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1.
Animals (Basel) ; 11(11)2021 Nov 02.
Artigo em Inglês | MEDLINE | ID: mdl-34827869

RESUMO

As the largest chamber of the ruminant stomach, the rumen not only serves as the principal absorptive surface and nutrient transport pathway from the lumen into the animal, but also plays an important short-chain fatty acid (SCFA) metabolic role in addition to protective functions. Accurate characterization of the gene expression profiles of genes of interest is essential to the exploration of the intrinsic regulatory mechanisms of rumen development in goats. Thus, the selection of suitable reference genes (RGs) is an important prerequisite for real-time quantitative PCR (RT-qPCR). In the present study, 16 candidate RGs were identified from our previous transcriptome sequencing of caprine rumen tissues. The quantitative expressions of the candidate RGs were measured using the RT-qPCR method, and the expression stability of the RGs was assessed using the geNorm, NormFinder, and BestKeeper programs. GeNorm analysis showed that the M values were less than 0.5 for all the RGs except GAPT4, indicating that they were stably expressed in the rumen tissues throughout development. RPS4X and RPS6 were the two most stable RGs. Furthermore, the expressions of two randomly selected target genes (IGF1 and TOP2A), normalized by the selected most stable RGs (RPS4X and RPS6), were consistent with the results of RNA sequencing, while the use of GAPDH and ACTB as RGs resulted in altered profiles. Overall, RPS4X and RPS6 showed the highest expression stability and the lowest coefficients of variation, and could be used as the optimal reference combination for quantifying gene expression in rumen tissues via RT-qPCR analysis.

2.
BMC Genomics ; 22(1): 769, 2021 Oct 28.
Artigo em Inglês | MEDLINE | ID: mdl-34706644

RESUMO

BACKGROUND: There is a long-term interest in investigating the genetic basis of the horned/polled phenotype in domestic goats. Here, we report a genome-wide association study (GWAS) to detect the genetic loci affecting the polled phenotype in goats. RESULTS: We obtained a total of 13,980,209 biallelic SNPs, using the genotyping-by-sequencing data from 45 Jintang Black (JT) goats, which included 32 female and nine male goats, and four individuals with the polled intersex syndrome (PIS). Using a mixed-model based GWAS, we identified two association signals, which were located at 150,334,857-150,817,260 bp (P = 5.15 × 10- 119) and 128,286,704-131,306,537 bp (P = 2.74 × 10- 15) on chromosome 1. The genotype distributions of the 14 most significantly associated SNPs were completely correlated with horn status in goats, based on the whole-genome sequencing (WGS) data from JT and two other Chinese horned breeds. However, variant annotation suggested that none of the detected SNPs within the associated regions were plausible causal mutations. Via additional read-depth analyses and visual inspections of WGS data, we found a 10.1-kb deletion (CHI1:g. 129424781_129434939del) and a 480-kb duplication (CHI1:150,334,286-150,818,098 bp) encompassing two genes KCNJ15 and ERG in the associated regions of polled and PIS-affected goats. Notably, the 10.1-kb deletion also served as the insertion site for the 480-kb duplication, as validated by PCR and Sanger sequencing. Our WGS genotyping showed that all horned goats were homozygous for the reference alleles without either the structural variants (SVs), whereas the PIS-affected goats were homozygous for both the SVs. We also demonstrated that horned, polled, and PIS-affected individuals among 333 goats from JT and three other Chinese horned breeds can be accurately classified via PCR amplification and agarose gel electrophoresis of two fragments in both SVs. CONCLUSION: Our results revealed that two genomic regions on chromosome 1 are major loci affecting the polled phenotypes in goats. We provided a diagnostic PCR to accurately classify horned, polled, and PIS-affected goats, which will enable a reliable genetic test for the early-in-life prediction of horn status in goats.


