Mouse ES Cells Express Endogenous ShRNAs, SiRNAs, and Other Microprocessor-independent, Dicer-dependent Small RNAs

Overview

Journal Genes Dev

Specialty Molecular Biology

Date 2008 Oct 17

PMID 18923076

Citations 497

Authors

Joshua E Babiarz

J Graham Ruby

Yangming Wang

David P Bartel

Robert Blelloch

Affiliations

Soon will be listed here.

Abstract

Canonical microRNAs (miRNAs) require two processing steps: the first by the Microprocessor, a complex of DGCR8 and Drosha, and the second by a complex of TRBP and Dicer. dgcr8Delta/Delta mouse embryonic stem cells (mESCs) have less severe phenotypes than dicer1Delta/Delta mESCs, suggesting a physiological role for Microprocessor-independent, Dicer-dependent small RNAs. To identify these small RNAs with unusual biogenesis, we performed high-throughput sequencing from wild-type, dgcr8Delta/Delta, and dicer1Delta/Delta mESCs. Several of the resulting DGCR8-independent, Dicer-dependent RNAs were noncanonical miRNAs. These derived from mirtrons and a newly identified subclass of miRNA precursors, which appears to be the endogenous counterpart of shRNAs. Our analyses also revealed endogenous siRNAs resulting from Dicer cleavage of long hairpins, the vast majority of which originated from one genomic locus with tandem, inverted short interspersed nuclear elements (SINEs). Our results extend the known diversity of mammalian small RNA-generating pathways and show that mammalian siRNAs exist in cell types other than oocytes.

Citing Articles

The functions and modifications of tRNA-derived small RNAs in cancer biology.

Saad A, Zhang K, Deng Q, Zhou J, Ge L, Wang H Cancer Metastasis Rev. 2025; 44(1):38.

PMID: 40072687 DOI: 10.1007/s10555-025-10254-6.

Natural compounds as regulators of miRNAs: exploring a new avenue for treating brain cancer.

Doghish A, El-Dakroury W, Abulsoud A, Abdelmaksoud N, Aly S, Elbadry A Naunyn Schmiedebergs Arch Pharmacol. 2025; .

PMID: 40047858 DOI: 10.1007/s00210-025-03934-1.

The miR-290 and miR-302 clusters are essential for reprogramming of fibroblasts to induced pluripotent stem cells.

Ye J, Boileau R, Parchem R, Judson-Torres R, Blelloch R Stem Cells. 2025; 43(2).

PMID: 40037390 PMC: 11879289. DOI: 10.1093/stmcls/sxae080.

The Role of MicroRNAs in Neurodegeneration: Insights from Huntington's Disease.

Mansour R, Shaker A, Abulsoud A, Mageed S, Ashraf A, Elsakka E Mol Neurobiol. 2025; .

PMID: 40009259 DOI: 10.1007/s12035-025-04750-7.

From fatty liver to fibrosis: the impact of miRNAs on NAFLD and NASH.

Mansour R, Mageed S, Abulsoud A, Sayed G, Lutfy R, Awad F Funct Integr Genomics. 2025; 25(1):30.

PMID: 39888504 DOI: 10.1007/s10142-025-01544-x.

References

Stark G, Kerr I, Williams B, Silverman R, Schreiber R . How cells respond to interferons. Annu Rev Biochem. 1998; 67:227-64. DOI: 10.1146/annurev.biochem.67.1.227. View

Ruby J, Stark A, Johnston W, Kellis M, Bartel D, Lai E . Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs. Genome Res. 2007; 17(12):1850-64. PMC: 2099593. DOI: 10.1101/gr.6597907. View

Denli A, Tops B, Plasterk R, Ketting R, Hannon G . Processing of primary microRNAs by the Microprocessor complex. Nature. 2004; 432(7014):231-5. DOI: 10.1038/nature03049. View

Landthaler M, Yalcin A, Tuschl T . The human DiGeorge syndrome critical region gene 8 and Its D. melanogaster homolog are required for miRNA biogenesis. Curr Biol. 2004; 14(23):2162-7. DOI: 10.1016/j.cub.2004.11.001. View

