Background:The role of non-coding RNAs in the porcine muscle metabolism is poorly understood,with few studies investigating their expression patterns in response to nutrient supply.Therefore,we aimed to investigate th...Background:The role of non-coding RNAs in the porcine muscle metabolism is poorly understood,with few studies investigating their expression patterns in response to nutrient supply.Therefore,we aimed to investigate the changes in microRNAs(miRNAs),long intergenic non-coding RNAs(lincRNAs)and mRNAs muscle expression before and after food intake.Results:We measured the miRNA,lincRNA and mRNA expression levels in the gluteus medius muscle of 12 gilts in a fasting condition(AL-T0)and 24 gilts fed ad libitum during either 5 h.(AL-T1,N=12)or 7 h.(AL-T2,N=12)prior to slaughter.The small RNA fraction was extracted from muscle samples retrieved from the 36 gilts and sequenced,whereas lincRNA and mRNA expression data were already available.In terms of mean and variance,the expression profiles of miRNAs and lincRNAs in the porcine muscle were quite different than those of mRNAs.Food intake induced the differential expression of 149(AL-T0/AL-T1)and 435(AL-T0/AL-T2)mRNAs,6(AL-T0/AL-T1)and 28(AL-T0/AL-T2)miRNAs and none lincRNAs,while the number of differentially dispersed genes was much lower.Among the set of differentially expressed miRNAs,we identified ssc-miR-148a-3p,ssc-miR-22-3p and ssc-miR-1,which play key roles in the regulation of glucose and lipid metabolism.Besides,co-expression network analyses revealed several miRNAs that putatively interact with mRNAs playing key metabolic roles and that also showed differential expression before and after feeding.One case example was represented by seven miRNAs(ssc-miR-148a-3p,ssc-miR-151-3p,ssc-miR-30a-3p,ssc-miR-30e-3p,ssc-miR-421-5p,ssc-miR-493-5p and ssc-miR-503)which putatively interact with the PDK4 mRNA,one of the master regulators of glucose utilization and fatty acid oxidation.Conclusions:As a whole,our results evidence that microRNAs are likely to play an important role in the porcine skeletal muscle metabolic adaptation to nutrient availability.展开更多
Pigs are globally farmed animals which provide protein for human consumption in the form of skeletal muscle. To better understand the function of long intergenic noncoding RNAs(linc RNAs) in porcine skeletal muscle gr...Pigs are globally farmed animals which provide protein for human consumption in the form of skeletal muscle. To better understand the function of long intergenic noncoding RNAs(linc RNAs) in porcine skeletal muscle growth and development, we collected RNA-seq data from porcine longissimus dorsi muscle(LDM) during embryonic development. We identified a total of 739 linc RNA transcripts, which were distributed on all chromosomes except the chromosome Y, and analyzed their molecular characteristics. Compared to protein-coding genes, linc RNAs showed shorter transcripts, longer exons, fewer exons and higher tissue specificity. In addition, the abundance of linc RNAs in five embryonic development stages were analyzed and 45 differentially expressed linc RNAs were screened, three of which were highly expressed in LDM during porcine embryonic development. Finally, we predicted the potential target genes and functions of the linc RNAs, and identified 1 537 cis-target genes and 8 571 trans-target genes. Furthermore, we identified two key candidate linc RNAs involved in muscle development, XLOC_024652 and XLOC_001832, for post-trial validation. Our results provide a genome-wide resource of linc RNAs which are potentially involved in porcine embryonic skeletal muscle development and lay a foundation for the further study of their functions.展开更多
Objective Cytokine responses to activation of innate immunity differ between individuals,yet the genomic and tissue-specific transcriptomic determinants of inflammatory responsiveness are not well understood. We hypot...Objective Cytokine responses to activation of innate immunity differ between individuals,yet the genomic and tissue-specific transcriptomic determinants of inflammatory responsiveness are not well understood. We hypothesized that tissue-specific mRNA and long intergenic non-coding RNA (lincRNA) induction differs between individuals with divergent evoked inflammatory responses.展开更多
