An insertion/deletion within the CREB1 gene identified using the RNA-sequencing is associated with sheep body morphometric traits

Whole exome sequencing identifies a novel mutation in Annexin A4 that is associated with recurrent spontaneous abortion

Background

Recurrent spontaneous abortion (RSA) is a multifactorial disease, the exact causes of which are still unknown. Environmental, maternal, and genetic factors have been shown to contribute to this condition. The aim of this study was to investigate the presence of mutations in the ANXA4 gene in patients with RSA.

Methods

Genomic DNA was extracted from 325 patients with RSA and 941 control women with a normal reproductive history for whole-exome sequencing (WES). The detected variants were annotated and filtered, and the pathogenicity of the variants was predicted through the SIFT online tool, functional enrichment analyses, Sanger sequencing validation, prediction of changes in protein structure, and evolutionary conservation analysis. Furthermore, plasmid construction, Western blotting, RT-qPCR, and cell migration, invasion and adhesion assays were used to detect the effects of ANXA4 mutations on protein function.

Results

An ANXA4 mutation (p.G8D) in 1 of the 325 samples from patients with RSA (RSA-219) was identified through WES. This mutation was not detected in 941 controls or included in public databases. Evolutionary conservation analysis revealed that the amino acid residue affected by the mutation (p.G8D) was highly conserved among 13 vertebrate species, and the SIFT program and structural modeling analysis predicted that this mutation was harmful. Furthermore, functional assays revealed that this mutation could inhibit cell migration, invasion and adhesion.

Conclusion

Our study suggests that an unreported novel ANXA4 mutation (p.G8D) plays an important role in the pathogenesis of RSA and may contribute to the genetic diagnosis of RSA.

Unlocking the Transcriptional Control of NCAPG in Bovine Myoblasts: CREB1 and MYOD1 as Key Players

Muscle formation directly determines meat production and quality. The non-SMC condensin I complex subunit G (NCAPG) is strongly linked to the growth features of domestic animals because it is essential in controlling muscle growth and development. This study aims to elucidate the tissue expression level of the bovine NCAPG gene, and determine the key transcription factors for regulating the bovine NCAPG gene. In this study, we observed that the bovine NCAPG gene exhibited high expression levels in longissimus dorsi and spleen tissues. Subsequently, we cloned and characterized the promoter region of the bovine NCAPG gene, consisting of a 2039 bp sequence, through constructing the deletion fragment double-luciferase reporter vector and site-directed mutation-identifying core promoter region with its key transcription factor binding site. In addition, the key transcription factors of the core promoter sequence of the bovine NCAPG gene were analyzed and predicted using online software. Furthermore, by integrating overexpression experiments and the electrophoretic mobility shift assay (EMSA), we have shown that cAMP response element binding protein 1 (CREB1) and myogenic differentiation 1 (MYOD1) bind to the core promoter region (-598/+87), activating transcription activity in the bovine NCAPG gene. In conclusion, these findings shed important light on the regulatory network mechanism that underlies the expression of the NCAPG gene throughout the development of the muscles in beef cattle.

Insertion/Deletion (InDel) Variants within the Sheep Fat-Deposition-Related PDGFD Gene Strongly Affect Morphological Traits

Platelet-derived growth factor D (PDGFD) is a member of the PDGF gene family, and it plays an important role in the regulation of adipocyte development in mammals. Furthermore, genome-wide association studies (GWAS) have previously identified it as a candidate gene associated with fleece fiber variation, body size, and the fat-tail phenotype in domestic Chinese sheep. In this study, a total of 1919 indigenous Chinese sheep were genotyped to examine the association between nucleotide sequence variations in PDGFD and body morphology. Our results detected both a 14 bp insertion in intron 2 and a 13 bp deletion in intron 4 of PDGFD. Moreover, these two InDel loci had low to moderate polymorphism. Notably, the 13 bp deletion mutation of PDGFD was found to significantly affect sheep body size. Yearling rams in the Luxi black-headed sheep (LXBH) containing a heterozygous genotype (insertion/deletion, ID) were found to have larger body length, chest depth, and body weight than those with wild genotypes. Furthermore, adult ewes in the Guiqian semi-fine wool sheep (GSFW) containing a homozygous mutation (deletion/deletion, DD) were found to have smaller chest width than their peers. Moreover, yearling ewes in this group with the same homozygous mutation were found to have lower body weight, chest width, and cannon circumference compared to those of other individuals. This study demonstrates that PDGFD InDel polymorphisms have the potential to be effective molecular markers to improve morphological traits in domestic Chinese sheep.

