Open Chromatin in Plant Genomes

Abstract

Sensitivity to DNase I digestion is an indicator of the accessibility and configuration of chromatin in eukaryotic genomes. Open chromatin exhibits high sensitivity to DNase I cleavage. DNase I hypersensitive sites (DHSs) in eukaryotic genomes can be identified through DNase I treatment followed by sequencing (DNase-seq). DHSs are most frequently associated with various cis-regulatory DNA elements, including promoters, enhancers, and silencers in both animal and plant genomes. Genome-wide identification of DHSs provides an efficient method to interpret previously un-annotated regulatory DNA sequences. In this review, we provide an overview of the historical perspective of DHS research in eukaryotes. We summarize the main achievements of DHS research in model animal species and review the recent progress of DHS research in plants. We finally discuss possible future directions of using DHS as a tool in plant genomics research.

Abundance and distribution of RNA polymerase II in Arabidopsis interphase nuclei

“…However, assuming that only one RNAPII Ser2ph molecule responsible for transcriptional elongation would be associated with only one gene, as mostly found in Drosophila , mouse, and human nuclei (Laird and Chooi, 1976; McKnight and Miller, 1976; Fakan et al , 1986; Jackson et al , 1998), then every second to third gene would be active in 2C–16C A. thaliana leaf nuclei (Table 1). Due to the presence of mainly non-cohesive chromatids in highly endopolyploid A. thaliana nuclei (Schubert et al , 2012), the resulting ‘open chromatin’ structure (Zhang et al , 2014) may allow the parallel transcription of multiple gene copies by RNAPII as demonstrated at the four well-separated chromatids in Drosophila embryo nuclei (Little et al , 2013). Thus, assuming that ~50% of the different genes are active in A. thaliana (see above), on average approximately one copy of the same gene would be transcriptionally active in 2C–16C nuclei.…”

Genome-wide mapping of DNase I hypersensitive sites reveals chromatin accessibility changes in Arabidopsis euchromatin and heterochromatin regions under extended darkness

“…Recently, light signalling has been reported to control nuclear architecture reorganization during establishment 17 . Changes in chromatin structure affect the binding of TFs to regulatory elements, thus altering the expression of the associated genes 18 . Consequently, DNase I hypersensitive sites (DHSs) represent chromatin regions that are accessible for TF binding and, thereby, can be used to predict the presence of TFs 19, 20 .…”

Towards genome-wide prediction and characterization of enhancers in plants

“…In contrast to the discoveries in rice, out of all DHSs identified in A. thaliana, approximately 15% were located in intergenic regions, representing likely distal enhancers, or other active CREs. DHSs within 1000 bp upstream of genes account for 45% and 27% of the total DHSs in Arabidopsis and rice genomes, respectively [25]. These results suggest that plant species with compact genomes such as Arabidopsis, may contain fewer distal CREs than those with large complex genomes.…”

“…NDRs show a pronounced susceptibility to cleavage by deoxyribonuclease I (DNase I), and are known as DNase I hypersensitive sites (DHSs) [22][23][24][25][26]. Thus, the extent of chromatin accessibility can be directly and reliably measured utilizing DNase I digestion in combination with next generation sequencing (DNase-seq) (Fig.…”

“…Thus, the extent of chromatin accessibility can be directly and reliably measured utilizing DNase I digestion in combination with next generation sequencing (DNase-seq) (Fig. 2B) [22][23][24][25][26][27]. A plethora of studies in human have utilized this strategy in an attempt to characterize DHS variability across cell-types in order to construct CRE catalogs for specific cells lines.…”