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Transcriptional Regulatory Elements in the Human Genome
Abstract
The faithful execution of biological processes requires a precise and carefully orchestrated set of steps that depend on the proper spatial and temporal expression of genes. Here we review the various classes of transcriptional regulatory elements (core promoters, proximal promoters, distal enhancers, silencers, insulators/boundary elements, and locus control regions) and the molecular machinery (general transcription factors, activators, and coactivators) that interacts with the regulatory elements to mediate precisely controlled patterns of gene expression. The biological importance of transcriptional regulation is highlighted by examples of how alterations in these transcriptional components can lead to disease. Finally, we discuss the methods currently used to identify transcriptional regulatory elements, and the ability of these methods to be scaled up for the purpose of annotating the entire human genome.
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“since transcriptional regulatory elements are likely to be contained within these intervals and that there is thus merit in capturing the variation within these regions42.”
From Psychiatric genome-wide association study analyses implicate neuronal, immune and histone pathways (2015) · cites this paper as [42]
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“…including promoters, enhancers, and insulators, in the genome influence RNA polymerase II (RNA pol II) complex activity during the transcription process by providing binding sites for transcription factors (TFs) and cofactors (Bulger and Groudine, 2010; Maston et al., 2006; Riethoven, 2010).”
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“Next to the transcription start site are the core and the proximal promoter (up to 250 base pairs), followed by the distal elements (the latter are more than 250 base pairs away from the transcription start site) [4].”
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“Transcription factors bind to CREs to modulate the expression of cell-type specific gene expression patterns [35,36].”
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“Viruses have evolved to contain strong promoters with multiple CREs, and the study of gene regulation in animal viruses has significantly shaped our understanding of eukaryotic gene con-trol, offering key insights into promoter architecture and transcriptional regulation [reviewed in [171,172]].”
NSD proteins in anti-tumor immunity and their therapeutic targeting by protein degraders
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“Spatially or temporally specific gene transcription is maintained through the enhancers and ciselements therein as well as transacting regulatory proteins (Maston et al., 2006).”
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“S5a) as previous studies in Arabidopsis suggests that 500 bp-1kbp is sufficient to emulate transcription behavior of a promoter (Maston et al. 2006; Srivastava et al. 2014; Mishra et al. 2022; Prasad et al. 2022).”
Regulatory variation: an emerging vantage point for cancer biology
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“…and specific TFs and results 214 HUMAN MUTATION, Vol. 33, No. 1, 209–217, 2012 in the disruption of normal processes of gene activation and transcriptional initiation [Cooper, 2002], and contribute to the pathophysiology of many human genetic disease including β-thalassemia [Maston et al., 2006].”
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Effects of gene regulatory reprogramming on gene expression in human and mouse developing hearts
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“It co-localizes with active enhancers and plays a critical role during embryonic development [31-36].”
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“In humans, approximately 60% of all promoters fall near a CpG island (Venter et al., 2001; Maston et al., 2006).”
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“Many specific functional elements, such as enhancer, transcription factor binding site, TATA box, transcription start site, and poly(A) site, are involved in these regulatory codes (Maston et al., 2006).”
BackgroundTranscriptional control analyses of the Xiphophorus melanoma oncogene
Regneri, J., Volff, J., & Schartl, M. (2015) · Comparative Biochemistry and Physiology Part C Toxicology & Pharmacology · doi:10.1016/j.cbpc.2015.09.001 · Cited by 6
“Distal cisregulatory elements such as enhancer and silencer elements, which often contribute to the spatial transcription pattern of genes, have been found up to over hundred kb up- or downstream of the proximal promoter (Maston et al., 2006; Miele and Dekker, 2008) and therefore are often missed in conventional plasm…”
BackgroundJiang, Q., Wang, Y., Gao, Y., Wang, H., Zhang, Z., Li, Q., Xu, S., Cai, W., & Li, L. (2021) · Human Genetics · doi:10.1007/s00439-020-02247-y · Cited by 6
“Indeed, the Human Genome Project has fruitfully revealed a widespread conservation of noncoding DNA, which harbors a variety of regulatory elements that either enhance (enhancers), suppress (silencers) or locally limit (insulators) the transcription of specific genes (Maston et al. 2006).”
