Evidence map›Paper›PMID 30675136›Full record

ArticleHereditas2019

Global mapping of binding sites for phic31 integrase in transgenic maden-darby bovine kidney cells using ChIP-seq.

Lijuan Qu, Lei Wang, Xueyuan Zhu, Yan Zhang, Qiang Ou, Aying Ma, Fengying Sheng, Xiaoqing Wei, Yue Dai, Guoting Li and 1 more

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

Article in Hereditas, 2019. 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, top 98% 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. Reprogramming Chromosome Ends by Functional Histone Acetylation.International journal of molecular sciences · 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

11 authors at 3 institutions in 1 country.

Lijuan QuDepartment of Laboratory Medicine, Shanghai Eighth People's Hospital, Shanghai, 200040 China.
Lei WangDepartment of Laboratory Medicine, Shanghai Eighth People's Hospital, Shanghai, 200040 China.
Xueyuan ZhuDepartment of Laboratory Medicine, Shanghai Eighth People's Hospital, Shanghai, 200040 China.
Yan ZhangDepartment of Laboratory Medicine, Shanghai Eighth People's Hospital, Shanghai, 200040 China.
Qiang OuDepartment of Laboratory Medicine, Shanghai Eighth People's Hospital, Shanghai, 200040 China.
Aying MaDepartment of Respiratory Medicine, Shanghai First People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 201620 China.
Fengying ShengDepartment of Laboratory Medicine, Shanghai Eighth People's Hospital, Shanghai, 200040 China.
Xiaoqing WeiDepartment of Laboratory Medicine, Shanghai Eighth People's Hospital, Shanghai, 200040 China.
Yue DaiDepartment of Laboratory Medicine, Shanghai Eighth People's Hospital, Shanghai, 200040 China.
Guoting LiLab of Reproductive Pharmacology, NHC Key Lab of Reproduction Regulation, Shanghai Institute of Planned Parenthood Research, Fudan University, Shanghai, 200032 China.
Shuwu XieLab of Reproductive Pharmacology, NHC Key Lab of Reproduction Regulation, Shanghai Institute of Planned Parenthood Research, Fudan University, Shanghai, 200032 China.
Shanghai Eighth People Hospital · CNShanghai Institute of Planned Parenthood Research · CNShanghai First People's Hospital · CN

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

backgroundΦC31 integrase, a site-specific recombinase, can efficiently target attB-bearing transgenes to endogenous pseudo attP sites within mammalian genomes. The sequence features of endogenous binding sites will help us to fully understand the site-specific recognition function by ΦC31 integrase. The present study was aimed to uncover the global map of ΦC31 integrase binding sites in bovine cells and analysis the features of these binding sites by comprehensive bioinformatics methods.

resultsIn this study, we constructed a ChIP-seq method that can be used to uncover the global binding sites by phiC31 integrase. 6740 potential ΦC31 integrase binding sites were identified. A sequence motif was found that contains inverted repeats and has similarities to wild-type attP site. Using REPEATMASKER, we identified a total of 20,183 repeat-regions distributed in 50 repeat types for the 6740 binding sites. These sites enriched in "regulation of GTPase activity" of in the GO category of biological process and KEGG pathway of signal transmembrane transporter activity.

conclusionThis study is the first time to uncover the global map of binding sites for ΦC31 integrase using ChIP-sequencing method and analysis the features of these binding sites. This method will help us to fully understand the mechanism of the site-specific integration function by phiC31 integrase and will potentially boost its genetic manipulations in both gene therapy and generation of transgenic animals.

Indexed as

Binding SitesProtein Interaction MappingAnimalsAnimals, Genetically ModifiedBacteriophagesCattleCell LineChromatin ImmunoprecipitationComputational BiologyIntegrasesIntegrasesBinding sitesChIP-seqSequence motifΦC31 integrase

Identifiers

PMID30675136
PMCPMC6332687
OpenAlexW2929673336

What OpenQuestion holds

Textmetadata
LicenceCC BY
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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.