CoChat
Sign Up
Cited by 78

The DOI matches its Crossref record; 4 of the 4 references it cites were found in a registry or an index.

Deep annotation of mouse iso-miR and iso-moR variation

Zhou, Hongjun, Arcila, Mary Luz, Li, Zhonghan, Lee, Eun Joo, Henzler, Christine, Liu, Jingya, Rana, Tariq M., Kosik, Kenneth S.·2012·Nucleic Acids Research
DOI 10.1093/nar/gks247PMC PMC3401436
Open this paper in CoChat — free account

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.

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

Integrity signals

Registry

Crossref · 10.1093/nar/gks247

Cites

4 of 4 references verified0 citation errors · 0 not checkable

Statistics

Figures

Figure 1. Total phased reads of miRNA/miRNA*, moRs and loops.
Figure 1. Total phased reads of miRNA/miRNA*, moRs and loops.CC BY-NC · PubMed Central
Figure 2. Correlation of 5p expression and 3p expression between Group I and II. The ratio of expressed 5′-strand and 3′-strand for each miRNA in each group were calculated and the log values plotted.
Figure 2. Correlation of 5p expression and 3p expression between Group I and II. The ratio of expressed 5′-strand and 3′-strand for each miRNA in each group were calculated and the log values plotted.CC BY-NC · PubMed Central
Figure 3. Phased read distributions of (A) miR-125b and (B) miR-191.
Figure 3. Phased read distributions of (A) miR-125b and (B) miR-191.CC BY-NC · PubMed Central
Figure 4. Distributions of isomiRs. (A) miR-124 isomiRs. IsomiRs were listed according their 5′-ends, and for each group with the same 5′-end, up to five most abundant isomiR with different 3′-ends are shown. (B) The distributions of all isomiRs grouped either by their 5′-end or 3′-end for both strands. IsomiRs were grouped by their distance of 5′-end or 3′-end compared to the dominant ones (X-axis). At most 3 nt variations at either end were allowed.
Figure 4. Distributions of isomiRs. (A) miR-124 isomiRs. IsomiRs were listed according their 5′-ends, and for each group with the same 5′-end, up to five most abundant isomiR with different 3′-ends are shown. (B) The distributions of all isomiRs grouped either by their 5′-end or 3′-end for both strands. IsomiRs were grouped by their distance of 5′-end or 3′-end compared to the dominant ones (X-axis). At most 3 nt variations at either end were allowed.CC BY-NC · PubMed Central
Figure 5. End variations of isomiRs at Drosha and Dicer cleavage sites. Two comparisons were performed: one was based on variations at the 5′-end of isomiRs and the other was based on variation at the 3′-ends. Both comparisons showed Drosha had a higher chance to match the sequences with the dominant isomiRs.
Figure 5. End variations of isomiRs at Drosha and Dicer cleavage sites. Two comparisons were performed: one was based on variations at the 5′-end of isomiRs and the other was based on variation at the 3′-ends. Both comparisons showed Drosha had a higher chance to match the sequences with the dominant isomiRs.CC BY-NC · PubMed Central
Figure 6. miRNAs with high isomiR variation. (A) Distributions of preferred and non-preferred isomiRs with high variation grouped by their 5′-ends. These miRNAs have second isomiRs with significant abundance, which usually shifted 2 or 3 nt’s compared to the dominant isomiR. (B) The distributions of three principle isomiRs of miR-495-3p positioned on the hairpin structure of miR-495 precursors. The dominant isomiR switched in Group II cells.
Figure 6. miRNAs with high isomiR variation. (A) Distributions of preferred and non-preferred isomiRs with high variation grouped by their 5′-ends. These miRNAs have second isomiRs with significant abundance, which usually shifted 2 or 3 nt’s compared to the dominant isomiR. (B) The distributions of three principle isomiRs of miR-495-3p positioned on the hairpin structure of miR-495 precursors. The dominant isomiR switched in Group II cells.CC BY-NC · PubMed Central
Figure 7. Distributions of isomiRs in different groups of samples for miRNAs with isomiR variation. (A) miR-485-3p which switched the dominant isomiR in Group II samples. (B) miR-543-5p; (C) miR-592-5p; (D) miR-137-3p; (E) miR-125b-2-3p which did not switch the dominant isomiR, but the second isomiR increased in Group II; (F) miR-690-3p which showed the difference between AGO-IP and total small RNA samples.
Figure 7. Distributions of isomiRs in different groups of samples for miRNAs with isomiR variation. (A) miR-485-3p which switched the dominant isomiR in Group II samples. (B) miR-543-5p; (C) miR-592-5p; (D) miR-137-3p; (E) miR-125b-2-3p which did not switch the dominant isomiR, but the second isomiR increased in Group II; (F) miR-690-3p which showed the difference between AGO-IP and total small RNA samples.CC BY-NC · PubMed Central
Figure 8. Untemplated nucleotide addition rate at the 3′-ends of miRNA/miRNA*.
Figure 8. Untemplated nucleotide addition rate at the 3′-ends of miRNA/miRNA*.CC BY-NC · PubMed Central

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.