Assuntos
Cabras , Cornos , Polimorfismo de Nucleotídeo Único , Alelos , Animais , Feminino , Estudos de Associação Genética/veterinária , Cabras/genética , Masculino , Fenótipo
3.
Anim Sci J ; 92(1): e13631, 2021 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-34545661

RESUMO

Insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1) plays essential roles in the proliferation of skeletal muscle satellite cells (MuSCs). Increasing evidence has shown that IGF2BP1 regulates the expression of noncoding RNAs and mRNAs. However, the related molecular network remains to be fully understood. Therefore, we performed RNA sequencing and analyzed the microRNAs (miRNAs), long noncoding RNAs (lncRNAs), and mRNAs differentially expressed in goat MuSCs treated with IGF2BP1 overexpressing and empty vectors. A total of 36 miRNAs, 59 lncRNAs, and 44 mRNAs were differentially expressed caused by IGF2BP1. Expectedly, they were enriched in muscle development-related Rap1, PI3K-AKT, and FoxO signaling pathways. Finally, we constructed a lncRNA-miRNA-mRNA interaction network containing 30 lncRNAs, 15 miRNAs, and 34 mRNAs, in which several miRNAs, including miR-133a-3p, miR-204-5p, miR-125a-3p, miR-145-3p, and miR-423-5p, relate with cell growth and participate in muscle development. Overall, we constructed an IGF2BP1-related network, which provides new insight into the myogenic proliferation of goat.

4.
FASEB J ; 35(9): e21868, 2021 09.
Artigo em Inglês | MEDLINE | ID: mdl-34449920

RESUMO

Brown adipose tissue (BAT) plays an important role on no shivering thermogenesis during cold exposure to maintain animal body temperature and energy homeostasis. However, knowledge of the cellular transition from white adipose tissue (WAT) to BAT is still limited. In this study, we provided a comprehensive metabolomics and transcriptional signatures of goat BAT and WAT. A total of 157 metabolites were significantly changed, including 81 upregulated and 76 downregulated metabolites. In addition, we identified the citric acid cycle, fatty acid elongation, and degradation pathways as coordinately activated in BAT. Interestingly, five unsaturated fatty acids (Eicosadienoic Acid, C20:2; γ-Linolenic acid, C20:3; Arachidonic Acid, C20:4; Adrenic acid, C22:4; Docosahexaenoic acid, C22:6), Succinate, L-carnitine, and L-palmitoyl-carnitine were found to be abundant in BAT. Furthermore, L-carnitine, an intermediate of fatty acid degradation, is required for goat brown adipocyte differentiation and thermogenesis through activating AMPK pathway. However, L-carnitine decreased lipid accumulation through inducing lipolysis and thermogenesis in white adipocytes. These results revealed that there are the significant alterations in transcriptomic and metabolomic profiles between goat WAT and BAT, which may contribute to better understanding the roles of metabolites in BAT thermogenesis process.


Assuntos
Tecido Adiposo Marrom/metabolismo , Cabras/metabolismo , Termogênese/fisiologia , Adipogenia/fisiologia , Tecido Adiposo Branco/metabolismo , Animais , Diferenciação Celular/fisiologia , Regulação para Baixo/fisiologia , Metabolismo Energético/fisiologia , Ácidos Graxos Insaturados/metabolismo , Homeostase/fisiologia , Lipólise/fisiologia , Metabolômica/métodos , RNA-Seq/métodos , Transdução de Sinais/fisiologia , Regulação para Cima/fisiologia
5.
Nat Commun ; 12(1): 4161, 2021 07 06.
Artigo em Inglês | MEDLINE | ID: mdl-34230488

RESUMO

Given the pleiotropic nature of coding sequences and that many loci exhibit multiple disease associations, it is within non-coding sequence that disease-specificity likely exists. Here, we focus on joint disorders, finding among replicated loci, that GDF5 exhibits over twenty distinct associations, and we identify causal variants for two of its strongest associations, hip dysplasia and knee osteoarthritis. By mapping regulatory regions in joint chondrocytes, we pinpoint two variants (rs4911178; rs6060369), on the same risk haplotype, which reside in anatomical site-specific enhancers. We show that both variants have clinical relevance, impacting disease by altering morphology. By modeling each variant in humanized mice, we observe joint-specific response, correlating with GDF5 expression. Thus, we uncouple separate regulatory variants on a common risk haplotype that cause joint-specific disease. By broadening our perspective, we finally find that patterns of modularity at GDF5 are also found at over three-quarters of loci with multiple GWAS disease associations.


