Student or educator? Sign up with your school email and get 6 months of Pro free.
CoChat
Sign Up
Cited by 429

The DOI matches its Crossref record; 6 of the 6 references it cites were found in a registry or an index.

The complex eukaryotic transcriptome: unexpected pervasive transcription and novel small RNAs

Jacquier, Alain·2009·Nature Reviews Genetics
DOI 10.1038/nrg2683
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 · 10.1038/nrg2683

Cites

6 of 6 references verified0 citation errors · 0 not checkable

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.

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

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 6 references

Research works printed but not linked: 74

  1. Carthew, R. W. & Sontheimer, E. J. Origins and mechanisms of miRNAs and siRNAs. Cell 136, 642–655 (2009). · DOI · Paper page
  2. Berretta, J. & Morillon, A. Pervasive transcription constitutes a new level of eukaryotic genome regulation. EMBO Rep. 10, 973–982 (2009). · DOI · Paper page
  3. Ponting, C. P., Oliver, P. L. & Reik, W. Evolution and functions of long noncoding RNAs. Cell 136, 629–641 (2009). · DOI · Paper page
  4. Yazgan, O. & Krebs, J. E. Noncoding but nonexpendable: transcriptional regulation by large noncoding RNA in eukaryotes. Biochem. Cell Biol. 85, 484–496 (2007). · DOI
  5. Velculescu, V. E. et al. Characterization of the yeast transcriptome. Cell 88, 243–251 (1997). · DOI · Paper page
  6. Goffeau, A. 1996: a vintage year for yeast and Yeast. Yeast 12, 1603–1605 (1996). · doi:10.1002/(sici)1097-0061(199612)12:16<1603::aid-yea117>3.0.co;2-z
  7. Okazaki, Y. et al. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature 420, 563–573 (2002). · DOI · Paper page
  8. Numata, K. et al. Identification of putative noncoding RNAs among the RIKEN mouse full-length cDNA collection. Genome Res. 13, 1301–1306 (2003). · DOI
  9. Hayashizaki, Y. & Carninci, P. Genome Network and FANTOM3: assessing the complexity of the transcriptome. PLoS Genet. 2, e63 (2006). · DOI
  10. Kapranov, P. et al. Large-scale transcriptional activity in chromosomes 21 and 22. Science 296, 916–919 (2002). · DOI · Paper page
  11. Ravasi, T. et al. Experimental validation of the regulated expression of large numbers of non-coding RNAs from the mouse genome. Genome Res. 16, 11–19 (2006). · DOI · Paper page
  12. Kampa, D. et al. Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22. Genome Res. 14, 331–342 (2004). · DOI · Paper page
  13. Cloonan, N. & Grimmond, S. M. Transcriptome content and dynamics at single-nucleotide resolution. Genome Biol. 9, 234 (2008). · DOI
  14. Kapranov, P., Sementchenko, V. I. & Gingeras, T. R. Beyond expression profiling: next generation uses of high density oligonucleotide arrays. Brief Funct. Genomic Proteomic 2, 47–56 (2003). · DOI
  15. He, Y., Vogelstein, B., Velculescu, V. E., Papadopoulos, N. & Kinzler, K. W. The antisense transcriptomes of human cells. Science 322, 1855–1857 (2008). · DOI · Paper page
  16. Carninci, P. Molecular biology: the long and short of RNAs. Nature 457, 974–975 (2009). · DOI
  17. Carninci, P., Yasuda, J. & Hayashizaki, Y. Multifaceted mammalian transcriptome. Curr. Opin. Cell Biol. 20, 274–280 (2008). · DOI
  18. Johnson, J. M., Edwards, S., Shoemaker, D. & Schadt, E. E. Dark matter in the genome: evidence of widespread transcription detected by microarray tiling experiments. Trends Genet. 21, 93–102 (2005). · DOI · Paper page
  19. Kapranov, P., Willingham, A. T. & Gingeras, T. R. Genome-wide transcription and the implications for genomic organization. Nature Rev. Genet. 8, 413–423 (2007). · DOI · Paper page
  20. Ponjavic, J. & Ponting, C. P. The long and the short of RNA maps. Bioessays 29, 1077–1080 (2007). · DOI
  21. Kapranov, P. et al. RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science 316, 1484–1488 (2007). The first description of promoter-associated ncRNAs in mammals. · DOI · Paper page
