Student or educator? Sign up with your school email and get 6 months of Pro free.
CoChat
Sign Up
Cited by 526

The DOI matches its Crossref record; 11 of the 11 references it cites were found in a registry or an index.

Metazoan promoters: emerging characteristics and insights into transcriptional regulation

Open access
Lenhard, Boris, Sandelin, Albin, Carninci, Piero·2012·Nature Reviews Genetics
DOI 10.1038/nrg3163
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/nrg3163

Cites

11 of 11 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 11 references

Research works printed but not linked: 91

  1. Sandelin, A. et al. Mammalian RNA polymerase II core promoters: insights from genome-wide studies. Nature Rev. Genet. 8, 424–436 (2007). · DOI · Paper page
  2. Valen, E. & Sandelin, A. Genomic and chromatin signals underlying transcription start-site selection. Trends Genet. 27, 475–485 (2011). · DOI
  3. Riethoven, J.-J. M. Regulatory regions in DNA: promoters, enhancers, silencers, and insulators. Methods Mol. Biol. 674, 33–42 (2010). · DOI
  4. Ohler, U. & Wassarman, D. A. Promoting developmental transcription. Development 137, 15–26 (2010). · DOI
  5. Deaton, A. M. & Bird, A. CpG islands and the regulation of transcription. Genes Dev. 25, 1010–1022 (2011). · DOI · Paper page
  6. Kadonaga, J. T. Perspectives on the RNA polymerase II core promoter. WIREs Dev. Biol. 1, 40–51 (2012). · DOI
  7. Yamashita, R., Suzuki, Y., Sugano, S. & Nakai, K. Genome-wide analysis reveals strong correlation between CpG islands with nearby transcription start sites of genes and their tissue specificity. Gene 350, 129–136 (2005). · DOI
  8. Yoshimura, K. et al. The cystic fibrosis gene has a “housekeeping”-type promoter and is expressed at low levels in cells of epithelial origin. J. Biol. Chem. 266, 9140–9144 (1991). · DOI
  9. Ponjavic, J. et al. Transcriptional and structural impact of TATA-initiation site spacing in mammalian core promoters. Genome Biol. 7, R78 (2006). · DOI
  10. Plessy, C. et al. Promoter architecture of mouse olfactory receptor genes. Genome Res. 22 Dec 2011 (doi:10.1101/gr.126201.111). · DOI
  11. Rach, E. A. et al. Transcription initiation patterns indicate divergent strategies for gene regulation at the chromatin level. PLoS Genet. 7, e1001274 (2011). This is a study that correlated TSS shapes with chromatin mark information, showing the link between the two features. · DOI
  12. FitzGerald, P. C., Sturgill, D., Shyakhtenko, A., Oliver, B. & Vinson, C. Comparative genomics of Drosophila and human core promoters. Genome Biol. 7, R53 (2006). · DOI
  13. Ohler, U. Identification of core promoter modules in Drosophila and their application in accurate transcription start site prediction. Nucleic Acids Res. 34, 5943–5950 (2006). · DOI
  14. Engstrom, P. G., Ho Sui, S. J., Drivenes, O., Becker, T. S. & Lenhard, B. Genomic regulatory blocks underlie extensive microsynteny conservation in insects. Genome Res. 17, 1898–1908 (2007). · DOI
  15. Akalin, A. et al. Transcriptional features of genomic regulatory blocks. Genome Biol. 10, R38 (2009). · DOI
  16. Rach, E. A., Yuan, H.-Y., Majoros, W. H., Tomancak, P. & Ohler, U. Motif composition, conservation and condition-specificity of single and alternative transcription start sites in the Drosophila genome. Genome Biol. 10, R73 (2009). · DOI
  17. Hoskins, R. A. et al. Genome-wide analysis of promoter architecture in Drosophila melanogaster. Genome Res. 21, 182–185 (2011). · DOI
  18. Hendrix, D. A., Hong, J.-W., Zeitlinger, J., Rokhsar, D. S. & Levine, M. S. Promoter elements associated with RNA Pol II stalling in the Drosophila embryo. Proc. Natl Acad. Sci. USA 105, 7762–7767 (2008). · DOI
  19. van Heeringen, S. J. et al. Nucleotide composition-linked divergence of vertebrate core promoter architecture. Genome Res. 21, 410–421 (2011). · DOI
  20. Grishkevich, V., Hashimshony, T. & Yanai, I. Core promoter T-blocks correlate with gene expression levels in C. elegans. Genome Res. 21, 707–717 (2011). · DOI
  21. Parry, T. J. et al. The TCT motif, a key component of an RNA polymerase II transcription system for the translational machinery. Genes Dev. 24, 2013–2018 (2010). · DOI
