Genome-wide analysis of mammalian promoter architecture and evolution

Cluster analysis and display of genome-wide expression patterns

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NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins

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The Transcriptional Landscape of the Mammalian Genome

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Sequence logos: a new way to display consensus sequences

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NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins

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The two NF-κB activation pathways and their role in innate and adaptive immunity

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The ENCODE (ENCyclopedia Of DNA Elements) Project

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The UCSC Genome Browser Database

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Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals

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Antisense Transcription in the Mammalian Transcriptome

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Multiple non-collinear TF-map alignments of promoter regions

Blanco, E., Guigó, R., & Messeguer, X. (2007) · BMC Bioinformatics · doi:10.1186/1471-2105-8-138 · Cited by 13

Distinct core promoter codes drive transcription initiation at key developmental transitions in a marine chordate

Danks, G., Navrátilová, P., Lenhard, B., & Thompson, E. M. (2018) · BMC Genomics · doi:10.1186/s12864-018-4504-5 · Cited by 13

CpG island mapping by epigenome prediction

Bock, C., Walter, J. E., Paulsen, M., & Lengauer, T. (2005) · PLoS Computational Biology · doi:10.1371/journal.pcbi.0030110.eor · Cited by 13

The Sp6 locus uses several promoters and generates sense and antisense transcripts

Hertveldt, V., Mees, C. D., Scohy, S., Vooren, P. V., Szpirer, J., & Szpirer, C. (2007) · Biochimie · doi:10.1016/j.biochi.2007.05.011 · Cited by 13

Multi-year whole-blood transcriptome data for the study of onset and progression of Parkinson’s Disease

Valentine, M. N. Z., Hashimoto, K., Fukuhara, T., Saiki, S., Ishikawa, K., Hattori, N., & Carninci, P. (2019) · Scientific Data · doi:10.1038/s41597-019-0022-9 · Cited by 13

Integration of high-resolution promoter profiling assays reveals novel, cell type–specific transcription start sites across 115 human cell and tissue typesPreprint

Moore, J. E., Zhang, X.-O., Elhajjajy, S. I., Fan, K., Pratt, H., Reese, F., Mortazavi, A., & Weng, Z. (2021) · Genome Research · doi:10.1101/gr.275723.121 · Cited by 13

A resource for transcriptomic analysis in the mouse brain

Plessy, C., Fagiolini, M., Wagatsuma, A., Harasawa, N., Kuji, T., Asaka-Oba, A., Kanzaki, Y., Fujishima, S., Waki, K., Nakahara, H., et al. (2008) · PLoS ONE · doi:10.1371/journal.pone.0003012 · Cited by 12

Mutational scans reveal differential evolvability of Drosophila promoters and enhancers

Li, X., Fuqua, T., van Breugel, M. E., & Crocker, J. (2023) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2022.0054 · Cited by 12

Quantitative analysis of transcription start site selection reveals control by DNA sequence, RNA polymerase II activity and NTP levels

Zhu, Y., Vvedenskaya, I. O., Sze, S., Nickels, B. E., & Kaplan, C. D. (2024) · Nature Structural & Molecular Biology · doi:10.1038/s41594-023-01171-9 · Cited by 12

ZC3H4/Restrictor Exerts a Stranglehold on Pervasive Transcription

Estell, C., & West, S. (2024) · Journal of Molecular Biology · doi:10.1016/j.jmb.2024.168707 · Cited by 12

Nucleosomal TATA-switch: Competing orientations of TATA on the nucleosome

Hapala, J., & Trifonov, E. N. (2013) · Gene · doi:10.1016/j.gene.2013.06.004 · Cited by 12

Identification and characterization of human PCDH10 gene promoter

Li, Z., Xie, J., Li, W., Tang, A., Li, X., Jiang, Z., Han, Y., Ye, J., Jing, J., Gui, Y., et al. (2011) · Gene · doi:10.1016/j.gene.2011.01.001 · Cited by 12