Assuntos
Éxons , Luxação do Quadril/genética , Luxação do Quadril/metabolismo , Osteoartrite do Joelho/genética , Osteoartrite do Joelho/metabolismo , Animais , Condrócitos , Modelos Animais de Doenças , Regulação da Expressão Gênica , Predisposição Genética para Doença , Estudo de Associação Genômica Ampla , Fator 5 de Diferenciação de Crescimento/genética , Fator 5 de Diferenciação de Crescimento/metabolismo , Humanos , Camundongos , Fenótipo , Sequências Reguladoras de Ácido Nucleico
6.
Animals (Basel) ; 11(5)2021 May 10.
Artigo em Inglês | MEDLINE | ID: mdl-34068539

RESUMO

Adipose tissues are mainly divided into brown adipose tissue (BAT) and white adipose tissue (WAT). WAT mainly functions to buffer excess calories, whereas BAT plays a role in the non-shivering thermogenesis to maintain body temperature and energy balance. Moreover, circRNAs play important roles in various biological processes. However, knowledge of the expression profile and function of circRNAs from BAT to WAT remains largely unknown. In this study, a total of 6610 unique circRNAs were identified in the perirenal adipose tissues of 1-day, 30-days, and 1-year goats. Functional annotation revealed that host genes of circRNAs were involved in some BAT-related pathways, such as the thyroid hormone signaling pathway, MAPK signaling pathway, and VEGF signaling pathway. Furthermore, a total of 61 DEcircRNAs were detected across three stages. Additionally, five selected circRNAs were validated by RNase R assay, qPCR, and Sanger sequencing. Finally, the circRNA-miRNA network was constructed between the DEcircRNAs and their miRNA binding sites.

7.
Int J Mol Sci ; 22(6)2021 Mar 23.
Artigo em Inglês | MEDLINE | ID: mdl-33806945

RESUMO

Circular RNA (circRNA) is a kind of novel endogenous noncoding RNA formed through back-splicing of mRNA precursor. The biogenesis, degradation, nucleus-cytoplasm transport, location, and even translation of circRNA are controlled by RNA-binding proteins (RBPs). Therefore, circRNAs and the chaperoned RBPs play critical roles in biological functions that significantly contribute to normal animal development and disease. In this review, we systematically characterize the possible molecular mechanism of circRNA-protein interactions, summarize the latest research on circRNA-protein interactions in muscle development and myocardial disease, and discuss the future application of circRNA in treating muscle diseases. Finally, we provide several valid prediction methods and experimental verification approaches. Our review reveals the significance of circRNAs and their protein chaperones and provides a reference for further study in this field.


Assuntos
Suscetibilidade a Doenças , Desenvolvimento Muscular/fisiologia , RNA Circular/genética , Proteínas de Ligação a RNA/metabolismo , Animais , Regulação da Expressão Gênica , Humanos , Edição de RNA , Transporte de RNA , RNA Mensageiro/genética
8.
Cell Mol Biol Lett ; 26(1): 4, 2021 Feb 10.
Artigo em Inglês | MEDLINE | ID: mdl-33568070

RESUMO

miRNAs are well known to be gene repressors. A newly identified class of miRNAs termed nuclear activating miRNAs (NamiRNAs), transcribed from miRNA loci that exhibit enhancer features, promote gene expression via binding to the promoter and enhancer marker regions of the target genes. Meanwhile, activated enhancers produce endogenous non-coding RNAs (named enhancer RNAs, eRNAs) to activate gene expression. During chromatin looping, transcribed eRNAs interact with NamiRNAs through enhancer-promoter interaction to perform similar functions. Here, we review the functional differences and similarities between eRNAs and NamiRNAs in myogenesis and disease. We also propose models demonstrating their mutual mechanism and function. We conclude that eRNAs are active molecules, transcriptional regulators, and partners of NamiRNAs, rather than mere RNAs produced during enhancer activation.


