التفاصيل البيبلوغرافية
| العنوان: |
Deep sequencing of short capped RNAs reveals novel families of noncoding RNAs |
| المؤلفون: |
de Hoon, Michiel, Bonetti, Alessandro, Plessy, Charles, Ando, Yoshinari, Hon, Chung-Chau, Ishizu, Yuri, Itoh, Masayoshi, Kato, Sachi, Lin, Dongyan, Maekawa, Sho, Murata, Mitsuyoshi, Nishiyori, Hiromi, Shin, Jay W., Stolte, Jens, Suzuki, Ana Maria, Tagami, Michihira, Takahashi, Hazuki, Forrest, Alistair R. R., Hayashizaki, Yoshihide, Kere, Juha, Carninci, Piero, Thongjuea, Supat |
| المساهمون: |
STEMM - Stem Cells and Metabolism Research Program, Juha Kere / Principal Investigator, Research Programs Unit, HUS Helsinki and Uusimaa Hospital District |
| بيانات النشر: |
Cold Spring Harbor Laboratory in association with the Genetical Society of Great Britain |
| سنة النشر: |
2023 |
| المجموعة: |
Helsingfors Universitet: HELDA – Helsingin yliopiston digitaalinen arkisto |
| مصطلحات موضوعية: |
ANALYSIS GENE-EXPRESSION, POL II, TRANSCRIPTION, DATABASE, ARCHIVE, ATLAS, Biochemistry, cell and molecular biology, Medical biotechnology, Biomedicine |
| الوصف: |
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. ; Peer reviewed |
| نوع الوثيقة: |
article in journal/newspaper |
| وصف الملف: |
application/pdf |
| اللغة: |
English |
| Relation: |
This work was supported by a grant-in-aid for Young Scientists B from the Japan Society for the Promotion of Science (JSPS KAKENHI grant number JP23710222) to M.d.H., a Research Grant from the Ministry of Education, Culture, Sports, Science and Technology (MEXT) for the RIKEN Omics Science Center, a Research Grant from MEXT for the RIKEN Center for Life Science Technologies, and a Research Grant from MEXT for the RIKEN Center for Integrative Medical Sciences.; de Hoon , M , Bonetti , A , Plessy , C , Ando , Y , Hon , C-C , Ishizu , Y , Itoh , M , Kato , S , Lin , D , Maekawa , S , Murata , M , Nishiyori , H , Shin , J W , Stolte , J , Suzuki , A M , Tagami , M , Takahashi , H , Forrest , A R R , Hayashizaki , Y , Kere , J , Carninci , P & Thongjuea , S 2022 , ' Deep sequencing of short capped RNAs reveals novel families of noncoding RNAs ' , Genome Research , vol. 32 , no. 9 , pp. 1727-1735 . https://doi.org/10.1101/gr.276647.122; http://hdl.handle.net/10138/358260; 0f37a116-e354-4710-b4f9-b9813fcd5baf; 000863738800007 |
| الاتاحة: |
http://hdl.handle.net/10138/358260 |
| Rights: |
cc_by_nc ; info:eu-repo/semantics/openAccess ; openAccess |
| رقم الانضمام: |
edsbas.B4F60B74 |
| قاعدة البيانات: |
BASE |