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

Abstract

BackgroundThere 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.ResultsWe 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.ConclusionsBy 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.Electronic supplementary materialThe online version of this article (10.1186/s13007-018-0381-9) contains supplementary material, which is available to authorized users.

Profiling of chromatin accessibility across Aspergillus species and identification of transcription factor binding sites in the Aspergillus genome using filamentous fungi ATAC-seq

“…The chromatin accessibility regions of A. niger CBS513.88 and SH2 were similarly distributed across the various elements of the genome; the chromatin accessibility regions were found in a high proportion at TSSs (∼70%) and in a low proportion at intergenic regions (∼5%). The proportional distribution of accessible regions is different from what is observed in humans (Ackermann et al 2016), Arabidopsis (Tannenbaum et al 2018) and tomato (Qiu et al 2016), which show a high distribution in intergenic regions and gene bodies. This difference may reflect the smaller size of the A. niger genome (35 Mb) compared with the larger and less compact genomes of humans (750 Mb), Arabidopsis (125 Mb) and tomato (900 Mb).…”

“…Prior works found that the accessible chromatin regions were positively correlated with gene expression changes of the nearest target genes (Wu et al 2016; Tannenbaum et al 2018; Toenhake et al 2018). We discovered that changing both the culture conditions and deleting TFs can slightly induce differential chromatin accessibility.…”

“…The accessible chromatin regions identified by ATAC-seq are particularly valuable for the identification of cis- regulatory DNA elements (Ackermann et al 2016; Lu et al 2017; Tannenbaum et al 2018; Toenhake et al 2018), which are bound by regulatory proteins such as transcription factors. We systematically identified genome-wide DNA footprints from candidate accessible regions and performed de novo motif enrichment analysis on the footprints from A. niger CBS513.88 and SH2 (Fig.…”

“…As a result, significantly lower amounts of starting nuclei are required for the investigation of CREs. ATAC-seq is now routinely being applied to systematically identify cis- regulatory regions and DNA footprints in humans (Buenrostro et al 2013), mice (Wu et al 2016), zebrafish (Fernandez-Minan et al 2016), Drosophila (Bozek et al 2019), Caenorhabditis elegans (Daugherty et al 2017), Arabidopsis thaliana (Tannenbaum et al 2018), Saccharomyces cerevisiae (Schep et al 2015) and so on. However, in Aspergillus species, the existence of cell walls and the purification of nuclei preparation prevented the routine application of this technique.…”

Integrating Peak Colocalization and Motif Enrichment Analysis for the Discovery of Genome-Wide Regulatory Modules and Transcription Factor Recruitment Rules

“…Similar estimates can be derived for other species and taxa, since nucleosome occupancy and DNA accessibility data are available for all the most widely studied species, as for example in Drosophila (Thomas et al, 2011), or Arabidopsis thaliana (Tannenbaum et al, 2018). In these two species the smaller genome size (hundreds of millions of base pairs) in turn results in a proportionally lower number of estimated accessible regions (tens of thousands).…”