Chromatin accessibility changes betweenArabidopsisstem cells and mesophyll cells illuminate cell type-specific transcription factor networks

Abstract

BackgroundCell differentiation is driven by changes in transcription factor (TF) activity and subsequent alterations in transcription. To study this process, differences in TF binding between cell types can be deduced by methods that probe chromatin accessibility. We used cell type-specific nuclei purification followed by the Assay for Transposase Accessible Chromatin (ATAC-seq) to delineate differences in chromatin accessibility and TF regulatory networks between stem cells of the shoot apical meristem (SAM) and differentiated leaf mesophyll cells of Arabidopsis thaliana.

The histone variant H2A.Z and chromatin remodeler BRAHMA act coordinately and antagonistically to regulate transcription and nucleosome dynamics in Arabidopsis

“…To identify TFs that may be associated with specific regulatory relationships between H2A.Z and BRM, we identified significantly enriched sequence motifs found in accessible chromatin regions associated with each of the eight DE gene classes we identified as targets of H2A.Z and BRM (Figure 1a). Accessible chromatin sites were defined in a previous study using an ATAC-seq dataset from leaf mesophyll cells (Sijacic et al, 2018), which is the predominant cell type in our tissue. The motifs enriched at accessible regions across seven of our DE gene classes are enriched for the target motifs of 78 different TFs (none were enriched for gene class 1) (Table S3).…”

“…ATAC-seq transposase hypersensitivity sites (THSs) from mesophyll cells were identified and annotated previously (Sijacic et al, 2018). We used python scripts to pull out the annotated mesophyll THSs that were associated with genes from our eight DE BRM and H2A.Z target gene classes (defined in Figure 1d).…”

Enhanced TF binding site maps improve regulatory networks learned from accessible chromatin data

“…The identification of highly accessible open chromatin regions throughout the genome helps to determine the location of potential regulatory elements. Recent advancements in experimental technologies have allowed researchers to map open chromatin regions in specific plant cell types (Maher et al, 2018;Sijacic et al, 2018). However, identifying which TFs are likely to bind these regions, and how they affect gene expression, is still a major challenge.…”

“…Recent advances in the profiling of open chromatin have increased our understanding of regulatory DNA in Arabidopsis (Zhang et al, 2012;Sullivan et al, 2014;Lu et al, 2017). Combined with cell type-specific nuclear purification, methods such as Assay for Transposase-Accessible Chromatin followed by DNA sequencing (ATAC-Seq) offer unprecedented opportunities to identify cell type-specific TF networks (Lu et al, 2017;Maher et al, 2018;Sijacic et al, 2018). Nevertheless, elucidation of GRNs from chromatin accessibility data requires detailed information about TF binding preferences in order to identify potential binding sites within accessible regions of the genome, and therefore infer TF-target gene regulatory interactions.…”

Epigenetic dynamics during flowering plant reproduction: evidence for reprogramming?

“…All cells arise from meristems, with reproductive cells formed specifically from the L2 layer of apical meristems. The epigenetic state of the L2 cells is largely unknown, although features of meristematic regions are beginning to be probed (Gutzat et al, 2018;Sijacic et al, 2018). Thus, the molecular epigenetic state of reproductive cells is often compared to leaf or seedling tissue, and it is unknown how reflective these tissues are of the relevant cells in meristems.…”