Regulatory chromatin landscape in Arabidopsis thaliana roots uncovered by coupling INTACT and ATAC-seq
Abstract Background There is a growing interest in the role of chromatin in acquiring and maintaining cell identity. Despite the ever-growing availability of genome-wide gene expression data, understanding how transcription programs are established and regulated to define cell identity remains a puz...
| Váldodahkkit: | , , , , , , , |
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| Materiálatiipa: | Artihkal |
| Giella: | English |
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BMC
2018-12-01
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| Ráidu: | Plant Methods |
| Fáttát: | |
| Liŋkkat: | http://link.springer.com/article/10.1186/s13007-018-0381-9 |
| _version_ | 1828841834706632704 |
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| author | Miriam Tannenbaum Avital Sarusi-Portuguez Ronen Krispil Michal Schwartz Olga Loza Jennifer I. C. Benichou Assaf Mosquna Ofir Hakim |
| author_facet | Miriam Tannenbaum Avital Sarusi-Portuguez Ronen Krispil Michal Schwartz Olga Loza Jennifer I. C. Benichou Assaf Mosquna Ofir Hakim |
| author_sort | Miriam Tannenbaum |
| collection | DOAJ |
| description | Abstract Background There is a growing interest in the role of chromatin in acquiring and maintaining cell identity. Despite the ever-growing availability of genome-wide gene expression data, understanding how transcription programs are established and regulated to define cell identity remains a puzzle. An important mechanism of gene regulation is the binding of transcription factors (TFs) to specific DNA sequence motifs across the genome. However, these sequences are hindered by the packaging of DNA to chromatin. Thus, the accessibility of these loci for TF binding is highly regulated and determines where and when TFs bind. We present a workflow for measuring chromatin accessibility in Arabidopsis thaliana and define organ-specific regulatory sites and binding motifs of TFs at these sites. Results We coupled the recently described isolation of nuclei tagged in specific cell types (INTACT) and assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) as a genome-wide strategy to uncover accessible regulatory sites in Arabidopsis based on their accessibility to nuclease digestion. By applying this pipeline in Arabidopsis roots, we revealed 41,419 accessible sites, of which approximately half are found in gene promoters and contain the H3K4me3 active histone mark. The root-unique accessible sites from this group are enriched for root processes. Interestingly, most of the root-unique accessible sites are found in nongenic regions but are correlated with root-specific expression of distant genes. Importantly, these gene-distant sites are enriched for binding motifs of TFs important for root development as well as motifs for TFs that may play a role as novel transcriptional regulators in roots, suggesting that these accessible loci are functional novel gene-distant regulatory elements. Conclusions By coupling INTACT with ATAC-seq methods, we present a feasible pipeline to profile accessible chromatin in plants. We also introduce a rapid measure of the experiment quality. We find that chromatin accessibility at promoter regions is strongly associated with transcription and active histone marks. However, root-specific chromatin accessibility is primarily found at intergenic regions, suggesting their predominance in defining organ identity possibly via long-range chromatin interactions. This workflow can be rapidly applied to study the regulatory landscape in other cell types, plant species and conditions. |
| first_indexed | 2024-12-12T20:10:52Z |
| format | Article |
| id | doaj.art-b8ac155cb1514c7294ff3d9535667f49 |
| institution | Directory Open Access Journal |
| issn | 1746-4811 |
| language | English |
| last_indexed | 2024-12-12T20:10:52Z |
| publishDate | 2018-12-01 |
| publisher | BMC |
| record_format | Article |
| series | Plant Methods |
