MelRNA-seq for Expression Analysis of SINE RNAs and Other Medium-Length Non-Coding RNAs.

ABSTRACT:

Background

Small interspersed elements (SINEs) are transcribed by RNA polymerase III (Pol III) to produce RNAs typically 100-500 nucleotides in length. Although their RNA abundance can be evaluated by Northern blotting and primer extension, the nature (sequence, exact length, and genomic origin) of these RNAs cannot be revealed by these methods. Moreover, mRNA sequencing (mRNA-seq) is not able to distinguish bona fide SINE RNAs or SINE sequences present in longer transcripts.

Results

To elucidate the abundance, source loci, and sequence nature of SINE RNAs, we established a deep sequencing method, designated as melRNA-seq (medium-length RNA-seq), which can determine whole-length RNA sequences. Total RNA samples were treated with 5' pyrophosphohydrolase (RppH), which allowed

SUBMITTER: Mori Y 

PROVIDER: S-EPMC8210359 | biostudies-literature | 2021 Jun

REPOSITORIES: biostudies-literature