Role of an SNP in Alternative Splicing of Bovine NCF4 and Mastitis Susceptibility

Functional impact of splicing variants in the elaboration of complex traits in cattle

GWAS conducted directly on imputed whole genome sequence have led to the identification of numerous genetic variants associated with agronomic traits in cattle. However, such variants are often simply markers in linkage disequilibrium with the actual causal variants, which is a limiting factor for the development of accurate genomic predictions. It is possible to identify causal variants by integrating information on how variants impact gene expression into GWAS output. RNA splicing plays a major role in regulating gene expression. Thus, assessing the effect of variants on RNA splicing may explain their function. Here, we use a high-throughput strategy to functionally analyse putative splice-disrupting variants in the bovine genome. Using GWAS, massively parallel reporter assay and deep learning algorithms designed to predict splice-disrupting variants, we identify 38 splice-disrupting variants associated with complex traits in cattle, three of which could be classified as causal. Our results indicate that splice-disrupting variants are widely found in the quantitative trait loci related to these phenotypes. Using our combined approach, we also assess the validity of splicing predictors originally developed to analyse human variants in the context of the bovine genome.

The Transcript Levels and the Serum Profile of Biomarkers Associated with Clinical Endometritis Susceptibility in Buffalo Cows

Determining the gene expression and serum profile of the indicators linked to clinical endometritis susceptibility in Egyptian buffalo cows was the aim of this investigation. The buffalo cows that were enrolled were divided into two groups: forty infected buffalo cows with clinical endometritis and forty seemingly healthy buffalo cows that served as the control group. For the purposes of gene expression and biochemical analysis, ten milliliters of blood was obtained via jugular venipuncture from each buffalo cow. TLR4, IL-8, IL-17, NFKB, SLCA11A1, NCF4, Keap1, HMOX1, OXSR1, ST1P1, and SERP1 were manifestly expressed at much higher levels in the buffaloes with endometritis. On the other hand, the genes that encode SOD, CAT, NDUFS6, Nrf2, and PRDX2 were down-regulated. There was a significant (p < 0.05) elevation of the serum levels of non-esterified fatty acids (NEFAs), beta hydroxy butyric acid (BHBA), triglycerides (TGs), globulin, creatinine, and cortisol, along with a reduction in the serum levels of glucose, cholesterol, total protein albumin, urea, estrogen (E2), progesterone (P4), follicle-stimulating hormone (FSH), luteinizing hormone (LH), thyroxine (T4), prostaglandin F2 α (PGF2α), calcium, iron, and selenium, in the endometritis group in comparison with the control. However, no significant change was observed in the values of phosphorus, magnesium, copper, or zinc in either group. Within the selective breeding of naturally resistant animals, the variation in the genes under study and the changes in the serum profiles of the indicators under investigation may serve as a reference guide for reducing endometritis in Egyptian buffalo cows.

Investigating Polymorphisms and Expression Profile of Immune, Antioxidant, and Erythritol-Related Genes for Limiting Postparturient Endometritis in Holstein Cattle

This study looked at genetic polymorphisms and transcript levels of immune, antioxidant, and erythritol-related markers for postparturient endometritis prediction and tracking in Holstein dairy cows. One hundred and thirty female dairy cows (65 endometritis affected and 65 apparently healthy) were used. Nucleotide sequence variations between healthy and endometritis-affected cows were revealed using PCR-DNA sequencing for immune (TLR4, TLR7, TNF-α, IL10, NCF4, and LITAF), antioxidant (ATOX1, GST, and OXSR1), and erythritol-related (TKT, RPIA, and AMPD1) genes. Chi-square investigation exposed a noteworthy variance amongst cow groups with and without endometritis in likelihood of dispersal of all distinguished nucleotide variants (p < 0.05). The IL10, ATOX1, and GST genes were expressed at substantially lower levels in endometritis-affected cows. Gene expression levels were considerably higher in endometritis-affected cows than in resistant ones for the genes TLR4, TLR7, TNF-α, NCF4, LITAF, OXSR1, TKT, RPIA, and AMPD1. The sort of marker and vulnerability or resistance to endometritis had a significant impact on the transcript levels of the studied indicators. The outcomes might confirm the importance of nucleotide variants along with gene expression patterns as markers of postparturient endometritis susceptibility/resistance and provide a workable control plan for Holstein dairy cows.

