Evidence map›Paper›PMID 39565284›Full record

ArticleJournal of animal science2024

Alternative polyadenylation landscape of longissimus dorsi muscle with high and low intramuscular fat content in cattle.

Chenglong Li, Junjie Xu, Yanfeng Zhang, Yanling Ding, Xiaonan Zhou, Zonghua Su, Chang Qu, Jiahao Liang, Yurun Han, Dingxiang Wang and 4 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Journal of animal science, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing 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

2 citing papers in PubMed.

  1. Article
  2. 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

14 authors.

Chenglong LiKey Laboratory of Ruminant Molecular and Cellular Breeding, College of Animal Science and Technology, Ningxia University, Yinchuan, China.
Junjie XuKey Laboratory of Ruminant Molecular and Cellular Breeding, College of Animal Science and Technology, Ningxia University, Yinchuan, China.
Yanfeng ZhangKey Laboratory of Ruminant Molecular and Cellular Breeding, College of Animal Science and Technology, Ningxia University, Yinchuan, China.
Yanling DingKey Laboratory of Ruminant Molecular and Cellular Breeding, College of Animal Science and Technology, Ningxia University, Yinchuan, China.
Xiaonan ZhouKey Laboratory of Ruminant Molecular and Cellular Breeding, College of Animal Science and Technology, Ningxia University, Yinchuan, China.
Zonghua SuKey Laboratory of Ruminant Molecular and Cellular Breeding, College of Animal Science and Technology, Ningxia University, Yinchuan, China.
Chang QuKey Laboratory of Ruminant Molecular and Cellular Breeding, College of Animal Science and Technology, Ningxia University, Yinchuan, China.
Jiahao LiangKey Laboratory of Ruminant Molecular and Cellular Breeding, College of Animal Science and Technology, Ningxia University, Yinchuan, China.
Yurun HanKey Laboratory of Ruminant Molecular and Cellular Breeding, College of Animal Science and Technology, Ningxia University, Yinchuan, China.
Dingxiang WangKey Laboratory of Ruminant Molecular and Cellular Breeding, College of Animal Science and Technology, Ningxia University, Yinchuan, China.
Yuangang ShiKey Laboratory of Ruminant Molecular and Cellular Breeding, College of Animal Science and Technology, Ningxia University, Yinchuan, China.
Cong-Jun LiAnimal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD 20705, USA.
George E LiuAnimal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD 20705, USA.
Xiaolong KangKey Laboratory of Ruminant Molecular and Cellular Breeding, College of Animal Science and Technology, Ningxia University, Yinchuan, China.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Intramuscular fat content is one of the most important factors affecting beef quality. However, the role of alternative polyadenylation (APA) in intramuscular fat deposition remains unclear. We compared APA events in muscle samples from high and low intramuscular fat (IMF) cattle, based on RNA-seq data. A total of 363 significant APAs were identified. Notably, the number of shortened 3'UTR events exceeded the number of lengthened 3'UTR events, and genes associated with shortened 3'UTR events were enriched in fatty acid metabolism-related pathways. Most APA events had alternative 3'UTR (aUTR) lengths of 200 to 300 bp. As the 3'UTR lengthened, the aUTR also lengthened (R2 = 0.79). These findings indicate that genes with longer 3'UTRs are more likely to be regulated by APA in the muscle of cattle with high IMF. To determine whether the identified APA events drove alterations in the expression of fat deposition-related genes, we analyzed the relationship between APA events and differentially expressed genes and identified several genes critical for fat deposition (e.g., PFKL and SLC1A5). Since miRNAs usually bind to the 3'UTR region of protein-coding genes and affect gene expression, we constructed an miRNA-APA network to detect several key miRNAs that may regulate fat deposition. We identified 10 important miRNAs that affect changes in IMF content, which may be gained (gained miRNA-binding sites) or lost (lost miRNA-binding sites) owing to 187 differential APA events. Our study characterized the APA profiles of cattle with high and low intramuscular fat content and provided further insights into the relationship between APA, miRNA, and fat deposition.

Indexed as

3' Untranslated RegionsMuscle, SkeletalPolyadenylationAdipose TissueAnimalsCattleGene Expression RegulationMicroRNAs3' Untranslated RegionsMicroRNAs3ʹUTRalternative polyadenylationcattleintramuscular fatmiRNA

Identifiers

PMID39565284
PMCPMC11641427

What Socratic 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 Socratic graph.