Many Novel Mammalian MicroRNA Candidates Identified by Extensive Cloning and RAKE Analysis

Overview

Journal Genome Res

Specialty Genetics

Date 2006 Sep 7

PMID 16954537

Citations 127

Authors

Eugene Berezikov

Geert van Tetering

Mark Verheul

Jose van de Belt

Linda Van Laake

Joost Vos

Robert Verloop

Marc van de Wetering

Victor Guryev

Shuji Takada

Anton Jan van Zonneveld

Hiroyuki Mano

Ronald Plasterk

Edwin Cuppen

Affiliations

Soon will be listed here.

Abstract

MicroRNAs are 20- to 23-nucleotide RNA molecules that can regulate gene expression. Currently > 400 microRNAs have been experimentally identified in mammalian genomes, whereas estimates go up to 1000 and beyond. Here we show that many more mammalian microRNAs exist. We discovered novel microRNA candidates using two approaches: testing of computationally predicted microRNAs by a modified microarray-based detection system, and cloning and sequencing of large numbers of small RNAs from different human and mouse tissues. Together these efforts experimentally identified 348 novel mouse and 81 novel human microRNA candidate genes. Most novel microRNAs candidates are not conserved beyond mammals, and ~10% are taxon-specific. Our analyses indicate that the entire microRNA repertoire is not remotely exhausted.

Citing Articles

Therapeutic potential of adipose-derived stem cell extracellular vesicles: from inflammation regulation to tissue repair.

Zhou B, Chen Q, Zhang Q, Tian W, Chen T, Liu Z Stem Cell Res Ther. 2024; 15(1):249.

PMID: 39113098 PMC: 11304935. DOI: 10.1186/s13287-024-03863-5.

The microRNA Let-7 and its exosomal form: Epigenetic regulators of gynecological cancers.

Wang F, Zhou C, Zhu Y, Keshavarzi M Cell Biol Toxicol. 2024; 40(1):42.

PMID: 38836981 PMC: 11153289. DOI: 10.1007/s10565-024-09884-3.

METTL1 drives tumor progression of bladder cancer via degrading ATF3 mRNA in an mG-modified miR-760-dependent manner.

Xie H, Wang M, Yu H, Wang H, Ding L, Wang R Cell Death Discov. 2022; 8(1):458.

PMID: 36396627 PMC: 9672058. DOI: 10.1038/s41420-022-01236-6.

Mesenchymal Stem Cell-Derived Exosomes and MicroRNAs in Cartilage Regeneration: Biogenesis, Efficacy, miRNA Enrichment and Delivery.

Foo J, Looi Q, How C, Lee S, Al-Masawa M, Chong P Pharmaceuticals (Basel). 2021; 14(11).

PMID: 34832875 PMC: 8618513. DOI: 10.3390/ph14111093.

Endogenous miRNA Sponges.

Alkan A, Akgul B Methods Mol Biol. 2021; 2257:91-104.

PMID: 34432275 DOI: 10.1007/978-1-0716-1170-8_5.

References

Lim L, Lau N, Garrett-Engele P, Grimson A, Schelter J, Castle J . Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature. 2005; 433(7027):769-73. DOI: 10.1038/nature03315. View

Nelson P, Baldwin D, Marie Scearce L, Oberholtzer J, Tobias J, Mourelatos Z . Microarray-based, high-throughput gene expression profiling of microRNAs. Nat Methods. 2005; 1(2):155-61. DOI: 10.1038/nmeth717. View

Lee R, Ambros V . An extensive class of small RNAs in Caenorhabditis elegans. Science. 2001; 294(5543):862-4. DOI: 10.1126/science.1065329. View

Alvarez-Garcia I, Miska E . MicroRNA functions in animal development and human disease. Development. 2005; 132(21):4653-62. DOI: 10.1242/dev.02073. View

He L, Thomson J, Hemann M, Hernando-Monge E, Mu D, Goodson S . A microRNA polycistron as a potential human oncogene. Nature. 2005; 435(7043):828-33. PMC: 4599349. DOI: 10.1038/nature03552. View

Du T, Zamore P . microPrimer: the biogenesis and function of microRNA. Development. 2005; 132(21):4645-52. DOI: 10.1242/dev.02070. View

Bentwich I, Avniel A, Karov Y, Aharonov R, Gilad S, Barad O . Identification of hundreds of conserved and nonconserved human microRNAs. Nat Genet. 2005; 37(7):766-70. DOI: 10.1038/ng1590. View

Steffen P, Voss B, Rehmsmeier M, Reeder J, Giegerich R . RNAshapes: an integrated RNA analysis package based on abstract shapes. Bioinformatics. 2005; 22(4):500-3. DOI: 10.1093/bioinformatics/btk010. View

Bonnet E, Wuyts J, Rouze P, Van de Peer Y . Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences. Bioinformatics. 2004; 20(17):2911-7. DOI: 10.1093/bioinformatics/bth374. View

10.

Lu J, Getz G, Miska E, Alvarez-Saavedra E, Lamb J, Peck D . MicroRNA expression profiles classify human cancers. Nature. 2005; 435(7043):834-8. DOI: 10.1038/nature03702. View

11.

Lewis B, Burge C, Bartel D . Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell. 2005; 120(1):15-20. DOI: 10.1016/j.cell.2004.12.035. View

12.

Khvorova A, Reynolds A, Jayasena S . Functional siRNAs and miRNAs exhibit strand bias. Cell. 2003; 115(2):209-16. DOI: 10.1016/s0092-8674(03)00801-8. View

13.

Schwarz D, Hutvagner G, Du T, Xu Z, Aronin N, Zamore P . Asymmetry in the assembly of the RNAi enzyme complex. Cell. 2003; 115(2):199-208. DOI: 10.1016/s0092-8674(03)00759-1. View

14.

Berezikov E, Guryev V, van de Belt J, Wienholds E, Plasterk R, Cuppen E . Phylogenetic shadowing and computational identification of human microRNA genes. Cell. 2005; 120(1):21-4. DOI: 10.1016/j.cell.2004.12.031. View

15.

Thompson J, Higgins D, Gibson T . CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994; 22(22):4673-80. PMC: 308517. DOI: 10.1093/nar/22.22.4673. View

16.

Sewer A, Paul N, Landgraf P, Aravin A, Pfeffer S, Brownstein M . Identification of clustered microRNAs using an ab initio prediction method. BMC Bioinformatics. 2005; 6:267. PMC: 1315341. DOI: 10.1186/1471-2105-6-267. View

17.

Aravin A, Tuschl T . Identification and characterization of small RNAs involved in RNA silencing. FEBS Lett. 2005; 579(26):5830-40. DOI: 10.1016/j.febslet.2005.08.009. View

18.

Wienholds E, Kloosterman W, Miska E, Alvarez-Saavedra E, Berezikov E, de Bruijn E . MicroRNA expression in zebrafish embryonic development. Science. 2005; 309(5732):310-1. DOI: 10.1126/science.1114519. View

19.

Berezikov E, Cuppen E, Plasterk R . Approaches to microRNA discovery. Nat Genet. 2006; 38 Suppl:S2-7. DOI: 10.1038/ng1794. View

20.

Wheeler G, Ntounia-Fousara S, Granda B, Rathjen T, Dalmay T . Identification of new central nervous system specific mouse microRNAs. FEBS Lett. 2006; 580(9):2195-200. DOI: 10.1016/j.febslet.2006.03.019. View