Single nucleotide polymorphisms can create alternative polyadenylation signals and affect gene expression through loss of microRNA-regulation.
Alternative polyadenylation (APA) can for example occur when a protein-coding gene has several polyadenylation (polyA) signals in its last exon, resulting in messenger RNAs (mRNAs) with different 3' untranslated region (UTR) lengths. Different 3'UTR lengths can give different microRNA (miR...
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Public Library of Science (PLoS)
2012-01-01
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| Series: | PLoS Computational Biology |
| Online Access: | https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1002621&type=printable |
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| author | Laurent F Thomas Pål Sætrom |
| author_facet | Laurent F Thomas Pål Sætrom |
| author_sort | Laurent F Thomas |
| collection | DOAJ |
| description | Alternative polyadenylation (APA) can for example occur when a protein-coding gene has several polyadenylation (polyA) signals in its last exon, resulting in messenger RNAs (mRNAs) with different 3' untranslated region (UTR) lengths. Different 3'UTR lengths can give different microRNA (miRNA) regulation such that shortened transcripts have increased expression. The APA process is part of human cells' natural regulatory processes, but APA also seems to play an important role in many human diseases. Although altered APA in disease can have many causes, we reasoned that mutations in DNA elements that are important for the polyA process, such as the polyA signal and the downstream GU-rich region, can be one important mechanism. To test this hypothesis, we identified single nucleotide polymorphisms (SNPs) that can create or disrupt APA signals (APA-SNPs). By using a data-integrative approach, we show that APA-SNPs can affect 3'UTR length, miRNA regulation, and mRNA expression--both between homozygote individuals and within heterozygote individuals. Furthermore, we show that a significant fraction of the alleles that cause APA are strongly and positively linked with alleles found by genome-wide studies to be associated with disease. Our results confirm that APA-SNPs can give altered gene regulation and that APA alleles that give shortened transcripts and increased gene expression can be important hereditary causes for disease. |
| format | Article |
| id | doaj-art-38877ad293b0454d9d5e8eb314ddcb3d |
| institution | DOAJ |
| issn | 1553-734X 1553-7358 |
| language | English |
| publishDate | 2012-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Computational Biology |
| spelling | doaj-art-38877ad293b0454d9d5e8eb314ddcb3d2025-08-20T03:01:15ZengPublic Library of Science (PLoS)PLoS Computational Biology1553-734X1553-73582012-01-0188e100262110.1371/journal.pcbi.1002621Single nucleotide polymorphisms can create alternative polyadenylation signals and affect gene expression through loss of microRNA-regulation.Laurent F ThomasPål SætromAlternative polyadenylation (APA) can for example occur when a protein-coding gene has several polyadenylation (polyA) signals in its last exon, resulting in messenger RNAs (mRNAs) with different 3' untranslated region (UTR) lengths. Different 3'UTR lengths can give different microRNA (miRNA) regulation such that shortened transcripts have increased expression. The APA process is part of human cells' natural regulatory processes, but APA also seems to play an important role in many human diseases. Although altered APA in disease can have many causes, we reasoned that mutations in DNA elements that are important for the polyA process, such as the polyA signal and the downstream GU-rich region, can be one important mechanism. To test this hypothesis, we identified single nucleotide polymorphisms (SNPs) that can create or disrupt APA signals (APA-SNPs). By using a data-integrative approach, we show that APA-SNPs can affect 3'UTR length, miRNA regulation, and mRNA expression--both between homozygote individuals and within heterozygote individuals. Furthermore, we show that a significant fraction of the alleles that cause APA are strongly and positively linked with alleles found by genome-wide studies to be associated with disease. Our results confirm that APA-SNPs can give altered gene regulation and that APA alleles that give shortened transcripts and increased gene expression can be important hereditary causes for disease.https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1002621&type=printable |
| spellingShingle | Laurent F Thomas Pål Sætrom Single nucleotide polymorphisms can create alternative polyadenylation signals and affect gene expression through loss of microRNA-regulation. PLoS Computational Biology |
| title | Single nucleotide polymorphisms can create alternative polyadenylation signals and affect gene expression through loss of microRNA-regulation. |
| title_full | Single nucleotide polymorphisms can create alternative polyadenylation signals and affect gene expression through loss of microRNA-regulation. |
| title_fullStr | Single nucleotide polymorphisms can create alternative polyadenylation signals and affect gene expression through loss of microRNA-regulation. |
| title_full_unstemmed | Single nucleotide polymorphisms can create alternative polyadenylation signals and affect gene expression through loss of microRNA-regulation. |
| title_short | Single nucleotide polymorphisms can create alternative polyadenylation signals and affect gene expression through loss of microRNA-regulation. |
| title_sort | single nucleotide polymorphisms can create alternative polyadenylation signals and affect gene expression through loss of microrna regulation |
| url | https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1002621&type=printable |
| work_keys_str_mv | AT laurentfthomas singlenucleotidepolymorphismscancreatealternativepolyadenylationsignalsandaffectgeneexpressionthroughlossofmicrornaregulation AT palsætrom singlenucleotidepolymorphismscancreatealternativepolyadenylationsignalsandaffectgeneexpressionthroughlossofmicrornaregulation |