Genome-wide analysis of mammalian promoter architecture and evolution

Cluster analysis and display of genome-wide expression patterns

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The ENCODE (ENCyclopedia Of DNA Elements) Project

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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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Noncanonical TATA Sequence in the UL44 Late Promoter of Human Cytomegalovirus Is Required for the Accumulation of Late Viral Transcripts

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Retrotransposition as a Source of New Promoters

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A Novel Protein Isoform of the Multicopy Human NAIP Gene Derives from Intragenic Alu SINE Promoters

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Identification of a novel temperature sensitive promoter in cho cells

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Dual-initiation promoters with intertwined canonical and TCT/TOP transcription start sites diversify transcript processing

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Bovine ncRNAs Are Abundant, Primarily Intergenic, Conserved and Associated with Regulatory Genes

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RNA degradome--its biogenesis and functions

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LncRNApred: Classification of Long Non-Coding RNAs and Protein-Coding Transcripts by the Ensemble Algorithm with a New Hybrid Feature

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Antisense transcription‐dependent chromatin signature modulates sense transcript dynamics

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Utilizing tiling microarrays for whole‐genome analysis in plants

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Natural antisense transcripts as versatile regulators of gene expression

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Nuclear export as a key arbiter of “mRNA identity” in eukaryotes

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Multiple Independent Retroelement Insertions in the Promoter of a Stress Response Gene Have Variable Molecular and Functional Effects in Drosophila

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Dynamic effects of genetic variation on gene expression revealed following hypoxic stress in cardiomyocytes

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Genetic and Molecular Analyses of PEG10 Reveal New Aspects of Genomic Organization, Transcription and Translation

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Chapter 6 Global Control Regions and Regulatory Landscapes in Vertebrate Development and Evolution

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Understanding the molecular diversity of synapses

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Complex Expression of the UL136 Gene of Human Cytomegalovirus Results in Multiple Protein Isoforms with Unique Roles in Replication

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Hypermethylation of Ron proximal promoter associates with lack of full-length Ron and transcription of oncogenic short-Ron from an internal promoter

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A cryptic promoter in the first exon of the SPG4gene directs the synthesis of the 60-kDa spastin isoform

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Computational annotation of miRNA transcription start sites

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STL-seq reveals pause-release and termination kinetics for promoter-proximal paused RNA polymerase II transcripts

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Promoter sequence and architecture determine expression variability and confer robustness to genetic variants

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Genome-wide inference reveals that feedback regulations constrain promoter-dependent transcriptional burst kinetics

Luo, S., Wang, Z., Zhang, Z., Zhou, T., & Zhang, J. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac1204 · Cited by 49

Contribution of Long Noncoding RNAs to Autism Spectrum Disorder Risk

Wilkinson, B., & Campbell, D. B. (2013) · International review of neurobiology · doi:10.1016/b978-0-12-418700-9.00002-2 · Cited by 49

Differential transcript isoform usage pre- and post-zygotic genome activation in zebrafish

Aanes, H., Østrup, O., Andersen, I. S., Moen, L. F., Mathavan, S., Collas, P., & Aleström, P. (2013) · BMC Genomics · doi:10.1186/1471-2164-14-331 · Cited by 48

Eukaryotic genomes may exhibit up to 10 generic classes of gene promoters

Gagniuc, P. A., & Ionescu-Tirgoviste, C. (2012) · BMC Genomics · doi:10.1186/1471-2164-13-512 · Cited by 49

A non-biased framework for the annotation and classification of the non-miRNA small RNA transcriptome

Pantano, L., Estivill, X., & Martı́, E. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr527 · Cited by 48

Polycomb recruitment attenuates retinoic acid–induced transcription of the bivalent NR2F1 gene

Laursen, K. B., Mongan, N. P., Zhuang, Y., Ng, M. M., Benoit, Y. D., & Gudas, L. J. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt367 · Cited by 48

E2F1 Transcription Factor Regulates O-linked N-acetylglucosamine (O-GlcNAc) Transferase and O-GlcNAcase Expression

Muthusamy, S., Hong, K. U., Dassanayaka, S., Hamid, T., & Jones, S. P. (2015) · Journal of Biological Chemistry · doi:10.1074/jbc.m115.677534 · Cited by 50

Divergence of CpG island promoters: A consequence or cause of evolution?

