Cited by 124

Functional Shifts in Insect microRNA Evolution

Marco, Antonio, Hui, Jerome H. L., Ronshaugen, Matthew, Griffiths-Jones, Sam·2010·Genome Biology and Evolution

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.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1093/gbe/evq053

Cites

Statistics

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.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • In some closely-related species, the preferred miRNA arm for homologous miRNA genes is not the same, consistent with the idea that, in at least some cases, miRNA arm switching could be evolutionarily favored.

    “Interestingly, in some closely‐related species, the preferred miRNA arm for homologous miRNA genes is not the same (de Wit et al., 2009; Griffiths‐Jones et al., 2011; Marco et al., 2010), consistent with the idea that, in at least some cases, miRNA arm switching could be evolutionarily favored.”

    From microRNA strand selection: Unwinding the rules (2021) · cites this paper as Marco et al., 2010

  • miRNA arm switching has been proposed to influence miRNA evolution, as altered selection of a miRNA strand by Argonaute would be expected to result in a different mRNA target repertoire.

    “Interestingly, miRNA arm switching has been proposed to influence miRNA evolution, as altered selection of a miRNA strand by Argonaute would be expected to result in a different mRNA target repertoire (de Wit, Linsen, Cuppen, & Berezikov, 2009; Griffiths‐Jones, Hui, Marco, & Ronshaugen, 2011; Marco, Hui, Ronshaugen, & Griffiths‐Jones, 2010).”

    From microRNA strand selection: Unwinding the rules (2021) · cites this paper as Marco, Hui, Ronshaugen, & Griffiths-Jones, 2010

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Cites

No references could be resolved yet.

