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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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“Silencers are distal cis -regulatory elements that repress their target gene promoters through physical interaction in an orientation-and position-independent manner (39, 41, 72).”
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“The best candidate SNPs for acting upon gene regulation are SNPs in regulatory regions and SNPs upstream of genes (‘‘upstream SNPs’’) because transcription is primarily regulated there (Birney et al., 2007; Maston et al., 2006).”
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“Promoters, enhancers and LCR are associated with gene expression activation, while insulators and silencers are associated with gene expression repression (8).”
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“The changes during embryonic development are driven by intricate gene expression programming (Maston et al., 2006), which reveals specific expression patterns in different types of cells at different development stages.”
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“Transcriptional activity is not only dependent on the formation of the initiation complex, but is tightly regulated by transcription factors and coactivators [173].”
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“An overview of transcriptional regulatory elements, illustrating how distal regulatory elements can interact with the core promoter (modified from Maston et al ., 2006). between CpG islands and promoter regions does not always have a syntenic relationship among different species.”
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Dissociated Pmch and Cre Expression in Lactating Pmch-Cre BAC Transgenic Mice
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“In the LHA, IHy, and PFx, as previously suggested by singlecell RNA sequencing data (Mickelsen et al., 2019), MCH-ir in all groups colocalized with Vglut2-Cre;eGFP (Figures 7A,C).”
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Gene regulatory network inference using out of equilibrium statistical mechanics
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“Finally, the small size of functional gene regulatory words (typically six to eight nucleotides) and their degeneracy lead to large numbers of false positive results (Maston et al. , 2006).”
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“Key in the regulation of gene expression are transcription factors (TFs), proteins that bind to short regulatory DNA sequences to either activate or silence the transcription of genes (Maston et al. 2006; Spitz and Fur-long 2012; Lambert et al. 2018; Kim and Wysocka 2023).”
BackgroundBeyond the Balance of Activator and Repressor
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“Similarly, gene data analysis for regulating transcription regulation by binding the sequence elements in protein sequences [19 – 22].”
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“(DME) It is well known that the enhancer is a short (50 ~ 1500 bp) DNA region upstream or downstream 1Mbp of TSS in the gene [42, 43].”
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“A gene promoter generically comprises a core promoter positioned +1bp to -120bp relative to the TSS, a proximal promoter -120bp to -1Kbp, and a distal promoter at an unknown distance from the TSS (Maston et al. 2006).”
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“Promoters can generally be influenced by distinct enhancer elements under varying conditions (Maston et al. 2006), while binding of factors that do not associate strongly with the promoter may ‘‘switch off’’ the enhancer as required.”
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“Furthermore, we uncovered several highly differentiated regions in noncoding regions of the genome, which, while their function is currently unknown, may play an important role in gene regulatory networks ( 59 ).”
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“Regarding the relatively low number of predicted promoters, we feel the main reason is that the candidate CREs contain a limited number of promoter-related regions, as experimentally validated promoters have been excluded from these candidate CREs (Supplementary Note 8).”
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“These values were chosen based on average distances of transcriptional regulatory elements from the genes they control [46,47].”
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“For example, when opting for a strategy where screening for a successful recombination event relies on expression of a resistance cassette with its own promotor sequence, special care should be taken in the design process to leave regulatory elements in the 3’ untranslated region intact [75], unless the cassette is re…”
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“Genes [1] are the genetic code of life, which direct the synthesis of various proteins [2] through transcription [3] and translation [4] processes to maintain the normal activities of life.”
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“Similar to enhancers, silencers can be found upstream of the gene they repress, downstream of a promoter within an intronic region or exon, as well as in the 3′ untranslated region (3′-UTR) [Ogbourne and Antalis, 1998; Maston et al., 2006].”