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?

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

Show all 4 references

Research works printed but not linked: 70

  1. Bartel, 2009, MicroRNAs: target recognition and regulatory functions, Cell, 136, 215, 10.1016/j.cell.2009.01.002 · DOI · Paper page
  2. Bartel, 2004, MicroRNAs: genomics, biogenesis, mechanism, and function, Cell, 116, 281, 10.1016/S0092-8674(04)00045-5 · DOI
  3. Okamura, 2007, The mirtron pathway generates microRNA-class regulatory RNAs in Drosophila, Cell, 130, 89, 10.1016/j.cell.2007.06.028 · DOI
  4. Ruby, 2007, Intronic microRNA precursors that bypass Drosha processing, Nature, 448, 83, 10.1038/nature05983 · DOI · Paper page
  5. Lee, 2003, The nuclear RNase III Drosha initiates microRNA processing, Nature, 425, 415, 10.1038/nature01957 · DOI
  6. Han, 2004, The Drosha-DGCR8 complex in primary microRNA processing, Genes Dev., 18, 3016, 10.1101/gad.1262504 · DOI
  7. Han, 2006, Molecular basis for the recognition of primary microRNAs by the Drosha-DGCR8 complex, Cell, 125, 887, 10.1016/j.cell.2006.03.043 · DOI
  8. Okada, 2009, A high-resolution structure of the pre-microRNA nuclear export machinery, Science, 326, 1275, 10.1126/science.1178705 · DOI
  9. Yi, 2003, Exportin-5 mediates the nuclear export of pre-microRNAs and short hairpin RNAs, Genes Dev., 17, 3011, 10.1101/gad.1158803 · DOI
  10. Bohnsack, 2004, Exportin 5 is a RanGTP-dependent dsRNA-binding protein that mediates nuclear export of pre-miRNAs, RNA, 10, 185, 10.1261/rna.5167604 · DOI
  11. Hutvágner, 2001, A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA, Science, 293, 834, 10.1126/science.1062961 · DOI · Paper page
  12. Gregory, 2005, Human RISC couples microRNA biogenesis and posttranscriptional gene silencing, Cell, 123, 631, 10.1016/j.cell.2005.10.022 · DOI · Paper page
  13. Leuschner, 2006, Cleavage of the siRNA passenger strand during RISC assembly in human cells, EMBO Rep., 7, 314, 10.1038/sj.embor.7400637 · DOI
  14. Hutvagner, 2008, Argonaute proteins: key players in RNA silencing, Nat. Rev. Mol. Cell Biol., 9, 22, 10.1038/nrm2321 · DOI
  15. Diederichs, 2007, Dual role for argonautes in microRNA processing and posttranscriptional regulation of microRNA expression, Cell, 131, 1097, 10.1016/j.cell.2007.10.032 · DOI
  16. Cheloufi, 2010, A dicer-independent miRNA biogenesis pathway that requires Ago catalysis, Nature, 465, 584, 10.1038/nature09092 · DOI · Paper page
  17. Cifuentes, 2010, A novel miRNA processing pathway independent of Dicer requires Argonaute2 catalytic activity, Science, 328, 1694, 10.1126/science.1190809 · DOI
  18. Khvorova, 2003, Functional siRNAs and miRNAs exhibit strand bias, Cell, 115, 209, 10.1016/S0092-8674(03)00801-8 · DOI · Paper page
  19. Schwarz, 2003, Asymmetry in the assembly of the RNAi enzyme complex, Cell, 115, 199, 10.1016/S0092-8674(03)00759-1 · DOI · Paper page
  20. Winter, 2009, Many roads to maturity: microRNA biogenesis pathways and their regulation, Nat. Cell Biol., 11, 228, 10.1038/ncb0309-228 · DOI
  21. Kuramochi-Miyagawa, 2010, MVH in piRNA processing and gene silencing of retrotransposons, Genes Dev., 24, 887, 10.1101/gad.1902110 · DOI
  22. Jazdzewski, 2009, Polymorphic mature microRNAs from passenger strand of pre-miR-146a contribute to thyroid cancer, Proc. Natl Acad. Sci. USA, 106, 1502, 10.1073/pnas.0812591106 · DOI · Paper page
  23. Czech, 2009, Hierarchical rules for Argonaute loading in Drosophila, Mol. Cell, 36, 445, 10.1016/j.molcel.2009.09.028 · DOI
  24. Okamura, 2009, Distinct mechanisms for microRNA strand selection by Drosophila Argonautes, Mol. Cell, 36, 431, 10.1016/j.molcel.2009.09.027 · DOI · Paper page
  25. Ghildiyal, 2010, Sorting of Drosophila small silencing RNAs partitions microRNA* strands into the RNA interference pathway, RNA, 16, 43, 10.1261/rna.1972910 · DOI · Paper page
