Evidence map›Paper›PMID 39582787›Full record

ArticleFrontiers in genetics2024

Analysis of cis-regulatory changes underlying phenotype divergence shaped by domestication in pigs.

Chunpeng Liu, Na Ao, Yuwen Liang, Tingting Ma, Qishan Wang, Zhen Wang, Fen Wu, Zhenyang Zhang, Yifei Fang, Minghui Wang and 2 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Frontiers in genetics, 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.

  1. Single nucleotide variations in theFrontiers in veterinary science · 2025
    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

12 authors.

Chunpeng Liu *College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, China.
Na Ao *College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, China.
Yuwen Liang *College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, China.
Tingting MaCollege of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, China.
Qishan WangCollege of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China.
Zhen WangCollege of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China.
Fen WuCollege of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China.
Zhenyang ZhangCollege of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China.
Yifei FangDepartment of Animal Science, Cornell University, Ithaca, NY, United States.
Minghui WangCenter for Life Science Ventures, Cornell University, Ithaca, NY, United States.
Yuchun PanCollege of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China.
Jing FuCollege of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, China.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Background: Cis-regulatory elements (CREs) are regions of DNA that regulate the expression of nearby genes. Changes in these elements can lead to phenotypic variations and adaptations in different populations. However, the regulatory dynamics underlying the local adaptation of traits remain poorly understood in Chinese and Western pigs. By comparing the chromatin accessibility profiles of skeletal muscle, liver, and fat between these two pig populations, we aimed to identify key regulatory elements that could explain phenotypic differences observed between the two groups. Results: Our results revealed that the genome-wide chromatin accessibility profiles were largely similar at a qualitative level within tissues. However, we also identified local regions that exhibited quantitative differences, most of which occurred in liver tissue. Interestingly, we found that most of the increased chromatin accessibility in the livers of Chinese pigs was associated with tissue-specific openness. Furthermore, we observed a positive correlation between the ATAC-seq signal at the transcript start site (TSS) and the expression levels of nearby genes. Motif enrichment analysis revealed Conclusion: Overall, our study provides valuable insights into the regulatory dynamics underlying phenotypic variation in pigs. By elucidating the role of CREs in driving phenotypic variation, we can better understand the genetic basis of complex traits and potentially identify targets for genetic improvement in livestock breeding programs.

Indexed as

allelic frequencyATAC-seqchromatin accessibilitycis-regulatory elementpig

Identifiers

PMID39582787
PMCPMC11581869

What Socratic holds

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Registered trials

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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 Socratic graph.