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 501–600 of 1,001
Characterization of the human DYRK1A promoter and its regulation by the transcription factor E2F1
Maenz, B., Hekerman, P., Vela, E. M., Galcerán, J., & Becker, W. B. (2008) · BMC Molecular Biology · doi:10.1186/1471-2199-9-30 · Cited by 37
Davis, M. R., Andersson, R., Severin, J., de Hoon, M., Bertin, N., Baillie, J. K., Kawaji, H., Sandelin, A., Forrest, A. R. R., & SUMMERS, K. M. (2013) · Molecular Genetics and Metabolism · doi:10.1016/j.ymgme.2013.12.006 · Cited by 39
Self-citationThe Precarious Prokaryotic Chromosome
Kuzminov, A. (2014) · Journal of Bacteriology · doi:10.1128/jb.00022-14 · Cited by 37
Simple and efficient profiling of transcription initiation and transcript levels with STRIPE-seqPreprint
Policastro, R. A., Raborn, R. T., Brendel, V., & Zentner, G. E. (2020) · Genome Research · doi:10.1101/gr.261545.120 · Cited by 37
The Core Promoter Is a Regulatory Hub for Developmental Gene Expression
Sloutskin, A., Shir-Shapira, H., Freiman, R. N., & Juven‐Gershon, T. (2021) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2021.666508 · Cited by 45
Prediction of RNA Polymerase II recruitment, elongation and stalling from histone modification data
Chen, Y., Jørgensen, M., Kolde, R., Zhao, X., Parker, B. J., Valen, E., Wen, J., & Sandelin, A. (2011) · BMC Genomics · doi:10.1186/1471-2164-12-544 · Cited by 37
Self-citationSpurious transcription and its impact on cell function
Wade, J. T., & Grainger, D. C. (2017) · Transcription · doi:10.1080/21541264.2017.1381794 · Cited by 38
Morioka, M. S., Kawaji, H., Nishiyori-Sueki, H., Murata, M., Kojima-Ishiyama, M., Carninci, P., & Itoh, M. (2020) · Methods in molecular biology · doi:10.1007/978-1-0716-0327-7_20 · Cited by 39
Self-citationFelder, T. K., Soyal, S. M., Oberkofler, H., Hahne, P., Auer, S., Weiss, R., Gadermaier, G., Miller, K. N., Krempler, F., Esterbauer, H., et al. (2011) · Journal of Biological Chemistry · doi:10.1074/jbc.m111.227496 · Cited by 36
Lennartsson, A., Arner, E., Fagiolini, M., Saxena, A., Andersson, R., Takahashi, H., Noro, Y., Sng, J., Sandelin, A., Hensch, T. K., et al. (2015) · Epigenetics & Chromatin · doi:10.1186/s13072-015-0043-3 · Cited by 37
Self-citationKim, N.-K., Tharakaraman, K., Mariño‐Ramírez, L., & Spouge, J. L. (2008) · BMC Bioinformatics · doi:10.1186/1471-2105-9-262 · Cited by 35
Genome-wide analysis of regions similar to promoters of histone genes
Chowdhary, R., Bajić, V. B., Dong, D., Wong, L., & Liu, J. S. (2010) · BMC Systems Biology · doi:10.1186/1752-0509-4-s1-s4 · Cited by 35
How to Recruit the Correct RNA Polymerase? Lessons from snRNA Genes
Dergai, O., & Hernandez, N. (2019) · Trends in Genetics · doi:10.1016/j.tig.2019.04.001 · Cited by 35
Nepal, C., Coolen, M., Hadzhiev, Y., Cussigh, D., Mydel, P., Steen, V. M., Carninci, P., Andersen, J. B., Bally-Cuif, L., Müller, F., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv1354 · Cited by 35
Self-citationCharacteristic bimodal profiles of RNA polymerase II at thousands of active mammalian promoters
Quinodoz, M., Gobet, C., Naef, F., & Gustafson, K. (2014) · Genome biology · doi:10.1186/gb-2014-15-6-r85 · Cited by 34
