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

Authors :
Seki M
Kuze Y
Zhang X
Kurotani KI
Notaguchi M
Nishio H
Kudoh H
Suzaki T
Yoshida S
Sugano S
Matsushita T
Suzuki Y
Source :
Nucleic acids research [Nucleic Acids Res] 2024 Jan 25; Vol. 52 (2), pp. e7.
Publication Year :
2024

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.<br /> (© The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Details

Language :
English
ISSN :
1362-4962
Volume :
52
Issue :
2
Database :
MEDLINE
Journal :
Nucleic acids research
Publication Type :
Academic Journal
Accession number :
37994784
Full Text :
https://doi.org/10.1093/nar/gkad1116