  26. Morin, 2008, Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells, Genome Res., 18, 610, 10.1101/gr.7179508 · DOI · Paper page
  27. Lee, 2010, Complexity of the microRNA repertoire revealed by next-generation sequencing, RNA, 16, 2170, 10.1261/rna.2225110 · DOI
  28. Berezikov, 2011, Deep annotation of Drosophila melanogaster microRNAs yields insights into their processing, modification, and emergence, Genome Res., 21, 203, 10.1101/gr.116657.110 · DOI
  29. Kozomara, 2011, miRBase: integrating microRNA annotation and deep-sequencing data, Nucleic Acids Res., 39, D152, 10.1093/nar/gkq1027 · DOI · Paper page
  30. Nelson, 2007, A novel monoclonal antibody against human Argonaute proteins reveals unexpected characteristics of miRNAs in human blood cells, RNA, 13, 1787, 10.1261/rna.646007 · DOI · Paper page
  31. Li, 2011, Small RNA-mediated regulation of iPS cell generation, EMBO J., 30, 823, 10.1038/emboj.2011.2 · DOI
  32. Takahashi, 2006, Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors, Cell, 126, 663, 10.1016/j.cell.2006.07.024 · DOI · Paper page
  33. Hu, 2009, Sequence features associated with microRNA strand selection in humans and flies, BMC Genomics, 10, 413, 10.1186/1471-2164-10-413 · DOI
  34. Chiang, 2010, Mammalian microRNAs: experimental evaluation of novel and previously annotated genes, Genes Dev., 24, 992, 10.1101/gad.1884710 · DOI · Paper page
  35. Warf, 2011, Improved annotation of C. elegans microRNAs by deep sequencing reveals structures associated with processing by Drosha and Dicer, RNA, 17, 563, 10.1261/rna.2432311 · DOI
  36. Ruby, 2007, Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs, Genome Res., 17, 1850, 10.1101/gr.6597907 · DOI
  37. Seitz, 2008, Argonaute loading improves the 5' precision of both MicroRNAs and their miRNA* strands in flies, Curr. Biol., 18, 147, 10.1016/j.cub.2007.12.049 · DOI · Paper page
  38. Ruby, 2006, Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans, Cell, 127, 1193, 10.1016/j.cell.2006.10.040 · DOI
  39. Wu, 2007, miRNA profiling of naive, effector and memory CD8 T cells, PLoS One, 2, e1020, 10.1371/journal.pone.0001020 · DOI
  40. Ramachandran, 2008, Degradation of microRNAs by a family of exoribonucleases in Arabidopsis, Science, 321, 1490, 10.1126/science.1163728 · DOI
  41. Kai, 2010, MicroRNA assassins: factors that regulate the disappearance of miRNAs, Nat. Struct. Mol. Biol., 17, 5, 10.1038/nsmb.1762 · DOI
  42. Pantano, 2010, SeqBuster, a bioinformatic tool for the processing and analysis of small RNAs datasets, reveals ubiquitous miRNA modifications in human embryonic cells, Nucleic Acids Res., 38, e34, 10.1093/nar/gkp1127 · DOI
  43. Ebhardt, 2009, Meta-analysis of small RNA-sequencing errors reveals ubiquitous post-transcriptional RNA modifications, Nucleic Acids Res., 37, 2461, 10.1093/nar/gkp093 · DOI
  44. Newman, 2011, Deep sequencing of microRNA precursors reveals extensive 3' end modification, RNA, 17, 1795, 10.1261/rna.2713611 · DOI
  45. Sewer, 2005, Identification of clustered microRNAs using an ab initio prediction method, BMC Bioinformatics, 6, 267, 10.1186/1471-2105-6-267 · DOI
  46. Mineno, 2006, The expression profile of microRNAs in mouse embryos, Nucleic Acids Res., 34, 1765, 10.1093/nar/gkl096 · DOI
  47. Ameres, 2010, Target RNA-directed trimming and tailing of small silencing RNAs, Science, 328, 1534, 10.1126/science.1187058 · DOI · Paper page
  48. Kim, 2010, Modifications of small RNAs and their associated proteins, Cell, 143, 703, 10.1016/j.cell.2010.11.018 · DOI
  49. Grimson, 2008, Early origins and evolution of microRNAs and Piwi-interacting RNAs in animals, Nature, 455, 1193, 10.1038/nature07415 · DOI
  50. Griffiths-Jones, 2011, MicroRNA evolution by arm switching, EMBO Rep., 12, 172, 10.1038/embor.2010.191 · DOI · Paper page
  51. Ro, 2007, Tissue-dependent paired expression of miRNAs, Nucleic Acids Res., 35, 5944, 10.1093/nar/gkm641 · DOI · Paper page