Reggiani, C., Coppens, S., Sékhara, T., Dimov, I., Pichon, B., Lufin, N., Addor, M., Belligni, E. F., Digilio, M. C., Faletra, F., et al. (2017) · Genome Medicine · doi:10.1186/s13073-017-0452-y · Cited by 35
Transcriptional regulation of the Alström syndrome gene ALMS1 by members of the RFX family and Sp1
Purvis, T. L., Hearn, T., Spalluto, C. M., Knorz, V. J., Hanley, K. P., Sánchez-Elsner, T., Hanley, N. A., & Wilson, D. I. (2010) · Gene · doi:10.1016/j.gene.2010.03.015 · Cited by 34
Reinemund, J., Seidel, K., Steckelings, U. M., Zaade, D., Klare, S., Rompe, F., Katerbaum, M., Schacherl, J., Li, Y., Menk, M., et al. (2009) · Biochemical Pharmacology · doi:10.1016/j.bcp.2009.02.025 · Cited by 34
Regional differences in gene expression and promoter usage in aged human brains
Pardo, L. M., Rizzu, P., Francescatto, M., Vitezic, M., Leday, G. G. R., Sanchez, J. S., Khamis, A. M., Takahashi, H., van de Berg, W. D. J., Medvedeva, Y. A., et al. (2013) · Neurobiology of Aging · doi:10.1016/j.neurobiolaging.2013.01.005 · Cited by 36
Self-citationCisView: A Browser and Database of cis-regulatory Modules Predicted in the Mouse Genome
Sharov, A. A., Dudekula, D. B., & Ko, M. S. H. (2006) · DNA Research · doi:10.1093/dnares/dsl005 · Cited by 34
Genome-wide primary transcriptome analysis of H2-producing archaeon Thermococcus onnurineus NA1
Cho, S., Kim, M., Jeong, Y., Lee, B.-R., Lee, J.-H., Kang, S. G., & Cho, B. (2017) · Scientific Reports · doi:10.1038/srep43044 · Cited by 34
Meers, M. P., Adelman, K., Duronio, R. J., Strahl, B. D., McKay, D. J., & Matera, A. G. (2018) · BMC Genomics · doi:10.1186/s12864-018-4510-7 · Cited by 34
Antisense Transcription in Gammaretroviruses as a Mechanism of Insertional Activation of Host Genes
Rasmussen, M. H., Ballarín-González, B., Liu, J., Lassen, L. B., Füchtbauer, A. C., Füchtbauer, E., Nielsen, A. L., & Pedersen, F. S. (2010) · Journal of Virology · doi:10.1128/jvi.02088-09 · Cited by 34
Synthetic Promoters in Gene Therapy: Design Approaches, Features and Applications
Artemyev, V., Gubaeva, A., Paremskaia, A. I., Dzhioeva, A. A., Deviatkin, A. A., Feoktistova, S. G., Mityaeva, O. N., & Volchkov, P. (2024) · Cells · doi:10.3390/cells13231963 · Cited by 34
Hume, D. A. (2012) · Journal of Leukocyte Biology · doi:10.1189/jlb.0312166 · Cited by 37
Self-citationNeininger, K., Marschall, T., & Helms, V. (2019) · PLoS ONE · doi:10.1371/journal.pone.0214816 · Cited by 33
Erb, I., & van Nimwegen, E. (2011) · PLoS ONE · doi:10.1371/journal.pone.0024279 · Cited by 33
When Cre-Mediated Recombination in Mice Does Not Result in Protein Loss
Turlo, K. A., Gallaher, S. D., Vora, R., Laski, F. A., & Iruela‐Arispe, M. L. (2010) · Genetics · doi:10.1534/genetics.110.121608 · Cited by 33
A yeast one‐hybrid and microfluidics‐based pipeline to map mammalian gene regulatory networks
Gubelmann, C., Waszak, S. M., Isakova, A., Holcombe, W., Hens, K., Hafner, A., Feuz, J., Raghav, S. K., Simicevic, J., & Deplancke, B. (2013) · Molecular Systems Biology · doi:10.1038/msb.2013.38 · Cited by 33
Small Genetic Circuits and MicroRNAs: Big Players in Polymerase II Transcriptional Control in Plants
Megraw, M. S., Cumbie, J. S., Ivanchenko, M. G., & Filichkin, S. A. (2016) · The Plant Cell · doi:10.1105/tpc.15.00852 · Cited by 33