猪和人类有相似的心血管系统、代谢特征和器官大小。因此,近些年猪逐渐成为研究能量代谢、人类肥胖和器官移植的理想医学动物模型。数千年的人工选择已经使家猪具有了巨大的表型多样性,例如,不同的品种猪的脂肪和肌肉含量有很大的差异...猪和人类有相似的心血管系统、代谢特征和器官大小。因此,近些年猪逐渐成为研究能量代谢、人类肥胖和器官移植的理想医学动物模型。数千年的人工选择已经使家猪具有了巨大的表型多样性,例如,不同的品种猪的脂肪和肌肉含量有很大的差异。因此,这些品系是研究脂肪沉积和肌肉发育的很好的模型。LincRNA是一类长链非编码RNA,在包括转录调控的多个生物学过程中发挥调控作用。在之前的研究中，科学家鉴定了4515个猪基因组内的lincRNA基因（zhou et al．2014）。然而，至今仍不清楚lincRNA是否在猪的脂肪沉积和肌肉发育过程中发挥调控作用。展开更多
Maintenance of pluripotency depends to diverse regulatory factors.Studies in embryonic stem cells(ESCs)have indicated that large intergenic non-coding RNAs(lincRNAs)are involved in the regulatory network of pluripoten...Maintenance of pluripotency depends to diverse regulatory factors.Studies in embryonic stem cells(ESCs)have indicated that large intergenic non-coding RNAs(lincRNAs)are involved in the regulatory network of pluripotency.However,the presence and function of pluripotency-associated lincRNAs in cancer cells with pluripotency features are unknown.In this study,we used embryonal carcinoma(EC)P19 cell lines to investigate the expression level of Halr1 in pluripotency and retinoic acid(RA)-induced differentiated states.Down-regulation of pluripotency associated factors such as OCT4,NANOG,SSEA1 and alkaline phosphatase at transcript and protein levels were used to confirm the differentiated status of P19 cells.Quantitative measurement of Halr1 transcript levels revealed a 79% decrease during RA-induced differentiation of P19 cells.These results indicate that upon exiting the pluripotency state the expression level of Halr1 similar to core pluripotency factors is remarkably reduced.展开更多
Over the past two decades, numerous non-coding RNAs(ncRNAs) have been identified in different biological systems including virology, especially in large DNA viruses such as herpesviruses. As a representative oncogenic...Over the past two decades, numerous non-coding RNAs(ncRNAs) have been identified in different biological systems including virology, especially in large DNA viruses such as herpesviruses. As a representative oncogenic alphaherpesvirus, Marek’s disease virus(MDV) causes an important immunosuppressive and rapid-onset neoplastic disease of poultry, namely Marek’s disease(MD). Vaccinations can efficiently prevent the onset of MD lymphomas and other clinical disease, often heralded as the first successful example of vaccination-based control of cancer. MDV infection is also an excellent model for research into virally-induced tumorigenesis. Recently, great progress has been made in understanding the functions of ncRNAs in MD biology.Herein, we give a review of the discovery and identification of MDV-encoded viral miRNAs, focusing on the genomics,expression profiles, and emerging critical roles of MDV-1 miRNAs as oncogenic miRNAs(oncomiRs) or tumor suppressor genes involved in the induction of MD lymphomas. We also described the involvements of host cellular miRNAs, lincRNAs, and circRNAs participating in MDV life cycle, pathogenesis, and/or tumorigenesis. The prospects, strategies, and new techniques such as the CRISPR/Cas9-based gene editing applicable for further investigation into the ncRNA-mediated regulatory mechanisms in MDV pathogenesis/oncogenesis were also discussed, together with the possibilities of future studies on antiviral therapy and the development of new efficient MD vaccines.展开更多
基金The research presented in this publication was funded by grants AGL2013–48742-C2–1-R and AGL2013–48742-C2–2-R awarded by the Spanish Ministry of Economy and Competitivity.We also acknowledge the support of the Spanish Ministry of Economy and Competitivity for the Center of Excellence Severo Ochoa 2016–2019(SEV-2015-0533)grant awarded to the Centre for Research in Agricultural Genomics(CRAG).E.Mármol-Sánchez was funded with a PhD fellowship FPU15/01733 awarded by the Spanish Ministry of Education and Culture(MECD).Y.Ramayo-Caldas is financially supported by the European Union H2020 Research and Innovation programme under Marie Skłodowska-Curie grant(P-Sphere)agreement N°6655919.T.F.Cardoso was funded with a fellowship from the CAPES Foundation-Coordination of Improvement of Higher Education,Ministry of Education of the Federal Government of Brazil.Thanks also to the CERCA Programme of the Generalitat de Catalunya.