Analysis of changes in transcription start site distribution by a classification approach

Liang, K., Suzuki, Y., Kumagai, Y., & Nakai, K. (2014) · Gene · doi:10.1016/j.gene.2013.12.038 · Cited by 12

Gene organization inside replication domains in mammalian genomes

Zaghloul, L., Baker, A., Audit, B., & Arnéodo, A. (2012) · Comptes Rendus Mécanique · doi:10.1016/j.crme.2012.10.023 · Cited by 12

Overlapping ETS and CRE Motifs (G/CCGGAAGTGACGTCA) Preferentially Bound by GABPα and CREB Proteins

Chatterjee, R., Zhao, J., He, X., Shlyakhtenko, A., Mann, I. K., Waterfall, J. J., Meltzer, P. S., Sathyanarayana, B. K., FitzGerald, P. C., & Vinson, C. (2012) · G3 Genes Genomes Genetics · doi:10.1534/g3.112.004002 · Cited by 12

Abundant and broad expression of transcription-induced chimeras and protein products in mammalian genomes

Lu, G., Wu, J., Zhao, G., Wang, Z., Chen, W., & Mu, S. (2015) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2015.12.084 · Cited by 12

Cap analysis of gene expression (CAGE) and noncoding regulatory elements

Guerrini, M. M., Oguchi, A., Suzuki, A., & Murakawa, Y. (2021) · Seminars in Immunopathology · doi:10.1007/s00281-021-00886-5 · Cited by 12

Hypothetical SNP markers that significantly affect the affinity of the TATA-binding protein to VEGFA, ERBB2, IGF1R, FLT1, KDR, and MET oncogene promoters as chemotherapy targets

Turnaev, I. I., Рассказов, Д. А., Arkova, O. V., Ponomarenko, M. P., Ponomarenko, P. M., Savinkova, L. K., & Kolchanov, N. A. (2016) · Molecular Biology · doi:10.1134/s0026893316010209 · Cited by 12

Decoding murine cytomegalovirus

Lodha, M., Muchsin, I., Jürges, C., Lisnić, V. J., L’Hernault, A., Rutkowski, A. J., Prusty, B. K., Grothey, A., Milić, A., Hennig, T., et al. (2023) · PLoS Pathogens · doi:10.1371/journal.ppat.1010992 · Cited by 12

Transcriptional noise as a driver of gene evolution

Polev, D. E. (2011) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2011.10.001 · Cited by 12

Predictive Models of Gene Regulation from High-Throughput Epigenomics Data

Althammer, S., Pagès, A., & Eyras, E. (2012) · Comparative and Functional Genomics · doi:10.1155/2012/284786 · Cited by 12

An update on recent methods applied for deciphering the diversity of the noncoding RNA genome structure and function

Spicuglia, S., Maqbool, M. A., Puthier, D., & Andrau, J. (2013) · Methods · doi:10.1016/j.ymeth.2013.04.003 · Cited by 17

Basal core promoters control the equilibrium between negative cofactor 2 and preinitiation complexes in human cells

Albert, T., Grote, K., Boeing, S., & Meisterernst, M. (2010) · Genome biology · doi:10.1186/gb-2010-11-3-r33 · Cited by 12

A methyl-sensitive element induces bidirectional transcription in TATA-less CpG island-associated promoters

Mahpour, A., Smiraglia, D. J., Scruggs, B. S., Gelman, I. H., & Ouchi, T. (2018) · PLoS ONE · doi:10.1371/journal.pone.0205608 · Cited by 12

Annotation of nuclear lncRNAs based on chromatin interactions

Agrawal, S., Kulakovskiy, I. V., Severin, J., Koido, M., Alam, T., Abugessaisa, I., Buyan, A., Chang, H. Y., Dostie, J., Itoh, M., et al. (2024) · PLoS ONE · doi:10.1371/journal.pone.0295971 · Cited by 12

Hepatic nutrient and hormonal regulation of the PANcreatic-DERived factor (PANDER) promoter

