Dicer-TRBP Complex Formation Ensures Accurate Mammalian MicroRNA Biogenesis

Wilson, Ross C.; Tambe, Akshay; Kidwell, Mary Anne; Noland, Cameron L.; Schneider, Catherine; Doudna, Jennifer A.

doi:10.1016/j.molcel.2014.11.030

Cited by 237 publications

(275 citation statements)

References 47 publications

Supporting

Mentioning

250

Contrasting

Unclassified

Order By: Relevance

“…4D, lower panel) indicating that either dimer formation is required to generate the dmDcr1-binding site on Loqs or that dimerization and dmDcr1 binding are alternative processes requiring the same protein surface. In agreement with the latter model, it has been shown recently that TRBP-dsRBD3 forms a highly similar interaction surface, which is used for direct Dicer binding (Wilson et al 2015).…”

Section: Loqs Forms Homodimerssupporting

confidence: 63%

“…Both dsRBPs have been implicated in miRNA biogenesis and contain three dsRNA binding domains (dsRBDs). It has been demonstrated that TRBP uses its first and second dsRBD to interact with the Dicer-produced miRNA intermediate while the third dsRBD is a protein-protein interaction domain and utilized for the interaction with the helicase domain of Dicer (Daniels et al 2009;Wilson et al 2015). In Drosophila, miRNA and short interfering RNA (siRNA) pathways are separated and two specialized Dicers exist.…”

Section: Introductionmentioning

confidence: 99%

“…The presumably unstructured linker between dsRBD2 and 3 supports this interaction (Forstemann et al 2005). While the interface between TRBP and human Dcr has recently been structurally characterized (Wilson et al 2015), the molecular basis of this interaction platform both on dmDcr1 and on the dsRBD3 of Loqs is not yet understood.…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Structural and functional insights into the fly microRNA biogenesis factor Loquacious

Jakob¹,

Treiber²,

Treiber³

et al. 2016

RNA

View full text Add to dashboard Cite

In the microRNA (miRNA) pathway, Dicer processes precursors to mature miRNAs. For efficient processing, double-stranded RNA-binding proteins support Dicer proteins. In flies, Loquacious (Loqs) interacts with Dicer1 (dmDcr1) to facilitate miRNA processing. Here, we have solved the structure of the third double-stranded RNA-binding domain (dsRBD) of Loqs and define specific structural elements that interact with dmDcr1. In addition, we show that the linker preceding dsRBD3 contributes significantly to dmDcr1 binding. Furthermore, our structural work demonstrates that the third dsRBD of Loqs forms homodimers. Mutations in the dimerization interface abrogate dmDcr1 interaction. Loqs, however, binds to dmDcr1 as a monomer using the identified dimerization surface, which suggests that Loqs might form dimers under conditions where dmDcr1 is absent or not accessible. Since critical sequence elements are conserved, we suggest that dimerization might be a general feature of dsRBD proteins in gene silencing.

show abstract

Section: Loqs Forms Homodimerssupporting

confidence: 63%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Structural and functional insights into the fly microRNA biogenesis factor Loquacious

Jakob¹,

Treiber²,

Treiber³

et al. 2016

RNA

View full text Add to dashboard Cite

show abstract

“…After their export into the cytoplasm, a further maturation step is executed by Dicer, assisted by TRBP, PACT, and Ago2 in a poised complex, by cleaving the precursor's loop and generating a short imperfect double-stranded RNA (dsRNA) stem (miRNA duplex) (Wilson et al 2015). Ago2 then orchestrates the last maturation step, preferentially incorporating one of the duplex RNA strands into the RISC, responsible for translational repression and RNA degradation.…”

Section: Introductionmentioning

confidence: 99%

Double-stranded microRNA mimics can induce length- and passenger strand–dependent effects in a cell type–specific manner

