GeF-seq: A Simple Procedure for Base-Pair Resolution ChIP-seq.

Onuma Chumsakul, Kensuke Nakamura, Kazuki Fukamachi, Shu Ishikawa, Taku Oshima

Abstract read

In one paragraph

Article in Methods in molecular biology (Clifton, N.J.), 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

–field-weighted citation impact

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.

Transcriptional Regulation in Bacteria.Microorganisms · 2024
Article

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

5 authors.

Onuma ChumsakulGraduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, Japan.

Kensuke NakamuraDivision of Informatics, Bioengineering and Bioscience, Maebashi Institute of Technology, Maebashi, Gunma, Japan.

Kazuki FukamachiDepartment of Biotechnology, Toyama Prefectural University, Imizu, Toyama, Japan.

Shu IshikawaGraduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, Japan. shu@people.kobe-u.ac.jp.

Taku OshimaGraduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, Japan. taku@pu-toyama.ac.jp.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Nucleotide sequences recognized and bound by DNA-binding proteins (DBPs) are critical to controlling and maintaining gene expression, replication, chromosome segregation, cell division, and nucleoid structure in bacterial cells. Therefore, determination of the binding sequences of DBPs is important not only to study DBP recognition mechanisms but also to understand the fundamentals of cell homeostasis. While ChIP-seq analysis appears to be an effective way to determine DBP binding sites on the genome, the resolution is sometimes not sufficient to identify the sites precisely. Here we introduce a simple and effective method named Genome Footprinting with high-throughput sequencing (GeF-seq) to determine binding sites of DBPs with single base-pair resolution. GeF-seq detects binding sites of DBPs as sharp peaks and thus makes it possible to identify the recognition sequence in each "binding peak" more easily and accurately compared to the common ChIP-seq.

Indexed as

Chromatin Immunoprecipitation SequencingDNA-Binding ProteinsHigh-Throughput Nucleotide SequencingBase PairingBinding SitesDNA FootprintingProtein BindingDNA-Binding ProteinsConsensus sequenceDNA-binding proteinsDNase I footprintingGeF-seqGenome footprintingHigh-resolution ChIP-seq

Identifiers

PMID39028501

DOI10.1007/978-1-0716-3930-6_3

What OpenQuestion holds

Textmetadata

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.