Ratliff, W. A., Athanason, M. G., Chechele, A. C., Kuehl, M. N., Fernandez, A. M., MarElia, C. B., & Burkhardt, B. R. (2015) · Molecular and Cellular Endocrinology · doi:10.1016/j.mce.2015.05.040 · Cited by 12

Promoter CpG methylation status in porcine Lyn is associated with its expression levels

Xiao, Z., Wang, C., Mo, D., Li, J., Chen, Y., Zhang, Z., & Cong, P. (2012) · Gene · doi:10.1016/j.gene.2012.08.050 · Cited by 12

Identification of Conserved Regulatory Elements in Mammalian Promoter Regions: A Case Study Using the PCK1 Promoter

Liu, G. E., Weirauch, M. T., Tassell, C. P. V., Li, R. W., Sonstegard, T. S., Matukumalli, L. K., Connor, E. E., Hanson, R. W., & Yang, J. (2008) · Genomics Proteomics & Bioinformatics · doi:10.1016/s1672-0229(09)60001-2 · Cited by 12

Análisis de la metilación de la región promotora del gen BMPR2 en pacientes con hipertensión arterial pulmonar

Pousada, G., Baloira, A., & Valverde, D. (2015) · Archivos de Bronconeumología · doi:10.1016/j.arbres.2015.10.006 · Cited by 12

Untranslated Gene Regions and Other Non-coding Elements

Barrett, L. W., Fletcher, S., & Wilton, S. D. (2013) · SpringerBriefs in biochemistry and molecular biology · doi:10.1007/978-3-0348-0679-4_1 · Cited by 13

Modeling promoter grammars with evolving hidden Markov models

Won, K., Sandelin, A., Marstrand, T. T., & Krogh, A. (2008) · Bioinformatics · doi:10.1093/bioinformatics/btn254 · Cited by 12

Isoforms of the Erythropoietin receptor in dopaminergic neurons of the Substantia Nigra

Marcuzzi, F., Zucchelli, S., Bertuzzi, M., Santoro, C., Tell, G., Carninci, P., & Gustincich, S. (2016) · Journal of Neurochemistry · doi:10.1111/jnc.13757 · Cited by 12

Monitoring transcription initiation activities in rat and dog

Lizio, M., Mukarram, A. K., Ohno, M., Watanabe, S., Itoh, M., Hasegawa, A., Lassmann, T., Severin, J., Harshbarger, J., Abugessaisa, I., et al. (2017) · Scientific Data · doi:10.1038/sdata.2017.173 · Cited by 12

Alternative TSS use is widespread in Cryptococcus fungi in response to environmental cues and regulated genome-wide by the transcription factor Tur1

Dang, T. T. V., Maufrais, C., Colin, J., Moyrand, F., Mouyna, I., Coppée, J., Onyishi, C. U., Lipecka, J., Guerrera, I. C., May, R. C., et al. (2024) · PLoS Biology · doi:10.1371/journal.pbio.3002724 · Cited by 12

Identification of TNF- -Responsive Promoters and Enhancers in the Intestinal Epithelial Cell Model Caco-2

Boyd, M., Coskun, M., Lilje, B., Andersson, R., Hoof, I., Bornholdt, J., Dahlgaard, K., Olsen, J., Vitezic, M., Bjerrum, J. T., et al. (2014) · DNA Research · doi:10.1093/dnares/dsu022 · Cited by 11

A two-stream convolutional neural network for microRNA transcription start site feature integration and identification

Cha, M., Zheng, H., Talukder, A., Barham, C., Li, X., & Hu, H. (2021) · Scientific Reports · doi:10.1038/s41598-021-85173-x · Cited by 11

Functional implications of the CpG island methylation in the pathogenesis of celiac disease

Ghosh, S., Khetarpal, P., & Senapati, S. (2022) · Molecular Biology Reports · doi:10.1007/s11033-022-07585-w · Cited by 11