Polymorphism in neutrophil cytosolic factor 4 (NCF4) of dairy cows had mastitis in previous lactations, and the relationship with the respiratory burst

Nicotinamide adenine dinucleotide phosphate oxidase (NADPH oxidase), as a key factor in innate immunity, consists of several components, one of them is p40phox which is encoded by neutrophil cytosolic factor 4 (NCF4). Respiratory burst and reactive oxygen species (ROS) production are antimicrobial mechanisms associated with NADPH oxidase. This study evaluated the effects of g.18174 A > G and g.18270C > T single-nucleotide polymorphisms (SNP) in NCF4 on bovine mastitis and the respiratory burst capacity of neutrophils. SNPs of 160 dairy cattle were determined using a novel PCR-RFLP protocol by employing restriction enzymes, MboI and FokI. Also, the flow cytometry measured respiratory burst in 82 blood samples. Our results indicated that only g.18174 A > G SNP reduced the respiratory burst capacity. However, both SNPs were not significantly correlated with clinical mastitis. We concluded that g.18174 A > G decreases the function of NADPH oxidase. However, both SNPs were not significantly correlated with clinical mastitis.

Genetic polymorphisms in immune- and inflammation-associated genes and their association with bovine mastitis resistance/susceptibility

Bovine mastitis, the inflammation of the mammary gland, is a contagious disease characterized by chemical and physical changes in milk and pathological changes in udder tissues. Depressed immunity and higher expression of inflammatory cytokines with an elevated milk somatic cell count can be observed during mastitis in dairy cattle. The use of somatic cell count (SCC) and somatic cell score (SCS) as correlated traits in the indirect selection of animals against mastitis resistance is in progress globally. Traditional breeding for mastitis resistance seems difficult because of the low heritability (0.10-0.16) of SCC/SCS and clinical mastitis. Thus, genetic-marker-selective breeding to improve host genetics has attracted considerable attention worldwide. Moreover, genomic selection has been found to be an effective and fast method of screening for dairy cattle that are genetically resistant and susceptible to mastitis at a very early age. The current review discusses and summarizes the candidate gene approach using polymorphisms in immune- and inflammation-linked genes (CD4, CD14, CD46, TRAPPC9, JAK2, Tf, Lf, TLRs, CXCL8, CXCR1, CXCR2, C4A, C5, MASP2, MBL1, MBL2, LBP, NCF1, NCF4, MASP2, A2M, and CLU, etc.) and their related signaling pathways (Staphylococcus aureus infection signaling, Toll-like receptor signaling, NF-kappa B signaling pathway, Cytokine-cytokine receptor, and Complement and coagulation cascades, etc.) associated with mastitis resistance and susceptibility phenotypic traits (IL-6, interferon-gamma (IFN-γ), IL17, IL8, SCS, and SCC) in dairy cattle.

Drug Discovery in Canine Pyometra Disease Identified by Text Mining and Microarray Data Analysis

Canine pyometra, which is accompanied by bacterial contamination of the dog uterus, is defined as a complex disease associated with the activation of several systems, including the immune system. This study uses text mining and microarray data analysis methods to discover some existing targeted gene drugs and expand potential new drug indications. Text mining ("canine pyometra") and microarray data analysis (GSE99877) were used to obtain a common set of genes. These genes and protein-protein interaction (PPI) networks were analyzed using Gene Ontology and the Kyoto Encyclopedia of Genes and Genomes. Then, the important genes clustered in the PPI network were selected for gene-drug interaction analysis to provide evidence for potential drug discovery. Through text mining and data analysis, we obtained 17,544 text mining genes (TMGs) and 399 differentially expressed genes (DEGs), respectively. There were 256 repeat genes between TMGs and DEGs, including 70 upregulated genes and 186 downregulated genes. Thirty-seven genes clustered in three significant gene modules. Eight of the 37 genes can target 23 existing drugs. In conclusion, the discovery of 8 immune response-related genes (BTK, CSF2RA, CSF2RB, ITGAL, NCF4, PLCG2, PTPRC, and TOP2A) targeting 23 existing drugs may expand the drug indications for pyometra-related diseases in dogs.