  22. Damgaard, C. K. & Lykke-Andersen, J. Translational coregulation of 5′TOP mRNAs by TIA-1 and TIAR. Genes Dev. 25, 2057–2068 (2011). · DOI
  23. Perry, R. P. The architecture of mammalian ribosomal protein promoters. BMC Evol. Biol. 5, 15 (2005). · DOI
  24. Ernst, J. & Kellis, M. Discovery and characterization of chromatin states for systematic annotation of the human genome. Nature Biotech. 28, 817–825 (2010). · DOI · Paper page
  25. Zeitlinger, J. et al. RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo. Nature Genet. 39, 1512–1516 (2007). This is one of several papers that used genomics methods to decipher stalling or poising; it also revealed functional tripartition of promoters based on RNAPII signal. · DOI · Paper page
  26. Schwartz, Y. B. et al. Alternative epigenetic chromatin states of Polycomb target genes. PLoS Genet. 6, e1000805 (2010). · DOI
  27. Kharchenko, P. V. et al. Comprehensive analysis of the chromatin landscape in Drosophila melanogaster. Nature 471, 480–485 (2011). This paper discusses a genome-wide chromatin landscape for D. melanogaster based on comprehensive histone modifications identifying combinatorial patterns, which is further integrated with chromosomes, genesand regulatory elements characteristics. · DOI · Paper page
  28. Izzo, A. & Schneider, R. Chatting histone modifications in mammals. Brief Funct. Genomics 9, 429–443 (2010). · DOI
  29. Lee, J.-S., Smith, E. & Shilatifard, A. The language of histone crosstalk. Cell 142, 682–685 (2010). · DOI · Paper page
  30. Nozaki, T. et al. Tight associations between transcription promoter type and epigenetic variation in histone positioning and modification. BMC Genomics 12, 416 (2011). · DOI
  31. Jiang, C. & Pugh, B. Nucleosome positioning and gene regulation: advances through genomics. Nature Rev. Genet. 10, 161–172 (2009). · DOI · Paper page
  32. Ioshikhes, I., Hosid, S. & Pugh, F. Variety of genomic DNA patterns for nucleosome positioning. Genome Res. 21, 1863–1871 (2011). · DOI
  33. Radman-Livaja, M., Liu, C. L., Friedman, N., Schreiber, S. L. & Rando, O. J. Replication and active demethylation represent partially overlapping mechanisms for erasure of H3K4me3 in budding yeast. PLoS Genet. 6, e1000837 (2010). · DOI
  34. Ramirez-Carrozzi, V. R. et al. A unifying model for the selective regulation of inducible transcription by CpG islands and nucleosome remodeling. Cell 138, 114–128 (2009). · DOI · Paper page
  35. Subtil-Rodríguez, A. & Reyes, J. C. BRG1 helps RNA polymerase II to overcome a nucleosomal barrier during elongation, in vivo. EMBO Rep. 11, 751–757 (2010). · DOI
  36. Hargreaves, D. C., Horng, T. & Medzhitov, R. Control of inducible gene expression by signal-dependent transcriptional elongation. Cell 138, 129–145 (2009). · DOI · Paper page
  37. Fu, Y., Sinha, M., Peterson, C. L., Weng, Z. & van Steensel, B. The insulator binding protein CTCF positions 20 nucleosomes around its binding sites across the human genome. PLoS Genet. 4, e1000138 (2008). · DOI · Paper page
  38. Kikuta, H. et al. Genomic regulatory blocks encompass multiple neighboring genes and maintain conserved synteny in vertebrates. Genome Res. 17, 545–555 (2007). · DOI · Paper page
  39. Mikkelsen, T. S. et al. Comparative epigenomic analysis of murine and human adipogenesis. Cell 143, 156–169 (2010). · DOI · Paper page
  40. Roider, H. G., Lenhard, B., Kanhere, A., Haas, S. A. & Vingron, M. CpG-depleted promoters harbor tissue-specific transcription factor binding signals—implications for motif overrepresentation analyses. Nucleic Acids Res. 37, 6305–6315 (2009). · DOI
  41. Soler, E. et al. A systems approach to analyze transcription factors in mammalian cells. Methods 53, 151–162 (2011). · DOI
  42. Dean, A. In the loop: long range chromatin interactions and gene regulation. Brief Funct. Genomics 10, 3–10 (2011). · DOI
  43. Cremer, T. & Cremer, M. Chromosome territories. Cold Spring Harb. Perspect. Biol. 2, a003889 (2010). · DOI · Paper page
  44. Guelen, L. et al. Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions. Nature 453, 948–951 (2008). · DOI
  45. Ferrai, C., de Castro, I. J., Lavitas, L., Chotalia, M. & Pombo, A. Gene positioning. Cold Spring Harb. Perspect. Biol. 2, a000588 (2010). · DOI