Integrated Analyses of DNA Methylation and Gene Expression of Rainbow Trout Muscle under Variable Ploidy and Muscle Atrophy Conditions

Salem, M., Al-Tobasei, R., Ali, A., & Kenney, B. (2022) · Genes · doi:10.3390/genes13071151 · Cited by 13

Comparative analysis of piRNA sequences, targets and functions in nematodes

Pastore, B., Hertz, H. L., & Tang, W. (2022) · RNA Biology · doi:10.1080/15476286.2022.2149170 · Cited by 11

Novel insights on the positive correlation between sense and antisense pairs on gene expression

Das, S., Rojas, M. P. Z., & Tran, E. J. (2024) · Wiley Interdisciplinary Reviews - RNA · doi:10.1002/wrna.1864 · Cited by 11

A Meta-Analysis of Microarray Gene Expression in Mouse Stem Cells: Redefining Stemness

Edwards, Y. J. K., Bryson, K., & Jones, D. T. (2008) · PLoS ONE · doi:10.1371/journal.pone.0002712 · Cited by 11

RainbowEnhancers Regulate Restrictive Transcription in Teleost Green, Red, and Blue Cones

Fang, W., Guo, C., & Wei, X. (2017) · Journal of Neuroscience · doi:10.1523/jneurosci.3421-16.2017 · Cited by 11

mRNA 5′ terminal sequences drive 200-fold differences in expression through effects on synthesis, translation and decay

van den Elzen, A. M. G., Watson, M. J., & Thoreen, C. C. (2022) · PLoS Genetics · doi:10.1371/journal.pgen.1010532 · Cited by 11

Sequence and epigenetic determinants in the regulation of the Math6 gene by Neurogenin3

Pujadas, G., Felipe, F., Ejarque, M., Sanchez, L., Cervantes, S., Lynn, F. C., Gomis, R., & Gasa, R. (2011) · Differentiation · doi:10.1016/j.diff.2011.05.006 · Cited by 11

Cis-Regulatory Elements in Mammals

Liu, X., Chen, M., Qu, X., Liu, W., Dou, Y., Liu, Q., Shi, D., Jiang, M., & Li, H. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms25010343 · Cited by 12

RNA-based Therapeutics: Past, Present and Future Prospects, Challenges in Cancer Treatment

Goel, A., Rastogi, A., Jain, M., & Niveriya, K. (2024) · Current Pharmaceutical Biotechnology · doi:10.2174/0113892010291042240130171709 · Cited by 10

lncRNA-disease association prediction based on matrix decomposition of elastic network and collaborative filtering

Wang, B., Liu, R., Zheng, X., Du, X., & Wang, Z. (2022) · Scientific Reports · doi:10.1038/s41598-022-16594-5 · Cited by 10

Alternative Transcription Start Site Usage and Functional Implications in Pathogenic Fungi

Dang, T. T. V., Colin, J., & Janbon, G. (2022) · Journal of Fungi · doi:10.3390/jof8101044 · Cited by 10

ATM suppresses c-Myc overexpression in the mammary epithelium in response to estrogen

Najnin, R. A., Mahmud, M. R. A., Rahman, M. M., Takeda, S., Sasanuma, H., Tanaka, H., Murakawa, Y., Shimizu, N., Akter, S., Takagi, M., et al. (2022) · Cell Reports · doi:10.1016/j.celrep.2022.111909 · Cited by 10

Polyamide-Scorpion Cyclam Lexitropsins Selectively Bind AT-Rich DNA Independently of the Nature of the Coordinated Metal

Lo, A. T. S., Salam, N. K., Hibbs, D. E., Rutledge, P. J., & Todd, M. H. (2011) · PLoS ONE · doi:10.1371/journal.pone.0017446 · Cited by 10

Linking Core Promoter Classes to Circadian Transcription

Westermark, P. O. (2016) · PLoS Genetics · doi:10.1371/journal.pgen.1006231 · Cited by 10

