Evidence map›Paper›PMID 37994784›Full record

ArticleNucleic acids research2024

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

Masahide Seki, Yuta Kuze, Xiang Zhang, Ken-Ichi Kurotani, Michitaka Notaguchi, Haruki Nishio, Hiroshi Kudoh, Takuya Suzaki, Satoko Yoshida, Sumio Sugano and 2 more

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nucleic acids research, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
0.2field-weighted citation impact, top 40% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed, 1 citations in OpenAlex.

  1. Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

12 authors at 7 institutions in 1 country.

Masahide SekiDepartment of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan.ORCID 0000-0001-6091-8698
Yuta KuzeDepartment of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan.
Xiang ZhangDivision of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Nara, Japan.
Ken-Ichi KurotaniBioscience and Biotechnology Center, Nagoya University, Aichi, Japan.
Michitaka NotaguchiBioscience and Biotechnology Center, Nagoya University, Aichi, Japan.
Haruki NishioData Science and AI Innovation Research Promotion Center, Shiga University, Shiga, Japan.ORCID 0000-0002-6124-782X
Hiroshi KudohCenter for Ecological Research, Kyoto University, Shiga, Japan.
Takuya SuzakiFaculty of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan.ORCID 0000-0001-9646-0279
Satoko YoshidaDivision of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Nara, Japan.ORCID 0000-0002-9999-7861
Sumio SuganoInstitute of Kashiwa-no-ha Omics Gate, Chiba, Japan.
Tomonao MatsushitaDepartment of Botany, Graduate School of Science, Kyoto University, Kyoto, Japan.ORCID 0000-0002-7735-8567
Yutaka SuzukiDepartment of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan.
Kyoto University · JPThe University of Tokyo · JPNara Institute of Science and Technology · JPChiba University · JPNagoya University · JPShiga University · JPUniversity of Tsukuba · JP

Funding

KAKENHIMEXT JP20H05905
6 · The paper itself

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.

Indexed as

Sequence Analysis, RNATranscription Initiation SiteBase SequenceGene Expression RegulationPromoter Regions, Genetic

Identifiers

PMID37994784
PMCPMC10810191
OpenAlexW4388939596

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.