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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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BackgroundInner and Outer DNA Loops in Cell Nuclei: Evidence from Pulsed-Field Comet Assay
Chopei, M., Olefirenko, V., Afanasieva, K. S., & Sivolob, A. (2022) · Cytology and Genetics · doi:10.3103/s0095452722040028 · Cited by 1
“In addition to the packaging of long DNA molecules in the limited space of the nucleus, chromatin plays a significant role in the regulation of transcription (Maston et al., 2006; Kadauke et al., 2009; Cook, 2010).”
BackgroundChiu, E. S., McDonald, C. A., Gagne, R. B., Dunkleberger, H., Moxcey, M., & VandeWoude, S. (2024) · Retrovirology · doi:10.1186/s12977-024-00635-0 · Cited by 3
“To better evaluate functional roles of enFeLV-LTR integration sites, we evaluated their influence on transcription by identifying coding regions of the cat genome 1Mbp of each integration, as this distance is generally accepted as the maximal distance for LTR enhancer function [28, 33].”
BackgroundMethodMethylSeqLogo: DNA methylation smart sequence logos
Hsu, F., & Horton, P. (2024) · BMC Bioinformatics · doi:10.1186/s12859-024-05896-2 · Cited by 1
“Thus we provide predefined promoter regions defined as 1000bp upstream to 200bp downstream of annotated major transcription start sites [26].”
Comparative study of the computer-aided design of MYCN-specific antigene oligonucleotides
Hincapié-López, M., Pinzón-Reyes, E. H., García-Zapirain, B., & Pabón-Martínez, Y. V. (2025) · Computational and Structural Biotechnology Reports · doi:10.1016/j.csbr.2025.100030 · Cited by 1
Transcriptome Complexity Disentangled: A Regulatory Molecules Approach
Asiaee, A., Abrams, Z. B., Pua, H. H., & Coombes, K. R. (2025) · International Journal of Molecular Sciences · doi:10.3390/ijms26062510 · Cited by 1
“Due to its ease of measurement, the transcriptome has played a significant role in advancing our understanding of differentiation [1], development [2], and disease [3].”
Ahmed, M., & Kim, D. R. (2019) · PeerJ · doi:10.7717/peerj.6509 · Cited by 1
Dysregulation of Cis-Regulatory Elements in Cancer
Barbour, J. A., & Wong, J. W. H. (2019) · Springer eBooks · doi:10.1007/978-981-13-8958-0_8 · Cited by 1
CaptureProbe: a java tool for designing probes for capture Hi-C applications
Yun-Fei, M., Adeola, A. C., Yan-bo, S., Xie, H., & Ya-ping, Z. (2020) · 动物学研究 · doi:10.24272/j.issn.2095-8137.2020.010 · Cited by 1
“Regulatory elements can act on multiple genes and distant target genes via chromatin looping (Maston et al., 2006).”
Three-dimensional genome rewiring during the development of antibody-secreting cells
Chan, W. F., Johanson, T. M., & Allan, R. S. (2020) · Biochemical Society Transactions · doi:10.1042/bst20191104 · Cited by 1
Integrative Ranking of Enhancer Networks Facilitates the Discovery of Epigenetic Markers in Cancer
Wang, Q., Wu, Y., Vorberg, T., Eils, R., & Herrmann, C. (2021) · Frontiers in Genetics · doi:10.3389/fgene.2021.664654
“Most of the enhancers are located within ± 1 Mb of the transcription start site (TSS) of their target genes (Maston et al., 2006).”
BackgroundHilbertEPIs: Enhancer-Promoter Interactions Prediction with Hilbert Curve and CNN Model
Hu, Y., Peng, R., Long, C., & Zhu, M. (2021) · International Conference on Bioinformatics and Computational Biology (ICBCB) · doi:10.1109/icbcb52223.2021.9459226 · Cited by 1
“Enhancers and promoters are important DNA cis-regulatory sequences in controlling transcriptional activity [1][2].”
BackgroundFinding and Verifying Enhancers for Endothelial-Expressed Genes
Neal, A., Rodriguez‐Caro, H., & Val, S. D. (2022) · Methods in molecular biology · doi:10.1007/978-1-0716-2059-5_28 · Cited by 1
Transcriptional Control Leading to Clinical Outcomes in Breast Cancer Cases
Aftab, A., Khan, R., Hameed, U., Abbas, T., & Ahmad, B. (2022) · Springer eBooks · doi:10.1007/978-981-19-0197-3_13 · Cited by 1
THE MOLECULAR, CELLULAR, AND GENETIC BASIS OF HEMOGLOBIN DISORDERS
Steinberg, M. H., Forget, B. G., Higgs, D. R., & Weatherall, D. J. (2009) · Cambridge University Press eBooks · doi:10.1017/cbo9780511596582.004 · Cited by 1
Identification of novel tumor predisposition families and underlying genetic defects
Aavikko, M. (2014) · Työväentutkimus Vuosikirja · Cited by 1
Efficiency and versatility of distal multisite transcription regulationPreprint
Saiz, L., & Vilar, J. M. G. (2007) · arXiv (Cornell University) · doi:10.48550/arxiv.0704.3264 · Cited by 1
“This strategy is widely used in eukaryotic enhancers [1] to integrate multiple signals into the control of the transcriptional machinery [1, 2], to the extent that transcription regulation through DNA looping is nowadays considered to be the rule”
BackgroundBioinformatics studies on the mechanisms of gene regulation in vertebrates
Ghazal, A. (2014) · Epsilon Open Archive (Sveriges lantbruksuniversitet biblioteket (Swedish University of Agricultural Sciences)) · Cited by 1
Aron, S. (2012) · University of the Witwatersrand, Johannesburg Institutional Repository on DSpace (University of the Witwatersrand, Johannesburg) · Cited by 1
Analysis of the cis-regulatory structure of developmentally regulated genes in zebrafish embryo
Kalmár, É. (2009) · heiDOK (Heidelberg University) · doi:10.11588/heidok.00009443 · Cited by 1
Wylie, D., Hofmann, H. A., & Zemelman, B. V. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/133934 · Cited by 1
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
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