Deconvolution of expression for nascent RNA-sequencing data (DENR) highlights pre-RNA isoform diversity in human cells

Zhao, Y., Dukler, N., Barshad, G., Toneyan, S., Danko, C. G., & Siepel, A. C. (2021) · Bioinformatics · doi:10.1093/bioinformatics/btab582 · Cited by 11

Sequence-based evaluation of promoter context for prediction of transcription start sites in Arabidopsis and rice

Hiratsuka, T., Makita, Y., & Yamamoto, Y. Y. (2022) · Scientific Reports · doi:10.1038/s41598-022-11169-w · Cited by 10

In-Depth Temporal Transcriptome Profiling of an Alphaherpesvirus Using Nanopore Sequencing

Tombácz, D., Kakuk, B., Torma, G., Csabai, Z., Gulyás, G. M., Tamás, V., Zádori, Z., Jefferson, V. A., Meyer, F., & Boldogkői, Z. (2022) · Viruses · doi:10.3390/v14061289 · Cited by 10

Evolutionary Transformations of Albumin Using the Example of Model Species of Jawless Agnatha and Bony Jawed Fish (Review)

Andreeva, A. M. (2022) · Inland Water Biology · doi:10.1134/s1995082922050029 · Cited by 10

Nuclear factor kappa B and tumor necrosis factor‐alpha modulation of transcription of the mouse testis‐ and pre‐implantation development‐specific Rnf33/Trim60 gene

Choo, K., Hsu, M., Tsai, Y., Lin, W., & Huang, C. (2010) · FEBS Journal · doi:10.1111/j.1742-4658.2010.08002.x · Cited by 10

Small RNA-Induced Transcriptional Gene Regulation in Mammals

Green, V. A., & Weinberg, M. S. (2011) · Progress in molecular biology and translational science · doi:10.1016/b978-0-12-415795-8.00005-2 · Cited by 10

CAGE-defined promoter regions of the genes implicated in Rett Syndrome

Vitezic, M., Bertin, N., Andersson, R., Lipovich, L., Kawaji, H., Lassmann, T., Sandelin, A., Heutink, P., Goldowitz, D., Ha, T. J., et al. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-1177 · Cited by 10

Transcription directed by human core promoters with a HomolD box sequence requires DDB1, RECQL and RNA polymerase II machinery

Contreras‐Levicoy, J., Moreira‐Ramos, S., Rojas, D., Urbina, F., & Maldonado, E. (2012) · Gene · doi:10.1016/j.gene.2012.05.059 · Cited by 10

Same same but different: The evolution of TBP in archaea and their eukaryotic offspring

Blombach, F., & Grohmann, D. (2017) · Transcription · doi:10.1080/21541264.2017.1289879 · Cited by 10

Global characterization of the Dicer-like protein DrnB roles in miRNA biogenesis in the social amoeba Dictyostelium discoideum

Liao, Z., Kjellin, J., Hoeppner, M. P., Grabherr, M. G., & Söderbom, F. (2018) · RNA Biology · doi:10.1080/15476286.2018.1481697 · Cited by 12

Evidence for compensatory evolution within pleiotropic regulatory elementsPreprint

Kliesmete, Z., Orchard, P., Lee, V. Y. K., Geuder, J., Krauß, S. M., Ohnuki, M., Jocher, J., Vieth, B., Enard, W., & Hellmann, I. (2024) · Genome Research · doi:10.1101/gr.279001.124 · Cited by 11

Interplay between the transcription preinitiation complex and the +1 nucleosome

Chen, X., & Xu, Y. (2024) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2023.12.001 · Cited by 9

ElemeNT 2023: an enhanced tool for detection and curation of core promoter elements

Adato, O., Sloutskin, A., Komemi, H., Brabb, I. M., Duttke, S. H. C., Bücher, P., Unger, R., & Juven‐Gershon, T. (2024) · Bioinformatics · doi:10.1093/bioinformatics/btae110 · Cited by 9

