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RNA-seq profiling reveals differentially expressed genes as potential markers for vital reaction in skin contusion: a pilot study.

ABSTRACT: Detection of the vitality of wounds is essential in forensic practice. The present study used Illumina RNA-seq technology to determine gene expression profiles in contused mouse skin. In obtained high quality sequencing reads, the reads were mapped onto a reference transcriptome (Mus_musculus.GRCm38.83). The results revealed that there were 659 up-regulated and 996 down-regulated differentially expressed genes (DEGs) in contused mouse skin. The DEGs were further analyzed using the Gene Ontology and the Kyoto Encyclopedia of Genes and Genomes databases. Genes from different functional categories and signalling pathways were enriched, including the immune system process, immune response, defense response, cytokine-cytokine receptor interaction, complement and coagulation cascades and chemokine signalling pathway. Expression patterns of 11 DEGs were verified by RT-qPCR in mice skins. In addition, alterations of five DEGs were also analyzed in postmortem human wound samples. The results were in concordance with the results of RNA-seq. These findings suggest that RNA-seq is a powerful tool to reveal DEGs as potential markers for vital reaction in terms of forensic practices.

SUBMITTER: Xu J

PROVIDER: S-EPMC6197083 | biostudies-other | 2018

REPOSITORIES: biostudies-other

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RNA-seq profiling reveals differentially expressed genes as potential markers for vital reaction in skin contusion: a pilot study.

Xu Jingtao J Zhao Rui R Xue Ye Y Xiao Huanqin H Sheng Yanliang Y Zhao Dong D He Jietao J Huang Hongyan H Wang Qi Q Wang Huijun H

Forensic sciences research 20170718 2

Detection of the vitality of wounds is essential in forensic practice. The present study used Illumina RNA-seq technology to determine gene expression profiles in contused mouse skin. In obtained high quality sequencing reads, the reads were mapped onto a reference transcriptome (Mus_musculus.GRCm38.83). The results revealed that there were 659 up-regulated and 996 down-regulated differentially expressed genes (DEGs) in contused mouse skin. The DEGs were further analyzed using the Gene Ontology ...[more]

PMID: 30483664

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Project description:BackgroundNowadays, both customers and producers prefer thin-tailed fat sheep. To effectively breed for this phenotype, it is important to identify candidate genes and uncover the genetic mechanism related to tail fat deposition in sheep. Accumulating evidence suggesting that post-transcriptional modification events of precursor-messenger RNA (pre-mRNA), including alternative splicing (AS) and alternative polyadenylation (APA), may regulate tail fat deposition in sheep. Differentially expressed transcripts (DETs) analysis is a way to identify candidate genes related to tail fat deposition. However, due to the technological limitation, post-transcriptional modification events in the tail fat of sheep and DETs between thin-tailed and fat-tailed sheep remains unclear.MethodsIn the present study, we applied pooled PacBio isoform sequencing (Iso-Seq) to generate transcriptomic data of tail fat tissue from six sheep (three thin-tailed sheep and three fat-tailed sheep). By comparing with reference genome, potential gene loci and novel transcripts were identified. Post-transcriptional modification events, including AS and APA, and lncRNA in sheep tail fat were uncovered using pooled Iso-Seq data. Combining Iso-Seq data with six RNA-sequencing (RNA-Seq) data, DETs between thin- and fat-tailed sheep were identified. Protein protein interaction (PPI) network, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were implemented to investigate the potential functions of DETs.ResultsIn the present study, we revealed the transcriptomic complexity of the tail fat of sheep, result in 9,001 potential novel gene loci, 17,834 AS events, 5,791 APA events, and 3,764 lncRNAs. Combining Iso-Seq data with RNA-Seq data, we identified hundreds of DETs between thin- and fat-tailed sheep. Among them, 21 differentially expressed lncRNAs, such as ENSOART00020036299, ENSOART00020033641, ENSOART00020024562, ENSOART00020003848 and 9.53.1 may regulate tail fat deposition. Many novel transcripts were identified as DETs, including 15.527.13 (DGAT2), 13.624.23 (ACSS2), 11.689.28 (ACLY), 11.689.18 (ACLY), 11.689.14 (ACLY), 11.660.12 (ACLY), 22.289.6 (SCD), 22.289.3 (SCD) and 22.289.14 (SCD). Most of the identified DETs have been enriched in GO and KEGG pathways related to extracellular matrix (ECM). Our result revealed the transcriptome complexity and identified many candidate transcripts in tail fat, which could enhance the understanding of molecular mechanisms behind tail fat deposition.

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RNA-seq profiling reveals differentially expressed genes as potential markers for vital reaction in skin contusion: a pilot study.

Publications

RNA-seq profiling reveals differentially expressed genes as potential markers for vital reaction in skin contusion: a pilot study.

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