Characterization of peripheral white blood cells transcriptome to unravel the regulatory signatures of bovine subclinical mastitis resistance

Subclinical bovine mastitis is a pathogenic infection of the breast characterized by a marked decrease in milk production and quality. As it has no obvious clinical symptoms, diagnosis and treatment are challenging. Therefore, searching for biomarkers in cows’ peripheral white blood cells is valuable for preventing and treating subclinical mastitis. Thus, in this study, the transcriptome of peripheral blood from healthy and subclinical mastitis cows was characterized to find the regulatory signatures of bovine subclinical mastitis using RNA-seq. A total of 287 differentially expressed genes (DEGs) and 70 differentially expressed lncRNAs (DELs) were detected, and 37 DELs were documented near known Quantitative Trait Loci (QTL) associated with the mastitis of cows. Bioinformatic analysis indicated that lncRNAs MSTRG25101.2, MSTRG.56327.1, and MSTRG.18968.1, which are adjacent to the SCS QTL and SCC QTL, may be candidate lncRNAs that influence the pathogenesis of mastitis in cows by up-regulating the expression of genes TLR4, NOD2, CXCL8, and OAS2. Moreover, the alternative splicing (AS) pattern of transcriptional sequence differences between healthy cows and subclinical mastitis cows suggested a molecular mechanism of mastitis resistance and susceptibility. A total of 2,212 differential alternative splicing (DAS) events, corresponding to 1,621 unique DAS genes, were identified in both groups and significantly enriched in immune and inflammatory pathways. Of these, 29 DAS genes were subject to regulation by 32 alternative splicing SNPs, showing diverse and specific splicing patterns and events. It is hypothesized that the PIK3C2B and PPRPF8 splice variants associated with AS SNPs (rs42705933 and rs133847062) may be risk factors for susceptibility to bovine subclinical mastitis. Altogether, these key blood markers associated with resistance to subclinical mastitis and SNPs associated with alternative splicing of genes provide the basis for genetic breeding for resistance to subclinical mastitis in cows.

Exploration of Alternative Splicing (AS) Events in MDV-Infected Chicken Spleens

Marek’s disease (MD) was an immunosuppression disease induced by Marek’s disease virus (MDV). MD caused huge economic loss to the global poultry industry, but it also provided an ideal model for studying diseases induced by the oncogenic virus. Alternative splicing (AS) simultaneously produced different isoform transcripts, which are involved in various diseases and individual development. To investigate AS events in MD, RNA-Seq was performed in tumorous spleens (TS), spleens from the survivors (SS) without any lesion after MDV infection, and non-infected chicken spleens (NS). In this study, 32,703 and 25,217 AS events were identified in TS and SS groups with NS group as the control group, and 1198, 1204, and 348 differently expressed (DE) AS events (p-value < 0.05 and FDR < 0.05) were identified in TS vs. NS, TS vs. SS, SS vs. NS, respectively. Additionally, Function enrichment analysis showed that ubiquitin-mediated proteolysis, p53 signaling pathway, and phosphatidylinositol signaling system were significantly enriched (p-value < 0.05). Small structural variations including SNP and indel were analyzed based on RNA-Seq data, and it showed that the TS group possessed more variants on the splice site region than those in SS and NS groups, which might cause more AS events in the TS group. Combined with previous circRNA data, we found that 287 genes could produce both circular and linear RNAs, which suggested these genes were more active in MD lymphoma transformation. This study has expanded the understanding of the MDV infection process and provided new insights for further analysis of resistance/susceptibility mechanisms.

