The DOI matches its Crossref record; 86 of the 86 references it cites were found in a registry or an index.
Origins and evolution of eukaryotic RNA interference
Open accessAbstract
Small interfering RNAs (siRNAs) and genome-encoded microRNAs (miRNAs) silence genes via complementary interactions with mRNAs. With thousands of miRNA genes identified and genome sequences of diverse eukaryotes available for comparison, the opportunity emerges for insights into origin and evolution of RNA interference (RNAi). The miRNA repertoires of plants and animals appear to have evolved independently. However, conservation of the key proteins involved in RNAi suggests that the last common ancestor of modern eukaryotes possessed siRNA-based mechanisms. Prokaryotes have a RNAi-like defense system that is functionally analogous but not homologous to eukaryotic RNAi. The protein machinery of eukaryotic RNAi seems to have been pieced together from ancestral proteins of archaeal, bacterial and phage origins that are involved in DNA repair and RNA-processing pathways.
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
1 retracted
RETRACTED: Secondary siRNAs Result from Unprimed RNA Synthesis and Form a Distinct Class
Sijen, T., Steiner, F. A., Thijssen, K. L., & Plasterk, R. H. A. (2007) · Science · doi:10.1126/science.1136699 · Cited by 383
RetractedBartel (2004) · doi:10.1016/s0092-8674(04)00045-5 · Cited by 34,714
MicroRNAs: small RNAs with a big role in gene regulation
He, L., & Hannon, G. J. (2004) · Nature Reviews Genetics · doi:10.1038/nrg1379 · Cited by 7,118
CRISPR Provides Acquired Resistance Against Viruses in Prokaryotes
Barrangou, R., Fremaux, C., Deveau, H., Richards, M., Boyaval, P., Moineau, S., Romero, D. A., & Horvath, P. (2007) · Science · doi:10.1126/science.1138140 · Cited by 5,947
The Transcriptional Landscape of the Mammalian Genome
Carninci, P., Kasukawa, T., Katayama, S., Gough, J., Frith, M. C., Maeda, N., Oyama, R., Ravasi, T., Lenhard, B., Wells, C., et al. (2005) · Science · doi:10.1126/science.1112014 · Cited by 3,499
Hutvágner, G., McLachlan, J., Pasquinelli, A. E., Bálint, E., Tuschl, T., & Zamore, P. D. (2001) · Science · doi:10.1126/science.1062961 · Cited by 2,781
MicroRNAs AND THEIR REGULATORY ROLES IN PLANTS
Jones-Rhoades, M. W., Bartel, D. P., & Bartel, B. (2006) · Annual Review of Plant Biology · doi:10.1146/annurev.arplant.57.032905.105218 · Cited by 2,686
Baulcombe, D. (2004) · Nature · doi:10.1038/nature02874 · Cited by 2,534
Principles of MicroRNA–Target Recognition
Brennecke, J., Stark, A., Russell, R. B., & Cohen, S. M. (2005) · PLoS Biology · doi:10.1371/journal.pbio.0030085 · Cited by 2,378
Identification of Mammalian microRNA Host Genes and Transcription Units
Rodriguez, A., Griffiths-Jones, S., Ashurst, J. L., & Bradley, A. (2004) · Genome Research · doi:10.1101/gr.2722704 · Cited by 2,128
Identification of hundreds of conserved and nonconserved human microRNAs
Bentwich, I., Avniel, A., Karov, Y., Aharonov, R., Gilad, S., Barad, O., Barzilai, A., Einat, P., Einav, U., Meiri, E., et al. (2005) · Nature Genetics · doi:10.1038/ng1590 · Cited by 1,841
Intronic microRNA precursors that bypass Drosha processing
Ruby, J. G., Jan, C. H., & Bartel, D. P. (2007) · Nature · doi:10.1038/nature05983 · Cited by 1,722
Dicer is essential for mouse development