Alternative transcription increases isoform complexity in Long Non-Coding RNAs and alters their functions in cancer

Bone, M., & Inman, G. J. (2025) · Non-coding RNA Research · doi:10.1016/j.ncrna.2025.04.008 · Cited by 9

H2A.Z is essential for oocyte maturation and fertility in female mouse

Xu, Q., Huang, C., Ming, J., Lu, X., Liu, L., Du, Z., Chen, Z., Na, J., Li, G., Xiang, Y., et al. (2025) · Nature Structural & Molecular Biology · doi:10.1038/s41594-025-01580-y · Cited by 9

Disruption of TAD hierarchy promotes LTR co-option in cancer

Wong, E. W. P., Şahin, M., Yang, R., Lee, U., Li, D., Zhan, Y. A., Misra, R., Tomas, F. V., Alomran, N., Polyzos, A., et al. (2025) · Nature Genetics · doi:10.1038/s41588-025-02239-6 · Cited by 10

TIPT2 and geminin interact with basal transcription factors to synergize in transcriptional regulation

Pitulescu, M. E., Teichmann, M., Luo, L., & Kessel, M. (2009) · BMC Biochemistry · doi:10.1186/1471-2091-10-16 · Cited by 9

Integrative transcription start site identification with iTiSS

Jürges, C., Dölken, L., & Erhard, F. (2021) · Bioinformatics · doi:10.1093/bioinformatics/btab170 · Cited by 9

The cap epitranscriptome: Early directions to a complex life as mRNA

Anreiter, I., Tian, Y. W., & Soller, M. (2022) · BioEssays · doi:10.1002/bies.202200198 · Cited by 9

Core promoterome of barley embryo

Pavlu, S., Nikumbh, S., Kovačik, M., An, T., Lenhard, B., Šimková, H., & Navrátilová, P. (2023) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2023.12.003 · Cited by 9

Positional requirements for the stimulation of mRNA nuclear export by ALREX-promoting elements

Tarnawsky, S. P., & Palazzo, A. F. (2012) · Molecular BioSystems · doi:10.1039/c2mb25016k · Cited by 9

The 5′ untranslated regions (UTRs) of CCN1, CCN2, and CCN4 exhibit cryptic promoter activity

Huang, B., Dornbach, L. M., & Lyons, K. M. (2007) · Journal of Cell Communication and Signaling · doi:10.1007/s12079-007-0003-1 · Cited by 9

Mesenchymal-to-Epithelial Transitions in Development and Cancer

Ng-Blichfeldt, J.-P., & Röper, K. (2020) · Methods in molecular biology · doi:10.1007/978-1-0716-0779-4_7 · Cited by 9

Influence of DAT1 Promotor Methylation on Sports Performance

Grzywacz, A., Chmielowiec, K., Boroń, A., Michałowska‐Sawczyn, M., Chmielowiec, J., Trybek, G., Mroczek, B., Leźnicka, K., Cięszczyk, P., & Masiak, J. (2021) · Genes · doi:10.3390/genes12091425 · Cited by 9

Genome-wide profiling of untranslated regions by paired-end ditag sequencing reveals unexpected transcriptome complexity in yeast

Kang, Y., Lai, D.-P., Ooi, H., Shen, T., Kou, Y., Tian, J., Czajkowsky, D. M., Shao, Z., & Zhao, X. (2014) · Molecular Genetics and Genomics · doi:10.1007/s00438-014-0913-6 · Cited by 9

Transcription of mouse Sp2 yields alternatively spliced and sub-genomic mRNAs in a tissue- and cell-type-specific fashion

Yin, H., Nichols, T. D., & Horowitz, J. M. (2010) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2010.03.002 · Cited by 9

Identification of a secondary promoter of CASP8 and its related transcription factor PURα

Lin, Z., Guo, Z., Yang, X., & Zhao, X. (2014) · International Journal of Oncology · doi:10.3892/ijo.2014.2436 · Cited by 9