Alternative splicing related genetic variants contribute to bladder cancer risk

Emerging evidence has shown that aberrant alternative splicing (AS) events are involved in the carcinogenesis. The association between genetic variants in AS and bladder cancer susceptibility remains to be fully elucidated. We searched for single nucleotide polymorphisms (SNPs) which are located in splicing quantitative trait loci (sQTLs) in bladder cancer through CancerSplicingQTL database and the 1000 Genomes Project. A case-control study including 580 cases and 1,101 controls was conducted to assess the association between the functional genetic variants and bladder cancer risk. Next, we used GTEx, TCGA, and GEO databases conducting sQTL analysis and gene expression differences analysis to evaluate the potential biological function of the candidate SNPs and related genes. We found that SNP rs4383 C>G was remarkably related with the reduced risk of bladder cancer (odds ratio = 0.68, 95% confidence interval = 0.59-0.79, P = 3.91 × 10^-7 ). Similar results were obtained in codominant, dominant and recessive model. Stratified analyses revealed that the effect of SNP rs4383 C>G on bladder cancer was more significant in the older subjects (age > 65), female and nonsmokers. sQTL analysis showed that SNP rs4383 was associated with the AS events of its downstream gene MAFF with a splicing event of alternative 5' splice site. The messenger RNA expression of MAFF in bladder tumor tissues was lowered compared with normal tissues. Patients with high expression of MAFF had higher survival rates. These findings indicated that SNP rs4383 related with the AS events of MAFF was associated with bladder cancer risk and could represent a possible biomarker for bladder cancer susceptibility.

Genome-wide methylation and transcriptome of blood neutrophils reveal the roles of DNA methylation in affecting transcription of protein-coding genes and miRNAs in E. coli-infected mastitis cows

Background

Neutrophils are the first effectors of inflammatory response triggered by mastitis infection, and are important defense cells against pathogenic Escherichia coli (E. coli). DNA methylation, as a critical epigenetic mechanism for regulating gene function, is involved in bovine mastitis.

Results

In this study, we sequenced the blood neutrophils of healthy and E. coli-infected mastitic half-sib cows for the overall DNA methylation levels using transcriptome sequencing and reduced representation bisulfite sequencing. The methylation levels in the mastitis cows (MCs) were decreased compared with healthy cows (HCs). A total of 494 differentially methylated regions were identified, among which 61 were up-methylated and 433 were down-methylated (MCs vs. HCs). The expression levels of 1094 differentially expressed genes were up-regulated, and 245 genes were down-regulated. Twenty-nine genes were found in methylation and transcription data, among which seven genes’ promoter methylation levels were negatively correlated with expression levels, and 11 genes were differentially methylated in the exon regions. The bisulfite sequencing PCR and quantitative real-time PCR validation results demonstrated that the promoter methylation of CITED2 and SLC40A1 genes affected differential expression. The methylation of LGR4 exon 5 regulated its own alternative splicing. The promoter methylation of bta-miR-15a has an indirect effect on the expression of its target gene CD163. The CITED2, SLC40A1, and LGR4 genes can be used as candidates for E. coli-induced mastitis resistance.

Conclusions

This study explored the roles of DNA methylation in affecting transcription of protein-coding genes and miRNAs in E. coli-induced mastitis, thereby helping explain the function of DNA methylation in the pathogenesis of mastitis and provided new target genes and epigenetic markers for mastitis resistance breeding in dairy cattle.

A single-nucleotide polymorphism induced alternative splicing in Tacr3 involves in hypoxic-ischemic brain damage

Single-nucleotide polymorphism (SNP) and Alternative splicing (AS) were found to be implicated in certain diseases, nevertheless, the contributions of mRNA SNPs and AS to pathogenesis in developing rat brains with hypoxic-ischemic encephalopathy (HIE) remained largely vague. Additionally, the disease associated with Tacr3 was normosmic congenital hypogonadotropic hypogonadism, while the relationship between HIE and Tacr3 remained largely elusive. The current study was designed to investigate the differentially expressed mRNAs and related SNPs as well as AS in neonatal rats subjected to HIE to identify if the exhibition of AS was associated with SNPs under pathological condition. Firstly, we used postnatal day 7 Sprague-Dawley rats to construct neonatal HIE model, and analyzed the expression profiles of SNP mRNA in hypoxic-ischemic (HI) and sham brains by using RNA sequencing. Then four genes, including Mdfic, Lpp, Bag3 and Tacr3, connecting with HIE and exhibiting SNPs and AS were identified by bioinformatics analysis. Moreover, combined with exonic splicing enhancer (ESE) and alternative splice site predictor (ASSP) analysis, we found that Tacr3 is associated specifically with HIE through 258547789 G > A SNP in inside the Alt First Exon and 258548573 G > A SNP in outside the Alt First Exon. Taken together, our study provides new evidence to understand the role of Tacr3 in HIE and it is possibly a potential target for the treatment of HIE in future clinic trial.

