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 ...
However, the structural contribution of RNA to chromatin organization remains undisputed: a large proportion of chromatin by mass corresponds to RNA (Holmes et al., 1972), mostly belonging to the loosely termed chromatin-associated RNA (caRNA) class. The functional roles of caRNAs are hinted by ...
An example of cross-cell-type comparison: enhancer-associated regulatory factors Learning a conditional-dependence network for all ENCODE cell types allows the comparison of within cell type connections across different cell types. Active enhancers are known to be flanked by a combination of the histon...
double strand break repair pathway that also recruits Fanconi Anaemia factors (Bochar et al., 2000; Otsuki et al., 2001). Finally, the SWI/SNF catalyticATPasesubunits BRM and BRG1 have been reported to be mutated in a variety of primary tumors and have been associated with a poor prognosis...
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...
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 ...
The most widely used strategy for assaying these factors is immunoprecipitation, whereby antibodies are used to pull down RNA associated with an epitope of interest from cell lysates2. The recovered RNA is then purified and used for downstream analysis such as Illumina sequencing3,4. Variations of...