Deep sequencing of short capped RNAs reveals novel families of noncoding RNAs

Michiel de Hoon, Alessandro Bonetti, Charles Plessy, Yoshinari Ando, Chung Chau Hon, Yuri Ishizu, Masayoshi Itoh, Sachi Kato, Dongyan Lin, Sho Maekawa, Mitsuyoshi Murata, Hiromi Nishiyori, Jay W. Shin, Jens Stolte, Ana Maria Suzuki, Michihira Tagami, Hazuki Takahashi, Supat Thongjuea, Alistair R.R. Forrest, Yoshihide HayashizakiJuha Kere, Piero Carninci

Research output: Contribution to journalArticlepeer-review


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.

Original languageEnglish
Pages (from-to)1727-1735
Number of pages9
JournalGenome Research
Issue number9
Publication statusPublished - Sep 2022


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