Assuntos
Núcleo Celular/genética , Elementos Facilitadores Genéticos/genética , MicroRNAs/genética , Desenvolvimento Muscular/genética , Transativadores/metabolismo , Animais , Humanos , MicroRNAs/metabolismo , MicroRNAs/uso terapêutico , Transcrição Genética
9.
Animals (Basel) ; 10(11)2020 Oct 23.
Artigo em Inglês | MEDLINE | ID: mdl-33114089

RESUMO

The rumen is an important digestive organ of ruminants. From the fetal to adult stage, the morphology, structure and function of the rumen change significantly. However, the knowledge of the intrinsic genetic regulation of these changes is still limited. We previously reported a genome-wide expression profile of miRNAs in pre-natal goat rumens. In this study, we combined and analyzed the transcriptomes of rumen miRNAs during pre-natal (E60 and E135) and post-natal (D30 and D150) stages. A total of 66 differentially expressed miRNAs (DEMs) were identified in the rumen tissues from D30 and D150 goats. Of these, 17 DEMs were consistently highly expressed in the rumens at the pre-weaning stages (E60, E135 and D30), while down-regulated at D150. Noteworthy, annotation analysis revealed that the target genes regulated by the DEMs were mainly enriched in MAPK signaling pathway, Jak-STAT signaling pathway and Ras signaling pathway. Interestingly, the expression of miR-148a-3p was significantly high in the embryonic stage and down-regulated at D150. The potential binding sites of miR-148a-3p in the 3'-UTR of QKI were predicted by the TargetScan and verified by the dual luciferase report assay. The co-localization of miR-148a-3p and QKI through in situ hybridization was observed in the rumen tissues but not in the intestinal tracts. Moreover, the expression of miR-148a-3p in the epithelium was significantly higher than that in the other layers of the rumen, suggesting that miR-148a-3p is involved in the development of the rumen epithelial cells by targeting QKI. Subsequently, miR-148a-3p inhibitor was found to induce the proliferation of GES-1 cells. Taken together, our study identified DEMs involved in the development of the rumen and provides insights into the regulation mechanism of rumen development in goats.

10.
Animals (Basel) ; 10(9)2020 Sep 10.
Artigo em Inglês | MEDLINE | ID: mdl-32927876

RESUMO

Brown adipose tissues have unique non-shivering thermogenesis functions, can be found in newborn ruminate animals, and then are gradually replaced by white adipose tissues in adulthood. For the purpose of exploring the intrinsic mechanism underlying the conversion process from brown (BAT) to white adipose tissue (WAT), it is necessary to utilize Quantitative PCR (qPCR) to study gene expression profiling. In this study, we identified reference genes that were consistently expressed during the transformation from goat BAT to WAT using RNA-seq data. Then, twelve genes were evaluated as candidate reference genes for qPCR in goat perirenal adipose tissue using three tools (geNorm, Normfinder, and BestKeeper). In addition, the selected reference genes were used to normalize the gene expression of PGC-1α and GPAT4. It was found that traditional reference genes, such as GAPDH, RPLP0, HPRT1, and PPIA were not suitable for target gene normalization. In contrast, CTNNB, PFDN5, and EIF3M, selected from RNA sequencing data, showed the least variation and were recommended as the best reference genes during the transformation from BAT to WAT.

11.
Cell ; 181(2): 362-381.e28, 2020 04 16.
Artigo em Inglês | MEDLINE | ID: mdl-32220312

RESUMO

During human evolution, the knee adapted to the biomechanical demands of bipedalism by altering chondrocyte developmental programs. This adaptive process was likely not without deleterious consequences to health. Today, osteoarthritis occurs in 250 million people, with risk variants enriched in non-coding sequences near chondrocyte genes, loci that likely became optimized during knee evolution. We explore this relationship by epigenetically profiling joint chondrocytes, revealing ancient selection and recent constraint and drift on knee regulatory elements, which also overlap osteoarthritis variants that contribute to disease heritability by tending to modify constrained functional sequence. We propose a model whereby genetic violations to regulatory constraint, tolerated during knee development, lead to adult pathology. In support, we discover a causal enhancer variant (rs6060369) present in billions of people at a risk locus (GDF5-UQCC1), showing how it impacts mouse knee-shape and osteoarthritis. Overall, our methods link an evolutionarily novel aspect of human anatomy to its pathogenesis.


