Current methods to identify sites of RNA interaction with the genome are limited to the study of a single RNA at a time. Here we describe a protocol for ChAR-seq, a strategy to identify all chromatin-associated RNAs and map their DNA contacts genome-wide. In ChAR-seq, proximity ligation ...
GRID-seq reveals the global RNA–chromatin interactome. Nat. Biotechnol. 35, 940–950 (2017). Article CAS PubMed PubMed Central Google Scholar Bell, J. C. et al. Chromatin-associated RNA sequencing (ChAR-seq) maps genome-wide RNA-to-DNA contacts. Elife 7, e27024 (2018). Article Pub...
correlations. This showed that RNA abundance was not associated with protein–RNA correlation (Fig.1e). Likewise, the gene-wise correlation analysis showed that 617 genes and 795 instances (including the same genes but different pairwise comparisons) had significant changes in the RNA and protein ...
NMuMG cells were treated for 6 or 30 h with BRM014 or with the vehicle DMSO (as a control), and the transcriptome was analyzed using duplicates of RNA sequencing (RNA-seq) and chromatin-associated RNA-seq (ChrRNA-seq) experiments. Chromatin-associated RNA is mostly constituted by nascent ...
Further, analysis by RNA chromatin immunoprecipitation (ChIP) indicates that the noncoding RNAs are physically associated with chromatin. These sterile ... C Epp,F Li,CA Howitt,... - RNA 被引量: 171发表: 2009年 RNA immunoprecipitation to determine RNA-protein associations in vivo chromatin immun...
Chromatin immunoprecipitation in combination with massive parallel DNA sequencing (ChIP-seq) analysis revealed that Setdb1 represses genes encoding developmental regulators [21]. These Setdb1-occupied genes constitute a subset of the “bivalent” genes, which contain nucleosomes with H3K4me3 and H3K27...
The integration of single cell transcriptome and chromatin accessibility datasets enables a deeper understanding of cell heterogeneity. We performed single nucleus ATAC (snATAC-seq) and RNA (snRNA-seq) sequencing to generate paired, cell-type-specific chromatin accessibility and transcriptional profiles of...
Recently, single-cell RNA sequencing (scRNA-seq) has been applied to root cells of Arabidopsis and rice and revealed the transcriptional programmes of major cell types, as well as the heterogeneity within a given population [1,2,3,4,5,6,7,8,9]. However, the mechanisms underlying these pro...
We next investigated additional features of lamina-associated chromatin across cell types. Compared to T2- and nonLADs, T1-LADs had the lowest proportion of expressed genes based on RNA-seq generated for this study and from published sources from matched cell types (Fig. 2C, Additional file 2...
[168]. DNA methyltransferases may regulate high levels of methylation associated with transcriptional silencing. For example, enhancer activity increased using PRO-seq sequencing in Dnmt1, Dnmt3a, and Dnmt3b triple-knockout mice, while enhancer activity decreased after the same measurement after TET ...