LCK rs10914542-G allele associates with type 1 diabetes in children via T cell hyporesponsiveness

BACKGROUND

Abnormal lymphocyte-specific protein tyrosine kinase (LCK)-related T cell hyporesponsiveness was discovered in type 1 diabetes (T1D). This study aims to investigate the potential associations between LCK single-nucleotide polymorphisms (SNPs) and the susceptibility of T1D.

METHODS

DNAs were extracted from blood samples of 589 T1D patients and 596 healthy controls to genotype seven SNPs of the LCK gene using PCR and Sanger sequencing. Associations of these SNPs with the susceptibility of T1D were determined by χ² test. LCKs were knocked out in peripheral blood mononuclear cells (PBMCs) using CRISPR-Cas9 to investigate the role of LCK SNP in T-lymphocyte activation in T1D.

RESULTS

SNP rs10914542 but not the other six SNPs of the LCK gene was significantly associated with (C vs. G, odds ratio (OR) = 0.581, 95% confidence interval (CI) = 0.470-0.718, P value = 4.13E - 7) the susceptibility of T1D. Peripheral T-lymphocyte activation in response to T cell receptor (TCR)/CD3 stimulation is significantly lower in the rs10914542-G-allele group than in the C-allele group. In vitro experiments revealed that rs10914542 G allele impaired the TCR/CD3-mediated T-cell activation in PBMCs.

CONCLUSIONS

This study reveals that the G allele of SNP rs10914542 of LCK impairs the TCR/CD3-mediated T-cell activation and increases the risk of T1D.

Digital gene expression analyses of mammary glands from meat ewes naturally infected with clinical mastitis

Clinical mastitis in sheep has gravely restrained production performance for a long time. Knowledge of mechanisms of its pathogenesis and resistance in meat sheep mammary gland with clinical mastitis are not yet understood, especially for clinical mastitis caused by natural infection. In this work, RNA-sequencing was firstly used to screen the differentially expressed genes (DEGs) in clinical mastitic mammary tissues (CMMTs) when compared with healthy mammary tissues (HMTs) from meat sheep flocks. We identified 420 DEGs including 316 upregulated and 104 downregulated genes in CMMTs. Gene ontology annotation revealed these DEGs were mainly engaged in immune response and inflammation response. Pathway enrichment showed they were primarily enriched in pathways relevant to inflammation, immune response and metabolism. Alternative splicing analysis showed most common differential splicing genes in CMMTs and HMTs were implicated in immune response. Immunostaining for three immune response-related proteins encoded by DEGs were mainly observed in mammary epithelium from both CMMTs and HMTs, and their positive signals were more intensive in CMMTs than those in HMTs. These findings provide experimental basis and reference for further researching the molecular genetic mechanisms, particularly immune defence mechanisms, of sheep mammary gland during clinical mastitis.

In silico genome-wide miRNA-QTL-SNPs analyses identify a functional SNP associated with mastitis in Holsteins

Background

Single-nucleotide polymorphisms (SNPs) in microRNAs (miRNAs) and their target binding sites affect miRNA function and are involved in biological processes and diseases, including bovine mastitis, a frequent inflammatory disease. Our previous study has shown that bta-miR-2899 is significantly upregulated in the mammary gland tissue of mastitis-infected cow than that of healthy cows.

Results

In the present study, we used a customized miRNAQTLsnp software and identified 5252 SNPs in 691 bovine pre-miRNAs, which are also located within the quantitative trait loci (QTLs) that are associated with mastitis and udder conformation-related traits. Using luciferase assay in the bovine mammary epithelial cells, we confirmed a candidate SNP (rs109462250, g. 42,198,087 G > A) in the seed region of bta-miR-2899 located in the somatic cell score (SCS)-related QTL (Chr.18: 33.9–43.9 Mbp), which affected the interaction of bta-miR-2899 and its putative target Spi-1 proto-oncogene (SPI1), a pivotal regulator in the innate and adaptive immune systems. Quantitative real-time polymerase chain reaction results showed that the relative expression of SPI1 in the mammary gland of AA genotype cows was significantly higher than that of GG genotype cows. The SNP genotypes were associated with SCS in Holstein cows.