Zeitz, M. J., Calhoun, P. J., James, C. C., Taetzsch, T., George, K. K., Robel, S., Valdez, G., & Smyth, J. W. (2019) · Cell Reports · doi:10.1016/j.celrep.2019.04.114 · Cited by 33
Finding the start site: redefining the human initiator elementPreprint
Kugel, J. F., & Goodrich, J. A. (2017) · Genes & Development · doi:10.1101/gad.295980.117 · Cited by 33
The origin and evolution of a distinct mechanism of transcription initiation in yeastsPreprint
Lu, Z., & Lin, Z. (2020) · Genome Research · doi:10.1101/gr.264325.120 · Cited by 33
Weinhouse, C., Bergin, I. L., Harris, C., & Dolinoy, D. C. (2015) · Epigenetics · doi:10.1080/15592294.2015.1107694 · Cited by 33
Xuan, P., Jia, L., Zhang, T., Sheng, N., Li, X., & Li, J. (2019) · International Journal of Molecular Sciences · doi:10.3390/ijms20184458 · Cited by 32
Mazar, J., Sinha, S., Dinger, M. E., Mattick, J. S., & Perera, R. J. (2010) · Molecular Genetics and Genomics · doi:10.1007/s00438-010-0543-6 · Cited by 32
Tissue-Specific and Ubiquitous Expression Patterns from Alternative Promoters of Human Genes
Jacox, E. H., Gotea, V., Ovcharenko, I., & Elnitski, L. L. (2010) · PLoS ONE · doi:10.1371/journal.pone.0012274 · Cited by 32
Hestand, M. S., Klingenhoff, A., Scherf, M., Ariyürek, Y., Ramos, Y. F., van Workum, W., Suzuki, M., Werner, T., van Ommen, G. B., den Dunnen, J. T., et al. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq602 · Cited by 32
Self-citationMetaProm: a neural network based meta-predictor for alternative human promoter prediction
Wang, J., Ungar, L., Tseng, H., & Hannenhalli, S. S. (2007) · BMC Genomics · doi:10.1186/1471-2164-8-374 · Cited by 32
Genome Network and FANTOM3: Assessing the Complexity of the Transcriptome
Hayashizaki, Y., & Carninci, P. (2006) · PLoS Genetics · doi:10.1371/journal.pgen.0020063 · Cited by 32
Self-citationKumar, V., Rayan, N. A., Muratani, M., Lim, S., Elanggovan, B., Xin, L., Lu, T. T.-H., Makhija, H., Poschmann, J., Lufkin, T., et al. (2016) · Genome Research · doi:10.1101/gr.201038.115 · Cited by 33
Dissecting the cis-regulatory syntax of transcription initiation with deep learningPreprint
Cochran, K., Yin, M., Mantripragada, A., Schreiber, J. M., Marinov, G. K., Shah, S. R., Yu, H., Lis, J. T., & Kundaje, A. B. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.05.28.596138 · Cited by 36
Alternative TSSs are co‐regulated in single cells in the mouse brain
Karlsson, K., Lönnerberg, P., & Linnarsson, S. (2017) · Molecular Systems Biology · doi:10.15252/msb.20167374 · Cited by 32
Rye, M. B., Sandve, G. K., Daub, C. O., Kawaji, H., Carninci, P., Forrest, A. R. R., & Drabløs, F. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-120 · Cited by 31
Self-citationGlobal approaches for profiling transcription initiation
Policastro, R. A., & Zentner, G. E. (2021) · Cell Reports Methods · doi:10.1016/j.crmeth.2021.100081 · Cited by 33
Makhnovskii, P. A., Gusev, O., Bokov, R. O., Gazizova, G. R., Vepkhvadze, T. F., Lysenko, E. A., Виноградова, О. Л., Kolpakov, F., & Викторович, П. Д. (2022) · Human Genomics · doi:10.1186/s40246-022-00399-8 · Cited by 31
Is sequencing enlightenment ending the dark age of the transcriptome?
