Concurrent mapping of multiple epigenetic marks and co-occupancy using ACT2-seq

Abstract Background Genome-wide profiling of epigenetic marks is a core technology in molecular genetics. Co-occupancy of different epigenetic marks or protein factors at the same genomic locations must often be inferred from multiple independently collected data sets. However, this strategy does no...

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Autores principales:	Benjamin Carter, Wai Lim Ku, Joe Pelt, Keji Zhao
Formato:	article
Lenguaje:	EN
Publicado:	BMC 2021
Materias:	Co-occupancy Co-enrichment ACT-seq Tagmentation Epigenetic marks Biotechnology TP248.13-248.65 Biology (General) QH301-705.5 Biochemistry QD415-436
Acceso en línea:	https://doaj.org/article/ea12137d935a4d0aa3970d12820b90d3
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spelling	oai:doaj.org-article:ea12137d935a4d0aa3970d12820b90d32021-12-05T12:20:14ZConcurrent mapping of multiple epigenetic marks and co-occupancy using ACT2-seq10.1186/s13578-021-00711-42045-3701https://doaj.org/article/ea12137d935a4d0aa3970d12820b90d32021-12-01T00:00:00Zhttps://doi.org/10.1186/s13578-021-00711-4https://doaj.org/toc/2045-3701Abstract Background Genome-wide profiling of epigenetic marks is a core technology in molecular genetics. Co-occupancy of different epigenetic marks or protein factors at the same genomic locations must often be inferred from multiple independently collected data sets. However, this strategy does not provide direct evidence of co-enrichment in the same cells due to the existence of cellular heterogeneity. To address this issue, we have developed a technique termed ACT2-seq that is capable of concurrently profiling multiple epigenetic marks in a single biological sample. In addition to reducing the numbers of samples required for experiments, ACT2-seq is capable of mapping co-occupancy of epigenetic factors on chromatin. This strategy provides direct evidence of co-enrichment without requiring complex single-molecule, single-cell, or magnetic bead-based approaches. Results We concurrently profiled pairs of two epigenetic marks using ACT2-seq as well as three marks in individual samples. Data obtained using ACT2-seq were found to be reproducible and robust. ACT2-seq was capable of cleanly partitioning concurrently mapped data sets that exhibited distinct enrichment patterns. Using ACT2-seq, we identified distinct relationships between co-occupancy of specific histone modifications and gene expression patterns. Conclusions We conclude that ACT2-seq presents an attractive option for epigenomic profiling due to its ease of use, potential for reducing sample and sequencing costs, and ability to simultaneously profile co-occupancy of multiple histone marks and/or chromatin-associated proteins.Benjamin CarterWai Lim KuJoe PeltKeji ZhaoBMCarticleCo-occupancyCo-enrichmentACT-seqTagmentationEpigenetic marksBiotechnologyTP248.13-248.65Biology (General)QH301-705.5BiochemistryQD415-436ENCell & Bioscience, Vol 11, Iss 1, Pp 1-12 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Co-occupancy Co-enrichment ACT-seq Tagmentation Epigenetic marks Biotechnology TP248.13-248.65 Biology (General) QH301-705.5 Biochemistry QD415-436
spellingShingle	Co-occupancy Co-enrichment ACT-seq Tagmentation Epigenetic marks Biotechnology TP248.13-248.65 Biology (General) QH301-705.5 Biochemistry QD415-436 Benjamin Carter Wai Lim Ku Joe Pelt Keji Zhao Concurrent mapping of multiple epigenetic marks and co-occupancy using ACT2-seq
description	Abstract Background Genome-wide profiling of epigenetic marks is a core technology in molecular genetics. Co-occupancy of different epigenetic marks or protein factors at the same genomic locations must often be inferred from multiple independently collected data sets. However, this strategy does not provide direct evidence of co-enrichment in the same cells due to the existence of cellular heterogeneity. To address this issue, we have developed a technique termed ACT2-seq that is capable of concurrently profiling multiple epigenetic marks in a single biological sample. In addition to reducing the numbers of samples required for experiments, ACT2-seq is capable of mapping co-occupancy of epigenetic factors on chromatin. This strategy provides direct evidence of co-enrichment without requiring complex single-molecule, single-cell, or magnetic bead-based approaches. Results We concurrently profiled pairs of two epigenetic marks using ACT2-seq as well as three marks in individual samples. Data obtained using ACT2-seq were found to be reproducible and robust. ACT2-seq was capable of cleanly partitioning concurrently mapped data sets that exhibited distinct enrichment patterns. Using ACT2-seq, we identified distinct relationships between co-occupancy of specific histone modifications and gene expression patterns. Conclusions We conclude that ACT2-seq presents an attractive option for epigenomic profiling due to its ease of use, potential for reducing sample and sequencing costs, and ability to simultaneously profile co-occupancy of multiple histone marks and/or chromatin-associated proteins.
format	article
author	Benjamin Carter Wai Lim Ku Joe Pelt Keji Zhao
author_facet	Benjamin Carter Wai Lim Ku Joe Pelt Keji Zhao
author_sort	Benjamin Carter
title	Concurrent mapping of multiple epigenetic marks and co-occupancy using ACT2-seq
title_short	Concurrent mapping of multiple epigenetic marks and co-occupancy using ACT2-seq
title_full	Concurrent mapping of multiple epigenetic marks and co-occupancy using ACT2-seq
title_fullStr	Concurrent mapping of multiple epigenetic marks and co-occupancy using ACT2-seq
title_full_unstemmed	Concurrent mapping of multiple epigenetic marks and co-occupancy using ACT2-seq
title_sort	concurrent mapping of multiple epigenetic marks and co-occupancy using act2-seq
publisher	BMC
publishDate	2021
url	https://doaj.org/article/ea12137d935a4d0aa3970d12820b90d3
work_keys_str_mv	AT benjamincarter concurrentmappingofmultipleepigeneticmarksandcooccupancyusingact2seq AT wailimku concurrentmappingofmultipleepigeneticmarksandcooccupancyusingact2seq AT joepelt concurrentmappingofmultipleepigeneticmarksandcooccupancyusingact2seq AT kejizhao concurrentmappingofmultipleepigeneticmarksandcooccupancyusingact2seq
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Concurrent mapping of multiple epigenetic marks and co-occupancy using ACT2-seq

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