miBiome Therapeutics, Mumbai 400102, India; (H.S.); (K.J.); (U.M.); (S.W.); (G.Z.); (S.R.)
| | - Kandarp Joshi
- miBiome Therapeutics, Mumbai 400102, India; (H.S.); (K.J.); (U.M.); (S.W.); (G.Z.); (S.R.)
| | - Upasana Mangrolia
- miBiome Therapeutics, Mumbai 400102, India; (H.S.); (K.J.); (U.M.); (S.W.); (G.Z.); (S.R.)
| | - Sanober Waghoo
- miBiome Therapeutics, Mumbai 400102, India; (H.S.); (K.J.); (U.M.); (S.W.); (G.Z.); (S.R.)
| | - Gulnaz Zaidi
- miBiome Therapeutics, Mumbai 400102, India; (H.S.); (K.J.); (U.M.); (S.W.); (G.Z.); (S.R.)
| | - Shravani Rawool
- miBiome Therapeutics, Mumbai 400102, India; (H.S.); (K.J.); (U.M.); (S.W.); (G.Z.); (S.R.)
| | - Ritesh P. Thakare
- Department of Molecular Cell and Cancer Biology, UMass Chan Medical School, Worcester, MA 01605, USA; (R.P.T.); (S.B.); (A.K.M.)
| | - Shahid Banday
- Department of Molecular Cell and Cancer Biology, UMass Chan Medical School, Worcester, MA 01605, USA; (R.P.T.); (S.B.); (A.K.M.)
| | - Alok K. Mishra
- Department of Molecular Cell and Cancer Biology, UMass Chan Medical School, Worcester, MA 01605, USA; (R.P.T.); (S.B.); (A.K.M.)
| | - Gautam Das
- miBiome Therapeutics, Mumbai 400102, India; (H.S.); (K.J.); (U.M.); (S.W.); (G.Z.); (S.R.)
| | - Sunil K. Malonia
- Department of Molecular Cell and Cancer Biology, UMass Chan Medical School, Worcester, MA 01605, USA; (R.P.T.); (S.B.); (A.K.M.)
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Huynh K, Smith BR, Macdonald SJ, Long AD. Genetic variation in chromatin state across multiple tissues in Drosophila melanogaster. PLoS Genet 2023; 19:e1010439. [PMID: 37146087 PMCID: PMC10191298 DOI: 10.1371/journal.pgen.1010439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 05/17/2023] [Accepted: 04/20/2023] [Indexed: 05/07/2023] Open
Abstract
We use ATAC-seq to examine chromatin accessibility for four different tissues in Drosophila melanogaster: adult female brain, ovaries, and both wing and eye-antennal imaginal discs from males. Each tissue is assayed in eight different inbred strain genetic backgrounds, seven associated with a reference quality genome assembly. We develop a method for the quantile normalization of ATAC-seq fragments and test for differences in coverage among genotypes, tissues, and their interaction at 44099 peaks throughout the euchromatic genome. For the strains with reference quality genome assemblies, we correct ATAC-seq profiles for read mis-mapping due to nearby polymorphic structural variants (SVs). Comparing coverage among genotypes without accounting for SVs results in a highly elevated rate (55%) of identifying false positive differences in chromatin state between genotypes. After SV correction, we identify 1050, 30383, and 4508 regions whose peak heights are polymorphic among genotypes, among tissues, or exhibit genotype-by-tissue interactions, respectively. Finally, we identify 3988 candidate causative variants that explain at least 80% of the variance in chromatin state at nearby ATAC-seq peaks.
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Affiliation(s)
- Khoi Huynh
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, United States of America
| | - Brittny R. Smith
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, United States of America
| | - Stuart J. Macdonald
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, United States of America
- Center for Computational Biology, University of Kansas, Lawrence, Kansas, United States of America
| | - Anthony D. Long
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, United States of America
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Wang L, Feng Y, Wang J, Jin X, Zhang Q, Ackah M, Wang Y, Xu D, Zhao W. ATAC-seq exposes differences in chromatin accessibility leading to distinct leaf shapes in mulberry. PLANT DIRECT 2022; 6:e464. [PMID: 36540416 PMCID: PMC9755926 DOI: 10.1002/pld3.464] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 10/30/2022] [Indexed: 06/17/2023]
Abstract
Mulberry leaf shape is an important agronomic trait indicating yield, growth, development, and habitat variation. China was the earliest country in the world to grow mulberry for sericulture, and it is also one of the great contributions of the Chinese nation to human civilization. ATAC-seq (Assay for Transposase Accessible Chromatin using sequencing) is a recently developed technique for genome-wide analysis of chromatin accessibility. The samples used for ATAC sequencing in this study were divided into two groups of whole leaves (CK-1 and CK-2) and lobed leaves (HL-1 and HL-2), with two replicates in each group. The related motif analysis, differential expression motif screening, and functional annotation of mulberry leaf shape differences were performed by raw letter analysis to finally obtain the transcription factors (TFs) that lead to the production of heteromorphic leaves. These transcription factors are common in plants, especially the TCP family, shown to be associated with leaf development and growth in other woody plants and are a potential transcription factor responsible for leaf shape differences in mulberry. Dissecting the regulatory mechanisms of leaf shape of different forms of mulberry leaves by ATAC-seq is an important way to protect mulberry germplasm resources and improve mulberry yield. It is conducive to cultivating mulberry varieties with high resistance to adversity, promoting the sustainable development of sericulture, and protecting and improving the ecological environment.
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Affiliation(s)
- Lei Wang
- School of Biology and TechnologyJiangsu University of Science and TechnologyZhenjiangChina
| | - Yuming Feng
- School of Biology and TechnologyJiangsu University of Science and TechnologyZhenjiangChina
| | - Jiangying Wang
- Leisure Agriculture LaboratoryLianyungang Academy of Agricultural SciencesLianyungangChina
| | - Xin Jin
- School of Biology and TechnologyJiangsu University of Science and TechnologyZhenjiangChina
| | - Qiaonan Zhang
- School of Biology and TechnologyJiangsu University of Science and TechnologyZhenjiangChina
| | - Michael Ackah
- School of Biology and TechnologyJiangsu University of Science and TechnologyZhenjiangChina
| | - Yuhua Wang
- School of Biology and TechnologyJiangsu University of Science and TechnologyZhenjiangChina
| | - Dayong Xu
- Leisure Agriculture LaboratoryLianyungang Academy of Agricultural SciencesLianyungangChina
| | - Weiguo Zhao
- School of Biology and TechnologyJiangsu University of Science and TechnologyZhenjiangChina
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