Conclusions

Altogether, miRNA-related SNPs, which influence the susceptibility to mastitis, are one of the plausible mechanisms underlying mastitis via modulating the interaction of miRNAs and immune-related genes. These miRNA-QTL-SNPs, such as the SNP (rs109462250) of bta-miR-2899 may have implication for the mastitis resistance breeding program in Holstein cattle.

Electronic supplementary material

The online version of this article (10.1186/s12863-019-0749-5) contains supplementary material, which is available to authorized users.

Production of an aberrant splice variant of CCL5 is not caused by genetic mutation in the mammary glands of mastitis‑infected Holstein cows

Genetic mutations, including single nucleotide polymorphisms (SNPs), result in aberrant alternatively splicing of gene and involves in susceptibility of inflammatory diseases, including bovine mastitis. C‑C motif chemokine ligand 5 (CCL5) is an immune‑associated gene, but its alternative splicing (AS) mechanism of gene expression has not yet been understood. The present study identified the splice variant of CCL5 and the compared differential expression of various transcripts between healthy and mastitic mammary gland tissue from cows. A novel transcript lacking exon 2 with a deletion of 112 bp (referred to as CCL5‑AS) was identified in the mammary gland. The expression of CCL5‑AS was lower compared with CCL5‑reference in the healthy and mastitic mammary tissues. A total of two novel SNPs (g.1647 C>T and g.1804 G>A) were identified in exon 2 of CCL5. Using the splicing mini‑gene reporter assay in bovine mammary epithelial cells (MAC‑T) and 293T cells, it was confirmed that the production of CCL5‑AS was not caused by the two SNPs. The present findings suggested that alternative splicing is one of the mechanisms of CCL5 expression regulation and is involved in mastitis infection, but that genetic mutation was not responsible for the generation of the abnormal transcript of CCL5 in cows.

Multiple QTL underlie milk phenotypes at the CSF2RB locus

Background

Over many years, artificial selection has substantially improved milk production by cows. However, the genes that underlie milk production quantitative trait loci (QTL) remain relatively poorly characterised. Here, we investigate a previously reported QTL located at the CSF2RB locus on chromosome 5, for several milk production phenotypes, to better understand its underlying genetic and molecular causes.

Results

Using a population of 29,350 taurine dairy cows, we conducted association analyses for milk yield and composition traits, and identified highly significant QTL for milk yield, milk fat concentration, and milk protein concentration. Strikingly, protein concentration and milk yield appear to show co-located yet genetically distinct QTL. To attempt to understand the molecular mechanisms that might be mediating these effects, gene expression data were used to investigate eQTL for 11 genes in the broader interval. This analysis highlighted genetic impacts on CSF2RB and NCF4 expression that share similar association signatures to those observed for lactation QTL, strongly implicating one or both of these genes as responsible for these effects. Using the same gene expression dataset representing 357 lactating cows, we also identified 38 novel RNA editing sites in the 3′ UTR of CSF2RB transcripts. The extent to which two of these sites were edited also appears to be genetically co-regulated with lactation QTL, highlighting a further layer of regulatory complexity that involves the CSF2RB gene.

Conclusions

This locus presents a diversity of molecular and lactation QTL, likely representing multiple overlapping effects that, at a minimum, highlight the CSF2RB gene as having a causal role in these processes.

Electronic supplementary material

The online version of this article (10.1186/s12711-019-0446-x) contains supplementary material, which is available to authorized users.