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CpG-depleted promoters harbor tissue-specific transcription factor binding signals—implications for motif overrepresentation analyses

Roider, H. G., Lenhard, B., Kanhere, A., Haas, S. A., & Vingron, M. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp682 · Cited by 48

Expression Specificity of Disease-Associated lncRNAs: Toward Personalized Medicine

Nguyen, Q. H., & Carninci, P. (2015) · Current topics in microbiology and immunology · doi:10.1007/82_2015_464 · Cited by 49

Decoding a Signature-Based Model of Transcription Cofactor Recruitment Dictated by Cardinal Cis-Regulatory Elements in Proximal Promoter Regions

Benner, C. W., Konovalov, S., Mackintosh, C., Hutt, K. R., Stunnenberg, R., & García-Bassets, I. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003906 · Cited by 47

NanoCAGE-XL and CapFilter: an approach to genome wide identification of high confidence transcription start sites

Cumbie, J. S., Ivanchenko, M. G., & Megraw, M. S. (2015) · BMC Genomics · doi:10.1186/s12864-015-1670-6 · Cited by 46

The unexpected traits associated with core promoter elements

Dikstein, R. (2011) · Transcription · doi:10.4161/trns.2.5.17271 · Cited by 46

Asap: A Framework for Over-Representation Statistics for Transcription Factor Binding Sites

Marstrand, T. T., Frellsen, J., Moltke, I., Thiim, M., Valen, E., Retelska, D., & Krogh, A. (2008) · PLoS ONE · doi:10.1371/journal.pone.0001623 · Cited by 46

The long and short of RNAs

Carninci, P. (2009) · Nature · doi:10.1038/457974b · Cited by 46

Characterization of GPR101 transcript structure and expression patterns

Trivellin, G., Bjelobaba, I. M., Daly, A., Larco, D. O., Palmeira, L., Faucz, F. R., Thiry, A., Leal, L. F., Rostomyan, L., Quezado, M., et al. (2016) · Journal of Molecular Endocrinology · doi:10.1530/jme-16-0045 · Cited by 46

YeasTSS: an integrative web database of yeast transcription start sites

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DNA Free Energy-Based Promoter Prediction and Comparative Analysis of Arabidopsis and Rice Genomes

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A global genomic transcriptional code associated with CNS-expressed genes

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Constructing the landscape of the mammalian transcriptome

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Probabilistic resolution of multi-mapping reads in massively parallel sequencing data using MuMRescueLite

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RNA-MATE: a recursive mapping strategy for high-throughput RNA-sequencing data

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Targeted discovery of novel human exons by comparative genomicsPreprint

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DDPC: Dragon Database of Genes associated with Prostate Cancer

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Methods for integration site distribution analyses in animal cell genomes

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A change-point model for identifying 3′UTR switching by next-generation RNA sequencing

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Characteristics of Antisense Transcript Promoters and the Regulation of Their Activity

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The Adipose Transcriptional Response to Insulin Is Determined by Obesity, Not Insulin Sensitivity

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Identification of putative promoters in 48 eukaryotic genomes on the basis of DNA free energy

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The ets-Related Transcription Factor GABP Directs Bidirectional Transcription

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Identification of neuronal target genes for CCAAT/Enhancer Binding Proteins

Kfoury, N., & Kapatos, G. (2008) · Molecular and Cellular Neuroscience · doi:10.1016/j.mcn.2008.11.004 · Cited by 45

SLIC-CAGE: high-resolution transcription start site mapping using nanogram-levels of total RNAPreprint

Cvetešić, N., Leitch, H. G., Borkowska, M., Müller, F., Carninci, P., Hájková, P., & Lenhard, B. (2018) · Genome Research · doi:10.1101/gr.235937.118 · Cited by 45

Distinct roles of LARP1 and 4EBP1/2 in regulating translation and stability of 5′TOP mRNAs

Hochstoeger, T., Papasaikas, P., Piskadlo, E., & Chao, J. A. (2024) · Science Advances · doi:10.1126/sciadv.adi7830 · Cited by 44

Genome-wide analysis of core promoter structures inSchizosaccharomyces pombewith DeepCAGE

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Transcription and Maturation of mRNA in Dinoflagellates

Roy, S., & Morse, D. (2013) · Microorganisms · doi:10.3390/microorganisms1010071 · Cited by 43

The role of chromatin dynamics in immune cell development

Winter, D. R., & Amit, I. (2014) · Immunological Reviews · doi:10.1111/imr.12200 · Cited by 44

Transcription-factor occupancy at HOT regions quantitatively predicts RNA polymerase recruitment in five human cell lines