Assuntos
Condrócitos/fisiologia , Articulação do Joelho/fisiologia , Osteoartrite/genética , Animais , Evolução Biológica , Condrócitos/metabolismo , Evolução Molecular , Predisposição Genética para Doença/genética , Fator 5 de Diferenciação de Crescimento/genética , Fator 5 de Diferenciação de Crescimento/metabolismo , Células HEK293 , Humanos , Joelho/fisiologia , Camundongos , Células NIH 3T3 , Sequências Reguladoras de Ácido Nucleico/genética , Fatores de Risco
12.
Front Genet ; 10: 1171, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31803241

RESUMO

Long noncoding RNAs (lncRNAs) have emerged as essential regulators of skeletal myogenesis, but few myogenesis-associated lncRNAs have been identified and our understanding of their regulatory mechanisms remains limited, particularly in goat. Here, we identified a novel lncRNA, TCONS_00006810 (named lncR-125b), from our previous lncRNA sequencing data on fetal (45, 60, and 105 days of gestation, three biological replicates for each point) and postnatal (3 days after birth, n = 3) goat skeletal muscle, and found that it is highly expressed in skeletal muscle and gradually upregulated during skeletal muscle satellite cell (SMSC) differentiation in goat. Notably, overexpression of lncR-125b accelerated the expression of myogenic differentiation 1 (MyoD 1) and myogenin (MyoG), and the formation of myotubes, and knockdown of lncR-125b showed opposite effects in SMSCs. Results of dual-luciferase assay and quantitative real-time polymerase chain reaction revealed that lncR-125b acts as a molecular sponge for miR-125b and that insulin-like growth factor 2 (IGF2), a critical regulator of skeletal myogenesis, is a direct target gene of miR-125b. Further analyses showed that lncR-125b negatively regulates miR-125b expression and positively regulates IGF2 expression in SMSCs. Mechanistically, lncR-125b promotes SMSC differentiation by functioning as a competing endogenous RNA (ceRNA) for miR-125b to control IGF2 expression. These findings identify lncR-125b as a novel noncoding regulator of muscle cell differentiation and skeletal muscle development in goat.

13.
PLoS One ; 13(11): e0202785, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-30388100

RESUMO

Given GDF5 involvement in hip development, and osteoarthritis (OA) and developmental hip dysplasia (DDH) risk, here we sought to assess the role(s) of GDF5 and its regulatory sequence on the development of hip morphology linked to injury risk. The brachypodism (bp) mouse, which harbors a Gdf5 inactivating mutation, was used to survey how Gdf5 loss of function impacts the development of hip morphology. Two transgenic Gdf5 reporter BAC lines were used to assess the spatiotemporal expression of Gdf5 regulatory sequences. Each BAC line was also used to assess the functional roles of upstream and downstream sequence on hip morphology. bp/bp mice had shorter femora with smaller femoral heads and necks as well as larger alpha angles, smaller anterior offsets, and smaller acetabula, compared to bp/+ mice (p<0.04). Regulatory sequences downstream of Gdf5 drove strong prenatal (E17) expression and low postnatal (6 months) expression across regions of femoral head and acetabulum. Conversely, upstream regulatory sequences drove very low expression at E17 and no detectable expression at 6 months. Importantly, downstream, but not upstream Gdf5 regulatory sequences fully restored all the key morphologic features disrupted in bp/bp mice. Hip morphology is profoundly affected by Gdf5 absence, and downstream regulatory sequences mediate its effects by controlling Gdf5 expression during development. This downstream region contains numerous enhancers harboring risk variants related to hip OA, DDH, and dislocation. We posit that subtle alterations to morphology driven by changes in downstream regulatory sequence underlie this locus' role in hip injury risk.