Carninci, P. (2009) · Nature Methods · doi:10.1038/nmeth1009-711 · Cited by 31
Self-citationTsuritani, K., Irie, T., Yamashita, R., Sakakibara, Y., Wakaguri, H., Kanai, A., Mizushima‐Sugano, J., Sugano, S., Nakai, K., & Suzuki, Y. (2007) · Genome Research · doi:10.1101/gr.6030107 · Cited by 31
Qu, Z., & Adelson, D. L. (2012) · PLoS ONE · doi:10.1371/journal.pone.0052275 · Cited by 30
Liu, B., Chen, J., & Shen, B. (2011) · BMC Systems Biology · doi:10.1186/1752-0509-5-s1-s2 · Cited by 30
Slobodin, B., & Dikstein, R. (2020) · EMBO Reports · doi:10.15252/embr.202050799 · Cited by 30
Davies, R. G., Liu, L., Sheng, T., Tuano, N., Chaturvedi, R., Huang, K. K., Itman, C., Mandoli, A., Qamra, A., Hu, C., et al. (2021) · Genome biology · doi:10.1186/s13059-021-02266-6 · Cited by 30
Diversity of Ca2+-activated K+ channel transcripts in inner ear hair cells
Beisel, K. W., Rocha-Sanchez, S. M., Ziegenbein, S. J., Morris, K. A., Kai, C., Kawai, J., Carninci, P., Hayashizaki, Y., & Davis, R. L. (2006) · Gene · doi:10.1016/j.gene.2006.07.023 · Cited by 30
Self-citationDiversification and Molecular Evolution of ATOH8, a Gene Encoding a bHLH Transcription Factor
Chen, J., Dai, F., Balakrishnan-Renuka, A., Leese, F., Schempp, W., Felix, S., Hoffmann, M. M., Moroşan‐Puopolo, G., Yusuf, F., Bisschoff, I. J., et al. (2011) · PLoS ONE · doi:10.1371/journal.pone.0023005 · Cited by 30
André‐Arpin, C., Laverdure, S., Barbeau, B., Gross, A., & Mesnard, J.-M. (2014) · Plasmid · doi:10.1016/j.plasmid.2014.06.001 · Cited by 30
Retrotransposons Influence the Mouse Transcriptome: Implication for the Divergence of Genetic Traits
Horie, K., Saito, E.-S., Keng, V. W., Ikeda, R., Ishihara, H., & Takeda, J. (2007) · Genetics · doi:10.1534/genetics.107.071647 · Cited by 33
Distinct roles of first exon variants of the tumor-suppressor Patched1 in Hedgehog signaling
Shimokawa, T., Svärd, J., Heby-Henricson, K., Teglund, S., Toftgård, R., & Zaphiropoulos, P. G. (2007) · Oncogene · doi:10.1038/sj.onc.1210301 · Cited by 30
Nucleotide composition-linked divergence of vertebrate core promoter architecturePreprint
van Heeringen, S. J., Akhtar, W., Jacobi, U. G., Akkers, R. C., Suzuki, Y., & Veenstra, G. J. C. (2011) · Genome Research · doi:10.1101/gr.111724.110 · Cited by 30
AAV genome modification for efficient AAV production
Asaad, W., Volos, P., Maksimov, D. O., Khavina, E. M., Deviatkin, A. A., Mityaeva, O. N., & Volchkov, P. (2023) · Heliyon · doi:10.1016/j.heliyon.2023.e15071 · Cited by 31
Core Promoter Functions in the Regulation of Gene Expression of Drosophila Dorsal Target Genes
Zehavi, Y., Kuznetsov, O., Ovadia-Shochat, A., & Juven‐Gershon, T. (2014) · Journal of Biological Chemistry · doi:10.1074/jbc.m114.550251 · Cited by 29
McInnis, E. A., Badhwar, A., Muthigi, A., Lardinois, O. M., Allred, S. C., Yang, J., Free, M. E., Jennette, J. C., Preston, G. A., Falk, R. J., et al. (2014) · Journal of the American Society of Nephrology · doi:10.1681/asn.2013101092 · Cited by 29
Nguyen, Q. H., Tellam, R. L., Naval-Sánchez, M., Porto-Neto, L. R., Barendse, W., Reverter, A., Hayes, B. J., Kijas, J., & Dalrymple, B. P. (2018) · GigaScience · doi:10.1093/gigascience/gix136 · Cited by 29
Gacita, A. M., Dellefave‐Castillo, L. M., Page, P., Barefield, D. Y., Wasserstrom, J. A., Puckelwartz, M. J., Nóbrega, M. A., & McNally, E. M. (2020) · Circulation Heart Failure · doi:10.1161/circheartfailure.120.006926 · Cited by 29