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“Following MASTON et al. (2006), it can be stated that regulatory systems of gene function in man are robust and redundant, and yet highly sensitive as well.”
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SEgene identifies links between super enhancers and gene expression across cell types
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“Given that enhancer-gene interactions typically fall within ±1 Mbp 63 – 65 , this distance is set as the default, though other values, such as 0.5 Mbp, are also implemented.”
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“If the promoter is otherwise conserved, then the clustering of substitutions might suggest adaptation (Pollard et al. 2006; Kim and Pritchard 2007; Holloway et al. 2008).”
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“Regulatory elements in 50 upstream control the gene expression by mRNA transcription (Maston et al., 2006).”
BackgroundCapturing the regulatory interactions of eukaryote genomes
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“Enhancers and silencers, while possessing opposing functions share common features in that they are generally orientation and distance independent in relation to the TSS [31, 33, 34].”
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Content and Variation of the Human Genome
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A Hemizygous Deletion Within the PGK1 Gene in Males with PGK1 Deficiency
Behlmann, A., Goyal, N., Yang, X., Chen, P. H., & Ankala, A. (2018) · JIMD Reports · doi:10.1007/8904_2018_147 · Cited by 4
“Gene expression (temporal and/or spatial) may also be altered by variants that disrupt chromosomal structure around a gene and/or of the cis-acting long-range regulatory elements (reviewed in Maston et al. 2006).”
BackgroundRegular expression based pattern extraction from a cell - Specific gene expression data
Subramanian, S., & Thomas, T. (2019) · Informatics in Medicine Unlocked · doi:10.1016/j.imu.2019.100269 · Cited by 4
Chen, Y., Jiang, B., Wang, W., Su, D., Xia, F., & Li, X. (2020) · Frontiers in Genetics · doi:10.3389/fgene.2020.00453 · Cited by 4
Molecular Genetics of Lung and Pleural Neoplasms
Cagle, P. T., Jagirdar, J. S., & Popper, H. (2008) · Springer eBooks · doi:10.1007/978-0-387-72114-9_2 · Cited by 4
Functions of AHR-1 and CYP-35A subfamily genes in caenorhabditis elegans
Aarnio, V. (2014) · UEF eRepo (University of Eastern Finland) · Cited by 4
EnhancerBD identifing sequence featurePreprint
Wang, Y. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.03.05.583459 · Cited by 4
Leveraging pre-trained AI models for robust promoter sequence design in synthetic biology
Yang, G., Chen, Y., Guo, Q., Li, X., & Zhou, Z. (2026) · Biophysics Reports · doi:10.52601/bpr.2025.240033 · Cited by 3
“…strength of core promoters is influenced by various factors, including component type and arrangement, transcription factor binding sites, and upstream and downstream regulatory elements (Browning et al. 2019; Butler and Kadonaga 2002; Lenhard et al. 2012; Maston et al. 2006; Vo Ngoc et al. 2017).”
AttnW2V-Enhancer: Leveraging attention and Word2Vec for enhanced enhancer prediction
Rehman, M. U., Abbas, Z., Ullah, F., & Hussain, I. (2025) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2025.07.008 · Cited by 3
Super-silencers are crucial for development and carcinogenesis in B cells
Huang, D., Petrykowska, H. M., Kumar, D., Kardava, L., Moir, S. L., Afzali, B., Elnitski, L. L., & Ovcharenko, I. (2025) · Nature Communications · doi:10.1038/s41467-025-63329-x · Cited by 3
“DNA regulatory elements (REs)play a crucialrole in gene transcription by recruiting diverse transcription factors (TFs) to either initiate, prepare, or inhibit gene transcription 1 – 3 .”
Sengupta, D., Mukhopadhyay, P., Banerjee, S., Ganguly, K., Mascharak, P., Mukherjee, N., Mitra, S., Bhattacharjee, S., Mitra, R., Sarkar, A., et al. (2023) · Scientific Reports · doi:10.1038/s41598-023-30962-9 · Cited by 3
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“Enhancers, which are cis ‐ acting elements, can be located up to 10 kb from genes [83, 84], which is why we included this third category in our DMR classification.”