Foley, J. W., & Sidow, A. (2013) · BMC Genomics · doi:10.1186/1471-2164-14-720 · Cited by 44

The Structures of Eukaryotic Transcription Pre-initiation Complexes and Their Functional Implications

Greber, B. J., & Nogales, E. (2019) · Sub-cellular biochemistry/Subcellular biochemistry · doi:10.1007/978-3-030-28151-9_5 · Cited by 43

The current status of cDNA cloning

Harbers, M. (2008) · Genomics · doi:10.1016/j.ygeno.2007.11.004 · Cited by 43

Integrated approaches to uncovering transcription regulatory networks in mammalian cells

Tan, K., Tegner, J. N., & Ravasi, T. (2008) · Genomics · doi:10.1016/j.ygeno.2007.11.005 · Cited by 43

ENCODE: More genomic empowermentPreprint

Weinstock, G. M. (2007) · Genome Research · doi:10.1101/gr.6534207 · Cited by 43

Identification of Arabidopsis genic and non‐genic promoters by paired‐end sequencing of TSS tags

Tokizawa, M., Kusunoki, K., Koyama, H., Kurotani, A., Sakurai, T., Suzuki, Y., Sakamoto, T., Kurata, T., & Yamamoto, Y. Y. (2017) · The Plant Journal · doi:10.1111/tpj.13511 · Cited by 42

Expression vector cassette engineering for recombinant therapeutic production in mammalian cell systems

Wang, T., & Guo, X. H. (2020) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-020-10640-w · Cited by 42

LncRNAs in vertebrates: Advances and challenges

Mallory, A. C., & Shkumatava, A. (2015) · Biochimie · doi:10.1016/j.biochi.2015.03.014 · Cited by 46

Identification and characterization of a novel promoter for the human ANO1 gene regulated by the transcription factor signal transducer and activator of transcription 6 (STAT6)

Mazzone, A., Gibbons, S. J., Bernard, C. E., Nowsheen, S., Middha, S., Almada, L. L., Ördög, T., Kendrick, M. L., Reid‐Lombardo, K., Shen, K. R., et al. (2014) · The FASEB Journal · doi:10.1096/fj.14-258541 · Cited by 42

Transcription initiation factor TBP: old friend new questions

Kramm, K., Engel, C., & Grohmann, D. (2019) · Biochemical Society Transactions · doi:10.1042/bst20180623 · Cited by 42

Inflammation drives alternative first exon usage to regulate immune genes including a novel iron-regulated isoform of Aim2

Robinson, E. K., Jagannatha, P., Covarrubias, S., Cattle, M. A., Safavi, R., SONG, R., Viswanathan, K., Shapleigh, B., Abu-Shumays, R. L., Jain, M., et al. (2021) · eLife · doi:10.7554/elife.69431 · Cited by 42

Dynamic regulation of N6,2′-O-dimethyladenosine (m6Am) in obesity

Ben-Haim, M. S., Pinto, Y., Moshitch-Moshkovitz, S., Hershkovitz, V., Kol, N., Diamant-Levi, T., Beeri, M. S., Amariglio, N., Cohen, H. Y., & Rechavi, G. (2021) · Nature Communications · doi:10.1038/s41467-021-27421-2 · Cited by 42

Collection and Comparative Analysis of 1888 Full-length cDNAs from Wild Rice Oryza rufipogon Griff. W1943

Lu, T., Yu, S., Fan, D., Mu, J., Shangguan, Y., Wang, Z., Minobe, Y., Lin, Z., & Han, B. (2008) · DNA Research · doi:10.1093/dnares/dsn018 · Cited by 42

Induction of a Unique Isoform of the NCOA7 Oxidation Resistance Gene by Interferon β-1b

Yu, L., Croze, E., Yamaguchi, K. D., Tran, T., Reder, A. T., Litvak, V., & Volkert, M. R. (2015) · Journal of Interferon & Cytokine Research · doi:10.1089/jir.2014.0115 · Cited by 41

Investigating the NRAS 5' UTR as a Target for Small Molecules

Balaratnam, S., Torrey, Z. R., Calabrese, D. R., Banco, M. T., Yazdani, K., Xiao, L., Fullenkamp, C. R., Seshadri, S., Holewinski, R. J., Andrésson, Þ., et al. (2022) · Cell chemical biology · doi:10.1016/j.chembiol.2023.05.004 · Cited by 42

