Evidence map›Paper›PMID 38479837›Full record

ArticleGenome research2024

Haplotype-resolved 3D chromatin architecture of the hybrid pig.

Yu Lin, Jing Li, Yiren Gu, Long Jin, Jingyi Bai, Jiaman Zhang, Yujie Wang, Pengliang Liu, Keren Long, Mengnan He and 27 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Genome research, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.

0numbers the graph read from it
0cells of the map it votes in
8citing 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

8 citing papers in PubMed.

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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

37 authors.

Yu Lin *State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
Jing Li *State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; lijing_2020@sicau.edu.cn tangqianzi@sicau.edu.cn mingzhou.li@sicau.edu.cn.ORCID 0000-0002-8850-454X
Yiren Gu *College of Animal and Veterinary Sciences, Southwest Minzu University, Chengdu 610041, China.
Long Jin *State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
Jingyi BaiState Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
Jiaman ZhangState Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
Yujie WangState Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
Pengliang LiuState Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
Keren LongState Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
Mengnan HeState Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
Diyan LiSchool of Pharmacy, Chengdu University, Chengdu 610106, China.
Can LiuState Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
Ziyin HanState Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
Yu ZhangState Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
Xiaokai LiState Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
Bo ZengState Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
Lu LuState Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
Fanli KongState Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
Ying SunState Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
Yongliang FanState Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
Xun WangState Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
Tao WangSchool of Pharmacy, Chengdu University, Chengdu 610106, China.
An'an JiangState Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
Jideng MaState Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
Linyuan ShenState Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
Li ZhuState Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
Yanzhi JiangState Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
Guoqing TangState Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
Xiaolan FanState Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
Qingyou LiuAnimal Molecular Design and Precise Breeding Key Laboratory of Guangdong Province, School of Life Science and Engineering, Foshan University, Foshan 528225, China.
Hua LiAnimal Molecular Design and Precise Breeding Key Laboratory of Guangdong Province, School of Life Science and Engineering, Foshan University, Foshan 528225, China.
Jinyong WangPig Industry Sciences Key Laboratory of Ministry of Agriculture and Rural Affairs, Chongqing Academy of Animal Sciences, Chongqing 402460, China.
Li ChenPig Industry Sciences Key Laboratory of Ministry of Agriculture and Rural Affairs, Chongqing Academy of Animal Sciences, Chongqing 402460, China.
Liangpeng GePig Industry Sciences Key Laboratory of Ministry of Agriculture and Rural Affairs, Chongqing Academy of Animal Sciences, Chongqing 402460, China.
Xuewei LiState Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
Qianzi TangState Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; lijing_2020@sicau.edu.cn tangqianzi@sicau.edu.cn mingzhou.li@sicau.edu.cn.
Mingzhou LiState Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; lijing_2020@sicau.edu.cn tangqianzi@sicau.edu.cn mingzhou.li@sicau.edu.cn.ORCID 0000-0001-8681-7684

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

In diploid mammals, allele-specific three-dimensional (3D) genome architecture may lead to imbalanced gene expression. Through ultradeep in situ Hi-C sequencing of three representative somatic tissues (liver, skeletal muscle, and brain) from hybrid pigs generated by reciprocal crosses of phenotypically and physiologically divergent Berkshire and Tibetan pigs, we uncover extensive chromatin reorganization between homologous chromosomes across multiple scales. Haplotype-based interrogation of multi-omic data revealed the tissue dependence of 3D chromatin conformation, suggesting that parent-of-origin-specific conformation may drive gene imprinting. We quantify the effects of genetic variations and histone modifications on allelic differences of long-range promoter-enhancer contacts, which likely contribute to the phenotypic differences between the parental pig breeds. We also observe the fine structure of somatically paired homologous chromosomes in the pig genome, which has a functional implication genome-wide. This work illustrates how allele-specific chromatin architecture facilitates concomitant shifts in allele-biased gene expression, as well as the possible consequential phenotypic changes in mammals.

Indexed as

ChromatinChromosomesAnimalsGenomeHaplotypesMammalsSwineChromatin

Identifiers

PMID38479837
PMCPMC10984390

What OpenQuestion holds

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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 OpenQuestion graph.