文摘Background:The role of non-coding RNAs in the porcine muscle metabolism is poorly understood,with few studies investigating their expression patterns in response to nutrient supply.Therefore,we aimed to investigate the changes in microRNAs(miRNAs),long intergenic non-coding RNAs(lincRNAs)and mRNAs muscle expression before and after food intake.Results:We measured the miRNA,lincRNA and mRNA expression levels in the gluteus medius muscle of 12 gilts in a fasting condition(AL-T0)and 24 gilts fed ad libitum during either 5 h.(AL-T1,N=12)or 7 h.(AL-T2,N=12)prior to slaughter.The small RNA fraction was extracted from muscle samples retrieved from the 36 gilts and sequenced,whereas lincRNA and mRNA expression data were already available.In terms of mean and variance,the expression profiles of miRNAs and lincRNAs in the porcine muscle were quite different than those of mRNAs.Food intake induced the differential expression of 149(AL-T0/AL-T1)and 435(AL-T0/AL-T2)mRNAs,6(AL-T0/AL-T1)and 28(AL-T0/AL-T2)miRNAs and none lincRNAs,while the number of differentially dispersed genes was much lower.Among the set of differentially expressed miRNAs,we identified ssc-miR-148a-3p,ssc-miR-22-3p and ssc-miR-1,which play key roles in the regulation of glucose and lipid metabolism.Besides,co-expression network analyses revealed several miRNAs that putatively interact with mRNAs playing key metabolic roles and that also showed differential expression before and after feeding.One case example was represented by seven miRNAs(ssc-miR-148a-3p,ssc-miR-151-3p,ssc-miR-30a-3p,ssc-miR-30e-3p,ssc-miR-421-5p,ssc-miR-493-5p and ssc-miR-503)which putatively interact with the PDK4 mRNA,one of the master regulators of glucose utilization and fatty acid oxidation.Conclusions:As a whole,our results evidence that microRNAs are likely to play an important role in the porcine skeletal muscle metabolic adaptation to nutrient availability.
基金financially supported by the National Natural Science Foundation of China (31601167, 31972537 and U1204326)the Natural Science Foundation of Henan Province, China (182300410027)+1 种基金the Central Plains Technological Innovation Leading Talents Project of Henan Province, China (194200510022)the Nanhu Scholars Program of Xinyang Normal University, China。
文摘Pigs are globally farmed animals which provide protein for human consumption in the form of skeletal muscle. To better understand the function of long intergenic noncoding RNAs(linc RNAs) in porcine skeletal muscle growth and development, we collected RNA-seq data from porcine longissimus dorsi muscle(LDM) during embryonic development. We identified a total of 739 linc RNA transcripts, which were distributed on all chromosomes except the chromosome Y, and analyzed their molecular characteristics. Compared to protein-coding genes, linc RNAs showed shorter transcripts, longer exons, fewer exons and higher tissue specificity. In addition, the abundance of linc RNAs in five embryonic development stages were analyzed and 45 differentially expressed linc RNAs were screened, three of which were highly expressed in LDM during porcine embryonic development. Finally, we predicted the potential target genes and functions of the linc RNAs, and identified 1 537 cis-target genes and 8 571 trans-target genes. Furthermore, we identified two key candidate linc RNAs involved in muscle development, XLOC_024652 and XLOC_001832, for post-trial validation. Our results provide a genome-wide resource of linc RNAs which are potentially involved in porcine embryonic skeletal muscle development and lay a foundation for the further study of their functions.