Novel Core Promoter Elements and a Cognate Transcription Factor in the Divergent Unicellular Eukaryote Trichomonas vaginalis

Smith, A. J., Chudnovsky, L., Simões-Barbosa, A., Delgadillo‐Correa, M. G., Jónsson, Z. O., Wohlschlegel, J. A., & Johnson, P. J. (2011) · Molecular and Cellular Biology · doi:10.1128/mcb.00745-10 · Cited by 41

The Determinants of Directionality in Transcriptional Initiation

Bagchi, D. N., & Iyer, V. R. (2016) · Trends in Genetics · doi:10.1016/j.tig.2016.03.005 · Cited by 46

Database for exploration of functional context of genes implicated in ovarian cancer

Kaur, M., Radovanović, A., Essack, M., Schaefer, U., Maqungo, M., Kibler, T. D., Schmeier, S., Christoffels, A. G., Narasimhan, K., Choolani, M. A., et al. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn593 · Cited by 40

Computational analyses of eukaryotic promoters

Zhang, M. Q. (2007) · BMC Bioinformatics · doi:10.1186/1471-2105-8-s6-s3 · Cited by 40

Alternative promoters in CpG depleted regions are prevalently associated with epigenetic misregulation of liver cancer transcriptomes

Nepal, C., & Andersen, J. B. (2023) · Nature Communications · doi:10.1038/s41467-023-38272-4 · Cited by 39

Relationship between maternal environment and DNA methylation patterns of estrogen receptor alpha in wild Eastern Bluebird (Sialia sialis) nestlings: a pilot study

Bentz, A. B., Sirman, A. E., Wada, H., Navara, K. J., & Hood, W. R. (2016) · Ecology and Evolution · doi:10.1002/ece3.2162 · Cited by 40

Role of epigenetics in zebrafish development

Balasubramanian, S., Raghunath, A., & Perumal, E. (2019) · Gene · doi:10.1016/j.gene.2019.144049 · Cited by 42

Regulation of Mouse Slo Gene Expression

Kundu, P., Alioua, A., Stefani, E., & Toro, L. (2007) · Journal of Biological Chemistry · doi:10.1074/jbc.m704777200 · Cited by 39

Coding region structural heterogeneity and turnover of transcription start sites contribute to divergence in expression between duplicate genes

Park, C., & Makova, K. D. (2009) · Genome biology · doi:10.1186/gb-2009-10-1-r10 · Cited by 39

Boosting with stumps for predicting transcription start sites

Zhao, X., Xuan, Z., & Zhang, M. Q. (2007) · Genome biology · doi:10.1186/gb-2007-8-2-r17 · Cited by 39

Histone modification profiles are predictive for tissue/cell-type specific expression of both protein-coding and microRNA genes

Zhang, Z., & Zhang, M. Q. (2011) · BMC Bioinformatics · doi:10.1186/1471-2105-12-155 · Cited by 38

Dynamic gene expression for metabolic engineering of mammalian cells in culture

Le, H., Vishwanathan, N., Kantardjieff, A., Doo, I., Srienc, M., Zheng, X., Somia, N. V., & Hu, W. (2013) · Metabolic Engineering · doi:10.1016/j.ymben.2013.09.004 · Cited by 39

Comprehensive profiling of the fission yeast transcription start site activity during stress and media response

Thodberg, M., Thieffry, A., Bornholdt, J., Boyd, M., Holmberg, C., Azad, A., Workman, C. T., Chen, Y., Ekwall, K., Nielsen, O., et al. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky1227 · Cited by 40

PAMP-triggered genetic reprogramming involves widespread alternative transcription initiation and an immediate transcription factor wave

Thieffry, A., López‐Márquez, D., Bornholdt, J., Malekroudi, M. G., Bressendorff, S., Barghetti, A., Sandelin, A., & Brodersen, P. (2022) · The Plant Cell · doi:10.1093/plcell/koac108 · Cited by 38

Systems biology of innate immunity

Tegner, J. N., Nilsson, R., Bajić, V. B., Björkegren, J., & Ravasi, T. (2006) · Cellular Immunology · doi:10.1016/j.cellimm.2007.01.010 · Cited by 38

Core promoter structure and genomic context reflect histone 3 lysine 9 acetylation patterns

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The Human IGF1R IRES likely operates through a Shine–Dalgarno‐like interaction with the G961 loop (E‐site) of the 18S rRNA and is kinetically modulated by a naturally polymorphic polyU loop

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