Nucleosomes Are Stably Evicted from Enhancers but Not Promoters upon Induction of Certain Pro-Inflammatory Genes in Mouse Macrophages

Gjidoda, A., Tagore, M. M., McAndrew, M. J., Woods, A., & Floer, M. (2014) · PLoS ONE · doi:10.1371/journal.pone.0093971 · Cited by 9

β3-Chimaerin, a novel member of the chimaerin Rac-GAP family

Zubeldía-Brenner, L., Gutiérrez-Uzquiza, Á., Barrio‐Real, L., Wang, H., Kazanietz, M. G., & Leskow, F. C. (2014) · Molecular Biology Reports · doi:10.1007/s11033-014-3055-3 · Cited by 9

Interindividual Transcriptional Regulation of the Human biglycan Gene Involves Three Common Molecular Haplotypes

Schmitz, B., Salomon, A., Rötrige, A., Ritter, M., Ringelstein, E. B., Fischer, J. W., Paul, M., Brand, E., & Brand, S. (2013) · Arteriosclerosis Thrombosis and Vascular Biology · doi:10.1161/atvbaha.112.301073 · Cited by 9

Regulatory interplay between TFIID’s conformational transitions and its modular interaction with core promoter DNA

Cianfrocco, M. A., & Nogales, E. (2013) · Transcription · doi:10.4161/trns.25291 · Cited by 9

Identification of novel motif patterns to decipher the promoter architecture of co-expressed genes in Arabidopsis thaliana

López, Y., Patil, A., & Nakai, K. (2013) · BMC Systems Biology · doi:10.1186/1752-0509-7-s3-s10 · Cited by 10

Predicting promoter activities of primary human DNA sequences

Irie, T., Park, S., Yamashita, R., Seki, M., Yada, T., Sugano, S., Nakai, K., & Suzuki, Y. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr173 · Cited by 9

Testis-specific products of the Drosophila melanogaster sbr gene, encoding nuclear export factor 1, are necessary for male fertility

Ginanova, V. R., Golubkova, E. V., Kliver, S. F., Bychkova, E., Markoska, K., Ivankova, N., Tretyakova, I., Evgen’ev, M. B., & Мамон, Л. А. (2015) · Gene · doi:10.1016/j.gene.2015.11.030 · Cited by 9

RNA interference: new mechanistic and biochemical insights with application in oral cancer therapy

Buduru, S. D., Zimța, A., Ciocan, C. A., Braicu, C., Dudea, D., Irimie, A. I., & Berindan‐Neagoe, I. (2018) · International Journal of Nanomedicine · doi:10.2147/ijn.s167383 · Cited by 9

Embryonic tissue differentiation is characterized by transitions in cell cycle dynamic-associated core promoter regulation

Wragg, J. W., Roos, L., Vučenović, D., Cvetešić, N., Lenhard, B., & Müller, F. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa563 · Cited by 9

Large-scale clustering of CAGE tag expression data

Shimokawa, K., Okamura-Oho, Y., Kurita, T., Frith, M. C., Kawai, J., Carninci, P., & Hayashizaki, Y. (2007) · BMC Bioinformatics · doi:10.1186/1471-2105-8-161 · Cited by 9

Combining TSS-MPRA and sensitive TSS profile dissimilarity scoring to study the sequence determinants of transcription initiation

Guzman, C., Duttke, S. H. C., Zhu, Y., Saldanha, C. D. A., Downes, N. L., Benner, C. W., & Heinz, S. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad562 · Cited by 7

Maternal per- and polyfluoroalkyl substance concentrations and placental DNA methylation of thyroid hormone-related genes

Xie, Z., Jin, L., Wu, Q., Ji, H., Miao, M., Song, X., Zhu, H., Su, H., Yuan, W., & Liang, H. (2025) · Journal of Hazardous Materials · doi:10.1016/j.jhazmat.2025.137545 · Cited by 9

Annotating genomes at increased scale and resolution

Ji, H. J., Pertea, M., & Salzberg, S. L. (2026) · Nature Reviews Genetics · doi:10.1038/s41576-026-00937-3 · Cited by 9