Assuntos
Regulação da Expressão Gênica no Desenvolvimento , Fator 5 de Diferenciação de Crescimento/genética , Quadril/anatomia & histologia , Quadril/crescimento & desenvolvimento , Animais , Deleção de Genes , Masculino , Camundongos Endogâmicos BALB C , Mutação , Sequências Reguladoras de Ácido Nucleico
14.
Gene ; 666: 158-164, 2018 Aug 05.
Artigo em Inglês | MEDLINE | ID: mdl-29751096

RESUMO

As a well-conserved microRNA, miR-183 is ubiquitously expressed in many tissues and cells including backfat and the 3T3-L1 adipocytes; however, the mechanisms regulating miR-183 in adipogenesis remain poorly understood. Here, we explored the expression pattern and role of miR-183 in adipogenesis using hircine preadipocytes. The results showed that miR-183 was up-regulated during preadipocyte differentiation, and overexpression of miR-183 enhanced lipid accumulation and dramatically increased the mRNA expression of the adipogenic genes PPARγ, C/EBPα, SREBP-1c, FAS, and ACC. Using bioinformatics tools, we predicted Smad4 to be a target of miR-183. This was subsequently validated with a luciferase reporter assay. Overexpression of miR-183 suppressed the mRNA and protein levels of Smad4 significantly, whereas inhibiting miR-183 had the opposite effect. However, inhibition of Smad4 greatly accelerated lipid deposition and increased the expression of adipogenic genes which consists with the results of miR-183 overexpression. In conclusion, these results indicate that miR-183 promotes hircine preadipocyte differentiation by targeting Smad4.


Assuntos
Adipogenia , Cabras/genética , MicroRNAs/fisiologia , Proteína Smad4/genética , Regiões 3' não Traduzidas , Adipócitos Brancos/fisiologia , Animais , Sequência de Bases , Sítios de Ligação , Células Cultivadas , Expressão Gênica , Cabras/metabolismo , Metabolismo dos Lipídeos , Interferência de RNA , Proteína Smad4/metabolismo , Gordura Subcutânea/citologia , Gordura Subcutânea/metabolismo
15.
Ann Rheum Dis ; 77(3): 450, 2018 03.
Artigo em Inglês | MEDLINE | ID: mdl-29311146

RESUMO

OBJECTIVES: Given the role of growth and differentiation factor 5 (GDF5) in knee development and osteoarthritis risk, we sought to characterise knee defects resulting from Gdf5 loss of function and how its regulatory regions control knee formation and morphology. METHODS: The brachypodism (bp) mouse line, which harbours an inactivating mutation in Gdf5, was used to survey how Gdf5 loss of function impacts knee morphology, while two transgenic Gdf5 reporter bacterial artificial chromosome mouse lines were used to assess the spatiotemporal activity and function of Gdf5 regulatory sequences in the context of clinically relevant knee anatomical features. RESULTS: Knees from homozygous bp mice (bp/bp) exhibit underdeveloped femoral condyles and tibial plateaus, no cruciate ligaments, and poorly developed menisci. Secondary ossification is also delayed in the distal femur and proximal tibia. bp/bp mice have significantly narrower femoral condyles, femoral notches and tibial plateaus, and curvier medial femoral condyles, shallower trochlea, steeper lateral tibial slopes and smaller tibial spines. Regulatory sequences upstream from Gdf5 were weakly active in the prenatal knee, while downstream regulatory sequences were active throughout life. Importantly, downstream but not upstream Gdf5 regulatory sequences fully restored all the key morphological features disrupted in the bp/bp mice. CONCLUSIONS: Knee morphology is profoundly affected by Gdf5 absence, and downstream regulatory sequences mediate its effects by controlling Gdf5 expression in knee tissues. This downstream region contains numerous enhancers harbouring human variants that span the osteoarthritis association interval. We posit that subtle alterations to morphology driven by changes in downstream regulatory sequence underlie this locus' role in osteoarthritis risk.


Assuntos
Fator 5 de Diferenciação de Crescimento/genética , Articulação do Joelho/embriologia , Osteoartrite do Joelho/genética , Animais , Predisposição Genética para Doença , Fator 5 de Diferenciação de Crescimento/metabolismo , Articulação do Joelho/metabolismo , Articulação do Joelho/patologia , Camundongos , Camundongos Endogâmicos BALB C , Camundongos Transgênicos , Mutação , Sequências Reguladoras de Ácido Nucleico/genética , Análise Espaço-Temporal , Microtomografia por Raio-X
16.
Funct Integr Genomics ; 18(1): 43-54, 2018 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-28993898