Bernstein, E., Kim, S. Y., Carmell, M. A., Murchison, E. P., Alcorn, H., Li, M. Z., Mills, A. A., Elledge, S. J., Anderson, K. V., & Hannon, G. J. (2003) · Nature Genetics · doi:10.1038/ng1253 · Cited by 1,627
Molecular Basis for the Recognition of Primary microRNAs by the Drosha-DGCR8 Complex
Han, J., Lee, Y., Yeom, K.-H., Nam, J.-W., Heo, I., Rhee, J.-K., Sohn, S. Y., Cho, Y., Zhang, B.-T., & Kim, V. N. (2006) · Cell · doi:10.1016/j.cell.2006.03.043 · Cited by 1,551
The evolution of gene regulation by transcription factors and microRNAs
Chen, K., & Rajewsky, N. (2007) · Nature Reviews Genetics · doi:10.1038/nrg1990 · Cited by 1,547
Argonaute proteins: key players in RNA silencing
Hutvagner, G., & Simard, M. J. (2008) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm2321 · Cited by 1,359
A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana
Rajagopalan, R., Vaucheret, H., Trejo, J., & Bartel, D. P. (2006) · Genes & Development · doi:10.1101/gad.1476406 · Cited by 1,298
Ribo-gnome: The Big World of Small RNAs
Zamore, P. D., & Haley, B. (2005) · Science · doi:10.1126/science.1111444 · Cited by 1,288
Makarova, K. S., Grishin, N. V., Shabalina, S. A., Wolf, Y. I., & Koonin, E. V. (2006) · Biology Direct · doi:10.1186/1745-6150-1-7 · Cited by 1,199
Self-citationFahlgren, N., Howell, M. D., Kasschau, K. D., Chapman, E. J., Sullivan, C. M., Cumbie, J. S., Givan, S. A., Law, T. F., Grant, S. R., Dangl, J. L., et al. (2007) · PLoS ONE · doi:10.1371/journal.pone.0000219 · Cited by 1,197
The Piwi-piRNA Pathway Provides an Adaptive Defense in the Transposon Arms Race
Aravin, A. A., Hannon, G. J., & Brennecke, J. (2007) · Science · doi:10.1126/science.1146484 · Cited by 1,096
Stark, A., Brennecke, J., Bushati, N., Russell, R. B., & Cohen, S. M. (2005) · Cell · doi:10.1016/j.cell.2005.11.023 · Cited by 1,080
The Mirtron Pathway Generates microRNA-Class Regulatory RNAs in Drosophila
Okamura, K., Hagen, J. W., Duan, H., Tyler, D. M., & Lai, E. C. (2007) · Cell · doi:10.1016/j.cell.2007.06.028 · Cited by 1,029
A biochemical framework for RNA silencing in plants
Tang, G., Reinhart, B. J., Bartel, D. P., & Zamore, P. D. (2003) · Genes & Development · doi:10.1101/gad.1048103 · Cited by 983
Gene silencing as an adaptive defence against viruses
Waterhouse, P. M., Wang, M.-B., & Lough, T. (2001) · Nature · doi:10.1038/35081168 · Cited by 980
Arabidopsis micro-RNA biogenesis through Dicer-like 1 protein functions
Kurihara, Y., & Watanabe, Y. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0403115101 · Cited by 965
Structural Basis for Double-Stranded RNA Processing by Dicer
MacRae, I. J., Zhou, K., Li, F., Repic, A., Brooks, A. N., Cande, W. Z., Adams, P. D., & Doudna, J. A. (2006) · Science · doi:10.1126/science.1121638 · Cited by 962
Sorek, R., Kunin, V., & Hugenholtz, P. (2008) · Nature Reviews Microbiology · doi:10.1038/nrmicro1793 · Cited by 907
RNAi-mediated pathways in the nucleus
Matzke, M. A., & Birchler, J. A. (2005) · Nature Reviews Genetics · doi:10.1038/nrg1500 · Cited by 844
microPrimer: the biogenesis and function of microRNA
Du, T., & Zamore, P. D. (2005) · Development · doi:10.1242/dev.02070 · Cited by 813
Clustering and conservation patterns of human microRNAs
Altuvia, Y. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki567 · Cited by 802
Berezikov, E., Chung, W.-J., Willis, J., Cuppen, E., & Lai, E. C. (2007) · Molecular Cell · doi:10.1016/j.molcel.2007.09.028 · Cited by 799