  22. Seila, A. C. et al. Divergent transcription from active promoters. Science 322, 1849–1851 (2008). A description of divergent small pervasive transcripts at gene promoters. · DOI · Paper page
  23. Taft, R. J. et al. Tiny RNAs associated with transcription start sites in animals. Nature Genet. 41, 572–578 (2009). · DOI · Paper page
  24. Core, L. J., Waterfall, J. J. & Lis, J. T. Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science 322, 1845–1848 (2008). This study produced a genome-wide map of run-on transcripts in mammals that reveals bidirectional transcription at gene promoters. · DOI · Paper page
  25. Muse, G. W. et al. RNA polymerase is poised for activation across the genome. Nature Genet. 39, 1507–1511 (2007). · DOI · Paper page
  26. Zeitlinger, J. et al. RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo. Nature Genet. 39, 1512–1516 (2007). · DOI · Paper page
  27. Gilmour, D. S. Promoter proximal pausing on genes in metazoans. Chromosoma 118, 1–10 (2009). · DOI
  28. Margaritis, T. & Holstege, F. C. Poised RNA polymerase II gives pause for thought. Cell 133, 581–584 (2008). · DOI
  29. Guenther, M. G., Levine, S. S., Boyer, L. A., Jaenisch, R. & Young, R. A. A chromatin landmark and transcription initiation at most promoters in human cells. Cell 130, 77–88 (2007). · DOI · Paper page
  30. Kim, T. H. et al. A high-resolution map of active promoters in the human genome. Nature 436, 876–880 (2005). · DOI · Paper page
  31. Fejes-Toth, K. et al. Post-transcriptional processing generates a diversity of 5′-modified long and short RNAs. Nature 457, 1028–1032 (2009). · DOI · Paper page
  32. Rasmussen, E. B. & Lis, J. T. In vivo transcriptional pausing and cap formation on three Drosophila heat shock genes. Proc. Natl Acad. Sci. USA 90, 7923–7927 (1993). · DOI · Paper page
  33. Houseley, J. & Tollervey, D. The many pathways of RNA degradation. Cell 136, 763–776 (2009). · DOI · Paper page
  34. Vanacova, S. et al. A new yeast poly(A) polymerase complex involved in RNA quality control. PLoS Biol. 3, e189 (2005). · DOI · Paper page
  35. LaCava, J. et al. RNA degradation by the exosome is promoted by a nuclear polyadenylation complex. Cell 121, 713–724 (2005). · DOI · Paper page
  36. Wyers, F. et al. Cryptic pol II transcripts are degraded by a nuclear quality control pathway involving a new poly(A) polymerase. Cell 121, 725–737 (2005). This study provided the first description of CUTs in yeast. In addition, in parallel with other reports, this article describes the novel poly(A) polymerase-containing complex TRAMP and its role in exosome-mediated nuclear RNA degradation. · DOI · Paper page
  37. Davis, C. A. & Ares, M. Jr. Accumulation of unstable promoter-associated transcripts upon loss of the nuclear exosome subunit Rrp6p in Saccharomyces cerevisiae. Proc. Natl Acad. Sci. USA 103, 3262–3267 (2006). · DOI · Paper page
  38. Neil, H. et al. Widespread bidirectional promoters are the major source of cryptic transcripts in yeast. Nature 457, 1038–1042 (2009). · DOI · Paper page
  39. Xu, Z. et al. Bidirectional promoters generate pervasive transcription in yeast. Nature 457, 1033–1037 (2009). References 42 and 43 report the genome-wide description of CUTs in yeast. In addition, the second article describes a novel type of more stable pervasive transcripts called SUTs. One main conclusion of both reports is that widespread bidirectional promoters generate most pervasive transcripts in yeast. · DOI · Paper page
  40. Lee, W. et al. A high-resolution atlas of nucleosome occupancy in yeast. Nature Genet. 39, 1235–1244 (2007). · DOI · Paper page
  41. O'Sullivan, J. M. et al. Gene loops juxtapose promoters and terminators in yeast. Nature Genet. 36, 1014–1018 (2004). · DOI · Paper page
