Identification and annotation of conserved promoters and macrophage-expressed genes in the pig genome

Abstract

BackgroundThe FANTOM5 consortium used Cap Analysis of Gene Expression (CAGE) tag sequencing to produce a comprehensive atlas of promoters and enhancers within the human and mouse genomes. We reasoned that the mapping of these regulatory elements to the pig genome could provide useful annotation and evidence to support assignment of orthology.ResultsFor human transcription start sites (TSS) associated with annotated human-mouse orthologs, 17% mapped to the pig genome but not to the mouse, 10% mapped only to the mouse, and 55% mapped to both pig and mouse. Around 17% did not map to either species. The mapping percentages were lower where there was not clear orthology relationship, but in every case, mapping to pig was greater than to mouse, and the degree of homology was also greater. Combined mapping of mouse and human CAGE-defined promoters identified at least one putative conserved TSS for >16,000 protein-coding genes. About 54% of the predicted locations of regulatory elements in the pig genome were supported by CAGE and/or RNA-Seq analysis from pig macrophages.ConclusionsComparative mapping of promoters and enhancers from humans and mice can provide useful preliminary annotation of other animal genomes. The data also confirm extensive gain and loss of regulatory elements between species, and the likelihood that pigs provide a better model than mice for human gene regulation and function.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2111-2) contains supplementary material, which is available to authorized users.

Functional Annotation of the Transcriptome of the Pig, Sus scrofa, Based Upon Network Analysis of an RNAseq Transcriptional Atlas

“…In the specific case of the immune system, pigs have provided a useful model for postnatal human development of acquired immunity (Butler et al, 2009); their macrophage-specific gene expression and response to stimulation by toll-like receptor agonists more closely resembles humans than commonly used mouse models (Kapetanovic et al, 2012;Schroder et al, 2012;Kapetanovic et al, 2013). Indeed, better identification of transcription start sites was previously validated by cross-species mapping of the large human FANTOM5 promoter data set (FANTOM Consortium et al, 2014;Robert et al, 2015). The potential for genomic selection and editing for production traits and the utility of the pig as a model organism has recently been expedited by the release of a highly contiguous reference genome (Sscrofa11.1) and parallel sequencing and annotation of a second genome (USMARCv1.0) (Warr et al, 2019).…”

“…Pigs are undoubtedly more human-like than mice (Beiki et al, 2019). Their promoters, identified by cross-mapping of transcription start sites from the human FANTOM5 data set, are more closely related at the DNA sequence level to human (FANTOM Consortium et al, 2014;Robert et al, 2015). But even for those genes for which orthology has been accepted and a gene name assigned, the extent to which expression and function are shared between pigs, humans, and other animals (notably rodent models) remains to be established (Schroder et al, 2012;Jubb et al, 2016).…”

A high-quality annotated transcriptome of swine peripheral blood

“…However, the widely used swine reference genome Sscrofa10.2 (SSC10.2 for short) [20] is neither well-assembled nor well-annotated [21]. For example, only 43% of the 25,510 transcripts of the 21,630 coding genes have both a 5′ and 3′ UTRs defined.…”

Swine blood transcriptomics: Application and advancement

“…However, further study showed that the current version of reference genome is neither well-assembled nor well-annotated [13]. For example, only 43% of the 25,510 transcripts of the 21,630 coding genes have both a 5" and 3" UTRs defined.…”

“…Published CAGE data from pig macrophages [13] were reanalyzed to estimate the proportion of PTs that have complete 5" ends. Briefly, adapter sequences and low quality bases were removed from the raw reads using Trimmomatic (v0.…”