RESUMO

Muscle growth and development from fetal to neonatal stages consist of a series of delicately regulated and orchestrated changes in expression of genes. In this study, we performed whole transcriptome profiling based on RNA-Seq of caprine longissimus dorsi muscle tissue obtained from prenatal stages (days 45, 60, and 105 of gestation) and neonatal stage (the 3-day-old newborn) to identify genes that are differentially expressed and investigate their temporal expression profiles. A total of 3276 differentially expressed genes (DEGs) were identified (Q value < 0.01). Time-series expression profile clustering analysis indicated that DEGs were significantly clustered into eight clusters which can be divided into two classes (Q value < 0.05), class I profiles with downregulated patterns and class II profiles with upregulated patterns. Based on cluster analysis, GO enrichment analysis found that 75, 25, and 8 terms to be significantly enriched in biological process (BP), cellular component (CC), and molecular function (MF) categories in class I profiles, while 35, 21, and 8 terms to be significantly enriched in BP, CC, and MF in class II profiles. KEGG pathway analysis revealed that DEGs from class I profiles were significantly enriched in 22 pathways and the most enriched pathway was Rap1 signaling pathway. DEGs from class II profiles were significantly enriched in 17 pathways and the mainly enriched pathway was AMPK signaling pathway. Finally, six selected DEGs from our sequencing results were confirmed by qPCR. Our study provides a comprehensive understanding of the molecular mechanisms during goat skeletal muscle development from fetal to neonatal stages and valuable information for future studies of muscle development in goats.


Assuntos
Desenvolvimento Fetal , Perfilação da Expressão Gênica/métodos , Regulação da Expressão Gênica no Desenvolvimento , Cabras/genética , Músculo Esquelético/metabolismo , Animais , Animais Recém-Nascidos , Feminino , Cabras/crescimento & desenvolvimento , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Desenvolvimento Muscular , Músculo Esquelético/crescimento & desenvolvimento , Análise de Sequência de RNA/métodos , Transdução de Sinais , Transcriptoma
17.
Nat Genet ; 49(8): 1202-1210, 2017 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-28671685

RESUMO

Variants in GDF5 are associated with human arthritis and decreased height, but the causal mutations are still unknown. We surveyed the Gdf5 locus for regulatory regions in transgenic mice and fine-mapped separate enhancers controlling expression in joints versus growing ends of long bones. A large downstream regulatory region contains a novel growth enhancer (GROW1), which is required for normal Gdf5 expression at ends of developing bones and for normal bone lengths in vivo. Human GROW1 contains a common base-pair change that decreases enhancer activity and colocalizes with peaks of positive selection in humans. The derived allele is rare in Africa but common in Eurasia and is found in Neandertals and Denisovans. Our results suggest that an ancient regulatory variant in GROW1 has been repeatedly selected in northern environments and that past selection on growth phenotypes explains the high frequency of a GDF5 haplotype that also increases arthritis susceptibility in many human populations.


Assuntos
Elementos Facilitadores Genéticos , Fator 5 de Diferenciação de Crescimento/genética , Osteoartrite/genética , Seleção Genética , Alelos , Animais , Cromossomos Artificiais Bacterianos , Evolução Molecular , Feminino , Predisposição Genética para Doença , Variação Genética , Humanos , Masculino , Camundongos , Camundongos Endogâmicos C57BL , Camundongos Endogâmicos CBA , Camundongos Transgênicos
18.
Mol Reprod Dev ; 83(11): 958-967, 2016 11.
Artigo em Inglês | MEDLINE | ID: mdl-27627189

