The DOI matches its Crossref record; 42 of the 42 references it cites were found in a registry or an index.
Genome-wide analysis of mammalian promoter architecture and evolution
Abstract
Mammalian promoters can be separated into two classes, conserved TATA box-enriched promoters, which initiate at a well-defined site, and more plastic, broad and evolvable CpG-rich promoters. We have sequenced tags corresponding to several hundred thousand transcription start sites (TSSs) in the mouse and human genomes, allowing precise analysis of the sequence architecture and evolution of distinct promoter classes. Different tissues and families of genes differentially use distinct types of promoters. Our tagging methods allow quantitative analysis of promoter usage in different tissues and show that differentially regulated alternative TSSs are a common feature in protein-coding genes and commonly generate alternative N termini. Among the TSSs, we identified new start sites associated with the majority of exons and with 3' UTRs. These data permit genome-scale identification of tissue-specific promoters and analysis of the cis-acting elements associated with them.
Overview
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
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 the citing paper
“Cap Analysis of Gene Expression Sequencing (CAGE-seq) determines the 5’-ends of TSSs at single nucleotide resolution11,12 and quantifies gene expression similar to RNA-seq13.”
From Alternative promoters in CpG depleted regions are prevalently associated with epigenetic misregulation of liver cancer transcriptomes (2023) · cites this paper as [11]
In the citing paper
“CAGE TCs overlapping reference promoters have significantly broader widths (Fig. 3e, f), which are termed broad promoters11”
From Alternative promoters in CpG depleted regions are prevalently associated with epigenetic misregulation of liver cancer transcriptomes (2023) · cites this paper as [11]
In the citing paper
“Contrary, CAGE TCs overlapping alternative promoters have narrow widths (Fig. 3e, f), which are termed sharp promoters11”
From Alternative promoters in CpG depleted regions are prevalently associated with epigenetic misregulation of liver cancer transcriptomes (2023) · cites this paper as [11]
In the citing paper
“Human promoters are mostly CG-rich35,62 and have distinct promoter architecture and regulation11 compared to CG-poor promoters which are mostly tissue-specific17”
From Alternative promoters in CpG depleted regions are prevalently associated with epigenetic misregulation of liver cancer transcriptomes (2023) · cites this paper as [11]
In the citing paper
“In addition, CGIs are often origins of replication31–33 and are generally associated with multiple TSSs dispersed over a 50–100 bp region.34,35”
From Adeno-Associated Virus Serotype-Specific Inverted Terminal Repeat Sequence Role in Vector Transgene Expression (2020) · cites this paper as [34]
In the citing paper
“This observation is further supported by the control of gene transcription largely through proximal promoters.64”
From Census and evaluation of p53 target genes (2017) · cites this paper as [64]
Citations
Cites
Cluster analysis and display of genome-wide expression patterns
Eisen, M. B., Spellman, P. T., Brown, P. O., & Botstein, D. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.25.14863 · Cited by 16,184
Pruitt, K. D., Tatusova, T. A., & Maglott, D. R. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl842 · Cited by 4,441
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. A., et al. (2005) · Science · doi:10.1126/science.1112014 · Cited by 3,492
Self-citationSequence logos: a new way to display consensus sequences
Schneider, T. D., & Stephens, R. M. (1990) · Nucleic Acids Research · doi:10.1093/nar/18.20.6097 · Cited by 3,354
Pruitt, K., Tatusova, T., & Maglott, D. (2004) · Nucleic Acids Res. · doi:10.1093/nar/gki025 · Cited by 3,248
The two NF-κB activation pathways and their role in innate and adaptive immunity
