Background The reproductive performance of chickens mainly depends on the development of follicles.Abnor-mal follicle development can lead to decreased reproductive performance and even ovarian disease among chick-ens...Background The reproductive performance of chickens mainly depends on the development of follicles.Abnor-mal follicle development can lead to decreased reproductive performance and even ovarian disease among chick-ens.Chicken is the only non-human animal with a high incidence of spontaneous ovarian cancer.In recent years,the involvement of circRNAs in follicle development and atresia regulation has been confirmed.Results In the present study,we used healthy and atretic chicken follicles for circRNA RNC-seq.The results showed differential expression of circRALGPS2.It was then confirmed that circRALGPS2 can translate into a protein,named cir-cRALGPS2-212aa,which has IRES activity.Next,we found that circRALGPS2-212aa promotes apoptosis and autophagy in chicken granulosa cells by forming a complex with PARP1 and HMGB1.Conclusions Our results revealed that circRALGPS2 can regulate chicken granulosa cell apoptosis and autophagy through the circRALGPS2-212aa/PARP1/HMGB1 axis.展开更多
【目的】利用转录组测序(transcriptome sequencing,RNA-Seq)和全长翻译组测序(ribosome-nascent-chain-complex sequencing,RNC-Seq)分析比对转录和翻译两个不同水平上牛骨骼肌的生长发育过程,解析其发育特征和规律,并筛选出可能在转...【目的】利用转录组测序(transcriptome sequencing,RNA-Seq)和全长翻译组测序(ribosome-nascent-chain-complex sequencing,RNC-Seq)分析比对转录和翻译两个不同水平上牛骨骼肌的生长发育过程,解析其发育特征和规律,并筛选出可能在转录组和翻译组共同参与牛肌肉生长发育过程的关键基因,为后续功能基因的筛选和利用提供目标靶点。【方法】采集4月龄牛胚胎的骨骼肌卫星细胞的增殖期(proliferative period,GM)和分化期第2天(the second day of differentiation,DM2)的样品进行RNA-Seq和RNC-Seq分析,对其差异表达基因进行生物信息学分析,从翻译调控的角度分析与骨骼肌发育相关的差异基因。【结果】BSMSCs的DM2期相较于GM期差异基因筛选表明,转录组共筛选获得2808个差异基因(上调基因1749个,下调基因1059个),翻译组共筛选获得3740个差异基因(上调基因1769个,下调基因1971个),转录组和翻译组共有的差异表达基因725个,其中表达趋势相同的基因618个,表达趋势相反的基因107个。功能富集分析获得103个与骨骼肌发育相关的基因。进一步深入分析发现,转录水平的调控和翻译水平的调控具有相对独立性,且翻译调控对转录调控具有一定的回调作用,筛选获得了22个与牛肌肉的生长发育密切相关的标靶基因(CDK1、SERPINE1、THBS1、IGFBP3、CNB1、GADD45A、CYCS、CDK2、CCND1、CCNE2、ZMAT3、ACTB、ACTA1、TNNT1、MYH7、ACTG1、TUBA1C、TNNC1、KIF20A、TUBB4B、MYL3、TUBB3)及13个存在翻译回调现象的关键基因(GREM1、EGR1、SFRP4、NKD2、DKK3、IGFBP3、CTSK、ITGAV、CTSV、CDKN1A、SESN3、GADD45A、ZMAT3)。【结论】本研究筛选获得了22个可能与牛肌肉的生长发育密切相关的关键基因和13个存在翻译回调的关键基因,为进一步利用分子手段调节牛肌肉生长发育过程及进行新品种培育提供了重要的靶点。展开更多
A great number of non-coding RNAs(ncRNAs) account for the majority of the genome. The translation of these ncRNAs has been noted but seriously underestimated due to both technological and theoretical limitations. Base...A great number of non-coding RNAs(ncRNAs) account for the majority of the genome. The translation of these ncRNAs has been noted but seriously underestimated due to both technological and theoretical limitations. Based on the development of ribosome profiling(Ribo-seq), full length translating RNA analysis(RNC-seq) and mass spectrometry technology, more and more ncRNAs are being found to be translated in different organism, and some of them can produce functional peptides. While recently, not only individual new functional proteins, but also a new proteome have been experimentally discovered to be encoded by endogenous lncRNAs and circRNAs. These new proteins are of biological significance, suggesting the connection of the translation of ncRNAs to human physiology and diseases. Therefore, an in-depth and systematic understanding of the coding capabilities of ncRNAs is necessary for basic biology and medicine. In this review, we summarize the advances in the field of discovering this new proteome, i.e. "ncRNA-coded" proteins.展开更多
基金This research was funded by The National Key Research and Development Program of China,grant number 2021YFD1300600China Agriculture Research System of MOF and MARA,grant number CARS-40+1 种基金Sichuan Science and Technology Program,grant number 2021YFYZ0007,2021YFYZ0031 and 2022YFYZ0005National Natural Science Foundation of China Grants,grant number 31972543.
