RT Journal
A1 de Hoon, Michiel
A1 Bonetti, Alessandro
A1 Plessy, Charles
A1 Ando, Yoshinari
A1 Hon, Chung-Chau
A1 Ishizu, Yuri
A1 Itoh, Masayoshi
A1 Kato, Sachi
A1 Lin, Dongyan
A1 Maekawa, Sho
A1 Murata, Mitsuyoshi
A1 Nishiyori, Hiromi
A1 Shin, Jay W.
A1 Stolte, Jens
A1 Suzuki, Ana Maria
A1 Tagami, Michihira
A1 Takahashi, Hazuki
A1 Thongjuea, Supat
A1 Forrest, Alistair R.R.
A1 Hayashizaki, Yoshihide
A1 Kere, Juha
A1 Carninci, Piero
T1 Deep sequencing of short capped RNAs reveals novel families of noncoding RNAs
JF Genome Research 
JO Genome Research 
YR 2022 
FD September 01 
VO 32 
IS 9 
SP 1727 
OP 1735 
DO 10.1101/gr.276647.122 
UL http://genome.cshlp.org/content/32/9/1727.abstract 
AB In eukaryotes, capped RNAs include long transcripts such as messenger RNAs and long noncoding RNAs, as well as shorter transcripts such as spliceosomal RNAs, small nucleolar RNAs, and enhancer RNAs. Long capped transcripts can be profiled using cap analysis gene expression (CAGE) sequencing and other methods. Here, we describe a sequencing library preparation protocol for short capped RNAs, apply it to a differentiation time course of the human cell line THP-1, and systematically compare the landscape of short capped RNAs to that of long capped RNAs. Transcription initiation peaks associated with genes in the sense direction have a strong preference to produce either long or short capped RNAs, with one out of six peaks detected in the short capped RNA libraries only. Gene-associated short capped RNAs have highly specific 3′ ends, typically overlapping splice sites. Enhancers also preferentially generate either short or long capped RNAs, with 10% of enhancers observed in the short capped RNA libraries only. Enhancers producing either short or long capped RNAs show enrichment for GWAS-associated disease SNPs. We conclude that deep sequencing of short capped RNAs reveals new families of noncoding RNAs and elucidates the diversity of transcripts generated at known and novel promoters and enhancers.