  46. Muse, G. W. et al. RNA polymerase is poised for activation across the genome. Nature Genet. 39, 1507–1511 (2007). · DOI · Paper page
  47. 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). This was one of several papers using genomics methods to decipher stalling or poising. · DOI
  48. Nechaev, S. & Adelman, K. Pol. II waiting in the starting gates: regulating the transition from transcription initiation into productive elongation. Biochim. Biophys. Acta 1809, 34–45 (2011). · DOI · Paper page
  49. Gilmour, D. S. & Lis, J. T. RNA polymerase II interacts with the promoter region of the noninduced hsp70 gene in Drosophila melanogaster cells. Mol. Cell. Biol. 6, 3984–3989 (1986). · DOI · Paper page
  50. 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). · DOI · Paper page
  51. Buratowski, S. Progression through the RNA polymerase II CTD Cycle. Mol. Cell 36, 541–546 (2009). · DOI · Paper page
  52. Ferrai, C. et al. Poised transcription factories prime silent uPA gene prior to activation. PLoS Biol. 8, e1000270 (2010). · DOI
  53. Shaevitz, J. W., Abbondanzieri, E. A., Landick, R. & Block, S. M. Backtracking by single RNA polymerase molecules observed at near-base-pair resolution. Nature 426, 684–687 (2003). · DOI · Paper page
  54. Gilchrist, D. A. et al. Pausing of RNA polymerase II disrupts DNA-specified nucleosome organization to enable precise gene regulation. Cell 143, 540–551 (2010). · DOI · Paper page
  55. Faulkner, G. J. et al. The regulated retrotransposon transcriptome of mammalian cells. Nature Genet. 41, 563–571 (2009). This paper showed the large number of retrotransposon elements that are potential TSSs. · DOI · Paper page
  56. Frith, M. C. et al. A code for transcription initiation in mammalian genomes. Genome Res. 18, 1–12 (2008). · DOI · Paper page
  57. Faulkner, G. J. & Carninci, P. Altruistic functions for selfish DNA. Cell Cycle 8, 2895–2900 (2009). · DOI
  58. Plessy, C. et al. Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan. Nature Methods 7, 528–534 (2010). · DOI
  59. Schoenberg, D. R. & Maquat, L. E. Re-capping the message. Trends Biochem. Sci. 34, 435–442 (2009). · DOI
  60. Jackowiak, P., Nowacka, M., Strozycki, P. M. & Figlerowicz, M. RNA degradome—its biogenesis and functions. Nucleic Acids Res. 39, 7361–7370 (2011). · DOI · Paper page
  61. Fejes-Toth, K. et al. Post-transcriptional processing generates a diversity of 5′-modified long and short RNAs. Nature 457, (2009) (1028). · DOI · Paper page
  62. Ni, T. et al. A paired-end sequencing strategy to map the complex landscape of transcription initiation. Nature Methods 7, 521–527 (2010). · DOI
  63. Mercer, T. R. et al. Regulated post-transcriptional RNA cleavage diversifies the eukaryotic transcriptome. Genome Res. 20, 1639–1650 (2010). · DOI
  64. O'Sullivan, J. M. et al. Gene loops juxtapose promoters and terminators in yeast. Nature Genet. 36, 1014–1018 (2004). · DOI
  65. Kaderi, El, B., Medler, S., Raghunayakula, S. & Ansari, A. Gene looping is conferred by activator-dependent interaction of transcription initiation and termination machineries. J. Biol. Chem. 284, 25015–25025 (2009). · DOI
  66. Perkins, K. J., Lusic, M., Mitar, I., Giacca, M. & Proudfoot, N. J. Transcription-dependent gene looping of the HIV-1 provirus is dictated by recognition of pre-mRNA processing signals. Mol. Cell 29, 56–68 (2008). · DOI
  67. Tan-Wong, S. M., French, J. D., Proudfoot, N. J. & Brown, M. A. Dynamic interactions between the promoter and terminator regions of the mammalian BRCA1 gene. Proc. Natl Acad. Sci. USA 105, 5160–5165 (2008). · DOI
  68. Kapranov, P. et al. RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science 316, 1484–1488 (2007). · DOI · Paper page
  69. Preker, P. et al. PROMoter uPstream Transcripts share characteristics with mRNAs and are produced upstream of all three major types of mammalian promoters. Nucleic Acids Res. 39, 7179–7193 (2011). · DOI
  70. Carninci, P. RNA dust: where are the genes? DNA Res. 17, 51–59 (2010). · DOI
  71. Jacquier, A. The complex eukaryotic transcriptome: unexpected pervasive transcription and novel small RNAs. Nature Rev. Genet. 10, 833–844 (2009). · DOI · Paper page
