A swine SINE (PRE-1 sequence) distribution in swine-related animal species and its phylogenetic analysis in swine genome

Origin, evolution, and tissue-specific functions of the porcine repetitive element 1

Background

The porcine repetitive element 1 (PRE1) is the most abundant short interspersed nuclear element (SINE) in the Sus scrofa genome and it has been suggested that some PRE1 can have regulatory functions. The million copies of PRE1 in the porcine genome have accumulated abundant CpG dinucleotides and unique structural variations, such as direct repeats and patterns of sequence degeneration. The aims of this study were to analyse these structural variations to trace the origin and evolutionary pattern of PRE1 and to investigate potential methylation-related functions of PRE1 based on methylation patterns of PRE1 CpG dinucleotides in different tissues.

Results

We investigated the evolutionary trajectory of PRE1 and found that PRE1 originated from the ancestral CHRS-S1 family through three main successive partial duplications. We found that the partial duplications and deletions of PRE1 were likely due to RNA splicing events during retrotransposition. Functionally, correlation analysis showed that the methylation levels of 103 and 261 proximal PRE1 were, respectively, negatively and positively correlated with the expression levels of neighboring genes (Spearman correlation, P < 0.01). Further epigenomic analysis revealed that, in the testis, demethylation of proximal PRE1 in the HORMAD1 and HACD3 genes had tissue-specific enhancer and promoter functions, while in the muscle, methylation of proximal PRE1 repeats in the TCEA3 gene had an enhancer function.

Conclusions

The characteristic sequences of PRE1 reflect unique patterns of origin and evolution and provide a structural basis for diverse regulatory functions.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12711-022-00745-3.

The sequence and analysis of a Chinese pig genome

Background

The pig is an economically important food source, amounting to approximately 40% of all meat consumed worldwide. Pigs also serve as an important model organism because of their similarity to humans at the anatomical, physiological and genetic level, making them very useful for studying a variety of human diseases. A pig strain of particular interest is the miniature pig, specifically the Wuzhishan pig (WZSP), as it has been extensively inbred. Its high level of homozygosity offers increased ease for selective breeding for specific traits and a more straightforward understanding of the genetic changes that underlie its biological characteristics. WZSP also serves as a promising means for applications in surgery, tissue engineering, and xenotransplantation. Here, we report the sequencing and analysis of an inbreeding WZSP genome.

Results

Our results reveal some unique genomic features, including a relatively high level of homozygosity in the diploid genome, an unusual distribution of heterozygosity, an over-representation of tRNA-derived transposable elements, a small amount of porcine endogenous retrovirus, and a lack of type C retroviruses. In addition, we carried out systematic research on gene evolution, together with a detailed investigation of the counterparts of human drug target genes.

Conclusion

Our results provide the opportunity to more clearly define the genomic character of pig, which could enhance our ability to create more useful pig models.

A SINE insertion causes the black-and-tan and saddle tan phenotypes in domestic dogs

Agouti Signaling Protein (ASIP) controls the localized expression of red and black pigment in the domestic dog through interaction with other genes, such as Melanocortin 1 Receptor and Beta-Defensin 103. Specific ASIP alleles are necessary for many of the coat color patterns, such as black-and-tan and saddle tan. Mutations in 2 ASIP alleles, a(y) and a, have previously been identified. Here, we characterize a mutation consisting of a short interspersed nuclear element (SINE) insertion in intron 1 of ASIP that allows for the differentiation of the a(w) wolf sable and a(t) black-and-tan alleles. The SINE insertion is present in dogs with the a(t) and a alleles but absent from dogs with the a(w) and a(y) alleles. Dogs with the saddle tan phenotype were all a(t)/a(t). Schnauzers were all a(w)/a(w). Genotypes of 201 dogs of 35 breeds suggest that there are only 4 ASIP alleles, as opposed to the 5 or 6 predicted in previous literature. These data demonstrate that the dominance hierarchy of ASIP is a(y) > a(w) > a(t) > a.

PCR amplification of repetitive sequences as a possible approach in relative species quantification

Both relative and absolute quantifications are possible in species quantification when single copy genomic DNA is used. However, amplification of single copy genomic DNA does not allow a limit of detection as low as one obtained from amplification of repetitive sequences. Amplification of repetitive sequences is therefore frequently used in absolute quantification but problems occur in relative quantification as the number of repetitive sequences is unknown. A promising approach was developed where data from amplification of repetitive sequences were used in relative quantification of species in binary mixtures. PCR LUX primers were designed that amplify repetitive and single copy sequences to establish the species dependent number (constants) (SDC) of amplified repetitive sequences per genome. The SDCs and data from amplification of repetitive sequences were tested for their applicability to relatively quantify the amount of chicken DNA in a binary mixture of chicken DNA and pig DNA. However, the designed PCR primers lack the specificity required for regulatory species control.

