SINE Insertion in 5’ Flanking of Porcine IGFBP3 May Associated with Gene Expression and Phenotypic Variations

Background: Insulin-like growth factor binding proteins (IGFBPs) have been considered important candidate genes for economic traits due to their involvement in physiological processes related to growth and development. However, most of the current studies on genetic markers of IGFBPs have focused on SNPs, and large fragment insertion mutations such as retrotransposons have rarely been considered.Results: In total twelve retrotransposon insertion polymorphisms (RIPs) were confirmed using bioinformatics prediction combined with the PCR-based amplification. By linkage genetic analysis, IGFBP3-1-RIP and IGFBP3-2-RIP are completely linked, showing only three genotypes, SINE+/+/LINE-/-, SINE-/-/LINE+/+ and SINE+/-/LINE-/+. The age of 100 kg body weight and longissimus muscle thickness of Large white individuals of SINE+/+/LINE-/-genotype were significantly (P<0.05) higher than those of other two genotypes. However, corrected backfat thickness of SINE+/+/LINE-/- individuals were significantly (P<0.05) thinner than those of SINE+/+/LINE-/- genotype. The expression of the IGFBP3 gene in liver and backfat of 30-day Sujiang piglets with SINE+/+/LINE-/- genotype were significantly higher (P<0.05) than those with SINE-/-/LINE+/+ genotype by qPCR. After the core promoter region of the IGFBP3 gene was identified locating within 482bp upstream of ATG by using the dual-luciferase activity assay, further study was conducted to confirm the effect of SINE of IGFBP3-1-RIP and LINE of IGFBP3-2-RIP on the promoter activity of IGFBP3 based on the PGL3-Promoter-Enhancer. The result revealed that only SINE insertion was significantly increased (P<0.05) promoter activity of the IGFBP3 gene, indicating that the SINE may act as an enhancer to regulate the promoter activity of the IGFBP3 gene.Conclusions: Overall, this study identified 12 RIPs in IGFBP gene clusters. Furthermore, SINE insertions in 5’ flanking of IGFBP3 may associated with variations of gene expression and phenotype.

SINE Insertion in 5’ Flanking of IGFBP3 May Associated With Gene Expression and Phenotypic Variations

Background: Insulin-like growth factor binding proteins (IGFBPs), specifically binding to IGF1 and IGF2, play an important role in regulating physiological functions of insulin-like growth factors (IGFs). IGFBPs have been considered important candidate genes for economic traits due to their involvement in physiological processes related to growth and development. However, most of the current studies on genetic markers of IGFBPs have focused on SNPs, and large fragment insertion mutations such as retrotransposons have rarely been considered. In this paper, we screened the porcine IGFBP genes (IGFBP1-8) for retrotransposon insertion polymorphisms (RIPs) using bioinformatics prediction combined with the PCR-based amplification. Furthermore, for two linked RIPs their population distribution and impact on promoter activity and phenotype were further evaluated.Results: Screening of IGFBPs identified RIPs in IGFBP1-5 and IGFBP7. In total twelve predicted RIPs were confirmed by PCR. These RIPs were detected in different breeds with an uneven distribution among them. By linkage genetic analysis and PCR verification, IGFBP3-1-RIP and IGFBP3-2-RIP are completely linked, showing only three genotypes, SINE+/+/LINE-/-, SINE-/-/LINE+/+ and SINE+/-/LINE-/+. The age of 100 kg body weight and longissimus muscle thickness of Large white individuals of SINE+/+/LINE-/-genotype were significantly (P<0.05) higher than those of SINE+/-/LINE+/- genotype and SINE-/-/LINE+/+ genotype. However, the longissimus muscle thickness and corrected backfat thickness of SINE+/+/LINE-/- individuals were significantly (P<0.05) thinner than those of SINE+/+/LINE-/- genotype. The expression of the IGFBP3 gene in liver, leg muscles and backfat of 30-day Sujiang piglets with SINE+/+/LINE-/- genotype were significantly higher (P<0.05) than those with SINE-/-/LINE+/+ genotype by the real-time quantitative polymerase chain reaction (qPCR). Further study was conducted to confirm the effect of SINE and LINE insertion on the promoter activity of IGFBP3. First, the core promoter region of the IGFBP3 gene was identified locating within 482bp upstream of ATG by using the dual-luciferase activity assay. Then SINE and LINE were combined with 482bp fragment to construct a recombinant vector respectively based on the PGL3-Promoter-Enhancer. The recombinant vector was transfected into C2C12, 3T3-L1, and Hela cells. The detection of the dual-luciferase reporter gene revealed that only SINE insertion was significantly increased (P<0.05) promoter activity of the IGFBP3 gene, indicating that the SINE may act as an enhancer to regulate the promoter activity of the IGFBP3 gene. Conclusions: Overall, this study identified 12 RIPs in IGFBP gene clusters, which provided useful markers for genetic analysis of pig populations. Furthermore, based on the dual-luciferase activity assay in cells and association analysis, the linked genetic variations generated by SINE and LINE insertions in 5’ flanking of IGFBP3 may associated with variations of gene expression and phenotype.