  42. Preker, P. et al. RNA exosome depletion reveals transcription upstream of active human promoters. Science 322, 1851–1854 (2008). · DOI · Paper page
  43. van Hoof, A., Lennertz, P. & Parker, R. Yeast exosome mutants accumulate 3′-extended polyadenylated forms of U4 small nuclear RNA and small nucleolar RNAs. Mol. Cell Biol. 20, 441–452 (2000). · DOI · Paper page
  44. Allmang, C. et al. Functions of the exosome in rRNA, snoRNA and snRNA synthesis. EMBO J. 18, 5399–5410 (1999). · DOI · Paper page
  45. Steinmetz, E. J., Conrad, N. K., Brow, D. A. & Corden, J. L. RNA-binding protein Nrd1 directs poly(A)-independent 3′-end formation of RNA polymerase II transcripts. Nature 413, 327–331 (2001). · DOI · Paper page
  46. Carroll, K. L., Pradhan, D. A., Granek, J. A., Clarke, N. D. & Corden, J. L. Identification of cis elements directing termination of yeast nonpolyadenylated snoRNA transcripts. Mol. Cell Biol. 24, 6241–6252 (2004). · DOI
  47. Vasiljeva, L. & Buratowski, S. Nrd1 interacts with the nuclear exosome for 3′ processing of RNA polymerase II transcripts. Mol. Cell 21, 239–248 (2006). · DOI · Paper page
  48. Ballarino, M., Morlando, M., Pagano, F., Fatica, A. & Bozzoni, I. The cotranscriptional assembly of snoRNPs controls the biosynthesis of H/ACA snoRNAs in Saccharomyces cerevisiae. Mol. Cell Biol. 25, 5396–5403 (2005). · DOI
  49. Yang, P. K. et al. Cotranscriptional recruitment of the pseudouridylsynthetase Cbf5p and of the RNA binding protein Naf1p during H/ACA snoRNP assembly. Mol. Cell Biol. 25, 3295–3304 (2005). · DOI
  50. Arigo, J. T., Eyler, D. E., Carroll, K. L. & Corden, J. L. Termination of cryptic unstable transcripts is directed by yeast RNA-binding proteins Nrd1 and Nab3. Mol. Cell 23, 841–851 (2006). · DOI · Paper page
  51. Thiebaut, M., Kisseleva-Romanova, E., Rougemaille, M., Boulay, J. & Libri, D. Transcription termination and nuclear degradation of cryptic unstable transcripts: a role for the Nrd1–Nab3 pathway in genome surveillance. Mol. Cell 23, 853–864 (2006). References 54 and 55 show that in yeast, the transcription of CUTs terminates by the same mechanism as the transcription of snoRNAs and that this mode of transcription termination is responsible for their rapid degradation by the nuclear exosome. · DOI · Paper page
  52. Gudipati, R. K., Villa, T., Boulay, J. & Libri, D. Phosphorylation of the RNA polymerase II C-terminal domain dictates transcription termination choice. Nature Struct. Mol. Biol. 15, 786–794 (2008). · DOI
  53. Thompson, D. M. & Parker, R. Cytoplasmic decay of intergenic transcripts in Saccharomyces cerevisiae. Mol. Cell Biol. 27, 92–101 (2007). · DOI
  54. Lee, A., Hansen, K. D., Bullard, J., Dudoit, S. & Sherlock, G. Novel low abundance and transient RNAs in yeast revealed by tiling microarrays and ultra high-throughput sequencing are not conserved across closely related yeast species. PLoS Genet. 4, e1000299 (2008). · DOI
  55. Preker, P., Nielsen, J., Schierup, M. H. & Jensen, T. H. RNA polymerase plays both sides: vivid and bidirectional transcription around and upstream of active promoters. Cell Cycle 8, 1106–1107 (2009). · doi:10.4161/cc.8.8.8236
  56. Wang, X. et al. Induced ncRNAs allosterically modify RNA-binding proteins in cis to inhibit transcription. Nature 454, 126–130 (2008). · DOI · Paper page
  57. Morris, K. V., Santoso, S., Turner, A. M., Pastori, C. & Hawkins, P. G. Bidirectional transcription directs both transcriptional gene activation and suppression in human cells. PLoS Genet. 4, e1000258 (2008). · DOI · Paper page
  58. Han, J., Kim, D. & Morris, K. V. Promoter-associated RNA is required for RNA-directed transcriptional gene silencing in human cells. Proc. Natl Acad. Sci. USA 104, 12422–12427 (2007). · DOI · Paper page
  59. Martianov, I., Ramadass, A., Serra Barros, A., Chow, N. & Akoulitchev, A. Repression of the human dihydrofolate reductase gene by a non-coding interfering transcript. Nature 445, 666–670 (2007). · DOI · Paper page