Aravin, A. A., Naumova, N. M., Tulin, A. V., Vagin, V. V., Rozovsky, Y. M., & Gvozdev, V. A. (2001) · Current Biology · doi:10.1016/s0960-9822(01)00299-8 · Cited by 795
Specialization and evolution of endogenous small RNA pathways
Chapman, E. J., & Carrington, J. C. (2007) · Nature Reviews Genetics · doi:10.1038/nrg2179 · Cited by 696
Structural basis for 5′-end-specific recognition of guide RNA by the A. fulgidus Piwi protein
Ma, J.-B., Yuan, Y.-R., Meister, G., Pei, Y., Tuschl, T., & Patel, D. J. (2005) · Nature · doi:10.1038/nature03514 · Cited by 657
Yigit, E., Batista, P. J., Bei, Y., Pang, K. M., Chen, C.-C. G., Tolia, N. H., Joshua-Tor, L., Mitani, S., Simard, M. J., & Mello, C. C. (2006) · Cell · doi:10.1016/j.cell.2006.09.033 · Cited by 650
Distinct Populations of Primary and Secondary Effectors During RNAi in C. elegans
Pak, J., & Fire, A. (2007) · Science · doi:10.1126/science.1132839 · Cited by 599
Keeling, P. J., Burger, G., Durnford, D. G., Lang, B. F., Lee, R. W., Pearlman, R. E., Roger, A. J., & Gray, M. W. (2005) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2005.09.005 · Cited by 579
Conserved domains in DNA repair proteins and evolution of repair systems
Aravind, L. (1999) · Nucleic Acids Research · doi:10.1093/nar/27.5.1223 · Cited by 560
Förstemann, K., Tomari, Y., Du, T., Vagin, V. V., Denli, A. M., Bratu, D. P., Klattenhoff, C., Theurkauf, W. E., & Zamore, P. D. (2005) · PLoS Biology · doi:10.1371/journal.pbio.0030236 · Cited by 545
Evolution of microRNA genes by inverted duplication of target gene sequences in Arabidopsis thaliana
Allen, E., Xie, Z., Gustafson, A. M., Sung, G.-H., Spatafora, J. W., & Carrington, J. C. (2004) · Nature Genetics · doi:10.1038/ng1478 · Cited by 520
Small RNAs Correspond to Centromere Heterochromatic Repeats
Reinhart, B. J., & Bartel, D. P. (2002) · Science · doi:10.1126/science.1077183 · Cited by 503
Diversity of microRNAs in human and chimpanzee brain
Berezikov, E., Thuemmler, F., van Laake, L. W., Kondova, I., Bontrop, R., Cuppen, E., & Plasterk, R. H. A. (2006) · Nature Genetics · doi:10.1038/ng1914 · Cited by 502
miRNAs control gene expression in the single-cell alga Chlamydomonas reinhardtii
Molnár, A., Schwach, F., Studholme, D. J., Thuenemann, E. C., & Baulcombe, D. C. (2007) · Nature · doi:10.1038/nature05903 · Cited by 501
Introns and the origin of nucleus–cytosol compartmentalization
Martin, W., & Koonin, E. V. (2006) · Nature · doi:10.1038/nature04531 · Cited by 501
Self-citationOn the origin and functions of RNA-mediated silencing: from protists to man
Cerutti, H., & Casas-Mollano, J. A. (2006) · Current Genetics · doi:10.1007/s00294-006-0078-x · Cited by 499
Ancient microRNA target sequences in plants
Floyd, S. K., & Bowman, J. L. (2004) · Nature · doi:10.1038/428485a · Cited by 408
Yuan, Y.-R., Pei, Y., Ma, J.-B., Kuryavyi, V., Zhadina, M., Meister, G., Chen, H.-Y., Dauter, Z., Tuschl, T., & Patel, D. J. (2005) · Molecular Cell · doi:10.1016/j.molcel.2005.07.011 · Cited by 396
Mechanism of RNA silencing by Hfq-binding small RNAs
Aiba, H. (2007) · Current Opinion in Microbiology · doi:10.1016/j.mib.2007.03.010 · Cited by 368
The expansion of the metazoan microRNA repertoire
Hertel, J., Lindemeyer, M., Missal, K., Fried, C., Tanzer, A., Flamm, C., Hofacker, I. L., Stadler, P. F., & 2005, T. S. O. B. C. L. 2. A. (2006) · BMC Genomics · doi:10.1186/1471-2164-7-25 · Cited by 355
