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Specific chromatin changes mark lateral organ founder cells in the Arabidopsis inflorescence meristem
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Frerichs, Anneke, Engelhorn, Julia, Altmüller, Janine, Gutierrez-Marcos, José F. and Werr, Wolfgang (2019) Specific chromatin changes mark lateral organ founder cells in the Arabidopsis inflorescence meristem. Journal of Experimental Botany, 70 (15). pp. 3867-3879. doi:10.1093/jxb/erz181 ISSN 0022-0957.
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Official URL: http://dx.doi.org/10.1093/jxb/erz181
Abstract
Fluorescence-activated cell sorting (FACS) and assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) were combined to analyse the chromatin state of lateral organ founder cells (LOFCs) in the peripheral zone of the Arabidopsis apetala1-1 cauliflower-1 double mutant inflorescence meristem. On a genome-wide level, we observed a striking correlation between transposase hypersensitive sites (THSs) detected by ATAC-seq and DNase I hypersensitive sites (DHSs). The mostly expanded DHSs were often substructured into several individual THSs, which correlated with phylogenetically conserved DNA sequences or enhancer elements. Comparing chromatin accessibility with available RNA-seq data, THS change configuration was reflected by gene activation or repression and chromatin regions acquired or lost transposase accessibility in direct correlation with gene expression levels in LOFCs. This was most pronounced immediately upstream of the transcription start, where genome-wide THSs were abundant in a complementary pattern to established H3K4me3 activation or H3K27me3 repression marks. At this resolution, the combined application of FACS/ATAC-seq is widely applicable to detect chromatin changes during cell-type specification and facilitates the detection of regulatory elements in plant promoters.
| Item Type: | Journal Article | ||||||||
|---|---|---|---|---|---|---|---|---|---|
| Divisions: | Faculty of Science, Engineering and Medicine > Science > Life Sciences (2010- ) | ||||||||
| Journal or Publication Title: | Journal of Experimental Botany | ||||||||
| Publisher: | Oxford University Press | ||||||||
| ISSN: | 0022-0957 | ||||||||
| Official Date: | 1 August 2019 | ||||||||
| Dates: |
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| Volume: | 70 | ||||||||
| Number: | 15 | ||||||||
| Page Range: | pp. 3867-3879 | ||||||||
| DOI: | 10.1093/jxb/erz181 | ||||||||
| Status: | Peer Reviewed | ||||||||
| Publication Status: | Published | ||||||||
| Access rights to Published version: | Open Access (Creative Commons) | ||||||||
| Description: | A correction has been published: |
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