SINE Insertion in the Intron of Pig GHR May Decrease Its Expression by Acting as a Repressor

The genetic diversity of the GH/IGF axis genes and their association with the variation of gene expression and phenotypic traits, principally represented by SNPs, have been extensively reported. Nevertheless, the impact of retrotransposon insertion polymorphisms (RIPs) on the GH/IGF axis gene activity has not been reported. In the present study, bioinformatic prediction and PCR verification were performed to screen RIPs in four GH/IGF axis genes (GH, GHR, IGF1 and IGF1R). In total, five RIPs, including one SINE RIP in intron 3 of IGF1, one L1 RIP in intron 7 of GHR, and three SINE RIPs in intron 1, intron 5 and intron 9 of GHR, were confirmed by PCR, displaying polymorphisms in diverse breeds. Dual luciferase reporter assay revealed that the SINE insertion in intron 1 of GHR significantly repressed the GHR promoter activity in PK15, Hela, C2C12 and 3T3-L1 cells. Furthermore, qPCR results confirmed that this SINE insertion was associated with a decreased expression of GHR in the leg muscle and longissimus dorsi, indicating that it may act as a repressor involved in the regulation of GHR expression. In summary, our data revealed that RIPs contribute to the genetic variation of GH/IGF axis genes, whereby one SINE RIP in the intron 1 of GHR may decrease the expression of GHR by acting as a repressor.

A SINE Insertion in F8 Gene Leads to Severe Form of Hemophilia A in a Family of Rhodesian Ridgebacks

Hemophilia A is the most common coagulation factor disorder in humans and dogs. The disease is characterized by the lack or diminished activity of Factor VIII (FVIII), caused by variants in the F8 gene and inherited as an X chromosomal trait. Two related male Rhodesian Ridgebacks were diagnosed with Hemophilia A due to reduced FVIII activity. The purpose of the study was to determine the genetic cause and give breeding advice for the remaining family members in order to eradicate the variant. By Sanger sequencing a short interspersed nuclear element (SINE) insertion in exon 14 of the F8 gene was found. Perfect correlation of this genetic variant with clinical signs of hemophilia A in the family tree, and the lack of this genetic variant in more than 500 unrelated dogs of the same and other breeds, confirms the hypothesis of this SINE being the underlying genetic cause of Hemophilia A in this family. The identification of clinically unaffected female carriers allows subsequent exclusion of these animals from breeding, to avoid future production of clinically affected male offspring and more subclinical female carriers.

