Characterization of Long Non-coding RNAs Modified by m6A RNA Methylation in Skeletal Myogenesis

Proper development of mammalian skeletal muscle relies on precise gene expression regulation. Our previous studies revealed that muscle development is regulated by both mRNA and long non-coding RNAs (lncRNAs). Accumulating evidence has demonstrated that N 6 -methyladenosine (m 6 A) plays important r...

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Published inFrontiers in cell and developmental biology Vol. 9; p. 762669
Main Authors Xie, Shu-Juan, Tao, Shuang, Diao, Li-Ting, Li, Pan-Long, Chen, Wei-Cai, Zhou, Zhi-Gang, Hu, Yan-Xia, Hou, Ya-Rui, Lei, Hang, Xu, Wan-Yi, Chen, Wen-Jie, Peng, Yan-Wen, Zhang, Qi, Xiao, Zhen-Dong
Format Journal Article
LanguageEnglish
Published Frontiers Media S.A 13.10.2021
Subjects
Brip1os
Cell and Developmental Biology
lncRNAs
m6A
METTL3
skeletal muscle development
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Abstract Proper development of mammalian skeletal muscle relies on precise gene expression regulation. Our previous studies revealed that muscle development is regulated by both mRNA and long non-coding RNAs (lncRNAs). Accumulating evidence has demonstrated that N 6 -methyladenosine (m 6 A) plays important roles in various biological processes, making it essential to profile m 6 A modification on a transcriptome-wide scale in developing muscle. Patterns of m 6 A methylation in lncRNAs in developing muscle have not been uncovered. Here, we reveal differentially expressed lncRNAs and report temporal m 6 A methylation patterns in lncRNAs expressed in mouse myoblasts and myotubes by RNA-seq and methylated RNA immunoprecipitation (MeRIP) sequencing. Many lncRNAs exhibit temporal differential expression, and m 6 A-lncRNAs harbor the consensus m 6 A motif “DRACH” along lncRNA transcripts. Interestingly, we found that m 6 A methylation levels of lncRNAs are positively correlated with the transcript abundance of lncRNAs. Overexpression or knockdown of m 6 A methyltransferase METTL3 alters the expression levels of these lncRNAs. Furthermore, we highlight that the function of m 6 A genic lncRNAs might correlate to their nearby mRNAs. Our work reveals a fundamental expression reference of m 6 A-mediated epitranscriptomic modifications in lncRNAs that are temporally expressed in developing muscle.
AbstractList Proper development of mammalian skeletal muscle relies on precise gene expression regulation. Our previous studies revealed that muscle development is regulated by both mRNA and long non-coding RNAs (lncRNAs). Accumulating evidence has demonstrated that N 6 -methyladenosine (m 6 A) plays important roles in various biological processes, making it essential to profile m 6 A modification on a transcriptome-wide scale in developing muscle. Patterns of m 6 A methylation in lncRNAs in developing muscle have not been uncovered. Here, we reveal differentially expressed lncRNAs and report temporal m 6 A methylation patterns in lncRNAs expressed in mouse myoblasts and myotubes by RNA-seq and methylated RNA immunoprecipitation (MeRIP) sequencing. Many lncRNAs exhibit temporal differential expression, and m 6 A-lncRNAs harbor the consensus m 6 A motif “DRACH” along lncRNA transcripts. Interestingly, we found that m 6 A methylation levels of lncRNAs are positively correlated with the transcript abundance of lncRNAs. Overexpression or knockdown of m 6 A methyltransferase METTL3 alters the expression levels of these lncRNAs. Furthermore, we highlight that the function of m 6 A genic lncRNAs might correlate to their nearby mRNAs. Our work reveals a fundamental expression reference of m 6 A-mediated epitranscriptomic modifications in lncRNAs that are temporally expressed in developing muscle.
