Ever-changing landscapes: transcriptional enhancers in development and evolution. On the dependency of cellular protein levels on mRNA abundance. The Regulation of rRNA Gene Transcription during Directed Differentiation of Human Embryonic Stem Cells. Replication landscape of the human genome. Petryk N., Kahli M., d'Aubenton-Carafa Y., et al. Deep sequencing of the cDNA identifies RNAs that are actively transcribed by RNAPII. After cap removal and end repair, the eluted RNA is reverse-transcribed to cDNA. RNAs are hydrolyzed and purified using beads coated with antibodies to 5-bromo-2-deoxyuridine (BrdU). In this method, active RNAPII is allowed to run on in the presence of 5-bromouridine 5'-triphosphate (Br-UTP). GRO-Seq maps the binding sites of transcriptionally active RNA polymerase II (RNAPII) (Core et al., 2008). Petryk N., Kahli M., d’Aubenton-Carafa Y., et al. Mammalian NET-seq analysis defines nascent RNA profiles and associated RNA processing genome-wide. Isolation of the protein and RNA content of active sites of transcription from mammalian cells. Melnik S., Caudron-Herger M., Brant L., et al. Functional genetic screens for enhancer elements in the human genome using CRISPR-Cas9. 7SK-BAF axis controls pervasive transcription at enhancers. Genome-wide nucleosome specificity and function of chromatin remodellers in ES cells. Comprehensive analysis of promoter-proximal RNA polymerase II pausing across mammalian cell types. The IL-4/STAT6 signaling axis establishes a conserved microRNA signature in human and mouse macrophages regulating cell survival via miR-342-3p. Cutoff Suppresses RNA Polymerase II Termination to Ensure Expression of piRNA Precursors. Transcription-associated processes cause DNA double-strand breaks and translocations in neural stem/progenitor cells. Getting up to speed with transcription elongation by RNA polymerase II. The identification of cis-regulatory elements: A review from a machine learning perspective. Enhanced Identification of Transcriptional Enhancers Provides Mechanistic Insights into Diseases. Murakawa Y., Yoshihara M., Kawaji H., Nishikawa M., Zayed H., et al. Illumina Library prep and Array Kit Selector Requires nascent RNAs of at least 18 nt (Mayer et al., 2016).Resolution is only 30_100 nt (Nojima et al., 2016).Physical impediments may block the polymerases.New initiation events may occur during the run-on step.Artifacts may be introduced during the preparation of the nuclei (Adelman et al., 2012).Limited to cell cultures and other artificial systems, due to the requirement for incubation in the presence of labeled nucleotides.Provides robust coverage of enhancer- and promoter-associated RNAs (Melnik et al., 2016).No prior knowledge of transcription sites is needed.Detects transcription anywhere on the genome.Detects sense and antisense transcription.Determines relative activity of transcription sites.Maps position of transcriptionally engaged RNA polymerases.In this method, active RNAPII is allowed to run on in the presence of 5-bromouridine 5′-triphosphate (Br-UTP).
0 kommentar(er)