Ruiz, J. L., Ranford-Cartwright, L. C., & Gómez‐Díaz, E. (2021) · NAR Genomics and Bioinformatics · doi:10.1093/nargab/lqaa113 · Cited by 33
Grapotte, M., Saraswat, M., Bessière, C., Menichelli, C., Ramilowski, J. A., Severin, J., Hayashizaki, Y., Itoh, M., Tagami, M., Murata, M., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-23143-7 · Cited by 32
Self-citationSalisbury, J., Hutchison, K. W., Wigglesworth, K., Eppig, J. J., & Graber, J. H. (2009) · PLoS ONE · doi:10.1371/journal.pone.0007479 · Cited by 29
Tanaka, T., Koyanagi, K. O., & Itoh, T. (2008) · PLANT PHYSIOLOGY · doi:10.1104/pp.108.131656 · Cited by 29
Zhu, Q., & Halfon, M. S. (2009) · BMC Genomics · doi:10.1186/1471-2164-10-9 · Cited by 29
Diverse DNA Methylation Statuses at Alternative Promoters of Human Genes in Various Tissues
Cheong, J., Yamada, Y. M. A., Yamashita, R., Irie, T., Kanai, A., Wakaguri, H., Nakai, K., Ito, T., Saito, I., Sugano, S., et al. (2006) · DNA Research · doi:10.1093/dnares/dsl008 · Cited by 29
Transcriptional Attenuation in Colon Carcinoma Cells in Response to Butyrate
Daroqui, M. C., & Augenlicht, L. H. (2010) · Cancer Prevention Research · doi:10.1158/1940-6207.capr-10-0083 · Cited by 29
Sauter, K. A. D., Bouhlel, M. A., O’Neal, J., Sester, D. P., Tagoh, H., Ingram, R. M., Pridans, C., Bonifer, C., & Hume, D. A. (2013) · PLoS ONE · doi:10.1371/journal.pone.0054935 · Cited by 28
Self-citationPervasive and CpG-dependent promoter-like characteristics of transcribed enhancers
Steinhaus, R., Gonzalez, T., Seelow, D., & Robinson, P. N. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa223 · Cited by 29
Yasuda, J., & Hayashizaki, Y. (2007) · Advances in cancer research · doi:10.1016/s0065-230x(07)99003-x · Cited by 30
Self-citationLung, J., Liu, K., Chang, J., Leu, S., & Shih, N. (2010) · FEBS Journal · doi:10.1111/j.1742-4658.2010.07819.x · Cited by 28
Isochores and the Regulation of Gene Expression in the Human Genome
Arhondakis, S., Auletta, F., & Bernardi, G. (2011) · Genome Biology and Evolution · doi:10.1093/gbe/evr017 · Cited by 28
Kalitsis, P., & Saffery, R. (2009) · BMC Genomics · doi:10.1186/1471-2164-10-498 · Cited by 30
Characterization of STAT6 Target Genes in Human B Cells and Lung Epithelial Cells
Kanai, A., Suzuki, K., Tanimoto, K., Mizushima‐Sugano, J., Suzuki, Y., & Sugano, S. (2011) · DNA Research · doi:10.1093/dnares/dsr025 · Cited by 28
Gan, Y., Guan, J., & Zhou, S. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp359 · Cited by 28
Where does transcription start? 5′-RACE adapted to next-generation sequencing
Leenen, F. A. D., Vernocchi, S., Hunewald, O. E., Schmitz, S., Molitor, A. M., Muller, C. P., & Turner, J. D. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv1328 · Cited by 28
Advances of DNase-seq for mapping active gene regulatory elements across the genome in animals
Chen, A., Chen, D., & Chen, Y. (2018) · Gene · doi:10.1016/j.gene.2018.05.033 · Cited by 28
Novel Promoters Derived from Chinese Hamster Ovary Cells via In Silico and In Vitro Analysis
Ly, N. N., Baumann, M., Dhiman, H., Marx, N., Schmieder, V., Hussein, M. K., Eisenhut, P., Hernandez, I., Koehn, J., & Borth, N. (2019) · Biotechnology Journal · doi:10.1002/biot.201900125 · Cited by 28
Locally acting transcription factors regulate p53-dependent cis-regulatory element activity
Catizone, A. N., Uzunbas, G. K., Celadova, P., Kuang, S., Bose, D. A., & Sammons, M. A. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa147 · Cited by 28
