Long noncoding RNAs(lncRNAs)have been confirmed to play a crucial role in various biological processes across several species.Though many efforts have been devoted to the expansion of the lncRNAs landscape,much about ...Long noncoding RNAs(lncRNAs)have been confirmed to play a crucial role in various biological processes across several species.Though many efforts have been devoted to the expansion of the lncRNAs landscape,much about lncRNAs is still unknown due to their great complexity.The development of high-throughput technologies and the constantly improved bioinformatic methods have resulted in a rapid expansion of lncRNA research and relevant databases.In this review,we introduced genome-wide research of lncRNAs in three parts:(i)novel lncRNA identification by high-throughput sequencing and computational pipelines;(ii)functional characterization of lncRNAs by expression atlas profiling,genome-scale screening,and the research of cancer-related lncRNAs;(iii)mechanism research by large-scale experimental technologies and computational analysis.Besides,primary experimental methods and bioinformatic pipelines related to these three parts are summarized.This review aimed to provide a comprehensive and systemic overview of lncRNA genome-wide research strategies and indicate a genome-wide lncRNA research system.展开更多
Skeletal muscle differentiation is a highly coordinated process that involves many cellular signaling pathways and microRNAs(miRNAs).A group of muscle-specific miRNAs has been reported to promote myogenesis by suppres...Skeletal muscle differentiation is a highly coordinated process that involves many cellular signaling pathways and microRNAs(miRNAs).A group of muscle-specific miRNAs has been reported to promote myogenesis by suppressing key signaling pathways for cell growth.However,the functional role and regulatory mechanism of most non-muscle-specific miRNAs with stage-specific changes during differentiation are largely unclear.Here,we describe the functional characterization of miR-101a/b,a pair of non-muscle-specific miRNAs that show the largest change among a group of transiently upregulated miRNAs during myogenesis in C2C12 cells.The overexpression of miR-101a/b inhibits myoblast differentiation by suppressing the p38/MAPK,Interferon Gamma,and Wnt pathways and enhancing the C/EBP pathway.Mef2a,a key protein in the p38/MAPK pathway,was identified as a direct target of miR-101a/b.Interestingly,we found that the long non-coding RNA(lncRNA)Malat1,which promotes muscle differentiation,interacts with miR-101a/b,and this interaction competes with Mef2a mRNA to relieve the inhibition of the p38/MAPK pathway during myogenesis.These results uncovered a“braking”role in differentiation of transiently upregulated miRNAs and provided new insights into the competing endogenous RNA(ceRNA)regulatory mechanism in myoblast differentiation and myogenesis.展开更多
基金supported by grants from the National Natural Science Foundation of China(No.82273158,81974436,81900559,and 31701116)the Natural Science Foundation of Guangdong Province,China(No.2022A1515010704,2022A1515011413,and 2021A1515010477)+2 种基金the Program for Guangdong Introducing Innovative and Entrepreneurial Teams(China)(No.2019ZT08Y485)Guangzhou Science and Technology Plan Projects(China)(No.202102020104)the Guangdong Province Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation(China)(No.2020B1212060018).
文摘Long noncoding RNAs(lncRNAs)have been confirmed to play a crucial role in various biological processes across several species.Though many efforts have been devoted to the expansion of the lncRNAs landscape,much about lncRNAs is still unknown due to their great complexity.The development of high-throughput technologies and the constantly improved bioinformatic methods have resulted in a rapid expansion of lncRNA research and relevant databases.In this review,we introduced genome-wide research of lncRNAs in three parts:(i)novel lncRNA identification by high-throughput sequencing and computational pipelines;(ii)functional characterization of lncRNAs by expression atlas profiling,genome-scale screening,and the research of cancer-related lncRNAs;(iii)mechanism research by large-scale experimental technologies and computational analysis.Besides,primary experimental methods and bioinformatic pipelines related to these three parts are summarized.This review aimed to provide a comprehensive and systemic overview of lncRNA genome-wide research strategies and indicate a genome-wide lncRNA research system.
基金supported by the National Natural Science Foundation of China(31970604,31701116,31770879,31771459,31900903,81870449,81974436)the Major Research Plan of the National Natural Science Foundation of China(91940000)+1 种基金the Fundamental Research Funds for the Central Universities(20lgpy112)Science and Technology New Star in ZhuJiang Guangzhou City(201806010151).
文摘Skeletal muscle differentiation is a highly coordinated process that involves many cellular signaling pathways and microRNAs(miRNAs).A group of muscle-specific miRNAs has been reported to promote myogenesis by suppressing key signaling pathways for cell growth.However,the functional role and regulatory mechanism of most non-muscle-specific miRNAs with stage-specific changes during differentiation are largely unclear.Here,we describe the functional characterization of miR-101a/b,a pair of non-muscle-specific miRNAs that show the largest change among a group of transiently upregulated miRNAs during myogenesis in C2C12 cells.The overexpression of miR-101a/b inhibits myoblast differentiation by suppressing the p38/MAPK,Interferon Gamma,and Wnt pathways and enhancing the C/EBP pathway.Mef2a,a key protein in the p38/MAPK pathway,was identified as a direct target of miR-101a/b.Interestingly,we found that the long non-coding RNA(lncRNA)Malat1,which promotes muscle differentiation,interacts with miR-101a/b,and this interaction competes with Mef2a mRNA to relieve the inhibition of the p38/MAPK pathway during myogenesis.These results uncovered a“braking”role in differentiation of transiently upregulated miRNAs and provided new insights into the competing endogenous RNA(ceRNA)regulatory mechanism in myoblast differentiation and myogenesis.