TY  - JOUR
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
Y1  - 2022/09/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 1727 
EP  - 1735 
DO  - 10.1101/gr.276647.122 
VL  - 32 
IS  - 9 
UR  - http://genome.cshlp.org/content/32/9/1727.abstract 
N2  - 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. 
ER  -