Evidence map›Paper›PMID 39349998›Full record

ArticleBMC genomics2024

Differential chromatin accessibility and Gene Expression Associated with Backfat Deposition in pigs.

Zhe Zhang, Lebin Chang, Bingjie Wang, Yilin Wei, Xinjian Li, Xiuling Li, Yongqian Zhang, Kejun Wang, Ruimin Qiao, Feng Yang and 2 more

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PubMed Full text at PMC Publisher
In one paragraph

Article in BMC genomics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing 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

3 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

12 authors.

Zhe ZhangCollege of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China.
Lebin ChangCollege of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China.
Bingjie WangCollege of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China.
Yilin WeiCollege of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China.
Xinjian LiCollege of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China.
Xiuling LiCollege of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China.
Yongqian ZhangHenan Yifa Animal Husbandry Co., Ltd, Hebi, 458000, China.
Kejun WangCollege of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China.
Ruimin QiaoCollege of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China.
Feng YangCollege of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China.
Tong YuCollege of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China.
Xuelei HanCollege of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China. hxl014@126.com.

Funding

14th Five-Year National Key R&D Program 2021YFD1301202Biological Breeding-Major Projects in National Science and Technology 2023ZD0404604the Agricultural Breeds Research Project of Henan Province 2022020101
6 · The paper itself

Abstract

backgroundBackfat serves as a vital fat reservoir in pigs, and its excessive accumulation will adversely impact pig growth performance, farming efficiency, and pork quality. The aim of this research is to integrate assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) and RNA sequencing (RNA-seq) to explore the molecular mechanisms underlying porcine backfat deposition.

resultsATAC-seq analysis identified 568 genes originating from 698 regions exhibiting differential accessibility, which were significantly enriched in pathways pertinent to adipocyte differentiation and lipid metabolism. Besides, a total of 283 transcription factors (TFs) were identified by motif analysis. RNA-seq analysis revealed 978 differentially expressed genes (DEGs), which were enriched in pathways related to energy metabolism, cell cycle and signal transduction. The integration of ATAC-seq and RNA-seq data indicates that DEG expression levels are associated with chromatin accessibility. This comprehensive study highlights the involvement of critical pathways, including the Wnt signaling pathway, Jak-STAT signaling pathway, and fatty acid degradation, in the regulation of backfat deposition. Through rigorous analysis, we identified several candidate genes (LEP, CTBP2, EHHADH, OSMR, TCF7L2, BCL2, FGF1, UCP2, CCND1, TIMP1, and VDR) as potentially significant contributors to backfat deposition. Additionally, we constructed TF-TF and TF-target gene regulatory networks and identified a series of potential TFs related to backfat deposition (FOS, STAT3, SMAD3, and ESR1).

conclusionsThis study represents the first application of ATAC-seq and RNA-seq, affording a novel perspective into the mechanisms underlying backfat deposition and providing invaluable resources for the enhancement of pig breeding programs.

Indexed as

ChromatinAdipose TissueAnimalsGene Expression ProfilingGene Expression RegulationHigh-Throughput Nucleotide SequencingRNA-SeqSwineTranscription FactorsChromatinTranscription FactorsATAC-seqBackfat depositionDuroc PigRegulatory mechanismsRNA-seqYunong Black Pig

Identifiers

PMID39349998
PMCPMC11441165

What OpenQuestion holds

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LicenceCC BY-NC-ND
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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 OpenQuestion graph.