Genomic gems: SINE RNAs regulate mRNA production

Mammalian short interspersed elements (SINEs) are abundant retrotransposons that have long been considered junk DNA; however, RNAs transcribed from mouse B2 and human Alu SINEs have recently been found to control mRNA production at multiple levels. Upon cell stress B2 and Alu RNAs bind RNA polymerase II (Pol II) and repress transcription of some protein-encoding genes. Bi-directional transcription of a B2 SINE establishes a boundary that places the growth hormone locus in a permissive chromatin state during mouse development. Alu RNAs embedded in Pol II transcripts can promote evolution and proteome diversity through exonization via alternative splicing. Given the diverse means by which SINE encoded RNAs impact production of mRNAs, this genomic junk is proving to contain hidden gems.

Mobile element-based forensic genomics

Mobile elements are commonly referred to as selfish repetitive DNA sequences. However, mobile elements represent a unique and underutilized group of molecular markers. Several of their characteristics make them ideally suited for use as tools in forensic genomic applications. These include their nature as essentially homoplasy-free characters, they are identical by descent, the ancestral state of any insertion is known to be the absence of the element, and many mobile element insertions are lineage specific. In this review, we provide an overview of mobile element biology and describe the application of certain mobile elements, especially the SINEs and other retrotransposons, to forensic genomics. These tools include quantitative species-specific DNA detection, analysis of complex biomaterials, and the inference of geographic origin of human DNA samples.

Quantitative intra-short interspersed element PCR for species-specific DNA identification

We have designed and evaluated four assays based upon PCR amplification of short interspersed elements (SINEs) for species-specific detection and quantitation of bovine, porcine, chicken, and ruminant DNA. The need for these types of approaches has increased drastically in response to the bovine spongiform encephalopathy epidemic. Using SYBR Green-based detection, the minimum effective quantitation levels were 0.1, 0.01, 5, and 1 pg of starting DNA template using our bovine, porcine, chicken, and ruminant species-specific SINE-based PCR assays, respectively. Background cross-amplification with DNA templates derived from 14 other species was negligible. Species specificity of the PCR amplicons was further demonstrated by the ability of the assays to accurately detect trace quantities of species-specific DNA from mixed (complex) sources. Bovine DNA was detected at 0.005% (0.5 pg), porcine DNA was detected at 0.0005% (0.05 pg), and chicken DNA was detected at 0.05% (5 pg) in a 10-ng mixture of bovine, porcine, and chicken DNA templates. We also tested six commercially purchased meat products using these assays. The SINE-based PCR methods we report here are species-specific, are highly sensitive, and will improve the detection limits for DNA sequences derived from these species.

Phylogenetic information in inter-SINE and inter-SSR fingerprints of the artiodactyla and evolution of the bov-tA SINE

Various interspersed repeated sequences and elements (IRSs) can be utilized to generate PCR-based multilocus fingerprint profiles by amplifying the interelement segments, using primers matching the elements themselves. We assessed the utility of inter-IRS fingerprinting in phylogenetic comparisons among six artiodactyl species using several primers derived from two abundant genomic components: the Bov-tA short interspersed nuclear elements (SINEs) and simple sequence repeats or microsatellites (SSRs). Character- and distance-based analyses of the fingerprint data produced trees conforming to the established phylogenetic relationships of species. The strength of phylogenetic signal from different primers varied; combining data from different experiments resulted in robust trees. Within the Cervidae, the hierarchical relationship [(Odocoileus, Rangifer) Alces] was strongly supported. Both methods appear useful tools for systematic studies at time scales <30 Myr. To elucidate the material basis of inter-SINE fingerprints, we obtained the first sequences of the 'bovid' Bov-tA element also from two cervids (reindeer and white-tailed deer) and analysed their relationship to a number of paralogous bovid elements. The differences among sequences, both intra- and interspecific, were relatively high (mean 18.5%); the sequences showed no clear clustering with the species from which they had been isolated. Most individual elements probably date back to the cervid-bovid ancestor >25 Myr ago, which is in line with the observed fingerprint distributions.

Conserved nucleotide differences and subfamily structure of porcine short interspersed elements

Interspersed elements are ubiquitous in the genomes of higher eukaryotes and account for over a third of the genomic DNA (Smit 1996). In swine the short interspersed elements, SINEs or PREs (porcine repetitive elements), have been found in a number of introns and 3' untranslated regions of different genes. However, compared to human Alu repeats the number of available PRE DNA sequences is still limited. In this study we have compared 85 PREs selected from DNA sequence database entries. The PREs were aligned and for each nucleotide position the relative frequencies of the four bases were calculated. A consensus sequence was derived from the first base usage. Similar to studies of SINEs in other species, the analysis showed that most mutations in PREs occur at CpG dinucleotide hot spots. The position variability for the two most frequent bases shows a bimodal distribution. The analysis suggests that the porcine SINEs can be divided into three major subfamilies sharing conserved nucleotide similarities.

Artiodactyl interspersed DNA repeats in cetacean genomes

Interspersed repeats that emerged at different evolutionary times are informative in mammalian phylogeny. Here we show that the ancient short interspersed elements (SINEs) ARE1 and ARE2 are abundantly present in the genomes of artiodactyls and cetaceans but not in other mammalian genomes. This supports the classification of the cetaceans with the artiodactyls by a shared character that is unlikely to be the result of convergence.