The DOI matches its Crossref record; 7 of the 7 references it cites were found in a registry or an index.
Dicer recognizes the 5′ end of RNA for efficient and accurate processing
Open accessAbstract
A hallmark of RNA silencing is a class of approximately 22-nucleotide RNAs that are processed from double-stranded RNA precursors by Dicer. Accurate processing by Dicer is crucial for the functionality of microRNAs (miRNAs). The current model posits that Dicer selects cleavage sites by measuring a set distance from the 3′ overhang of the double-stranded RNA terminus. Here we report that human Dicer anchors not only the 3′ end but also the 5′ end, with the cleavage site determined mainly by the distance (∼22 nucleotides) from the 5′ end (5′ counting rule). This cleavage requires a 5′-terminal phosphate group. Further, we identify a novel basic motif (5′ pocket) in human Dicer that recognizes the 5′-phosphorylated end. The 5′ counting rule and the 5′ anchoring residues are conserved in Drosophila Dicer-1, but not in Giardia Dicer. Mutations in the 5′ pocket reduce processing efficiency and alter cleavage sites in vitro. Consistently, miRNA biogenesis is perturbed in vivo when Dicer-null embryonic stem cells are replenished with the 5′-pocket mutant. Thus, 5′-end recognition by Dicer is important for precise and effective biogenesis of miRNAs. Insights from this study should also afford practical benefits to the design of small hairpin RNAs.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing
Benjamini, Y., & Hochberg, Y. (1995) · Journal of the Royal Statistical Society Series B: Statistical Methodology · doi:10.1111/j.2517-6161.1995.tb02031.x · Cited by 109,482
Fast and accurate short read alignment with Burrows-Wheeler transform
Li, H., & Durbin, R. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp324 · Cited by 58,607
MicroRNAs: Target Recognition and Regulatory Functions
Bartel, D. P. (2009) · Cell · doi:10.1016/j.cell.2009.01.002 · Cited by 20,068
Ketting, R. F., Fischer, S. E. J., Bernstein, E., Sijen, T., Hannon, G. J., & Plasterk, R. H. A. (2001) · Genes & Development · doi:10.1101/gad.927801 · Cited by 1,852
miRNPs: a novel class of ribonucleoproteins containing numerous microRNAs
Mourelatos, Z., Dostie, J., Paushkin, S., Sharma, A., Charroux, B., Abel, L., Rappsilber, J., Mann, M., & Dreyfuss, G. (2002) · Genes & Development · doi:10.1101/gad.974702 · Cited by 1,105
Mammalian microRNAs: experimental evaluation of novel and previously annotated genes
Chiang, H. R., Schoenfeld, L. W., Ruby, J. G., Auyeung, V. C., Spies, N., Baek, D., Johnston, W. K., Russ, C., Luo, S., Babiarz, J. E., et al. (2010) · Genes & Development · doi:10.1101/gad.1884710 · Cited by 825
Characterization of Dicer-deficient murine embryonic stem cells
Murchison, E. P., Partridge, J. F., Tam, O. H., Cheloufi, S., & Hannon, G. J. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0505479102 · Cited by 800
Cited by
Regulation of microRNA biogenesis
Ha, M., & Kim, V. N. (2014) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm3838 · Cited by 5,462
Self-citationBartel, D. P. (2018) · Cell · doi:10.1016/j.cell.2018.03.006 · Cited by 3,751
microRNAs in action: biogenesis, function and regulation
Shang, R., Lee, S., Senavirathne, G., & Lai, E. C. (2023) · Nature Reviews Genetics · doi:10.1038/s41576-023-00611-y · Cited by 897