Wertheim, B. (2012) · InTech eBooks · doi:10.5772/48239 · Cited by 3
“These cisregulatory elements can consist of Transcription Factor Binding Motifs (TFBM), promotors, enhancers, silencers and other sequence motifs that regulate the genes [22].”
Assessing the Effects of Symmetry on Motif Discovery and Modeling
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“But having a model for the specificity of the transcription factor allows one to have a finer scale resolution of the binding sites [4,10,11,12] and to infer the effects of genetic variations on gene expression [13,14].”
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“[ 33 ].”
BackgroundNucleosomal packaging of eukaryotic DNA and regulation of transcription
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“se pairs in length and harbor binding sites for several transcription factors, which are responsible for specific activation of enhancer-regulated genes [92, 93].”
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Budd, A. (2012) · Methods in molecular biology · doi:10.1007/978-1-61779-582-4_1 · Cited by 3
Ageing and Alzheimer’s Disease
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Cross‐sectional study of students' molecular explanations of inheritance patterns
Castro‐Faix, M., & Duncan, R. G. (2021) · Science Education · doi:10.1002/sce.21692 · Cited by 3
Exploring the role of eRNA in regulating gene expression
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Intronic variants in inborn errors of metabolism: Beyond the exome
Hertzog, A., Selvanathan, A., Farnsworth, E., Tchan, M. C., Adams, L., Lewis, K., Tolun, A. A., Bennetts, B., Ho, G., & Bhattacharya, K. (2022) · Frontiers in Genetics · doi:10.3389/fgene.2022.1031495 · Cited by 3
Unexploited Performance of NLS in the dCas9-VPR-Mediated Transcriptional Activation
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Gecaj, R. M., Behluli, B., & Youngs, C. R. (2024) · Current Issues in Molecular Biology · doi:10.3390/cimb46070394 · Cited by 3
“Transcription factors (TFs) are important proteins that regulate the transcription of specific genes, including miRNA genes, and are crucial in the process of gene expression [52].”
BackgroundSilva, D., & Jemc, J. C. (2015) · Genetics · doi:10.1534/genetics.115.179911 · Cited by 3
“Transcriptional regulatory elements are composed of two distinct families: promoters and distal regulatory elements, including enhancers and silencers (Maston et al. 2006).”
BackgroundInfluentialBhakuni, T., Sharma, A. K., Ali, M. F., Mahapatra, M., Saxena, R., & Jairajpuri, M. A. (2016) · Clinical and Applied Thrombosis/Hemostasis · doi:10.1177/1076029616652725 · Cited by 3
“Variations in the promoter region are a known putative cause of diseases such as b-thalassemia, hemophilia, bladder cancer, and familial hypercholesterolemia.(14,15) Although more than 250 mutations and polymorphisms spanning the introns, exons, and flanking regions in SERPINC1 gene causing DVT are known, only a singl…”
Background
Metadata
- Authors
- Maston, G. A., Evans, S. K., & Green, M. R.
- Affiliations
- Howard Hughes Medical Institute (US)
- Venue
- Annual Review of Genomics and Human Genetics
- Publisher
- Annual Reviews
- Published
- 2006-09-01
- Volume
- 7
- Issue
- 1
- Pages
- 29-59
- ISSN
- 1527-8204 (ISSN-L)
- 1545-293X
- OpenAlex
- W2159164310
- Cited by
- 937
- References
- 202
- Citations by year
- 2026: 18 · 2025: 45 · 2024: 45 · 2023: 39 · 2022: 51 · 2021: 57 · 2020: 57 · 2019: 55 · 2018: 55 · 2017: 45 · 2016: 51 · 2015: 59 · 2014: 61 · 2013: 72 · 2012: 54
- FWCI
- 2.53
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Annual Review of Genomics and Human Genetics (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Human Genome Research Institute
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Keywords
- transcriptional regulatory elements, core promoter, proximal promoter, distal enhancers, silencers, insulators, locus control region, general transcription factors, transcriptional activator, transcriptional coactivator, gene expression regulation, human genome annotation
- MeSH terms
- Gene Expression Regulation, Humans, Transcription Factors, Genome, Human, Regulatory Elements, Transcriptional
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.
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