Study on the Association between LRRC8B Gene InDel and Sheep Body Conformation Traits

Marker-assisted selection is an important method for livestock breeding. In recent years, this technology has been gradually applied to livestock breeding to improve the body conformation traits. In this study, the LRRC8B (Leucine Rich Repeat Containing 8 VRAC Subunit B) gene was selected to evaluate the association between its genetic variations and the body conformation traits in two native sheep breeds in China. Four body conformation traits, including withers height, body length, chest circumference, and body weight, were collected from 269 Chaka sheep. We also collected the body length, chest width, withers height, chest depth, chest circumference, cannon bone circumference, and height at hip cross of 149 Small-Tailed Han sheep. Two different genotypes, ID and DD, were detected in all sheep. Our data showed that the polymorphism of the LRRC8B gene was significantly associated with chest depth (p < 0.05) in Small-Tailed Han sheep, and it is greater in sheep with DD than those with ID. In conclusion, our data suggested that the LRRC8B gene could serve as a candidate gene for marker-assisted selection in Small-Tailed Han sheep.

Polymorphism detection of PRKG2 gene and its association with the number of thoracolumbar vertebrae and carcass traits in Dezhou donkey

BACKGROUND

Previous studies have shown that the protein kinase cGMP-dependent 2 (PRKG2) gene is associated with dwarfism in humans, dogo Argentines, and Angus cattle, as well as with height and osteoblastogenesis in humans. Therefore, the PRKG2 gene was used as the target gene to explore whether this gene is associated with several thoracolumbar vertebrae and carcass traits in Dezhou donkeys.

RESULTS

In this study, fifteen SNPs were identified by targeted sequencing, all of which were located in introns of the PRKG2 gene. Association analysis illustrated that the g.162153251 G > A, g.162156524 C > T, g.162158453 C > T and, g.162163775 T > G were significantly different from carcass weight. g.162166224 G > A, g.162166654 T > A, g.162167165 C > A, g.162167314 A > C and, g.162172653 G > C were significantly associated with the number of thoracic vertebrae. g.162140112 A > G was significantly associated with the number and the length of lumbar vertebrae, and g.162163775 T > G was significantly associated with the total number of thoracolumbar vertebrae.

CONCLUSION

Overall, the results of this study suggest that PRKG2 gene polymorphism can be used as a molecular marker to breed high-quality Dezhou donkeys.

miR-125b-5p upregulation by TRIM28 induces cisplatin resistance in non-small cell lung cancer through CREB1 inhibition

OBJECTIVE

miR-125b-5p plays an important role in the development of cancer and drug resistance. However, in cisplatin resistance of non-small cell lung cancer (NSCLC), the function and potential mechanism of miR-125b-5p is still unclear. The aim of this study was to investigate the role and molecular mechanism of miR-125b-5p in cisplatin resistance of NSCLC.

METHODS

A GEO dataset (GSE168707) was analyzed to find high miR-125b-5p levels were associated with DDP resistance. miR-125b-5p expression levels were detected in A549 and A549/DDP cells via real-time quantitative RT-PCR (qRT-PCR). Luciferase reporter assays, western blots and mouse model xenografted were performed to identify CREB1 as a direct target gene of miR-125b-5p. Cell proliferation and apoptosis were also performed to identify whether miR-125b-5p upregulation by TRIM28 induces DDP resistance in NSCLC through CREB1 inhibition.

RESULTS

In A549/DDP cells, miR-125b-5p expression was upregulated compared to A549 cells. Then miR-125b-5p was found to increase DDP resistance in NSCLC in vivo and in vitro by increasing cell proliferation and suppressing cell apoptosis. Bioinformatic analyses were used to search for gene which miR-125b-5p can target. We identified miR-125b-5p can regulate CREB1 via luciferase reporter assays, qRT-PCR and western blots. Cell proliferation and apoptosis were also performed to confirm miR-125b-5p could impact on CREB1 and induce the DDP resistance in NSCLC. Additionally, we used bioinformatic analyses to find tripartite motif-containing 28 (TRIM28) as a transcriptional enhance factor of miR-125b-5p. The expression of TRIM28 was upregulated in A549/DDP cells compared with that in A549 cells by qRT-PCR. Finally, we found TRIM28 could mediate DDP resistance through miR-125b-5p/CREB1 axis via cell proliferation, western blot and apoptosis assay.

CONCLUSIONS

Overall, our findings demonstrated novel functions and mechanisms underlying DDP resistance in NSCLC through the TRIM28/miR-125b-5p/CREB1 axis. These may serve as novel therapeutic targets to improve the treatment efficacy using DDP for NSCLC in the future.