RESUMO

Extensive variation in reproduction has arisen in Chinese Mongolian sheep during recent domestication. Hu and Small-tailed Han sheep, for example, have become non-seasonal breeders and exhibit higher fecundity than Tan and Ujumqin breeds. We therefore scanned reproduction-related single-nucleotide variations from methylated DNA-immunoprecipitation sequencing data generated from each of those four breeds to uncover potential mechanisms underlying this breed variation. We generated a high-quality map of single nucleotide variations (SNVs) in DNA methylation enriched regions, and found that the majority of variants are located within non-coding regions. We identified 359 SNVs within the Sheep Quantitative Trait Locus (QTL) database. Nineteen of these SNVs associated with the Aseasonal Reproduction QTL, and 10 out of the 19 reside close to genes with known reproduction functions. We also identified the well-known FecB mutation in high-fecundity sheep (Hu and Small-tailed Han sheep). When we applied these FecB finding to our breeding system, we improved lambing rate by 175%. In summary, this study provided strong candidate SNVs associated with sheep fecundity that can serve as targets for functional testing and to enhance selective breeding strategies. Mol. Reprod. Dev. 83: 958-967, 2016 © 2016 Wiley Periodicals, Inc.


Assuntos
Bases de Dados de Ácidos Nucleicos , Loci Gênicos , Polimorfismo de Nucleotídeo Único , Reprodução/genética , Ovinos/genética , Animais , Feminino , Masculino
19.
Sci Rep ; 6: 26770, 2016 05 27.
Artigo em Inglês | MEDLINE | ID: mdl-27230812

RESUMO

Tibetan sheep have lived on the Tibetan Plateau for thousands of years; however, the process and consequences of adaptation to this extreme environment have not been elucidated for important livestock such as sheep. Here, seven sheep breeds, representing both highland and lowland breeds from different areas of China, were genotyped for a genome-wide collection of single-nucleotide polymorphisms (SNPs). The FST and XP-EHH approaches were used to identify regions harbouring local positive selection between these highland and lowland breeds, and 236 genes were identified. We detected selection events spanning genes involved in angiogenesis, energy production and erythropoiesis. In particular, several candidate genes were associated with high-altitude hypoxia, including EPAS1, CRYAA, LONP1, NF1, DPP4, SOD1, PPARG and SOCS2. EPAS1 plays a crucial role in hypoxia adaption; therefore, we investigated the exon sequences of EPAS1 and identified 12 mutations. Analysis of the relationship between blood-related phenotypes and EPAS1 genotypes in additional highland sheep revealed that a homozygous mutation at a relatively conserved site in the EPAS1 3' untranslated region was associated with increased mean corpuscular haemoglobin concentration and mean corpuscular volume. Taken together, our results provide evidence of the genetic diversity of highland sheep and indicate potential high-altitude hypoxia adaptation mechanisms, including the role of EPAS1 in adaptation.


Assuntos
Aclimatação , Altitude , Ovinos/genética , Animais , Mapeamento Cromossômico , Feminino , Genoma , Genótipo , Masculino , Filogeografia , Polimorfismo de Nucleotídeo Único , Seleção Genética
20.
Sci Rep ; 6: 24360, 2016 Apr 11.
Artigo em Inglês | MEDLINE | ID: mdl-27063570

RESUMO

Recent advances in our ability to design DNA binding factors with specificity for desired sequences have resulted in a revolution in genetic engineering, enabling directed changes to the genome to be made relatively easily. Technologies that facilitate specific and precise genome editing, such as knock-in, are critical for determining the functions of genes and for understanding fundamental biological processes. The CRISPR/Cas9 system has recently emerged as a powerful tool for functional genomic studies in mammals. Rosa26 gene can encode a non-essential nuclear RNA in almost all organizations, and become a hot point of exogenous gene insertion. Here, we describe efficient, precise CRISPR/Cas9-mediated Integration using a donor vector with tGFP sequence targeted in the sheep genomic Rosa26 locus. We succeeded in integrating with high efficiency an exogenous tGFP (turboGFP) gene into targeted genes in frame. Due to its simplicity, design flexibility, and high efficiency, we propose that CRISPR/Cas9-mediated knock-in will become a standard method for the generation transgenic sheep.


Assuntos
Sistemas CRISPR-Cas/genética , Técnicas de Introdução de Genes/métodos , RNA Guia/genética , Animais , Animais Geneticamente Modificados/metabolismo , Linhagem Celular , Feminino , Fibroblastos/citologia , Fibroblastos/metabolismo , Genes Reporter , Loci Gênicos , Vetores Genéticos/genética , Vetores Genéticos/metabolismo , Microscopia de Fluorescência , Ovário/metabolismo , Ovinos
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