Question

Although mutations in the coding region of a genes can lead to changes in protein sequence (non-synonomous, nonsense, frameshift) there are plenty of mutations in non-coding regions within the genome that can alter how gene are expressed. In the scenarios below, please indicate what non-coding regions might contain a SNP (Single Nucleotide Polymorphism) mutation, and how this SNP mutation might lead to the given scenario: a. no transcription occurs for a particular gene b. Transcription occurs, but the mRNA is shorter than normal (by 100 bp) c. Transcription occurs, but the mRNA is longer than normal (100 bp longer)

Answer 1

A single-nucleotide polymorphism (SNP) is a mutation in the DNA sequence that occurs when a single nucleotide A, T, G or C differs between members of a species or paired chromosomes in an individual. Ps can occur in coding, non-coding and intergenic regions of the genome. Nearly 90% SNPs occur in non-coding regions. RNAs, introns, promoters and other control sequences, repeated sequences, and retroviruses are included in non-coding regions.

Most non-coding variants are concentrated in Deoxyribonuclease I (DNase I) hypersensitive sites, enhancer regions, and chromatin marks. If the SNP is an Inversion, then it will affect more than one gene. Transitions from purine to pyrimidine or vice versa (A to G or G to A or   T to C or C to T) and transversions from Purine to pyrimidine or pyrimidine to purine may occur.

a. Polymorphisms in the TATA box inhibit promoter activity. Hence, it can inhibit gene transcription as it is part of the core promoter. For example, a A>C point mutation (A > C) at position -27 in the putative TATA box of the EDH17B2 gene decreased promoter activity and inhibited transcription. SNPs in regions of the promoter where transcription factor binds, will also inhibit transcription. Promoter region SNPs can affect binding between transcription factors such as SP1, c-Myb, E2F1, Ets, and GATA-1 and promoter. There may be deletion of transcription factor binding site affecting transcription. If mutation occurs in the CpG island of promoter site, which may increase methylation at this site, decreasing transcription due to gene silencing. Mutation in binding sites for transcription factors such as SP1 and CTCF, which forms a methylation site, may inhibit transcription. If promoter SNPs cause histone modifications (acetylation, methylation, phosphorylation, ubiquitination, and Glycosylation) will inhibit transcription. Due to increased modification, the RNA polymerase cannot access the promoter, inhibiting transcription. Formation of MicroRNAs will also decrease transcription as miRNA bind to untranslated regions.

b. SNPs in intronic regions affect mRNA splicing. If a splicing site is created prematurely, then it may result in formation of a smaller coding region. As a result, a smaller mRNA transcript is formed, due to splicing after transcription. If sites are created in intronic regions that stall the RNA polymerase, then the mRNA will be shorter due to RNA polymerase not being able to carry out transcription beyond a certain length.

c. If the intronic region splice sites are removed, then the mRNA will be longer than normal. Removal of splice site will include the introns in the coding region, casuing increase in the mRNA length. If untranslated regions are mutated, then there can be increased transcription beyond these sites.