DNA methylation rather than single nucleotide polymorphisms regulates the production of an aberrant splice variant of IL6R in mastitic cows

Interleukin-6 receptor-alpha (IL6R) interacts with IL6 and forms a ligand-receptor complex, which can stimulate various cellular responses, such as cell proliferation, cell differentiation, and activation of inflammatory processes. Both genetic mutation and epigenetic modification regulate gene transcription. We identified a novel splice variant of bovine IL6R, designated as IL6R-TV, which is characterized by the skipping of exon 2 of the NCBI-referenced IL6R gene (IL6R-reference). The expression levels of IL6R-TV and IL6R-reference transcripts were lower in normal mammary gland tissues. These transcripts play a potential role during inflammatory infection. We also detected two putative functional SNPs (g.19711 T > C and g.19731 G > C) located within the upstream 100 bp of exon 2. These SNPs formed two haplotypes (T-G and C-C). Two mutant pSPL3 exon-trapping plasmids (pSPL3-T-G and pSPL3-C-C) were transferred into the bovine mammary epithelial cells (MAC-T) and human embryonic kidney 293 T cells (HEK293T) to investigate the relationship between the two SNPs and the aberrant splicing of IL6R. DNA methylation levels of the alternatively spliced exon in normal and mastitis-infected mammary gland tissues were quantified through nested bisulfate sequencing PCR (BSP) and cloning sequencing. We found that DNA methylation regulated IL6R transcription. The DNA methylation level was high in mastitis-infected mammary gland tissues and stimulated IL6R expression, thereby promoting the inclusion of the alternatively spliced exon. The upregulated expression of the two transcripts was due to DNA methylation modification rather than genetic mutations.

Blocking the 5' splice site of exon 4 by a morpholino oligomer triggers APOL1 protein isoform switch

APOL1 risk alleles G1 or G2 are associated with a kidney disease phenotype exclusively in people of recent African ancestry. Here we show that exon 4 encoding a part of the APOL1 signal peptide is constitutively spliced in major APOL1 transcripts expressed in kidney glomerular and tubular cells. We demonstrate that constitutive splicing of exon 4 results from a suboptimal hnRNP A1 binding motif found in exon 4. Accordingly, a robust binding of hnRNP A1 protein to a consensus hnRNP A1 cis-acting element in exon 4 results in almost complete exclusion of exon 4 from the APOL1 minigene transcripts. Blocking the 5' splice site at the exon 4/intron boundary with a specific antisense morpholino oligonucleotide excludes exon 4 from the splicing pattern of endogenous APOL1 transcripts. These transcripts are fully functional and produce APOL1 protein isoform that is not normally detectable in podocytes. Together with our previous data showing no cytotoxicity of overexpressed APOL1 isoform lacking exon 4, we propose that morpholino-induced APOL1 isoform switch may provide a new tool to identify in vivo molecular mechanism(s) by which risk alleles promote or mediate the kidney disease phenotype.

Genetic variants of microRNA processing genes and risk of non-syndromic orofacial clefts

OBJECTIVE

MicroRNA (miRNA) processing genes play important roles in the craniofacial development. The aim of this study was to explore the associations between single nucleotide polymorphisms (SNPs) of miRNA processing genes with the risk of non-syndromic orofacial clefts (NSOC).

METHODS

We genotyped 12 potentially functional SNPs from seven miRNA processing genes (GEMIN3, DROSHA, DGCR8, GEMIN4, PIWIL1, XPO5, and DICER) in a case-control study of 602 NSOC cases and 605 controls.

RESULTS

Two SNPs were associated with the susceptibility of CL/P: rs10719 in DROSHA led to an increased risk of cleft lip with or without palate (CL/P) (GA/AA: p = .024, OR = 1.33, 95% CI = [1.04, 1.70]; GG + GA/AA: p = .037, OR = 1.29, 95% CI = [1.02, 1.63]), while rs493760 in DROSHA (CC/TT: p = .049, OR = 0.58, 95% CI = [0.34, 0.99]) could reduce the risk of CL/P. In addition, rs10719 (A)-rs493760 (C) haplotype contributed to a decreased risk of CL/P (OR = 0.77, 95% CI = [0.63, 0.94]), whereas the rs10719 (G)-rs493760 (C) haplotype contributed to the increased risk of cleft palate only (CPO) (OR = 2.70, 95% CI = [1.15, 6.35]). However, there was no difference observed in these SNPs after the Bonferroni correction.

CONCLUSION

Taken together, our results provided the potential evidence that rs10719 and rs493760 might contribute to the risk of CL/P and suggested potential genetic basis and mechanisms of CL/P. The lack of association between these SNPs and CPO might be due to the limited sample size of CPO subgroup.