SINE Retrotransposons Import Polyadenylation Signals to 3’UTRs in Dog (Canis familiaris)

BackgroundMessenger RNA 3’ untranslated regions (3’UTRs) control many aspects of gene expression and determine where the transcript will terminate. The polyadenylation signal (PAS) AAUAAA is a key regulator of transcript termination and this hexamer, or a similar sequence, is very frequently found within 30 bp of 3’UTR ends. Short interspersed element (SINE) retrotransposons are found throughout genomes in high copy number. When inserted into genes they can disrupt expression, alter splicing, or cause nuclear retention of mRNAs. The genomes of the domestic dog and other carnivores carry hundreds of thousands Can-SINEs, a tRNA-related SINE with transcription termination potential. Because of this we asked whether Can-SINEs may help terminate transcript in some dog genes.ResultsDog 3’UTRs have several peaks of AATAAA PAS frequency within 40 bp of the 3’UTR end, including four bp-interval peaks at 28, 32, and 36 bp from the end. The periodicity is partly explained by TAAA(n) repeats within Can-SINE AT-rich tails. While density of antisense-oriented Can-SINEs in 3’UTRs is fairly constant with distances from 3’end, sense-oriented Can-SINEs are common at the 3’end but nearly absent farther upstream. There are nine Can-SINE sub-types in the dog genome and the consensus sequence sense strands (head to tail) all carry at least three PASs while antisense strands usually have none. We annotated all repeat-masked Can-SINE copies in the Boxer reference genome and found that the young SINEC_Cf type has a mode of 15 bp for target site duplications (TSDs). We find that all Can-SINE types favor integration at TSDs beginning with A(4). The count of AATAAA PASs differs significantly between sense and antisense-oriented retrotransposons in transcripts. Can-SINEs near 3’UTR ends are very likely to carry AATAAA on the mRNA sense strand while those farther upstream are not. We also identified loci where Can-SINE insertion has truncated or altered a dog 3’UTR compared to the human ortholog.ConclusionDog Can-SINE activity has imported AATAAA PASs into gene transcripts and led to alteration of 3’UTRs. AATAAA sequences are selectively removed from Can-SINEs in introns and upstream 3’UTR regions but are retained at the far downstream end of 3’UTRs, which we infer reflects their role as termination sequences for these transcripts.

ATP2A2 SINE Insertion in an Irish Terrier with Darier Disease and Associated Infundibular Cyst Formation

A 4-month-old female Irish Terrier presented with a well demarcated ulcerative and crusting lesion in the right ear canal. Histological analysis revealed epidermal hyperplasia with severe acantholysis affecting all suprabasal layers of the epidermis, which prompted a presumptive diagnosis of canine Darier disease. The lesion was successfully treated by repeated laser ablation of the affected epidermis. Over the course of three years, the dog additionally developed three dermal nodules of up to 4 cm in diameter that were excised and healed without complications. Histology of the excised tissue revealed multiple infundibular cysts extending from the upper dermis to the subcutis. The cysts were lined by squamous epithelium, which presented with abundant acantholysis of suprabasal keratinocytes. Infundibular cysts represent a novel finding not previously reported in Darier patients. Whole genome sequencing of the affected dog was performed, and the functional candidate genes for Darier disease (ATP2A2) and Hailey-Hailey disease (ATP2C1) were investigated. The analysis revealed a heterozygous SINE insertion into the ATP2A2 gene, at the end of intron 14, close to the boundary of exon 15. Analysis of the ATP2A2 mRNA from skin of the affected dog demonstrated a splicing defect and marked allelic imbalance, suggesting nonsense-mediated decay of the resulting aberrant transcripts. As Darier disease in humans is caused by haploinsufficiency of ATP2A2, our genetic findings are in agreement with the clinical and histopathological data and support the diagnosis of canine Darier disease.

SINE Retrotransposon variation drives Ecotypic disparity in natural populations of Coilia nasus