| spelling | doaj.art-b8ac155cb1514c7294ff3d9535667f492022-12-22T00:13:30ZengBMCPlant Methods1746-48112018-12-0114111210.1186/s13007-018-0381-9Regulatory chromatin landscape in Arabidopsis thaliana roots uncovered by coupling INTACT and ATAC-seqMiriam Tannenbaum0Avital Sarusi-Portuguez1Ronen Krispil2Michal Schwartz3Olga Loza4Jennifer I. C. Benichou5Assaf Mosquna6Ofir Hakim7The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan UniversityThe Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan UniversityThe Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan UniversityThe Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan UniversityThe Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan UniversityThe Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan UniversityRobert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, Hebrew University of JerusalemThe Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan UniversityAbstract Background There is a growing interest in the role of chromatin in acquiring and maintaining cell identity. Despite the ever-growing availability of genome-wide gene expression data, understanding how transcription programs are established and regulated to define cell identity remains a puzzle. An important mechanism of gene regulation is the binding of transcription factors (TFs) to specific DNA sequence motifs across the genome. However, these sequences are hindered by the packaging of DNA to chromatin. Thus, the accessibility of these loci for TF binding is highly regulated and determines where and when TFs bind. We present a workflow for measuring chromatin accessibility in Arabidopsis thaliana and define organ-specific regulatory sites and binding motifs of TFs at these sites. Results We coupled the recently described isolation of nuclei tagged in specific cell types (INTACT) and assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) as a genome-wide strategy to uncover accessible regulatory sites in Arabidopsis based on their accessibility to nuclease digestion. By applying this pipeline in Arabidopsis roots, we revealed 41,419 accessible sites, of which approximately half are found in gene promoters and contain the H3K4me3 active histone mark. The root-unique accessible sites from this group are enriched for root processes. Interestingly, most of the root-unique accessible sites are found in nongenic regions but are correlated with root-specific expression of distant genes. Importantly, these gene-distant sites are enriched for binding motifs of TFs important for root development as well as motifs for TFs that may play a role as novel transcriptional regulators in roots, suggesting that these accessible loci are functional novel gene-distant regulatory elements. Conclusions By coupling INTACT with ATAC-seq methods, we present a feasible pipeline to profile accessible chromatin in plants. We also introduce a rapid measure of the experiment quality. We find that chromatin accessibility at promoter regions is strongly associated with transcription and active histone marks. However, root-specific chromatin accessibility is primarily found at intergenic regions, suggesting their predominance in defining organ identity possibly via long-range chromatin interactions. This workflow can be rapidly applied to study the regulatory landscape in other cell types, plant species and conditions.http://link.springer.com/article/10.1186/s13007-018-0381-9Chromatin accessibilityChromatin structureRegulatory elementTranscriptionTranscription factorArabidopsis thaliana |
| spellingShingle | Miriam Tannenbaum Avital Sarusi-Portuguez Ronen Krispil Michal Schwartz Olga Loza Jennifer I. C. Benichou Assaf Mosquna Ofir Hakim Regulatory chromatin landscape in Arabidopsis thaliana roots uncovered by coupling INTACT and ATAC-seq Plant Methods Chromatin accessibility Chromatin structure Regulatory element Transcription Transcription factor Arabidopsis thaliana |
| title | Regulatory chromatin landscape in Arabidopsis thaliana roots uncovered by coupling INTACT and ATAC-seq |
| title_full | Regulatory chromatin landscape in Arabidopsis thaliana roots uncovered by coupling INTACT and ATAC-seq |
| title_fullStr | Regulatory chromatin landscape in Arabidopsis thaliana roots uncovered by coupling INTACT and ATAC-seq |
| title_full_unstemmed | Regulatory chromatin landscape in Arabidopsis thaliana roots uncovered by coupling INTACT and ATAC-seq |
| title_short | Regulatory chromatin landscape in Arabidopsis thaliana roots uncovered by coupling INTACT and ATAC-seq |
| title_sort | regulatory chromatin landscape in arabidopsis thaliana roots uncovered by coupling intact and atac seq |
| topic | Chromatin accessibility Chromatin structure Regulatory element Transcription Transcription factor Arabidopsis thaliana |
| url | http://link.springer.com/article/10.1186/s13007-018-0381-9 |
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