Evidence map›Paper›PMID 29409445›Full record

ArticleBMC genomics2018

Integrative analysis of methylomic and transcriptomic data in fetal sheep muscle tissues in response to maternal diet during pregnancy.

Hadjer Namous, Francisco Peñagaricano, Marcello Del Corvo, Emanuele Capra, David L Thomas, Alessandra Stella, John L Williams, Paolo Ajmone Marsan, Hasan Khatib

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

Article in BMC genomics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
19citing papers in PubMed, 1 pooled it
1.4field-weighted citation impact, top 19% 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

19 citing papers in PubMed, 1 synthesis or guideline pooled it, 45 citations in OpenAlex.

  1. Pooled it
  2. Review
  3. Article
  4. Article
  5. Article
  6. Pan-Omics in Sheep: Unveiling Genetic Landscapes.Animals : an open access journal from MDPI · 2024
    Review
  7. Article
  8. Article
  9. Article
  10. Article
  11. Article
  12. Article
  13. Article
  14. Article
  15. Article
  16. Article
  17. Article
  18. Article
  19. 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

9 authors at 5 institutions in 3 countries.

Hadjer NamousDepartment of Animal Sciences, University of Wisconsin, 1675 Observatory Drive, Madison, WI, 53706, USA.
Francisco PeñagaricanoDepartment of Animal Sciences, University of Florida Genetics Institute, University of Florida, Florida, USA.
Marcello Del CorvoInstitute of Zootechnics and PRONUTRIGEN Research Center, Faculty of Agricultural, Food and Environmental Sciences, Università Cattolica del S. Cuore, Piacenza, Italy.
Emanuele CapraIstituto di Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche, Lodi, Italy.
David L ThomasDepartment of Animal Sciences, University of Wisconsin, 1675 Observatory Drive, Madison, WI, 53706, USA.
Alessandra StellaIstituto di Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche, Lodi, Italy.
John L WilliamsDavies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, Australia.
Paolo Ajmone MarsanInstitute of Zootechnics and PRONUTRIGEN Research Center, Faculty of Agricultural, Food and Environmental Sciences, Università Cattolica del S. Cuore, Piacenza, Italy.
Hasan KhatibDepartment of Animal Sciences, University of Wisconsin, 1675 Observatory Drive, Madison, WI, 53706, USA. hkhatib@wisc.edu.
University of Wisconsin–Madison · USIstituto di Biologia e Biotecnologia Agraria · ITUniversità Cattolica del Sacro Cuore · ITUniversity of Adelaide · AUUniversity of Florida · US

Funding

College of Agricultural and Life Sciences AAA3936
6 · The paper itself

Abstract

backgroundNumerous studies have established a link between maternal diet and the physiological and metabolic phenotypes of their offspring. In previous studies in sheep, we demonstrated that different maternal diets altered the transcriptome of fetal tissues. However, the mechanisms underlying transcriptomic changes are poorly understood. DNA methylation is an epigenetic mark regulating transcription and is largely influenced by dietary components of the one-carbon cycle that generate the methyl group donor, SAM. Therefore, in the present study, we tested whether different maternal diets during pregnancy would alter the DNA methylation and gene expression patterns in fetal tissues.

resultsPregnant ewes were randomly divided into two groups which received either hay or corn diet from mid-gestation (day 67 ± 5) until day 131 ± 1 when fetuses were collected by necropsy. A total of 1516 fetal longissimus dorsi (LD) tissues were used for DNA methylation analysis and gene expression profiling. Whole genome DNA methylation using methyl-binding domain enrichment analysis revealed 60 differentially methylated regions (DMRs) between hay and corn fetuses with 39 DMRs more highly methylated in the hay fetuses vs. 21 DMRs more highly methylated in the corn fetuses. Three DMRs (LPAR3, PLIN5-PLIN4, and the differential methylation of a novel lincRNA) were validated using bisulfite sequencing. These DMRs were associated with differential gene expression. Additionally, significant DNA methylation differences were found at the single CpG level. Integrative methylome and transcriptome analysis revealed an association between gene expression and inter-/intragenic methylated regions. Furthermore, intragenic DMRs were found to be associated with expression of neighboring genes.

conclusionsThe findings of this study imply that maternal diet from mid- to late-gestation can shape the epigenome and the transcriptome of fetal tissues, and putatively affect phenotypes of the lambs.

Indexed as

DietDNA MethylationEpigenesis, GeneticMaternal ExposureTranscriptomeAnimalsComputational BiologyFemaleFetusGene Expression RegulationGenomeLinkage DisequilibriumMusclesPregnancyReproducibility of ResultsSequence Analysis, DNADifferentially-methylated regionDNA methylationGene expressionMaternal diet

Identifiers

PMID29409445
PMCPMC5801776
OpenAlexW2801970373

What OpenQuestion holds

Textmetadata
LicenceCC BY
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 OpenQuestion graph.