  72. Taft, R. J., Kaplan, C. D., Simons, C. & Mattick, J. S. Evolution, biogenesis and function of promoter-associated RNAs. Cell Cycle 8, 2332–2338 (2009). · DOI
  73. Valen, E. et al. Biogenic mechanisms and utilization of small RNAs derived from human protein-coding genes. Nature Struct. Mol. Biol. 18, 1075–1082 (2011). · DOI
  74. Cernilogar, F. M. et al. Chromatin-associated RNA interference components contribute to transcriptional regulation in Drosophila. Nature 480, 391–395 (2011). · DOI
  75. Basehoar, A. D., Zanton, S. J. & Pugh, B. F. Identification and distinct regulation of yeast TATA box-containing genes. Cell 116, 699–709 (2004). · DOI · Paper page
  76. Yamamoto, Y. Y. et al. Heterogeneity of Arabidopsis core promoters revealed by high-density TSS analysis. Plant J. 60, 350–362 (2009). · DOI
  77. Seila, A. C. et al. Divergent transcription from active promoters. Science 322, 1849–1851 (2008). · DOI · Paper page
  78. Taft, R. J. et al. Tiny RNAs associated with transcription start sites in animals. Nature Genet. 41, 572–578 (2009). · DOI · Paper page
  79. Taft, R. J. et al. Nuclear-localized tiny RNAs are associated with transcription initiation and splice sites in metazoans. Nature Struct. Mol. Biol. 17, 1030–1034 (2010). · DOI
  80. Mandal, S. S. et al. Functional interactions of RNA-capping enzyme with factors that positively and negatively regulate promoter escape by RNA polymerase II. Proc. Natl Acad. Sci. USA 101, 7572–7577 (2004). · DOI
  81. Wasserman, W. W. & Sandelin, A. Applied bioinformatics for the identification of regulatory elements. Nature Rev. Genet. 5, 276–287 (2004). · DOI · Paper page
  82. Valen, E. et al. Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE. Genome Res. 19, 255–265 (2009). · DOI
  83. Kanamori-Katayama, M. et al. Unamplified cap analysis of gene expression on a single-molecule sequencer. Genome Res. 21, 1150–1159 (2011). · DOI
  84. Affymetrix/Cold Spring Harbor Laboratory ENCODE Transcriptome Project. Post-transcriptional processing generates a diversity of 5′-modified long and short RNAs. Nature 457, 1028–1032 (2009). This study shows the large diversity of ncRNAs around promoters. · DOI · Paper page
  85. Hashimoto, S.-I. et al. 5′-end SAGE for the analysis of transcriptional start sites. Nature Biotech. 22, 1146–1149 (2004). · DOI
  86. Ng, P. et al. Gene identification signature (GIS) analysis for transcriptome characterization and genome annotation. Nature Methods 2, 105–111 (2005). · DOI
  87. Thomas, M. F. & Ansel, K. M. Construction of small RNA cDNA libraries for deep sequencing. Methods Mol. Biol. 667, 93–111 (2010). · DOI
  88. Kawaji, H. et al. Hidden layers of human small RNAs. BMC Genomics 9, 157 (2008). · DOI · Paper page
  89. The ENCODE Project Consortium. A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol. 9, e1001046 (2011). · DOI · Paper page
  90. Gilchrist, D. A. et al. NELF-mediated stalling of Pol II can enhance gene expression by blocking promoter-proximal nucleosome assembly. Genes Dev. 22, 1921–1933 (2008). · DOI · Paper page
  91. Gries, T. J., Kontur, W. S., Capp, M. W., Saecker, R. M. & Record, M. T. One-step DNA melting in the RNA polymerase cleft opens the initiation bubble to form an unstable open complex. Proc. Natl Acad. Sci. USA 107, 10418–10423 (2010). · DOI

Cited by

See all 526

Metadata

Authors
Lenhard, B., Sandelin, A., & Carninci, P.
Venue
Nature Reviews Genetics
Publisher
Springer Science and Business Media LLC
Published
2012-03-06
Volume
13
Issue
4
Pages
233-245
ISSN
  • 1471-0056 (ISSN-L)
  • 1471-0064
DOI
10.1038/nrg3163
OpenAlex
W2083073732
Cited by
526
References
11
FWCI
3.15
Type
journal article
Language
en
Open access
green
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: Metazoan promoters: emerging characteristics and insights into transcriptional regulation. https://app.cochat.ai/papers/10.1038/nrg3163
The paper
Lenhard, B., Sandelin, A., & Carninci, P. (2012). Metazoan promoters: emerging characteristics and insights into transcriptional regulation. Nature Reviews Genetics. https://doi.org/10.1038/nrg3163

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.