Proper development of mammalian skeletal muscle relies on precise gene expression regulation. Our previous studies revealed that muscle development is regulated by both mRNA and long non-coding RNAs (lncRNAs). Accumulating evidence has demonstrated that N6-methyladenosine (m6A) plays important roles in various biological processes, making it essential to profile m6A modification on a transcriptome-wide scale in developing muscle. Patterns of m6A methylation in lncRNAs in developing muscle have not been uncovered. Here, we reveal differentially expressed lncRNAs and report temporal m6A methylation patterns in lncRNAs expressed in mouse myoblasts and myotubes by RNA-seq and methylated RNA immunoprecipitation (MeRIP) sequencing. Many lncRNAs exhibit temporal differential expression, and m6A-lncRNAs harbor the consensus m6A motif "DRACH" along lncRNA transcripts. Interestingly, we found that m6A methylation levels of lncRNAs are positively correlated with the transcript abundance of lncRNAs. Overexpression or knockdown of m6A methyltransferase METTL3 alters the expression levels of these lncRNAs. Furthermore, we highlight that the function of m6A genic lncRNAs might correlate to their nearby mRNAs. Our work reveals a fundamental expression reference of m6A-mediated epitranscriptomic modifications in lncRNAs that are temporally expressed in developing muscle.Proper development of mammalian skeletal muscle relies on precise gene expression regulation. Our previous studies revealed that muscle development is regulated by both mRNA and long non-coding RNAs (lncRNAs). Accumulating evidence has demonstrated that N6-methyladenosine (m6A) plays important roles in various biological processes, making it essential to profile m6A modification on a transcriptome-wide scale in developing muscle. Patterns of m6A methylation in lncRNAs in developing muscle have not been uncovered. Here, we reveal differentially expressed lncRNAs and report temporal m6A methylation patterns in lncRNAs expressed in mouse myoblasts and myotubes by RNA-seq and methylated RNA immunoprecipitation (MeRIP) sequencing. Many lncRNAs exhibit temporal differential expression, and m6A-lncRNAs harbor the consensus m6A motif "DRACH" along lncRNA transcripts. Interestingly, we found that m6A methylation levels of lncRNAs are positively correlated with the transcript abundance of lncRNAs. Overexpression or knockdown of m6A methyltransferase METTL3 alters the expression levels of these lncRNAs. Furthermore, we highlight that the function of m6A genic lncRNAs might correlate to their nearby mRNAs. Our work reveals a fundamental expression reference of m6A-mediated epitranscriptomic modifications in lncRNAs that are temporally expressed in developing muscle.
Proper development of mammalian skeletal muscle relies on precise gene expression regulation. Our previous studies revealed that muscle development is regulated by both mRNA and long non-coding RNAs (lncRNAs). Accumulating evidence has demonstrated that N6-methyladenosine (m6A) plays important roles in various biological processes, making it essential to profile m6A modification on a transcriptome-wide scale in developing muscle. Patterns of m6A methylation in lncRNAs in developing muscle have not been uncovered. Here, we reveal differentially expressed lncRNAs and report temporal m6A methylation patterns in lncRNAs expressed in mouse myoblasts and myotubes by RNA-seq and methylated RNA immunoprecipitation (MeRIP) sequencing. Many lncRNAs exhibit temporal differential expression, and m6A-lncRNAs harbor the consensus m6A motif “DRACH” along lncRNA transcripts. Interestingly, we found that m6A methylation levels of lncRNAs are positively correlated with the transcript abundance of lncRNAs. Overexpression or knockdown of m6A methyltransferase METTL3 alters the expression levels of these lncRNAs. Furthermore, we highlight that the function of m6A genic lncRNAs might correlate to their nearby mRNAs. Our work reveals a fundamental expression reference of m6A-mediated epitranscriptomic modifications in lncRNAs that are temporally expressed in developing muscle.
Author Peng, Yan-Wen
Zhang, Qi
Lei, Hang
Tao, Shuang
Hu, Yan-Xia
Zhou, Zhi-Gang
Chen, Wei-Cai
Diao, Li-Ting
Xie, Shu-Juan
Xu, Wan-Yi
Chen, Wen-Jie
Li, Pan-Long
Hou, Ya-Rui
Xiao, Zhen-Dong
AuthorAffiliation 1 Vaccine Research Institute of Sun Yat-sen University, The Third Affiliated Hospital of Sun Yat-sen University , Guangzhou , China
2 Biotherapy Center, The Third Affiliated Hospital of Sun Yat-sen University , Guangzhou , China
3 Department of Orthopedics, First Affiliated Hospital, Jinan University , Guangzhou , China
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These authors have contributed equally to this work
This article was submitted to Epigenomics and Epigenetics, a section of the journal Frontiers in Cell and Developmental Biology
Reviewed by: Zhanpeng Huang, The First Affiliated Hospital of Sun Yat-sen University, China; Chao Shen, City of Hope National Medical Center, United States
Edited by: Huilin Huang, Sun Yat-sen University Cancer Center (SYSUCC), China
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Snippet Proper development of mammalian skeletal muscle relies on precise gene expression regulation. Our previous studies revealed that muscle development is...
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SubjectTerms Brip1os
Cell and Developmental Biology
lncRNAs
m6A
METTL3
skeletal muscle development
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Title Characterization of Long Non-coding RNAs Modified by m6A RNA Methylation in Skeletal Myogenesis
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