Background SINEs are a type of nonautonomous retrotransposon that can transpose from one site to be integrated elsewhere in an organism genome. SINE insertion can give rise to genetic variants and regulate gene expression, allowing organisms to acquire new adaptive capacity. Studies on this subject have focused on the impacts of SINEs on genes. However, ecological disparities in fish have not yet been explained by SINEs. Results New SINEs were isolated from Coilia nasus, which has two ecotypes—migratory and resident—that differ in their spawning and migration behaviors. The SINEs possess two structures that resemble a tRNA gene and a LINE retrotransposon tail. Comparison of olfactory tissue transcriptomes, intact SINE transcript copies were detected in only the migratory fish at the initial retrotransposition stage. The SINE DNA copy numbers were higher in the resident type than in the migratory type, while the frequency of SINE insertion was higher in the migratory type than in the resident type. Furthermore, SINE insertions can lead to new repeats of short DNA fragments in the genome, along with target site duplications. SINEs in the resident type have undergone excision via a mechanism in which predicted cleavage sites are formed by mutations, resulting in gaps that are then filled by microsatellites via microhomology-induced replication. Conclusions Notably, SINEs in the resident type have undergone strong natural selection, causing genomic heteroplasmy and driving ecological diversity of C. nasus. Our results reveal possible evolutionary mechanisms underlying the ecological diversity at the interface between SINE mobilization and organism defense.

Effects of equine myostatin (MSTN) genotype variation on transcriptional responses in Thoroughbred skeletal muscle

Myostatin gene (MSTN) variation influences distance aptitude in Thoroughbreds as a consequence of functional physiological effects including skeletal muscle fibre type and muscle hypertrophy variation. A promotor region short interspersed nuclear element (SINE) insertion, tagged by SNP g.66493737-C, alters MSTN mRNA expression. We tested the hypothesis that skeletal muscle gene expression varies among MSTN genotypes due to differential up- or down-stream gene signalling pathways that may be influenced by exercise and training and consequently contribute to variation in exercise phenotypes. Skeletal muscle biopsies were collected from Thoroughbreds previously genotyped for MSTN (n=35 CC, n=50 CT, n=9 TT) at three different time-points: untrained at rest (UR), untrained after exercise (UE) and trained at rest (TR). Gene differential expression (DE) was determined from RNAseq data using DESeq2 (Benjamini-Hochberg P-value <0.05). Functional over-representation analysis was performed in DAVID. In UR samples, one, nine and 47 genes were DE between CC vs CT, CT vs TT and C:C vs TT, respectively. The OSGEPL1 gene, located <250 Kb proximal to MSTN, was DE among all cohorts. Six genes were DE in UE between CC vs TT including OSGEPL1, FGF10 and COQ8A. There was significant enrichment for GO categories related to mitochondria in TR. Comparison of the exercise response (UR vs UE) revealed patterns of expression that were opposing; i.e. CHRNG was 0.857 log2FC in the TT cohort but 2.055 log2FC in the CC cohort. Genes located in proximity to MSTN and involved in mitochondrial function were most significantly different among genotype cohorts. Patterns of DE among genotypes suggests gene-regulated influence on the phenotype. Understanding these patterns may assist genotype-guided training strategies.

Merle allele variations in the Mudi dog breed and their effects on phenotypes

A retrotransposon insertion in the SILV gene is associated with a peculiar phenotype of dog, known as a merle. It is characterised by various areas of their coat colour becoming diluted due to a malfunction in the eumelanin-producing pigment cells. Recent studies have shown that the exact size of the short interspersed element (SINE) insertion is in correlation with specific phenotypic attributes, but was not able to absolutely confine dogs to a certain colour pattern. Our study focused on the merle variations occurring in the Mudi breed. Altogether, 123 dog samples from 11 countries were tested and genotyped. The exact length of the merle alleles were determined by automated fluorescent capillary fragment analysis. The most frequent merle genotype in this Mudi sample collection was the ‘classic’ merle (m/M: 61.8%), whereas other variants, such as atypical (m/Ma and m/Ma+: 5.7%), harlequin (m/Mh: 13.8%), double merle (M/M: 0.8%) and mosaic profiles (17.9%) were also observed. The practical significance of testing this mutation is that, phenotypically, not only merle dogs are carriers of this insertion, but also the so-called hidden merle individuals (where the merle phenotype is fully covered by the pheomelanin-dominated colouration) are potentially capable of producing unintentionally homozygous ‘double merle’ progeny with ophthalmologic, viability and auditory impairments.