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ARS Home » Plains Area » Clay Center, Nebraska » U.S. Meat Animal Research Center » Genetics and Animal Breeding » Research » Publications at this Location » Publication #364270

Research Project: Identifying Genomic Solutions to Improve Efficiency of Swine Production

Location: Genetics and Animal Breeding

Title: Transcriptome and genome-wide histone modifications in swine fetal liver

item NIU, BUYUE - Iowa State University
item LIU, HAIBO - Iowa State University
item Nonneman, Danny - Dan
item TUGGLE, CHRISTOPHER - Iowa State University

Submitted to: Plant and Animal Genome Conference Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: 12/1/2018
Publication Date: 1/16/2019
Citation: Niu, B., Liu, H., Nonneman, D.J., Tuggle, C.K. 2019. Transcriptome and genome-wide histone modifications in swine fetal liver [abstract]. Plant and Animal Genome Conference Proceedings, San Diego, CA, 12-16 January 2019. pg. 212, PE0420. Available:

Interpretive Summary:

Technical Abstract: Histone modifications play important roles in regulating gene expression; however, they have not been widely studied in swine tissues. The aim of this study was to illustrate the correlation between histone modifications and gene expression in swine fetal liver. Here, to determine gene expression and chromatin modifications, four 70-day fetal liver tissues from a Meishan x White Composite reciprocal crosses were collected and mRNA expression were assessed using Illumina short read sequencing (RNA-seq). Then, chromatin immunoprecipitation for four selected histone markers (H3K4me1, H3K4me3, H3K27me3 and H3K27ac) followed by quantitative-PCR (ChIP-qPCR) and high throughput sequence (ChIP-seq) were performed to analyze the chromatin modifications. RNA-seq data showed 12,508 genes expressed in the fetal liver, by using a minimal cutoff of 0.07 FPKM (equivalent to 1 CPM). Genes highly expressed (RPL30 and FETUB), and genes with undetectable expression (WNT10A) or gene desert regions in the fetal liver were selected as quality controls for ChIP-qPCR assays. ChIP-qPCR results showed that the percentage of H3K4me3 enrichment relative to the input was high at RPL30 (14% in average), whereas the percentage of H3K27me3 enrichment relative to the input was significant at WNT10A loci (3% in average). Additionally, the fold enrichment for H3K4me3 (RPL30/WNT10A), H3K27ac (RPL30/WNT10A), H3K27me3 (WNT10A/RPL30) and H3K4me1 (FETUB/gene desert) were all significant. Integrated RNA-seq and ChIP-seq analysis are ongoing. In conclusion, research in this study will provide association between swine gene expression and chromatin histone modification, which will contribute to the functional annotation of the pig genome.