By integrating MNase-seq and siRNA-seq data, we found that regions of mCHH islands accumulate 21nt-siRNAs in a tissue-specific manner, marking the transition to open chromatin, thereby ensuring the accessibility of TFs for tissue-specific gene regulation.Our ROI-directed RRBS pipeline is ...
The DNA methylation and MNase data for 100-bp bins were compared with the TIR annotation gff using bedtools closest to identify the 100-bp bins within 4 kb of each TIR element. Only 100-bp bins that are closest to a single TIR element are used for analysis of chromatin properties at ...
Additionally, 57 QTL were located in non-genic regions, of which 89.7% were identified close to MNase hyposensitive (HS) proximal regions [28], and 53.4% and 55.1% resided in accessible chromatin regions identified in leaf and inflorescence [29], all were significantly higher than expected by...
Genome-wide identifications of CREs based on open chromatin using DNase I hypersensitive sites (DHSs) and MNase- hypersensitive (MNase HS) regions have been carried out in Arabidopsis, rice, cotton, and maize, which greatly promoted the study of plant functional genome [1, 2, 4, 6, 9, 24...
the SNPs with minor allele frequency ≥ 0.05 in this panel, in a linear regression model including the PEER factors from [22] as covariates, using GEMMA 0.98.1 [94]. Chromatin accessibility was characterized by hotspots of MNase hypersensitivity in germinating shoot or germinating root [21,95]...
ARF peaks overlap with regions of open chromatin.aOverlap of DAP-seq peaks with open chromatin regions from different tissues. Gray bars represent coverage of open chromatin datasets relative to leaf dataset (ATAC-seq plus MNase datasets which contained the greatest coverage). Clade A ARFs (orange...
As shown in Fig. S5 A and B, nucleosome densities at the upstream of transcription start sites (UTSs) were dramatically decreased in R101 and RS1 compared to those of WT, which is consistent with results of the MNase experiment. Especially, the nucleosome density at UTS that is essential...