Regulatory chromatin landscape in Arabidopsis thaliana roots uncovered by coupling INTACT and ATAC-seq

Miriam Tannenbaum, Avital Sarusi-Portuguez, Ronen Krispil, Michal Schwartz, Olga Loza, Jennifer I.C. Benichou, Assaf Mosquna, Ofir Hakim

Research output: Contribution to journalArticlepeer-review

30 Scopus citations

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.

Original languageEnglish
Article number113
JournalPlant Methods
Volume14
Issue number1
DOIs
StatePublished - 20 Dec 2018

Bibliographical note

Publisher Copyright:
© 2018 The Author(s).

Funding

This work is supported in part by Marie Curie Integration Grant (CIG)‑FP7‑PEO‑ PLE‑20013‑CIG‑618763 and I‑CORE Program of the Planning and Budgeting Committee and The Israel Science Foundation Grant No. 41/11. ASP is sup‑ ported by the Nehemia Levtzion Fellowship.

FundersFunder number
Seventh Framework Programme618763
Marie CurieFP7‑PEO‑ PLE‑20013‑CIG‑618763
Israel Science Foundation41/11

    Keywords

    • ATAC-seq
    • Arabidopsis thaliana
    • Chromatin accessibility
    • Chromatin structure
    • INTACT
    • Regulatory element
    • Transcription
    • Transcription factor

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