Goldgraben

Russell

Rueda

et al. 2015

RNA

View full text Add to dashboard Cite

MicroRNAs are short (17-26) noncoding RNAs driving or modulating physiological and pathological cellular events. Overexpression of miR-155 is pathogenic in B-cell malignancy but was also reported in a number of solid tumors-in particular, in breast cancer, where its role remains unclear and often contradictory. Using representative cell line models, we sought to determine whether the discrepant miR-155 effects in breast cancer could be explained by the heterogeneity of the disease. The growth of six breast cancer cell lines transfected with several miRNA mimics was analyzed. We found MCF-7 cell growth to be inhibited by miR-155 and miR-145 mimics, both 23-nt long, but not by a number of shorter mimics, including a universal commercial negative control. Microarray and Western blot analyses revealed induction of apoptosis, associated with interferon-β after activation of the double-stranded RNA sensor pathway. 3 ′ Trimming of the miRNA mimics to 21 nt substantially reduced their growth-inhibitory potency. Mutating the canonical seed of the miR-155 mimic had no effect on the induced inhibition, which was abolished by mutating the miRNA seed of the artificial passenger strand. A panel of breast cancer cell lines showed a wide range of sensitivities to 23-mer mimics, broadly consistent with the sensitivity of the cell lines to Poly (I:C). We demonstrate two sources for nonspecific in vitro effects by miRNA mimics: duplex length and the artificial passenger strand. We highlight the danger of a universal 21-mer negative control and the importance of using matched seed mutants for reliable interpretation of phenotypes.

show abstract

“…Human Dicer also associates with two different dsRNA-binding proteins, TRBP and PACT (17,18). These dsRNA-binding proteins are not required for dicing activity but function as key regulatory factors in defining the dicing site and facilitating RISC formation (19)(20)(21).…”

mentioning

confidence: 99%

RNA-binding protein DUS16 plays an essential role in primary miRNA processing in the unicellular alga Chlamydomonas reinhardtii

Yamasaki

Onishi

Kim

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

Canonical microRNAs (miRNAs) are embedded in duplexed stemloops in long precursor transcripts and are excised by sequential cleavage by DICER nuclease(s). In this miRNA biogenesis pathway, dsRNA-binding proteins play important roles in animals and plants by assisting DICER. However, these RNA-binding proteins are poorly characterized in unicellular organisms. Here we report that a unique RNA-binding protein, Dull slicer-16 (DUS16), plays an essential role in processing of primary-miRNA (pri-miRNA) transcripts in the unicellular green alga Chlamydomonas reinhardtii. In animals and plants, dsRNA-binding proteins involved in miRNA biogenesis harbor two or three dsRNA-binding domains (dsRBDs), whereas DUS16 contains one dsRBD and also an ssRNA-binding domain (RRM). The null mutant of DUS16 showed a drastic reduction in most miRNA species. Production of these miRNAs was complemented by expression of full-length DUS16, but the expression of RRM-or dsRBDtruncated DUS16 did not restore miRNA production. Furthermore, DUS16 is predominantly localized to the nucleus and associated with nascent (unspliced form) pri-miRNAs and the DICER-LIKE 3 protein. These results suggest that DUS16 recognizes pri-miRNA transcripts cotranscriptionally and promotes their processing into mature miRNAs as a component of a microprocessor complex. We propose that DUS16 is an essential factor for miRNA production in Chlamydomonas and, because DUS16 is functionally similar to the dsRNA-binding proteins involved in miRNA biogenesis in animals and land plants, our report provides insight into this mechanism in unicellular eukaryotes.Chlamydomonas | microRNA biogenesis | dsRNA-binding protein | small RNA-seq | mutagenesis

show abstract

Dicer-TRBP Complex Formation Ensures Accurate Mammalian MicroRNA Biogenesis

Cited by 237 publications

References 47 publications

Structural and functional insights into the fly microRNA biogenesis factor Loquacious

Structural and functional insights into the fly microRNA biogenesis factor Loquacious

Double-stranded microRNA mimics can induce length- and passenger strand–dependent effects in a cell type–specific manner

RNA-binding protein DUS16 plays an essential role in primary miRNA processing in the unicellular alga Chlamydomonas reinhardtii

Contact Info

Product

Resources

About