文摘Objective Cytokine responses to activation of innate immunity differ between individuals,yet the genomic and tissue-specific transcriptomic determinants of inflammatory responsiveness are not well understood. We hypothesized that tissue-specific mRNA and long intergenic non-coding RNA (lincRNA) induction differs between individuals with divergent evoked inflammatory responses.
文摘猪和人类有相似的心血管系统、代谢特征和器官大小。因此,近些年猪逐渐成为研究能量代谢、人类肥胖和器官移植的理想医学动物模型。数千年的人工选择已经使家猪具有了巨大的表型多样性,例如,不同的品种猪的脂肪和肌肉含量有很大的差异。因此,这些品系是研究脂肪沉积和肌肉发育的很好的模型。LincRNA是一类长链非编码RNA,在包括转录调控的多个生物学过程中发挥调控作用。在之前的研究中，科学家鉴定了4515个猪基因组内的lincRNA基因（zhou et al．2014）。然而，至今仍不清楚lincRNA是否在猪的脂肪沉积和肌肉发育过程中发挥调控作用。
基金supported by a Ferdowsi University of Mashhad grant to HD(No.22534).
文摘Maintenance of pluripotency depends to diverse regulatory factors.Studies in embryonic stem cells(ESCs)have indicated that large intergenic non-coding RNAs(lincRNAs)are involved in the regulatory network of pluripotency.However,the presence and function of pluripotency-associated lincRNAs in cancer cells with pluripotency features are unknown.In this study,we used embryonal carcinoma(EC)P19 cell lines to investigate the expression level of Halr1 in pluripotency and retinoic acid(RA)-induced differentiated states.Down-regulation of pluripotency associated factors such as OCT4,NANOG,SSEA1 and alkaline phosphatase at transcript and protein levels were used to confirm the differentiated status of P19 cells.Quantitative measurement of Halr1 transcript levels revealed a 79% decrease during RA-induced differentiation of P19 cells.These results indicate that upon exiting the pluripotency state the expression level of Halr1 similar to core pluripotency factors is remarkably reduced.
基金supported by the National Natural Science Foundation of China(U21A20260)the Natural Science Foundation of Henan Province(212300410359)+1 种基金the Independent innovation project of Henan Academy of Agricultural Sciences(2022ZC65)the BBSRC Newton Fund Joint Centre Awards on“UK-China Centre of Excellence for Research on Avian Diseases”(BBS/OS/NW/000007)。
文摘Over the past two decades, numerous non-coding RNAs(ncRNAs) have been identified in different biological systems including virology, especially in large DNA viruses such as herpesviruses. As a representative oncogenic alphaherpesvirus, Marek’s disease virus(MDV) causes an important immunosuppressive and rapid-onset neoplastic disease of poultry, namely Marek’s disease(MD). Vaccinations can efficiently prevent the onset of MD lymphomas and other clinical disease, often heralded as the first successful example of vaccination-based control of cancer. MDV infection is also an excellent model for research into virally-induced tumorigenesis. Recently, great progress has been made in understanding the functions of ncRNAs in MD biology.Herein, we give a review of the discovery and identification of MDV-encoded viral miRNAs, focusing on the genomics,expression profiles, and emerging critical roles of MDV-1 miRNAs as oncogenic miRNAs(oncomiRs) or tumor suppressor genes involved in the induction of MD lymphomas. We also described the involvements of host cellular miRNAs, lincRNAs, and circRNAs participating in MDV life cycle, pathogenesis, and/or tumorigenesis. The prospects, strategies, and new techniques such as the CRISPR/Cas9-based gene editing applicable for further investigation into the ncRNA-mediated regulatory mechanisms in MDV pathogenesis/oncogenesis were also discussed, together with the possibilities of future studies on antiviral therapy and the development of new efficient MD vaccines.