IsomiRs – the overlooked repertoire in the dynamic microRNAome
Neilsen, C. T., Goodall, G. J., & Bracken, C. P. (2012) · Trends in Genetics · doi:10.1016/j.tig.2012.07.005 · Cited by 499
Beyond Secondary Structure: Primary-Sequence Determinants License Pri-miRNA Hairpins for Processing
Auyeung, V. C., Ulitsky, I., McGeary, S. E., & Bartel, D. P. (2013) · Cell · doi:10.1016/j.cell.2013.01.031 · Cited by 434
From guide to target: molecular insights into eukaryotic RNA-interference machinery
Ipsaro, J. J., & Joshua-Tor, L. (2015) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2931 · Cited by 281
A tale of non-canonical tails: gene regulation by post-transcriptional RNA tailing
Yu, S., & Kim, V. N. (2020) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-020-0246-8 · Cited by 142
Self-citationDeletion of Human tarbp2 Reveals Cellular MicroRNA Targets and Cell-Cycle Function of TRBP
Kim, Y., Yeo, J., Lee, J. H., Cho, J., Seo, D., Kim, J.-S., & Kim, V. N. (2014) · Cell Reports · doi:10.1016/j.celrep.2014.09.039 · Cited by 124
Self-citationGain-of-function mutation of microRNA-140 in human skeletal dysplasia
Grigelioniene, G., Suzuki, H. I., Taylan, F., Mirzamohammadi, F., Borochowitz, Z. U., Ayturk, U. M., Tzur, S., Horemuzova, E., Lindstrand, A., Weis, M. A., et al. (2019) · Nature Medicine · doi:10.1038/s41591-019-0353-2 · Cited by 103
“4d, e); this finding is consistent with the critical role of the 5 ′ -end structure of pre-miRNAs and miRNA duplexes in Dicer processing and in asymmetric miRNA strand selection 19,20 .”
A Mechanism for microRNA Arm Switching Regulated by Uridylation
Kim, H., Kim, J., Yu, S., Lee, Y.-Y., Park, J., Choi, R. J., Yoon, S.-J., Kang, S.-G., & Kim, V. N. (2020) · Molecular Cell · doi:10.1016/j.molcel.2020.04.030 · Cited by 99
Self-citationStructural basis of microRNA biogenesis by Dicer-1 and its partner protein Loqs-PB
Jouravleva, K., Golovenko, D., Demo, G., Dutcher, R. C., Hall, T. M. T., Zamore, P. D., & Korostelev, A. A. (2022) · Molecular Cell · doi:10.1016/j.molcel.2022.09.002 · Cited by 57
Martin, E. C., Elliott, S., Rhodes, L. V., Antoon, J. W., Fewell, C., Zhu, Y., Driver, J. L., Jodari‐Karimi, M., Taylor, C. W., Flemington, E. K., et al. (2014) · Molecular Carcinogenesis · doi:10.1002/mc.21946 · Cited by 54
Gao, Z., Harwig, A., Berkhout, B., & Herrera-Carrillo, E. (2017) · Transcription · doi:10.1080/21541264.2017.1322170 · Cited by 47
Caenorhabditis elegans Dicer acts with the RIG-I-like helicase DRH-1 and RDE-4 to cleave dsRNA
Consalvo, C. D., Aderounmu, A. M., Donelick, H. M., Aruscavage, P. J., Eckert, D. M., Shen, P. S., & Bass, B. L. (2024) · eLife · doi:10.7554/elife.93979.3 · Cited by 12
C. elegans Dicer acts with the RIG-I-like helicase DRH-1 and RDE-4 to cleave dsRNA
Consalvo, C. D., Aderounmu, A. M., Donelick, H. M., Aruscavage, P. J., Eckert, D. M., Shen, P. S., & Bass, B. L. (2023) · doi:10.1101/2023.09.21.558868 · Cited by 1
Metadata
- Authors
- Park, J.-E., Heo, I., Tian, Y., Simanshu, D. K., Chang, H., Jee, D., Patel, D. J., & Kim, V. N.
- Venue
- Nature
- Published
- 2011-07
- Volume
- 475
- Issue
- 7355
- Pages
- 201-205
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- OpenAlex
- W1991737083
- Cited by
- 512
- References
- 7
- FWCI
- 14.69
- Type
- journal article
- Language
- en
- Open access
- green
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
