An improved method for the highly specific detection of transcription start sites-Reference-Cited by-同舟云学术

An improved method for the highly specific detection of transcription start sites

Published:2023-11-22 Issue:2 Volume:52 Page:e7-e7
ISSN:0305-1048
Container-title:Nucleic Acids Research
language:en
Short-container-title:

Author:

Seki Masahide¹^ORCID,Kuze Yuta¹,Zhang Xiang²,Kurotani Ken-ichi³,Notaguchi Michitaka³⁴⁵,Nishio Haruki⁶^ORCID,Kudoh Hiroshi⁷,Suzaki Takuya⁸⁹^ORCID,Yoshida Satoko²^ORCID,Sugano Sumio¹⁰¹¹,Matsushita Tomonao⁴^ORCID,Suzuki Yutaka¹

Affiliation:

1. Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo , Chiba , Japan

2. Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology , Nara , Japan

3. Bioscience and Biotechnology Center, Nagoya University , Aichi , Japan

4. Department of Botany, Graduate School of Science, Kyoto University , Kyoto , Japan

5. Graduate School of Bioagricultural Sciences, Nagoya University , Aichi , Nagoya , Japan

6. Data Science and AI Innovation Research Promotion Center, Shiga University , Shiga , Japan

7. Center for Ecological Research, Kyoto University , Shiga , Japan

8. Faculty of Life and Environmental Sciences, University of Tsukuba , Ibaraki , Japan

9. Tsukuba Plant-Innovation Research Center, University of Tsukuba , Ibaraki , Japan

10. Institute of Kashiwa-no-ha Omics Gate , Chiba , Japan

11. Future Medicine Education and Research Organization, Chiba University , Chiba , Japan

Abstract

Abstract Precise detection of the transcriptional start site (TSS) is a key for characterizing transcriptional regulation of genes and for annotation of newly sequenced genomes. Here, we describe the development of an improved method, designated ‘TSS-seq2.’ This method is an iterative improvement of TSS-seq, a previously published enzymatic cap-structure conversion method to detect TSSs in base sequences. By modifying the original procedure, including by introducing split ligation at the key cap-selection step, the yield and the accuracy of the reaction has been substantially improved. For example, TSS-seq2 can be conducted using as little as 5 ng of total RNA with an overall accuracy of 96%; this yield a less-biased and more precise detection of TSS. We then applied TSS-seq2 for TSS analysis of four plant species that had not yet been analyzed by any previous TSS method.

Funder

MEXT

KAKENHI

Publisher

Oxford University Press (OUP)

Subject

Genetics

Link

https://academic.oup.com/nar/article-pdf/52/2/e7/56418912/gkad1116.pdf

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