High-resolution RNA 3′-ends mapping of bacterial Rho-dependent transcripts

Optimized rapid amplification of cDNA ends (RACE) for mapping bacterial mRNA transcripts.

A simple, efficient and sensitive RACE-based procedure was developed for the determination of unknown 5' regions from bacterial cDNA. A number of critical modifications were made to the standard RACE method, including the optimization of the RNA extraction, reverse transcription and PCR conditions. This procedure was used to accurately determine the site of transcript initiation and structure o...

High-resolution profiling of protein occupancy on polyadenylated RNA transcripts.

A key prerequisite to understand how gene regulatory processes are controlled by the interplay of RNA-binding proteins and ribonucleoprotein complexes with RNAs is the generation of comprehensive high-resolution maps of protein-RNA interactions. Recent advances in next-generation sequencing technology accelerated the development of various crosslinking and immunoprecipitation (CLIP) approaches ...

Synthesis of small RNA transcripts with discrete 5' and 3' ends.

Mapping of ribosomal RNA transcripts in wheat.

Ribosomal RNA transcripts in wheat have been studied by RNA gel blotting and their termini determined from electrophoretic analysis of S1 nuclease-resistant RNA/DNA hybrids and also of hybrids created by primer extension. A major putative transcription initiation site has been localized 1132 base pairs upstream from the 5' end of the 18S RNA sequence. A major putative processing site occurs 640...

Strand‐specific, high‐resolution mapping of modified RNA polymerase II

Reversible modification of the RNAPII C-terminal domain links transcription with RNA processing and surveillance activities. To better understand this, we mapped the location of RNAPII carrying the five types of CTD phosphorylation on the RNA transcript, providing strand-specific, nucleotide-resolution information, and we used a machine learning-based approach to define RNAPII states. This reve...