Bonizzi, G., & Karin, M. (2004) · Trends in Immunology · doi:10.1016/j.it.2004.03.008 · Cited by 2,535
The ENCODE (ENCyclopedia Of DNA Elements) Project
(2004) · Science · doi:10.1126/science.1105136 · Cited by 2,390
The UCSC Genome Browser Database
Karolchik, D. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg129 · Cited by 1,890
Xie, X., Lu, J., Kulbokas, E. J., Golub, T. R., Mootha, V., Lindblad-Toh, K., Lander, E. S., & Kellis, M. (2005) · Nature · doi:10.1038/nature03441 · Cited by 1,872
Antisense Transcription in the Mammalian Transcriptome
Katayama, S., Tomaru, Y., Kasukawa, T., Waki, K., Nakanishi, M., Nakamura, M., Nishida, H., Yap, C.-S., Suzuki, M., Kawai, J., et al. (2005) · Science · doi:10.1126/science.1112009 · Cited by 1,699
Self-citation
Flagged first, then by citations
Cited by
Sorted by citations
Items 1,001–1,001 of 1,001
CAGE-TSSchip: promoter-based expression profiling using the 5'-leading label of capped transcripts
Katayama, S., Kanamori-Katayama, M., Yamaguchi, K., Carninci, P., & Hayashizaki, Y. (2007) · Genome biology · doi:10.1186/gb-2007-8-3-r42 · Cited by 4
Self-citation
Metadata
- Authors
- Carninci, P., Sandelin, A., Lenhard, B., Katayama, S., Shimokawa, K., Ponjavic, J., Semple, C. A. M., Taylor, M. S., Engström, P. G., Frith, M. C., Forrest, A. R. R., Alkema, W. B., Tan, S. L., Plessy, C., Kodzius, R., Ravasi, T., Kasukawa, T., Fukuda, S., Kanamori-Katayama, M., Kitazume, Y., Kawaji, H., Kai, C., Nakamura, M., Konno, H., Nakano, K., Mottagui-Tabar, S., Arner, P., Chesi, A., Gustincich, S., Persichetti, F., Suzuki, H., Grimmond, S. M., Wells, C. A., Orlando, V., Wahlestedt, C., Liu, E. T., Harbers, M., Kawai, J., Bajic, V. B., Hume, D. A., & Hayashizaki, Y.
- Affiliations
- RIKEN (JP)
- Karolinska Institutet (SE)
- University of Helsinki (FI)
- Western General Hospital (GB)
- University of Oxford (GB)
- Australian Research Council (AU)
- Institute for Infocomm Research (SG)
- NTT (Japan) (JP)
- Scuola Internazionale Superiore di Studi Avanzati (IT)
- Griffith University (AU)
- Dulbecco Telethon Institute (IT)
- Genome Institute of Singapore (SG)
- University of Tsukuba (JP)
- Corresponding author
- Hume, David A
- Hayashizaki, Yoshihide
- ORCID
- Carninci, Piero
- Sandelin, Albin
- Lenhard, Boris
- Katayama, Shintaro
- Shimokawa, Kazuro
- Semple, Colin A M
- Taylor, Martin S
- Engström, Pär G
- Frith, Martin C
- Forrest, Alistair R R
- Alkema, Wynand B
- Plessy, Charles
- Kodzius, Rimantas
- Ravasi, Timothy
- Kasukawa, Takeya
- Fukuda, Shiro
- Kawaji, Hideya
- Nakamura, Mari
- Arner, Peter
- Chesi, Alessandra
- Gustincich, Stefano
- Persichetti, Francesca
- Suzuki, Harukazu
- Grimmond, Sean M
- Wells, Christine A
- Orlando, Valerio
- Liu, Edison T
- Harbers, Matthias
- Kawai, Jun
- Hume, David A
- Hayashizaki, Yoshihide
- Venue
- Nature Genetics
- Published
- 2006-04-28
- Volume
- 38
- Issue
- 6
- Pages
- 626-635
- ISSN
- 1061-4036 (ISSN-L)
- 1546-1718
- OpenAlex
- W2057692691
- Cited by
- 1,350
- References
- 41
- Citations by year
- 2026: 25 · 2025: 36 · 2024: 52 · 2023: 46 · 2022: 53 · 2021: 54 · 2020: 60 · 2019: 73 · 2018: 46 · 2017: 56 · 2016: 58 · 2015: 63 · 2014: 81 · 2013: 72 · 2012: 66
- FWCI
- 42.97
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Nature Genetics (publishedVersion)
- PubMed (publishedVersion)
- Data Archiving and Networked Services (DANS) (submittedVersion)
- SDL (submittedVersion)
- Griffith Research Online (submittedVersion)
- Funders
- Biotechnology and Biological Sciences Research Council (BB/H531586/1, S17961)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Keywords
- promoter architecture, transcription start sites, TATA box, promoter evolution, alternative promoters, tissue-specific promoters, cis-regulatory elements, gene expression regulation
- MeSH terms
- Animals, Base Sequence, DNA, Promoter Regions, Genetic, TATA Box, Genome, Evolution, Molecular, 3' Untranslated Regions, Proteome
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
