In ChAR-seq, proximity ligation of RNA and DNA to a linker molecule is used to construct a chimeric RNA-DNA molecule that is converted to DNA for sequencing. In a single assay, ChAR-seq can discover de novo chromatin interactions of distinct RNAs, including nascent transcripts, splicing RNAs...
Comparing TBP-chromatin residence times with nascent RNA transcription rates18, we found that a median value of ~5 TBP binding events were associated with productive RNA synthesis across Pol II genes. Our results paint a highly dynamic, stochastic picture of pre-initiation complex formation with ...
RNA Sequencing and analysis Total RNA from cells transfected with siRNA for the time indicated were prepared with RNeasy Mini kit (QIAGEN) and treated with ribo-Zero kit (illumina) to remove ribosomal RNA. RNA-seq libraries were prepared with a NEBNext® Ultra RNA Library Prep Kit for Illum...
Analysis of high-throughput sequencing datasets Available paired-end RNA-seq data was downloaded from the ENCODE portal (https://www.encodeproject.org/), which compiles both ENCODE and ROADMAP data. Percent of inclusion (PSI) of alternatively spliced exons was calculated using the raw fastq files...
Nanopore direct RNA sequencing maps the complexity of Arabidopsis mRNA processing and m(6)A modification Elife, 9 (2020), p. e49658, 10.7554/eLife.49658 View in ScopusGoogle Scholar 55 L. Touat-Todeschini, Y. Shichino, M. Dangin, N. Thierry-Mieg, B. Gilquin, E. Hiriart, R. Sachida...
T. Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science 322, 1845–1848 (2008). Article CAS Google Scholar Yildirim, E., Sadreyev, R. I., Pinter, S. F. & Lee, J. T. X-chromosome hyperactivation in mammals via nonlinear relationships ...
We next examined how CBX7 binding sites in the RNA (dCLIP-seq) relate to CBX7's chromatin binding sites (chromatin immunoprecipitation sequencing [ChIP-seq]). Previous work demonstrated that CBX7 tends to bind large numbers of genomic loci in mouse ESCs (Morey et al., 2012). Therefore, ...
Methods that measure the production of nascent RNAs, such as GRO-seq (Global run-on sequencing), may be more precise to study the effect of chromatin accessibility on gene expression [54]. In conclusion, we comprehensively investigated and compared the landscape of chromatin accessibility in GT ...