Transcriptome profiling of LncRNAs in sheep tail fat deposition

LncRNAs have recently received special attention due to their critical role in many important biological processes. There are few reports on its regulatory function in sheep fat deposition. In this study, two sheep populations with different tail types in Xinjiang, Bashibai sheep (fat-tailed) and the hybrid population of Bashibai sheep and wild argali (small-tailed) were selected for whole transcriptome sequencing from their tail tissues. First, 728 differentially expressed LncRNAs of tail fat between Bashibai and F2 sheep were identified by RNA-seq. Second, the tissue expression profile and relative expression difference between Bashibai and F2 sheep of 2 of 728 DE LncRNAs were analyzed by RT-PCR. LncRNA-MSTRG.24995 was highly expressed in tail fat, while lncRNA-MSTRG.36913 was highly expressed in subcutaneous fat. In addition, the expressions of LncRNA-MSTRG.24995 and LncRNA-MSTRG.36913 in tail fat of F2 sheep were significantly lower than that of Bashibai sheep, while those patterns in longissimus dorsi, quadriceps femoris and rumen were reversed. Third, the expression pattern of target genes FASN and THRSP in each tissue was similar with that of corresponding LncRNAs. The LncRNA-MSTRG.24995 directly affects tail fat deposition by FASN gene, while the LncRNA-MSTRG.36913 indirectly affects that by THRSP gene. This will help us to understand molecular mechanism of fat tail deposition from transcriptomic perspectives.

Five SNPs Within the FGF5 Gene Significantly Affect Both Wool Traits and Growth Performance in Fine-Wool Sheep (Ovis aries)

Fibroblast growth factor 5 (FGF5) gene, a member of fibroblast growth factor superfamily, plays significant roles in the regulation of the hair growth cycle during the development of mammalian hair follicles as well as the skeletal muscle development. In this study, DNA sequencing was used to scan the putative SNPs within the full-length of FGF5 gene, and SNPscan high-throughput technique was applied in the individual genotyping of 604 crossbred sheep. 10 SNPs were identified within FGF5 gene while five of them located in intron 1 could be genotyped, namely SNP1 (g. 105914953 G > A), SNP2 (g. 105922232 T > C), SNP3 (g. 105922244 A > G), SNP4 (g. 105922334 A > T) and SNP5 (g. 105922340 G > T). All these SNPs were in accord with the Hardy-Weinberg equilibrium (P > 0.05), and displayed the moderate polymorphism with PIC values ranging from 0.302 to 0.374. Thereafter, the correlation analysis between each SNP locus and economic traits including wool length, greasy wool weight and growth performance of sheep was systematically implemented. In our results, SNP1, SNP3, SNP4 and SNP5 were significantly associated with wool length, greasy wool weight and growth traits of SG sheep (P < 0.05); SNP1, SNP2, SNP3, and SNP4 were significantly correlated with wool length and growth traits of SSG sheep (P < 0.05). Meanwhile, our study revealed a strong linkage disequilibrium (LD) relationship among these SNPs (r² > 0.33), except for SNP3 and SNP4 sites (r² = 0.30). Combination genotype analysis showed that combination genotypes were significantly associated with mean fiber diameter of SG (P < 0.05), and body weight trait of SSG (P < 0.01). The above findings suggested that these SNP loci might affect economic traits synergistically and could be regarded as potential molecular markers for improving both wool production and growth performance of fine-wool sheep, which lay a molecular foundation for the breeding of fine dual-purpose sheep thereby accelerating the pace of sheep breeding.

A deletion mutation within the goat AKAP13 gene is significantly associated with litter size

A-kinase anchoring protein 13 (AKAP13) is one of the AKAP protein family members, which is correlated with estrogen receptors (ERs) and progesterone receptor (PR) activity. Consequently, the AKAP13 gene is considered to be one of the candidate genes for regulating female fertility. Hence, the objectives of this study were to discover the potential insertion/deletion (indel) variants within the AKAP13 gene and evaluate their associations with litter size of Shaanbei white cashmere goats (SBWC) to screen candidate genes for the molecular marker-assisted selection (MAS). Ultimately, we found the 16-bp deletion of AKAP13 gene which displayed three genotypes (II, ID and DD). However, it was not confirmed to Hardy-Weinberg equilibrium (HWE) in the tested population. Statistical analysis demonstrated that this 16-bp indel locus was significantly associated with litter size in goats (p < 0.05), in which the ID genotype was a key genotype for increasing litter size in goats. Besides, independent χ² tests between different genotypes and litter size showed that high-prolific groups had higher frequency of the 'D' allele (p < 0.05). Briefly, AKAP13 gene is a candidate gene for improving fertility, and its 16-bp indel locus can be used as a valid DNA molecular marker for the MAS in goat breeding.