Journal of Genetics & Genomic Sciences Category: Genetics Type: Review Article
Regulatory Potential of Mobile Genetic Elements in the Human MGMT Gene
- Lukash Lyubov Leonidovna1*, Olga Pidpala2
- 1 Institute Of Molecular Biology And Genetics, National Academy Of Sciences Of Ukraine, 03680, 150 Zabolotnogo St., Kiev, Ukraine
- 2 Institute Of Molecular Biology And Genetics, National Academy Of Sciences Of Ukraine, Kiev, Ukraine
*Corresponding Author:Lukash Lyubov Leonidovna
Institute Of Molecular Biology And Genetics, National Academy Of Sciences Of Ukraine, 03680, 150 Zabolotnogo St., Kiev, Ukraine
Received Date: Apr 15, 2018 Accepted Date: May 24, 2018 Published Date: Jun 07, 2018
Mobile Genetic Elements (MGE) make up a large part of the DNA of eukaryotes, in particular, almost 45% of the human genome. Numerous data show the diverse role of these elements in the genome from plasticity factors to mutability or stability. They discuss their role in the evolution of genomes and the evolution of gene regulation. The purpose of this work was to investigate the distribution of MGE in human MGMT gene and their regulatory potential. It has been shown at first that in the human MGMT gene, MGE is present both in the intron sequences and in the promoter region. In the intron sequences, MGEs form composite cluster structures that are the source of various regulatory sequences and have the potential to form alternative promoters. In the promoter region, three sequences of MGE were identified: two LTR repeats and a fragment of the DNA transposon. The MGE fragments in the promoter region of human MGMT also enriched with potential cis-regulatory sequences that may be involved in the regulation of this gene.
The eukaryotic genome is a complex and dynamic structure. About 50% of the human genome, and possibly more is covered by Mobile Genetic Elements (MGE), which for a long time were considered unnecessary ballast [1,2]. Studies of recent years convincingly testify to the important role of these elements in the evolution of genomes and in the evolution of gene regulation [3-15]. They are not only mutagenic factors, but they can also be the source of a variety of regulatory sequences, such as sites of alternative splicing, cis-regulatory modules, which are clusters of binding sites of transcription factors, or play the role of alternative promoters [16-24]. MGE tends to integrate into non-coding genome sites (introns, flanked genes and intergenic sites) . On average, in the human introns, MGE is approximately 89.5%; in exons, they account for slightly more than 10%, in particular about 4% for protein-encoding genes . Up to 20% of the genes contain MGE in non-translated regions of mRNA, where they can affect the regulation of gene expressions; in particular, the MGE in 5'UTR affects the initiation of translation . It is known that about 25% of human genes contain MGE in promoter regions, and today there is convincing evidence of their involvement, in particular promoters of retroelements, in the regulation of gene transcriptional activity [21,26]. There are cases where MGE plays the role of alternative promoters, which leads either to increase the level of expression of the corresponding gene, or to change the tissue specificity of its expression .
Human MGMT gene encodes a reparative enzyme called O6-methylguanine-DNA methyltransferase, which removes alkylated groups from the O6 position of guanine in DNA and protects cells from their toxic and mutagenic effects. Expression of this gene and the activity of the enzyme themselves have wide limits both in between and intrinsically individual variations, indicating that its regulation is complicated . Given the complexity of this problem, it might be worthwhile to focus on MGE, the role of which in gene regulation has recently been discussed quite widely. Numerous databases today have enormous material on the availability of mobile elements, but the data array is not characterized and not generalized. Perhaps the MGE of MGMT gene is also a source of a variety of regulatory sequences, which led us to focus our attention on the study of this issue.
MATERIALS AND METHODS
The nucleotide sequence of the MGMT gene is taken on the Ensembl site. Data on the promoter region of the gene were obtained from GenBank (X61657), about the potential promotor regions of the gene being studied from the AceView database. The results of the search and identification of IHE are done with the CENSOR program. The homology between the sequences studied was determined by the BLAST 2.2.32 program. Functional sites are defined by TFSEARCH: Searching Transcription Factor Binding Sites (ver 1.3). The search for potential regulatory sequences was performed by SITECON, SiteGA, BLASTN 2.2.26 using the TRRD database resources (Transcription Regulatory Regions Database) and CISTER: Cis-element Cluster Finder, WWW Signal Scan and Tfsitescan. These methods and databases were used in the relevant sections of the article.