Cap‐seq reveals complicated miRNA transcriptional mechanisms in C. elegans and mouse

Chen, J., Zhu, D., & Sun, Y. (2017) · Quantitative Biology · doi:10.1007/s40484-017-0123-4 · Cited by 8

Complex transcriptional regulation of the BCL2L12 gene: Novel, active promoter in K562 cells

Nikčević, G., Dražilov, S. S., Karan-Djurašević, T., Tos̆ić, N., Kontos, C. K., Scorilas, A., & Pavlović, S. (2020) · Gene · doi:10.1016/j.gene.2020.144723 · Cited by 8

Regional-specific calibration enables application of computational evidence for clinical classification of 5′ cis-regulatory variants in Mendelian disease

Villani, R. M., McKenzie, M. E., Davidson, A. L., & Spurdle, A. B. (2024) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2024.05.002 · Cited by 8

Drosophila Piwi distinguishes transposons from mRNAs by piRNA complementarity and abundance

Ariura, M., Solberg, T., Ishizu, H., Takahashi, H., Carninci, P., Siomi, H., & Iwasaki, Y. W. (2024) · Cell Reports · doi:10.1016/j.celrep.2024.115020 · Cited by 8

Intronic promoters and their noncoding transcripts: A new source of cancer‐associated genes

Relle, M., Becker, M., Meyer, R. G., Stassen, M., & Schwarting, A. (2012) · Molecular Carcinogenesis · doi:10.1002/mc.21955 · Cited by 8

Transcription-controlling regulatory elements of the eukaryotic genome

Razin, S. V., Gavrilov, A. A., & Ulianov, S. V. (2015) · Molecular Biology · doi:10.1134/s0026893315020119 · Cited by 8

The Activator/Dissociation Transposable Elements Comprise a Two-Component Gene Regulatory Switch That Controls Endogenous Gene Expression in Maize

Bai, L., & Brutnell, T. P. (2011) · Genetics · doi:10.1534/genetics.110.124149 · Cited by 8

Epigenetic regulation of the human genome: coherence between promoter activity and large-scale chromatin environment

Julienne, H., Zoufir, A., Audit, B., & Arnéodo, A. (2013) · Frontiers in Life Science · doi:10.1080/21553769.2013.832706 · Cited by 10

A Single Nucleotide Polymorphism (rs3811792) Affecting Human SCD5 Promoter Activity Is Associated with Diabetes Mellitus

Zámbó, V., Orosz, G., Szabó, L., Tibori, K., Sipeki, S., Molnár, K., Csala, M., & Kereszturi, É. (2022) · Genes · doi:10.3390/genes13101784 · Cited by 8

Mice and Men: Their Promoter Properties

Bajić, V. B., Tan, S. L., Christoffels, A. G., Schönbach, C., Lipovich, L., Yang, L., Hofmann, O., Kruger, A., Hide, W., Kai, C., et al. (2006) · PLoS Genetics · doi:10.1371/journal.pgen.0020054 · Cited by 116

Mammalian RNA polymerase II core promoters: insights from genome-wide studies

Sandelin, A., Carninci, P., Lenhard, B., Ponjavic, J., Hayashizaki, Y., & Hume, D. A. (2007) · Nature Reviews Genetics · doi:10.1038/nrg2026 · Cited by 526

Architectural and evolutionary features of TE-derived TSSs shape tissue-specific promoter activity in the human genome

Zhang, Y. P., Fan, Y., Wu, H., & Zhang, X.-O. (2026) · Nature Communications · doi:10.1038/s41467-026-68934-y · Cited by 2

Charting the functional landscape of the mammalian genome

Skipper, M. (2006) · Nature Reviews Genetics · doi:10.1038/nrg1885

Multiple novel promoter-architectures revealed by decoding the hidden heterogeneity within the genome

Narlikar, L. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku924 · Cited by 15