Han J, Lee Y, Yeom K, Kim Y, Jin H, Kim V . The Drosha-DGCR8 complex in primary microRNA processing. Genes Dev. 2004; 18(24):3016-27. PMC: 535913. DOI: 10.1101/gad.1262504. View

Pruitt K, Tatusova T, Maglott D . NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 2004; 33(Database issue):D501-4. PMC: 539979. DOI: 10.1093/nar/gki025. View

Dykxhoorn D, Lieberman J . The silent revolution: RNA interference as basic biology, research tool, and therapeutic. Annu Rev Med. 2005; 56:401-23. DOI: 10.1146/annurev.med.56.082103.104606. View

Kanellopoulou C, Muljo S, Kung A, Ganesan S, Drapkin R, Jenuwein T . Dicer-deficient mouse embryonic stem cells are defective in differentiation and centromeric silencing. Genes Dev. 2005; 19(4):489-501. PMC: 548949. DOI: 10.1101/gad.1248505. View

Siepel A, Bejerano G, Pedersen J, Hinrichs A, Hou M, Rosenbloom K . Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 2005; 15(8):1034-50. PMC: 1182216. DOI: 10.1101/gr.3715005. View

10.

Harfe B, McManus M, Mansfield J, Hornstein E, Tabin C . The RNaseIII enzyme Dicer is required for morphogenesis but not patterning of the vertebrate limb. Proc Natl Acad Sci U S A. 2005; 102(31):10898-903. PMC: 1182454. DOI: 10.1073/pnas.0504834102. View

11.

Murchison E, Partridge J, Tam O, Cheloufi S, Hannon G . Characterization of Dicer-deficient murine embryonic stem cells. Proc Natl Acad Sci U S A. 2005; 102(34):12135-40. PMC: 1185572. DOI: 10.1073/pnas.0505479102. View

12.

Margulies M, Egholm M, Altman W, Attiya S, Bader J, Bemben L . Genome sequencing in microfabricated high-density picolitre reactors. Nature. 2005; 437(7057):376-80. PMC: 1464427. DOI: 10.1038/nature03959. View

13.

Hammond S . Dicing and slicing: the core machinery of the RNA interference pathway. FEBS Lett. 2005; 579(26):5822-9. DOI: 10.1016/j.febslet.2005.08.079. View

14.

Verdel A, Moazed D . RNAi-directed assembly of heterochromatin in fission yeast. FEBS Lett. 2005; 579(26):5872-8. DOI: 10.1016/j.febslet.2005.08.083. View

15.

Maniataki E, Mourelatos Z . A human, ATP-independent, RISC assembly machine fueled by pre-miRNA. Genes Dev. 2005; 19(24):2979-90. PMC: 1315402. DOI: 10.1101/gad.1384005. View

16.

Lee S, Collins K . Two classes of endogenous small RNAs in Tetrahymena thermophila. Genes Dev. 2005; 20(1):28-33. PMC: 1356098. DOI: 10.1101/gad.1377006. View

17.

Han J, Lee Y, Yeom K, Nam J, Heo I, Rhee J . Molecular basis for the recognition of primary microRNAs by the Drosha-DGCR8 complex. Cell. 2006; 125(5):887-901. DOI: 10.1016/j.cell.2006.03.043. View

18.

Watanabe T, Takeda A, Tsukiyama T, Mise K, Okuno T, Sasaki H . Identification and characterization of two novel classes of small RNAs in the mouse germline: retrotransposon-derived siRNAs in oocytes and germline small RNAs in testes. Genes Dev. 2006; 20(13):1732-43. PMC: 1522070. DOI: 10.1101/gad.1425706. View

19.

Strauss W, Chen C, Lee C, Ridzon D . Nonrestrictive developmental regulation of microRNA gene expression. Mamm Genome. 2006; 17(8):833-40. DOI: 10.1007/s00335-006-0025-7. View

20.

Blelloch R, Wang Z, Meissner A, Pollard S, Smith A, Jaenisch R . Reprogramming efficiency following somatic cell nuclear transfer is influenced by the differentiation and methylation state of the donor nucleus. Stem Cells. 2006; 24(9):2007-13. PMC: 3000431. DOI: 10.1634/stemcells.2006-0050. View