文摘Background The reproductive performance of chickens mainly depends on the development of follicles.Abnor-mal follicle development can lead to decreased reproductive performance and even ovarian disease among chick-ens.Chicken is the only non-human animal with a high incidence of spontaneous ovarian cancer.In recent years,the involvement of circRNAs in follicle development and atresia regulation has been confirmed.Results In the present study,we used healthy and atretic chicken follicles for circRNA RNC-seq.The results showed differential expression of circRALGPS2.It was then confirmed that circRALGPS2 can translate into a protein,named cir-cRALGPS2-212aa,which has IRES activity.Next,we found that circRALGPS2-212aa promotes apoptosis and autophagy in chicken granulosa cells by forming a complex with PARP1 and HMGB1.Conclusions Our results revealed that circRALGPS2 can regulate chicken granulosa cell apoptosis and autophagy through the circRALGPS2-212aa/PARP1/HMGB1 axis.
文摘【目的】利用转录组测序(transcriptome sequencing,RNA-Seq)和全长翻译组测序(ribosome-nascent-chain-complex sequencing,RNC-Seq)分析比对转录和翻译两个不同水平上牛骨骼肌的生长发育过程,解析其发育特征和规律,并筛选出可能在转录组和翻译组共同参与牛肌肉生长发育过程的关键基因,为后续功能基因的筛选和利用提供目标靶点。【方法】采集4月龄牛胚胎的骨骼肌卫星细胞的增殖期(proliferative period,GM)和分化期第2天(the second day of differentiation,DM2)的样品进行RNA-Seq和RNC-Seq分析,对其差异表达基因进行生物信息学分析,从翻译调控的角度分析与骨骼肌发育相关的差异基因。【结果】BSMSCs的DM2期相较于GM期差异基因筛选表明,转录组共筛选获得2808个差异基因(上调基因1749个,下调基因1059个),翻译组共筛选获得3740个差异基因(上调基因1769个,下调基因1971个),转录组和翻译组共有的差异表达基因725个,其中表达趋势相同的基因618个,表达趋势相反的基因107个。功能富集分析获得103个与骨骼肌发育相关的基因。进一步深入分析发现,转录水平的调控和翻译水平的调控具有相对独立性,且翻译调控对转录调控具有一定的回调作用,筛选获得了22个与牛肌肉的生长发育密切相关的标靶基因(CDK1、SERPINE1、THBS1、IGFBP3、CNB1、GADD45A、CYCS、CDK2、CCND1、CCNE2、ZMAT3、ACTB、ACTA1、TNNT1、MYH7、ACTG1、TUBA1C、TNNC1、KIF20A、TUBB4B、MYL3、TUBB3)及13个存在翻译回调现象的关键基因(GREM1、EGR1、SFRP4、NKD2、DKK3、IGFBP3、CTSK、ITGAV、CTSV、CDKN1A、SESN3、GADD45A、ZMAT3)。【结论】本研究筛选获得了22个可能与牛肌肉的生长发育密切相关的关键基因和13个存在翻译回调的关键基因,为进一步利用分子手段调节牛肌肉生长发育过程及进行新品种培育提供了重要的靶点。
基金supported by the National Key Research and Development Program (2017YFA0505100, 2017YFA0505001, 2018YFC0910202)the National Natural and Science Foundation of China (81372135 to TW+1 种基金81322028 and 31300649 to GZ31570828 and 31770888 to Q.Y.H.)。
文摘A great number of non-coding RNAs(ncRNAs) account for the majority of the genome. The translation of these ncRNAs has been noted but seriously underestimated due to both technological and theoretical limitations. Based on the development of ribosome profiling(Ribo-seq), full length translating RNA analysis(RNC-seq) and mass spectrometry technology, more and more ncRNAs are being found to be translated in different organism, and some of them can produce functional peptides. While recently, not only individual new functional proteins, but also a new proteome have been experimentally discovered to be encoded by endogenous lncRNAs and circRNAs. These new proteins are of biological significance, suggesting the connection of the translation of ncRNAs to human physiology and diseases. Therefore, an in-depth and systematic understanding of the coding capabilities of ncRNAs is necessary for basic biology and medicine. In this review, we summarize the advances in the field of discovering this new proteome, i.e. "ncRNA-coded" proteins.