Origin and Evolution of Human microRNAs From Transposable Elements
Piriyapongsa, J., Mariño-Ramírez, L., & Jordan, I. K. (2007) · Genetics · doi:10.1534/genetics.107.072553 · Cited by 353
Sempere, L. F., Cole, C. N., Mcpeek, M. A., & Peterson, K. J. (2006) · Journal of Experimental Zoology Part B: Molecular and Developmental Evolution · doi:10.1002/jez.b.21118 · Cited by 309
Ufd2, a Novel Autoantigen in Scleroderma, Regulates Sister Chromatid Separation
Spinette, S., Lengauer, C., Mahoney, J. A., Jallepalli, P. V., Wang, Z., Casciola-Rosen, L., & Rosen, A. (2004) · Cell Cycle · doi:10.4161/cc.3.12.1345 · Cited by 309
Lineage-specific loss and divergence of functionally linked genes in eukaryotes
Aravind, L., Watanabe, H., Lipman, D. J., & Koonin, E. V. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.200346997 · Cited by 295
Self-citationDual coding of siRNAs and miRNAs by plant transposable elements
Piriyapongsa, J., & Jordan, I. K. (2008) · RNA · doi:10.1261/rna.916708 · Cited by 289
Bacterial Small RNA Regulators
Majdalani, N., Vanderpool, C. K., & Gottesman, S. (2005) · Critical Reviews in Biochemistry and Molecular Biology · doi:10.1080/10409230590918702 · Cited by 286
A Family of Human MicroRNA Genes from Miniature Inverted-Repeat Transposable Elements
Piriyapongsa, J., & Jordan, I. K. (2007) · PLoS ONE · doi:10.1371/journal.pone.0000203 · Cited by 283
Plant and animal microRNAs: similarities and differences
Millar, A. A., & Waterhouse, P. M. (2005) · Functional & Integrative Genomics · doi:10.1007/s10142-005-0145-2 · Cited by 281
Iyer, L. M., Koonin, E. V., & Aravind, L. (2003) · BMC Structural Biology · doi:10.1186/1472-6807-3-1 · Cited by 265
Self-citationmicroRNAs: Runts of the Genome Assert Themselves
Lai, E. C. (2003) · Current Biology · doi:10.1016/j.cub.2003.11.017 · Cited by 264
The birth and death of microRNA genes in Drosophila
Lu, J., Shen, Y., Wu, Q., Kumar, S., He, B., Shi, S., Carthew, R. W., Wang, S. M., & Wu, C.-I. (2008) · Nature Genetics · doi:10.1038/ng.73 · Cited by 252
Mammalian microRNAs derived from genomic repeats
SMALHEISER, N., & TORVIK, V (2005) · Trends in Genetics · doi:10.1016/j.tig.2005.04.008 · Cited by 251
Ribonuclease revisited: structural insights into ribonuclease III family enzymes
MacRae, I. J., & Doudna, J. A. (2007) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2006.12.002 · Cited by 247
Hairpin RNA: a secondary structure of primary importance
Svoboda, P., & Cara, A. D. (2006) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-005-5558-5 · Cited by 241
Complex Spliceosomal Organization Ancestral to Extant Eukaryotes
Collins, L., & Penny, D. (2005) · Molecular Biology and Evolution · doi:10.1093/molbev/msi091 · Cited by 240
Role of Dicer in Posttranscriptional RNA Silencing
Jaskiewicz, L., & Filipowicz, W. (2008) · Current Topics in Microbiology and Immunology · doi:10.1007/978-3-540-75157-1_4 · Cited by 202
Evolution of plant microRNA gene families
Li, A., & Mao, L. (2007) · Cell Research · doi:10.1038/sj.cr.7310113 · Cited by 200
Conserved themes in small-RNA-mediated transposon control
Girard, A., & Hannon, G. J. (2008) · Trends in Cell Biology · doi:10.1016/j.tcb.2008.01.004 · Cited by 183
Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell
Makarova, K. S. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki775 · Cited by 181
The mammalian transcriptome and the function of non-coding DNA sequences.