Research works printed but not linked: 57

  1. Altschul SF Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Nucleic Acids Res 1997 25 3389 3402 9254694 PMC146917
  2. Altuvia Y Clustering and conservation patterns of human microRNAs Nucleic Acids Res 2005 33 2697 2706 15891114 PMC1110742
  3. Aravin AA The small RNA profile during Drosophila melanogaster development Dev Cell 2003 5 337 350 12919683
  4. Ashburner M Golic KG Hawley RS Drosophila: a laboratory handbook 2004 2nd ed New York Cold Spring Harbor Laboratory Press
  5. Bartel DP MicroRNAs: genomics, biogenesis, mechanism, and function Cell 2004 116 281 297 14744438
  6. Bartel DP MicroRNAs: target recognition and regulatory functions Cell 2009 136 215 233 19167326 PMC3794896
  7. Baskerville S Bartel DP Microarray profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes RNA 2005 11 241 247 15701730 PMC1370713
  8. Behura SK Insect microRNAs: structure, function and evolution Insect Biochem Mol Biol 2007 37 3 9 17175441
  9. Bell ML Buvoli M Leinwand LA Uncoupling of expression of an intronic microRNA and its myosin host gene by exon skipping Mol Cell Biol 2010 30 1937 1945 20154144 PMC2849460
  10. Berezikov E Evolutionary flux of canonical microRNAs and mirtrons in Drosophila Nat Genet 2010 42 6 9 20037610 PMC4136759
  11. Brown SJ Denell RE Beeman RW Beetling around the genome Genet Res 2003 82 155 161 15134194
  12. Cai Y Novel microRNAs in silkworm (Bombyx mori) Funct Integr Genomics 2010 doi:10.1007/s10142-010-0162-7 20229201 · DOI
  13. Chen K Rajewsky N The evolution of gene regulation by transcription factors and microRNAs Nat Rev Genet 2007 8 93 103 17230196
  14. Cheng L Pastrana E Tavazoie M Doetsch F miR-124 regulates adult neurogenesis in the subventricular zone stem cell niche Nat Neurosci 2009 12 399 408 19287386 PMC2766245
  15. Chiang HR Mammalian microRNAs: experimental evaluation of novel and previously annotated genes Genes Dev 2010 24 992 1009 20413612 PMC2867214
  16. Clark AM The microRNA miR-124 controls gene expression in the sensory nervous system of Caenorhabditis elegans Nucleic Acids Res 2010 doi:10.1093/nar/gkq083 PMC2887956 20176573 · DOI
  17. Cloonan N RNA-MATE: a recursive mapping strategy for high-throughput RNA-sequencing data Bioinformatics 2009 25 2615 19648138 PMC2752615
  18. Davis GK Patel NH Short, long, and beyond: molecular and embryological approaches to insect segmentation Annu Rev Entomol 2002 47 669 699 11729088
  19. de Wit E Linsen S Cuppen E Berezikov E Repertoire and evolution of miRNA genes in four divergent nematode species Genome Res 2009 19 2064 2074 19755563 PMC2775598
  20. Glazov EA A microRNA catalog of the developing chicken embryo identified by a deep sequencing approach Genome Res 2008 18 957 964 18469162 PMC2413163
  21. Griffiths-Jones S RALEE—RNA ALignment editor in Emacs Bioinformatics 2005 21 257 259 15377506
  22. Griffiths-Jones S Rfam: annotating non-coding RNAs in complete genomes Nucleic Acids Res 2005 33 D121 D124 15608160 PMC540035
  23. Griffiths-Jones S Saini HK van Dongen S Enright AJ miRBase: tools for microRNA genomics Nucleic Acids Res 2008 36 D154 D158 17991681 PMC2238936
  24. Guerra-Assunção JA Enright A MapMi: automated mapping of microRNA loci BMC Bioinformatics 2010 11 133 20233390 PMC2858034
  25. Jagadeeswaran G Deep sequencing of small RNA libraries reveals dynamic regulation of conserved and novel microRNAs and microRNA-stars during silkworm development BMC Genomics 2010 11 52 20089182 PMC2824724
  26. Kloosterman WP Plasterk RHA The diverse functions of microRNAs in animal development and disease Dev Cell 2006 11 441 450 17011485
  27. Langmead B Trapnell C Pop M Salzberg SL Ultrafast and memory-efficient alignment of short DNA sequences to the human genome Genome Biol 2009 10 R25 19261174 PMC2690996
  28. Lee Y The nuclear RNase III Drosha initiates microRNA processing Nature 2003 425 415 419 14508493
  29. Lee Y Jeon K Lee J Kim S Kim VN MicroRNA maturation: stepwise processing and subcellular localization EMBO J 2002 21 4663 4670 12198168 PMC126204
  30. Liu S MicroRNAs show diverse and dynamic expression patterns in multiple tissues of Bombyx mori BMC Genomics 2010 11 85 20122259 PMC2835664
  31. Lowe TM Eddy SR tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence Nucleic Acids Res 1997 25 955 964 9023104 PMC146525
  32. Lu J The birth and death of microRNA genes in Drosophila Nat Genet 2008 40 351 355 18278047
  33. Luo Q Genome-wide mapping of conserved microRNAs and their host transcripts in Tribolium castaneum J Genet Genomics 2008 35 349 355 18571123
  34. Makeyev EV Zhang J Carrasco MA Maniatis T The MicroRNA miR-124 promotes neuronal differentiation by triggering brain-specific alternative pre-mRNA splicing Mol Cell 2007 27 435 448 17679093 PMC3139456
  35. Marques-Souza H Aranda M Tautz D Delimiting the conserved features of hunchback function for the trunk organization of insects Development 2008 135 881 888 18216167
  36. Nawrocki EP Kolbe DL Eddy SR Infernal 1.0: inference of RNA alignments Bioinformatics 2009 25 1335 1337 19307242 PMC2732312
  37. Niwa R Slack FJ The evolution of animal microRNA function Curr Opin Genet Dev 2007 17 145 150 17317150
  38. Okamura K The regulatory activity of microRNA* species has substantial influence on microRNA and 3' UTR evolution Nat Struct Mol Biol 2008 15 354 363 18376413 PMC2698667
  39. Peel AD Forward genetics in Tribolium castaneum: opening new avenues of research in arthropod biology J Biol 2009 8 106 20053302 PMC2804280
  40. Richards S The genome of the model beetle and pest Tribolium castaneum Nature 2008 452 949 955 18362917
  41. Rodriguez A Griffiths-Jones S Ashurst JL Bradley A Identification of mammalian microRNA host genes and transcription units Genome Res 2004 14 1902 1910 15364901 PMC524413
  42. Ronshaugen M Biemar F Piel J Levine M Lai EC The Drosophila microRNA iab-4 causes a dominant homeotic transformation of halteres to wings Genes Dev 2005 19 2947 2952 16357215 PMC1315399
  43. Ruby JG Jan CH Bartel DP Intronic microRNA precursors that bypass Drosha processing Nature 2007 448 83 86 17589500 PMC2475599
  44. Ruby JG Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs Genome Res 2007 17 1850 1864 17989254 PMC2099593
  45. Saini HK Enright AJ Griffiths-Jones S Annotation of mammalian primary microRNAs BMC Genomics 2008 9 564 19038026 PMC2632650
  46. Saini HK Griffiths-Jones S Enright AJ Genomic analysis of human microRNA transcripts Proc Natl Acad Sci USA 2007 104 17719 17724 17965236 PMC2077053
  47. Savard J Tautz D Lercher MJ Genome-wide acceleration of protein evolution in flies (Diptera) BMC Evol Biol 2006 6 7 16436210 PMC1369000
  48. Shippy TD Analysis of the Tribolium homeotic complex: insights into mechanisms constraining insect Hox clusters Dev Genes Evol 2008 218 127 139 18392875 PMC2292473
  49. Singh J Nagaraju J In silico prediction and characterization of microRNAs from red flour beetle (Tribolium castaneum) Insect Mol Biol 2008 17 427 436 18651924
  50. Stark A Systematic discovery and characterization of fly microRNAs using 12 Drosophila genomes Genome Res 2007 17 1865 1879 17989255 PMC2099594
  51. Tang G Maxwell ES Xenopus microRNA genes are predominantly located within introns and are differentially expressed in adult frog tissues via post-transcriptional regulation Genome Res 2008 18 104 112 18032731 PMC2134782
  52. Thompson JD Higgins DG Gibson TJ 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 4673 4680 7984417 PMC308517
  53. Tyler DM Functionally distinct regulatory RNAs generated by bidirectional transcription and processing of microRNA loci Genes Dev 2008 22 26 36 18172163 PMC2151012
  54. Wang L Wang S Li Y Paradesi MSR Brown SJ BeetleBase: the model organism database for Tribolium castaneum Nucleic Acids Res 2007 35 D476 D479 17090595 PMC1669707
  55. Wheeler B The deep evolution of metazoan microRNAs Evol Dev 2009 11 50 68 19196333
  56. Wiegmann BM Kim J Tratwein MD Hedges SB Kumar S Holometabola The timetree of life 2009 New York Oxford University Press US 260 263
  57. Yekta S Shih I Bartel DP MicroRNA-directed cleavage of HOXB8 mRNA Science 2004 304 594 596 15105502

Cited by

Sorted by citations

Authors
Marco, A., Hui, J. H. L., Ronshaugen, M., & Griffiths-Jones, S.
Affiliations
Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, United Kingdom
Venue
Genome Biology and Evolution
Published
2010-01-01
Volume
2
Pages
686-696
ISSN
1759-6653
Cited by
124
References
0
Language
en

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