Pathway analysis of microRNAs in mouse heart development

MicroRNAs (miRNAs) are non-coding RNAs, which regulate gene expression by promoting degradation or repressing translation of targeted transcripts. Current researches indicate that microRNAs play essential roles in heart development, but their regulating mechanisms are still elusive. Using computational methods, we analysed microRNAs associated pathways in mouse heart development and found that 24 pathways were enriched with target genes of microRNAs. Some of these pathways are reported important in heart development, while others are associated with cancer. The computational results could be used to guide experimental design for the further understanding of the microRNAs function in heart development.

[1]  Yang Wang,et al.  MicroRNA: past and present. , 2007, Frontiers in bioscience : a journal and virtual library.

[2]  Doron Betel,et al.  The microRNA.org resource: targets and expression , 2007, Nucleic Acids Res..

[3]  Yvonne Tay,et al.  A Pattern-Based Method for the Identification of MicroRNA Binding Sites and Their Corresponding Heteroduplexes , 2006, Cell.

[4]  Janan T. Eppig,et al.  The mouse Gene Expression Database (GXD): 2017 update , 2016, Nucleic Acids Res..

[5]  A. Hatzigeorgiou,et al.  A guide through present computational approaches for the identification of mammalian microRNA targets , 2006, Nature Methods.

[6]  Martin Reczko,et al.  The database of experimentally supported targets: a functional update of TarBase , 2008, Nucleic Acids Res..

[7]  Xiaowei Wang,et al.  Sequence analysis Prediction of both conserved and nonconserved microRNA targets in animals , 2007 .

[8]  K. Gunsalus,et al.  Combinatorial microRNA target predictions , 2005, Nature Genetics.

[9]  E. Olson,et al.  microRNA-133a regulates cardiomyocyte proliferation and suppresses smooth muscle gene expression in the heart. , 2008, Genes & development.

[10]  Michael Kertesz,et al.  The role of site accessibility in microRNA target recognition , 2007, Nature Genetics.

[11]  T. Callis,et al.  Taking microRNAs to heart. , 2008, Trends in molecular medicine.

[12]  Thomas Thum,et al.  MicroRNAs: novel regulators in cardiac development and disease. , 2008, Cardiovascular research.

[13]  Kuo-Fen Lee,et al.  Essential roles of Her2/erbB2 in cardiac development and function. , 2004, Recent progress in hormone research.

[14]  C. Croce,et al.  A microRNA expression signature of human solid tumors defines cancer gene targets , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[15]  Zhou Jun-mei.  Role of Human Heart Developmental Candidate Gene hole in MAPK Signaling Pathway , 2005 .

[16]  Tongbin Li,et al.  miRecords: an integrated resource for microRNA–target interactions , 2008, Nucleic Acids Res..

[17]  中尾 光輝,et al.  KEGG(Kyoto Encyclopedia of Genes and Genomes)〔和文〕 (特集 ゲノム医学の現在と未来--基礎と臨床) -- (データベース) , 2000 .

[18]  Xiaowei Wang.  miRDB: a microRNA target prediction and functional annotation database with a wiki interface. , 2008, RNA.

[19]  Yuriy Gusev,et al.  Computational methods for analysis of cellular functions and pathways collectively targeted by differentially expressed microRNA. , 2008, Methods.

[20]  R. Yeh,et al.  MicroRNA regulation of cell lineages in mouse and human embryonic stem cells. , 2008, Cell stem cell.

[21]  Lawrence S. Hon,et al.  The roles of binding site arrangement and combinatorial targeting in microRNA repression of gene expression , 2007, Genome Biology.

[22]  D. Bartel.  MicroRNAs Genomics, Biogenesis, Mechanism, and Function , 2004, Cell.

[23]  Melynda Boerm,et al.  Mekk3 is essential for early embryonic cardiovascular development , 2000, Nature Genetics.

[24]  I. Kishimoto,et al.  Cardiotrophin-1 phosphorylates akt and BAD, and prolongs cell survival via a PI3K-dependent pathway in cardiac myocytes. , 2000, Journal of molecular and cellular cardiology.

[25]  Yong Zhao,et al.  Serum response factor regulates a muscle-specific microRNA that targets Hand2 during cardiogenesis , 2005, Nature.

[26]  C. Burge,et al.  Conserved Seed Pairing, Often Flanked by Adenosines, Indicates that Thousands of Human Genes are MicroRNA Targets , 2005, Cell.

[27]  R. Giegerich,et al.  Fast and effective prediction of microRNA/target duplexes. , 2004, RNA.

[28]  G. D. De Keulenaer,et al.  Role of Neuregulin-1/ErbB Signaling in Cardiovascular Physiology and Disease: Implications for Therapy of Heart Failure , 2007, Circulation.