Shabalina, S. A., & Spiridonov, N. A. (2004) · Genome biology · doi:10.1186/gb-2004-5-4-105 · Cited by 180
Self-citationComparison of approaches for rational siRNA design leading to a new efficient and transparent method
Matveeva, O., Nechipurenko, Y., Rossi, L., Moore, B., Saetrom, P., Ogurtsov, A. Y., Atkins, J. F., & Shabalina, S. A. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm088 · Cited by 179
Self-citationComputational models with thermodynamic and composition features improve siRNA design
Shabalina, S. A., Spiridonov, A. N., & Ogurtsov, A. Y. (2006) · BMC Bioinformatics · doi:10.1186/1471-2105-7-65 · Cited by 170
Self-citationRapid evolution of an X-linked microRNA cluster in primates
Zhang, R., Peng, Y., Wang, W., & Su, B. (2007) · Genome Research · doi:10.1101/gr.6146507 · Cited by 160
Alu elements within human mRNAs are probable microRNA targets
Smalheiser, N. R., & Torvik, V. I. (2006) · Trends in Genetics · doi:10.1016/j.tig.2006.08.007 · Cited by 157
Evidence for a microRNA expansion in the bilaterian ancestor
Prochnik, S. E., Rokhsar, D. S., & Aboobaker, A. A. (2006) · Development Genes and Evolution · doi:10.1007/s00427-006-0116-1 · Cited by 142
Evolution of plant microRNA gene families
Aili, Li, Long, L., & Mao, M. (2007) · Cell Research · Cited by 132
Antiviral silencing in animals
Li, H., & Ding, S. (2005) · FEBS Letters · doi:10.1016/j.febslet.2005.08.034 · Cited by 116
Molecular evolution of the rice miR395 gene family
GUDDETI, S., ZHANG, D. C., Li, A. L., LESEBERG, C. H., Kang, H., Li, X. G., Wen Xue, Z. H. A. I., Johns, M. A., & Mao, L. (2005) · Cell Research · doi:10.1038/sj.cr.7290333 · Cited by 112
Nishino, T., Komori, K., Tsuchiya, D., Ishino, Y., & Morikawa, K. (2005) · Structure · doi:10.1016/j.str.2004.11.008 · Cited by 99
Komori, K., Hidaka, M., Horiuchi, T., Fujikane, R., Shinagawa, H., & Ishino, Y. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m409243200 · Cited by 93
The Structure of an RNAi Polymerase Links RNA Silencing and Transcription
Salgado, P. S., Koivunen, M. R. L., Makeyev, E. V., Bamford, D. H., Stuart, D. I., & Grimes, J. M. (2006) · PLoS Biology · doi:10.1371/journal.pbio.0040434 · Cited by 92
Adaptive Evolution of Newly Emerged Micro-RNA Genes in Drosophila
Lü, J., Fu, Y., Kumar, S., Shen, Y., Zeng, K., Xu, A., Carthew, R. W., & Wu, C.-I. (2008) · Molecular Biology and Evolution · doi:10.1093/molbev/msn040 · Cited by 84
Patterns of intron gain and conservation in eukaryotic genes
Carmel, L., Rogozin, I. B., Wolf, Y. I., & Koonin, E. V. (2007) · BMC Evolutionary Biology · doi:10.1186/1471-2148-7-192 · Cited by 81
Self-citationMatranga, C. B., & Zamore, P. D. (2007) · Current Biology · doi:10.1016/j.cub.2007.07.014 · Cited by 79
An unusual Dicer-like1 protein fuels the RNA interference pathway in Trypanosoma brucei
Shi, H., Tschudi, C., & Ullu, E. (2006) · RNA · doi:10.1261/rna.246906 · Cited by 75
Free energy lights the path toward more effective RNAi
Silva, J. M., Sachidanandam, R., & Hannon, G. J. (2003) · Nature Genetics · doi:10.1038/ng1203-303 · Cited by 27
Cited by
The HCV Life Cycle: In vitro Tissue Culture Systems and Therapeutic Targets
Gerold, G., & Pietschmann, T. (2014) · Digestive Diseases · doi:10.1159/000360830 · Cited by 4,854
Bartel, D. P. (2018) · Cell · doi:10.1016/j.cell.2018.03.006 · Cited by 3,751
Transposable Elements, Epigenetics, and Genome Evolution
Fedoroff, N. V. (2012) · Science · doi:10.1126/science.338.6108.758 · Cited by 634
Origins and evolution of CRISPR-Cas systems
Koonin, E. V., & Makarova, K. S. (2019) · Philosophical Transactions of the Royal Society B: Biological Sciences · doi:10.1098/rstb.2018.0087 · Cited by 494
Self-citationEpigenetic Regulation in Plants
Pikaard, C. S., & Mittelsten Scheid, O. (2014) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a019315 · Cited by 440
Metadata
- Authors
- SHABALINA, S., & KOONIN, E.
- Venue
- Trends in Ecology & Evolution
- Publisher
- Elsevier BV
- Published
- 2008-10
- Volume
- 23
- Issue
- 10
- Pages
- 578-587
- ISSN
- 0169-5347 (ISSN-L)
- OpenAlex
- W2054268736
- Cited by
- 561
- References
- 86
- FWCI
- 8.07
- 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.