Hume, D. A., Sasmono, R. T., Himes, S. R., Sharma, S. M., Bronisz, A., Constantin, M., Ostrowski, M. C., & Ross, I. L. (2008) · The Journal of Immunology · doi:10.4049/jimmunol.180.10.6733 · Cited by 28
Self-citationSystems biology of transcription control in macrophages
Ravasi, T., Wells, C. A., & Hume, D. A. (2007) · BioEssays · doi:10.1002/bies.20683 · Cited by 29
Self-citationPrediction and analysis of nucleosome exclusion regions in the human genome
Radwan, A., Younis, A. A., Luykx, P., & Khuri, S. (2008) · BMC Genomics · doi:10.1186/1471-2164-9-186 · Cited by 28
Sala, S. C., Perteghella, T., Lagarde, J., Nishiyori, H., Palumbo, E., Arnan, C., Takahashi, H., Carninci, P., Uszczyńska-Ratajczak, B., & Guigó, R. (2024) · Nature Communications · doi:10.1038/s41467-024-49523-3 · Cited by 27
Self-citationShao, W., Alcantara, S. G.-M., & Zeitlinger, J. (2019) · eLife · doi:10.7554/elife.41461 · Cited by 27
Saminathan, T., Chen, P., Lai, M., Chen, J., & Jauh, G. (2012) · The Plant Journal · doi:10.1111/j.1365-313x.2012.04989.x · Cited by 27
Bonham, A. J., Neumann, T., Tirrell, M., & Reich, N. O. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp424 · Cited by 27
Itoh, M., Kojima, M., Nagao-Sato, S., Saijo, E., Lassmann, T., Kanamori-Katayama, M., Kaiho, A., Lizio, M., Kawaji, H., Carninci, P., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0030809 · Cited by 27
Self-citationMaeda, N., Nishiyori, H., Nakamura, M., Kawazu, C., Murata, M., Sano, H., Hayashida, K., Fukuda, S., Tagami, M., Hasegawa, A., et al. (2008) · BioTechniques · doi:10.2144/000112814 · Cited by 27
Self-citationTranscription Start Site Evolution in Drosophila
Main, B. J., Smith, A. D., Jang, H. J., & Nuzhdin, S. V. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mst085 · Cited by 27
Telomerase Reverse Transcriptase Regulates microRNAs
Lassmann, T., Maida, Y., Tomaru, Y., Yasukawa, M., Ando, Y., Kojima, M., Kasim, V., Simon, C., Daub, C. O., Carninci, P., et al. (2015) · International Journal of Molecular Sciences · doi:10.3390/ijms16011192 · Cited by 27
Self-citationBornholdt, J., Saber, A. T., Lilje, B., Boyd, M., Jørgensen, M., Chen, Y., Vitezic, M., Jacobsen, N. R., Poulsen, S. S., Berthing, T., et al. (2017) · ACS Nano · doi:10.1021/acsnano.6b07533 · Cited by 28
Self-citationSEASTAR: systematic evaluation of alternative transcription start sites in RNA
Qin, Z., Stoilov, P., Zhang, X., & Xing, Y. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky053 · Cited by 27
Mapping of Small RNAs in the Human ENCODE Regions
Borel, C., Gagnebin, M., Gehrig, C., Kriventseva, E. V., Zdobnov, E. M., & Antonarakis, S. E. (2008) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2008.02.016 · Cited by 27
DDEC: Dragon database of genes implicated in esophageal cancer
Essack, M., Radovanović, A., Schaefer, U., Schmeier, S., Seshadri, S. V., Christoffels, A. G., Kaur, M., & Bajić, V. B. (2009) · BMC Cancer · doi:10.1186/1471-2407-9-219 · Cited by 27
SCS: Signal, Context, and Structure Features for Genome-Wide Human Promoter Recognition
Zeng, J., Zhao, X.-Y., Cao, X.-Q., & Yan, H. (2008) · IEEE Transactions on Computational Biology and Bioinformatics · doi:10.1109/tcbb.2008.95 · Cited by 27
Barnes, M. R. (2006) · Briefings in Bioinformatics · doi:10.1093/bib/bbl021 · Cited by 27
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
