Changes in chromatin accessibility between Arabidopsis stem cells and mesophyll cells illuminate cell type‐specific transcription factor networks

• Published in: The Plant journal : for cell and molecular biology 2018-04, Vol.94 (2), p.215-231
• Main Authors: Sijacic, Paja, Bajic, Marko, McKinney, Elizabeth C., Meagher, Richard B., Deal, Roger B.
• Format: Article
• Language: English
• Subjects: Accessibility; Arabidopsis - cytology; Arabidopsis - metabolism; Arabidopsis Proteins - physiology; Arabidopsis thaliana; ATAC‐seq; Binding; Cell differentiation; Chromatin; Chromatin - metabolism; Developmental plasticity; Differentiation (biology); Gene expression; Gene Expression Regulation, Plant; Gene regulation; INTACT; Leaves; Meristem - cytology; Meristem - metabolism; Mesophyll; Mesophyll Cells - metabolism; Plant Leaves - cytology; Plant Leaves - metabolism; Plant Shoots - cytology; Plant Shoots - metabolism; Purification; Regulatory sequences; shoot meristem; stem cell; Stem cells; Stem Cells - metabolism; T cell receptors; transcription factor; Transcription factors; Transcription Factors - physiology; Transposase
• ISSN: 0960-7412; 1365-313X
• DOI: 10.1111/tpj.13882

Summary Cell differentiation is driven by changes in the activity of transcription factors (TFs) and subsequent alterations in transcription. To study this process, differences in TF binding between cell types can be deduced by probing chromatin accessibility. We used cell type‐specific nuclear 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 in Arabidopsis thaliana. Chromatin accessibility profiles of SAM stem cells and leaf mesophyll cells were very similar at a qualitative level, yet thousands of regions having quantitatively different chromatin accessibility were also identified. Analysis of the genomic regions preferentially accessible in each cell type identified hundreds of overrepresented TF‐binding motifs, highlighting sets of TFs that are probably important for each cell type. Within these sets, we found evidence for extensive co‐regulation of target genes by multiple TFs that are preferentially expressed in each cell type. Interestingly, the TFs within each of these cell type‐enriched sets also showed evidence of extensively co‐regulating each other. We further found that preferentially accessible chromatin regions in mesophyll cells tended to also be substantially accessible in the stem cells, whereas the converse was not true. This observation suggests that the generally higher accessibility of regulatory elements in stem cells might contribute to their developmental plasticity. This work demonstrates the utility of cell type‐specific chromatin accessibility profiling for the rapid development of testable models of regulatory control differences between cell types. Significance Statement Differences in transcription factor (TF) activity between plant cells of different types remain largely unexplored. We used cell type‐specific nuclear purification followed by chromatin accessibility assays to delineate TF networks in stem cells of the shoot apical meristem and differentiated leaf mesophyll cells in Arabidopsis thaliana, providing insight into how the transcriptomes of these cell types are established and maintained.