RESULTS AND DISCUSSION
Distribution of MGE in the gene of human MGMT reparative enzyme
Figure 1: MGE in the human MGMT gene and in its introns.
|Intron number (bp)||% MGE, (bp)|
|DNA- transposons||Endogenous retroviruses||LTR retrotransposons||Non-LTR retrotransposons||In total|
|intron 1 (68.944)||6.05 (4169)||2.36 (1625)||19.26 (13281)||27.67 (19075)|
|intron 2 (171.517)||4.14 (7102)||2.19 (3762)||0.24 (409)||20.75 (35590)||27.32 (46863)|
|intron 3 (51.158)||2.26 (1158)||2.63 (1345)||39.85 (20388)||44.74 (22891)|
|intron 4 (7.446)||2.25 (167)||4.71 (351)||1.3 (97)||8.26 (615)|
|Gene (300824)||4.21 (12676)||2.35 (7083)||0.24 (409)||23.03 (69275)||29.73 (89443)|
|Coordinates within the intron||MGE||Length bp||Class / family||Chain||Number cluster|
Table 2: MGE clusters in human MGMT intron 2.
|Coordinates within the intron||MGE||Length bp||Class / family||Chain||Number cluster|
Table 3: MGE clusters in human MGMT intron 3.
Composite cluster structures of MGE in the introns of the investigated gene as a source of potential regulatory sequences
|Ingredients of composite clusters|
|intron 2 (cluster 1)||intron 3 (cluster 1)|
Table 4: Representation of potential sites of binding the boundaries of composite cluster structures of MGE in human MGMT gene introns.
Motives of regulatory sequences in the promoter regions of the MGMT gene within the MGE
The promoted gene promoter (X61657) has a length of 1157 bp and covers exon 1 part intron 1. It is devoid of TATA or CAAT sequences, contains CG-rich regions and is structurally reminiscent of genes of the household. It also contains SP1, AP-1 and AP-2, NF-kapBsites, two elements that bind the Glucocorticoid Receptor (GRE) and a 59-bp size element, which is located on the first eccentric-intron boundary, necessary for effective transcription of the reporter designs [46,47].
Fragments of MGE in the promoter region of the investigated gene
|Referential promoter, symbolic||Data on MGE|
|Element||Class||Length||Direction||Coordinates within promotor|
Table 5: Fragments of MGE in the promoter region of human MGMT gene.
Potential cis-elements within the fragments of mobile genetic elements in the promoter regions of the investigated gene
Figure 2: Potential cis-regulatory elements in the MGE fragments identified within the sequence of the refracted promoter of human MGMT gene.
Fragments of the MGE as components of potential alternative promoters
Fragments of the MGE in alternative promoter regions of the investigated gene
|Symbolic designation||Data on MGE|
|for the promoter||Element||Class||Length||Direction||Coordinates within promoter|
Table 6: Sequence of MGE in potential alternative promoter regions of the MGMT human reparative enzyme gene.
Potential regulatory sequences within identified MGE fragments
|Conditional designation of the promoter||Mobile genetic elements||Regulatory sequences|
|Name||Species affiliation||Linking sites for transcription factors||Regulatory elements|
TATA box; YY1; GATA; SF1;Sp1;CAAT box; OCT1; SREBP; PAX2;
Locus Control Region-like region
Table 7: Regulatory potential sequences of MGE, inherent in the genome of the man, within the potential promoters of the human MGMT gene.
In the human MGMT gene, MGE is present both in the intron sequences and in the promoter region. In the intron sequences, MGEs form composite cluster structures that are the source of various regulatory sequences and have the potential to form alternative promoters. In the promoter region, three sequences of MGE were identified: two LTR-repeats and a fragment of the DNA-transposon. The fact that one of the LTR-repeats contains the described response elements of the Glucocorticoid hormones (GRE) and that the minimal promoter and sequence of the SP1 site are located within the fragment of DNA-transposon confirms the important role of MGE in gene regulation. In addition, the MGE fragments in the promoter region of human MGMT enriched with potential cis regulatory sequences that may also be involved in the regulation of this gene.
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Citation:Pidpala O, Leonidovna LL (2018) Regulatory Potential of Mobile Genetic Elements in the Human MGMT Gene. J Genet Genomic Sci 3: 008.
Copyright: © 2018 Lukash Lyubov Leonidovna, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.