  52. de Wit, 2009, Repertoire and evolution of miRNA genes in four divergent nematode species, Genome Res., 19, 2064, 10.1101/gr.093781.109 · DOI · Paper page
  53. Seitz, 2008, Argonaute loading improves the 5' precision of both MicroRNAs and their miRNA* strands in flies, Curr. Biol., 18, 147, 10.1016/j.cub.2007.12.049 · DOI · Paper page
  54. Azuma-Mukai, 2008, Characterization of endogenous human Argonautes and their miRNA partners in RNA silencing, Proc. Natl Acad. Sci. USA, 105, 7964, 10.1073/pnas.0800334105 · DOI
  55. Czech, 2008, An endogenous small interfering RNA pathway in Drosophila, Nature, 453, 798, 10.1038/nature07007 · DOI
  56. Okamura, 2008, The regulatory activity of microRNA* species has substantial influence on microRNA and 3' UTR evolution, Nat. Struct. Mol. Biol., 15, 354, 10.1038/nsmb.1409 · DOI · Paper page
  57. Goff, 2009, Ago2 immunoprecipitation identifies predicted microRNAs in human embryonic stem cells and neural precursors, PLoS One, 4, e7192, 10.1371/journal.pone.0007192 · DOI
  58. Czech, 2011, Small RNA sorting: matchmaking for Argonautes, Nat. Rev. Genet., 12, 19, 10.1038/nrg2916 · DOI · Paper page
  59. Burroughs, 2011, Deep-sequencing of human Argonaute-associated small RNAs provides insight into miRNA sorting and reveals Argonaute association with RNA fragments of diverse origin, RNA Biol., 8, 158, 10.4161/rna.8.1.14300 · DOI
  60. Yang, 2011, Widespread regulatory activity of vertebrate microRNA* species, RNA, 17, 312, 10.1261/rna.2537911 · DOI · Paper page
  61. Kuchenbauer, 2011, Comprehensive analysis of mammalian miRNA* species and their role in myeloid cells, Blood, 118, 3350, 10.1182/blood-2010-10-312454 · DOI
  62. Schulte, 2010, Deep sequencing reveals differential expression of microRNAs in favorable versus unfavorable neuroblastoma, Nucleic Acids Res., 38, 5919, 10.1093/nar/gkq342 · DOI
  63. Kim, 2008, Identification and characterization of new microRNAs from pig, Mamm. Genome, 19, 570, 10.1007/s00335-008-9111-3 · DOI
  64. Reese, 2010, Identification of novel microRNA-like molecules generated from herpesvirus and host tRNA transcripts, J. Virol., 84, 10344, 10.1128/JVI.00707-10 · DOI
  65. de Hoon, 2010, Cross-mapping and the identification of editing sites in mature microRNAs in high-throughput sequencing libraries, Genome Res., 20, 257, 10.1101/gr.095273.109 · DOI
  66. Fernandez-Valverde, 2010, Dynamic isomiR regulation in Drosophila development, RNA, 16, 1881, 10.1261/rna.2379610 · DOI · Paper page
  67. Guo, 2011, A comprehensive survey of miRNA repertoire and 3' addition events in the placentas of patients with pre-eclampsia from high-throughput sequencing, PLoS One, 6, e21072, 10.1371/journal.pone.0021072 · DOI
  68. Burroughs, 2012, pre-miRNA profiles obtained through application of locked nucleic acids and deep sequencing reveals complex 5'/3' arm variation including concomitant cleavage and polyuridylation patterns, Nucleic Acids Res., 40, 1424, 10.1093/nar/gkr903 · DOI
  69. Babiarz, 2008, Mouse ES cells express endogenous shRNAs, siRNAs, and other Microprocessor-independent, Dicer-dependent small RNAs, Genes Dev., 22, 2773, 10.1101/gad.1705308 · DOI
  70. Shi, 2009, A distinct class of small RNAs arises from pre-miRNA-proximal regions in a simple chordate, Nat. Struct. Mol. Biol., 16, 183, 10.1038/nsmb.1536 · DOI

Cited by

Sorted by citations

Metadata

Authors
Zhou, H., Arcila, M. L., Li, Z., Lee, E. J., Henzler, C., Liu, J., Rana, T. M., & Kosik, K. S.
Venue
Nucleic Acids Research
Publisher
Oxford University Press (OUP)
Published
2012-03-19
Volume
40
Issue
13
Pages
5864-5875
ISSN
  • 1362-4962
  • 0305-1048
DOI
10.1093/nar/gks247
PMC
PMC3401436
Cited by
78
References
4
Language
en
Licence
creativecommons.org/licenses/by-nc/3.0 (vor, 1660 d)

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