Deep sequencing of short capped RNAs reveals novel families of noncoding RNAs
- Michiel Jan Laurens De Hoon1,8,
- Alessandro Bonetti1,
- Charles Plessy1,
- Yoshinari Ando1,
- Chung-Chau Hon1,
- Yuri Ishizu2,
- Masayoshi Itoh3,
- Sachi Katoh1,
- Dongyan Lin1,
- Sho Maekawa4,
- Mitsuyoshi Murata1,
- Hiromi Nishiyori1,
- Jay W Shin1,
- Jens Stolte2,
- Ana Maria Suzuki1,
- Michihira Tagami1,
- Hazuki Takahashi1,
- Supat Thongjuea2,
- Alistair RR Forrest5,
- Yoshihide Hayashizaki6,
- Juha Kere7 and
- Piero Carninci1
- 1 RIKEN Center for Integrative Medical Sciences;
- 2 RIKEN Center for Life Science Technologies;
- 3 RIKEN Preventive Medicine and Diagnosis Innovation Program;
- 4 RIKEN Omics Science Center;
- 5 Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia;
- 6 RIKEN Preventive Medicine and Diagnosis Innovation Program, RIKEN Omics Science Center;
- 7 Karolinska Institutet, University of Helsinki, Folkhälsan Research Center
Abstract
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 had a strong preference to produce either long or short capped RNAs, with 1 out of 6 peaks detected in the short capped RNA libraries only. Gene-associated short capped RNAs had highly specific 3' ends, typically overlapping splice sites. Enhancers also preferentially generated either short or long capped RNAs, with 10% of enhancers observed in the short capped RNA libraries only. Both enhancers producing short or long capped RNAs showed 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.
- Received January 28, 2022.
- Accepted August 9, 2022.
- Published by Cold Spring Harbor Laboratory Press
This manuscript is Open Access.
This article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International license), as described at http://creativecommons.org/licenses/by/4.0/.