  60. Martens, J. A., Wu, P. Y. & Winston, F. Regulation of an intergenic transcript controls adjacent gene transcription in Saccharomyces cerevisiae. Genes Dev. 19, 2695–2704 (2005). A landmark article that, with reference 66, analyses the first example of gene regulation by transcription interference in budding yeast. · DOI · Paper page
  61. Martens, J. A., Laprade, L. & Winston, F. Intergenic transcription is required to repress the Saccharomyces cerevisiae SER3 gene. Nature 429, 571–574 (2004). · DOI · Paper page
  62. Jenks, M. H., O'Rourke, T. W. & Reines, D. Properties of an intergenic terminator and start site switch that regulate IMD2 transcription in yeast. Mol. Cell Biol. 28, 3883–3893 (2008). · DOI
  63. Kopcewicz, K. A., O'Rourke, T. W. & Reines, D. Metabolic regulation of IMD2 transcription and an unusual DNA element that generates short transcripts. Mol. Cell Biol. 27, 2821–2829 (2007). · doi:10.1128/mcb.02159-06
  64. Kuehner, J. N. & Brow, D. A. Regulation of a eukaryotic gene by GTP-dependent start site selection and transcription attenuation. Mol. Cell 31, 201–211 (2008). · DOI
  65. Steinmetz, E. J. et al. Genome-wide distribution of yeast RNA polymerase II and its control by Sen1 helicase. Mol. Cell 24, 735–746 (2006). · DOI · Paper page
  66. Thiebaut, M. et al. Futile cycle of transcription initiation and termination modulates the response to nucleotide shortage in S. cerevisiae. Mol. Cell 31, 671–682 (2008). · DOI
  67. Kwapisz, M. et al. Mutations of RNA polymerase II activate key genes of the nucleoside triphosphate biosynthetic pathways. EMBO J. 27, 2411–2421 (2008). · DOI
  68. Arigo, J. T., Carroll, K. L., Ames, J. M. & Corden, J. L. Regulation of yeast NRD1 expression by premature transcription termination. Mol. Cell 21, 641–651 (2006). · DOI
  69. Carninci, P. et al. The transcriptional landscape of the mammalian genome. Science 309, 1559–1563 (2005). · DOI · Paper page
  70. Shiraki, T. et al. Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage. Proc. Natl Acad. Sci. USA 100, 15776–15781 (2003). · DOI · Paper page
  71. Wei, C. L. et al. 5′ Long serial analysis of gene expression (LongSAGE) and 3′ LongSAGE for transcriptome characterization and genome annotation. Proc. Natl Acad. Sci. USA 101, 11701–11706 (2004). · DOI
  72. Gingeras, T. R. Origin of phenotypes: genes and transcripts. Genome Res. 17, 682–690 (2007). · DOI · Paper page
  73. Vasiljeva, L., Kim, M., Mutschler, H., Buratowski, S. & Meinhart, A. The Nrd1–Nab3–Sen1 termination complex interacts with the Ser5-phosphorylated RNA polymerase II C-terminal domain. Nature Struct. Mol. Biol. 15, 795–804 (2008). · DOI · Paper page
  74. Carroll, K. L., Ghirlando, R., Ames, J. M. & Corden, J. L. Interaction of yeast RNA-binding proteins Nrd1 and Nab3 with RNA polymerase II terminator elements. RNA 13, 361–373 (2007). · DOI

Cited by

See all 429

Metadata

Authors
Jacquier, A.
Venue
Nature Reviews Genetics
Publisher
Springer Science and Business Media LLC
Published
2009-12
Volume
10
Issue
12
Pages
833-844
ISSN
  • 1471-0056 (ISSN-L)
  • 1471-0064
DOI
10.1038/nrg2683
OpenAlex
W2088722891
Cited by
429
References
6
FWCI
2.21
Type
journal article
Language
en
Open access
closed
Licence
www.springer.com/tdm (tdm)

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

How to cite

Cite CoChat for the checks on this page, and the paper for its own findings.

This page
CoChat. (2026). Citation check: The complex eukaryotic transcriptome: unexpected pervasive transcription and novel small RNAs. https://app.cochat.ai/papers/10.1038/nrg2683
The paper
Jacquier, A. (2009). The complex eukaryotic transcriptome: unexpected pervasive transcription and novel small RNAs. Nature Reviews Genetics. https://doi.org/10.1038/nrg2683

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.