BackgroundNúñez-Olvera, S. I., Puente-Rivera, J., Ramos‐Payán, R., Pérez‐Plasencia, C., Salinas-Vera, Y. M., Aguilar‐Arnal, L., & López‐Camarillo, C. (2021) · Cells · doi:10.3390/cells11010075 · Cited by 8
“Alternatively, a repressor may block transcription by inhibiting PIC assembly [2,24].”
BackgroundKörbelin, J., Klein, J., Matuszcak, C., Runge, J., Harbaum, L., Klose, H. F. E., & Hennigs, J. K. (2023) · Frontiers in Cardiovascular Medicine · doi:10.3389/fcvm.2022.1036096 · Cited by 8
“Cooperation between multiple copies of the same TF, or between different TFs, can stimulate transcriptional synergy in which the regulatory effect of TFs working together is greater than the sum of the individual TFs (143).”
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“Enhancers and promoters are two of the most critical regulatory elements of gene transcription in the eukaryotic genome (Maston et al., 2006).”
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“The current list of these regulatory elements includes promoters, enhancers, silencers, and locus control regions [92] .”
Background3CDB: a manually curated database of chromosome conformation capture data
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“Gene expression in eukaryotes is tightly regulated by both cis- and trans-regulatory elements (1).”
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“…and then imported to the nucleus where it binds as homodimer or heterodimer, to a specific cis-acting sequence located in promoters of target genes, which allows the interaction with the basal transcription machinery and other tissue-specific factors to stimulate transcription (Maston et al. 2006).”
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“…elements that control gene expression levels, we observe the maximum of average attention mask weights across all promoters occurs at the center of input sequences, which corresponds to core promoter elements required for recruitment of transcriptional machinery [Maston et al., 2006] (Figure 3C).”
BackgroundPromID: human promoter prediction by deep learningPreprint
Umarov, R. K., Kuwahara, H., Li, Y., Gao, X., & Solovyev, V. V. (2018) · arXiv (Cornell University) · doi:10.48550/arxiv.1810.01414 · Cited by 9
“This is important especially in the prediction of human promoters since the structural features of many promoters are still unknown [8, 16].”
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Evaluation of Bayesian Linear Regression models for gene set prioritization in complex diseases
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“Signal-dependent transcriptional activation of RNA polymerase II (Pol II)-transcribed genes is a hallmark of metazoan gene regulation (1, 2) and is largely governed by gene-distal enhancers (3–5).”
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“Proximal promoter regions (PPRs, for a comprehensive list of abbreviations Supplementary File 1) of RNA polymerase II transcribed genes usually extend up to 1Kb upstream from transcription start sites (TSSs) (1).”
BackgroundInterrogating cell type-specific cooperation of transcriptional regulators in 3D chromatin
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“However, when and how these elements and TRs cooperatively regulate gene expression and cellular function remain largely unknown (Kazemian et al., 2013; Maston et al., 2006; Spitz and Furlong, 2012; Voss and Hager, 2014).”
BackgroundGenotype-Based Test in Mapping Cis-Regulatory Variants from Allele-Specific Expression Data
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Genomic features of human limb specific enhancers
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“…it is obvious that the elements regulating transcription can be located not only in the 5′-regions, but also in introns, 3′-regions and they may be even incorporated into the structure of neighboring genes (Broos et al., 2011; Jothi et al., 2008; Lettice et al., 2003, Maston et al., 2006).”
BackgroundCharacterization of a proximal Sp1 response element in the mouse Dlk2 gene promoter
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“These elements are presented as the core promoter, the proximal promoter and the distal promoter, located approximately –40 to þ50 nucleotides,(4) up to 200 nucleotides(5) and up to 1 mega nucleotides upstream of the transcription initiation site (TIS) respectively.(6) The core promoter plays an essential role in regu…”
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Pan, J.-H., & Du, P.-F. (2023) · Briefings in Bioinformatics · doi:10.1093/bib/bbad494 · Cited by 7
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A TWO-STAGE EVOLUTIONARY APPROACH FOR EFFECTIVE CLASSIFICATION OF HYPERSENSITIVE DNA SEQUENCES
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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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