Enrichment of rare alleles within epigenetic chromatin marks in the first intron
In previous studies, we demonstrated that some sites in the first intron likely regulate gene expression. In the present work, we sought to further confirm the functional relevance of first intron sites by estimating the quantity of rare alleles in the first intron. A basic hypothesis posited herein...
Saved in:
| Main Authors: | , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BioMed Central
2019-03-01
|
| Series: | Genomics & Informatics |
| Subjects: | |
| Online Access: | http://genominfo.org/upload/pdf/gi-2019-17-1-e9.pdf |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1832570106013548544 |
|---|---|
| author | Shin-Sang Jo Sun Shim Choi |
| author_facet | Shin-Sang Jo Sun Shim Choi |
| author_sort | Shin-Sang Jo |
| collection | DOAJ |
| description | In previous studies, we demonstrated that some sites in the first intron likely regulate gene expression. In the present work, we sought to further confirm the functional relevance of first intron sites by estimating the quantity of rare alleles in the first intron. A basic hypothesis posited herein is that genomic regions carrying more functionally important sites will have a higher proportion of rare alleles. We estimated the proportions of rare single nucleotide polymorphisms with a minor allele frequency < 0.01 located in several histone marks in the first introns of various genes, and compared them with those in other introns and those in 2-kb upstream regions. As expected, rare alleles were found to be significantly enriched in most of the regulatory sites located in the first introns. Meanwhile, transcription factor binding sites were significantly more enriched in the 2-kb upstream regions (i.e., the regions of putative promoters of genes) than in the first introns. These results strongly support our proposal that the first intron sites of genes may have important regulatory functions in gene expression independent of promoters. |
| format | Article |
| id | doaj-art-e9503d30f6f244cea1d9d79cdc64860a |
| institution | Kabale University |
| issn | 2234-0742 |
| language | English |
| publishDate | 2019-03-01 |
| publisher | BioMed Central |
| record_format | Article |
| series | Genomics & Informatics |
| spelling | doaj-art-e9503d30f6f244cea1d9d79cdc64860a2025-02-02T17:54:24ZengBioMed CentralGenomics & Informatics2234-07422019-03-0117110.5808/GI.2019.17.1.e9551Enrichment of rare alleles within epigenetic chromatin marks in the first intronShin-Sang Jo0Sun Shim Choi1 Division of Biomedical Convergence, College of Biomedical Science, Institute of Bioscience & Biotechnology, Kangwon National University, Chuncheon 24341, Korea Division of Biomedical Convergence, College of Biomedical Science, Institute of Bioscience & Biotechnology, Kangwon National University, Chuncheon 24341, KoreaIn previous studies, we demonstrated that some sites in the first intron likely regulate gene expression. In the present work, we sought to further confirm the functional relevance of first intron sites by estimating the quantity of rare alleles in the first intron. A basic hypothesis posited herein is that genomic regions carrying more functionally important sites will have a higher proportion of rare alleles. We estimated the proportions of rare single nucleotide polymorphisms with a minor allele frequency < 0.01 located in several histone marks in the first introns of various genes, and compared them with those in other introns and those in 2-kb upstream regions. As expected, rare alleles were found to be significantly enriched in most of the regulatory sites located in the first introns. Meanwhile, transcription factor binding sites were significantly more enriched in the 2-kb upstream regions (i.e., the regions of putative promoters of genes) than in the first introns. These results strongly support our proposal that the first intron sites of genes may have important regulatory functions in gene expression independent of promoters.http://genominfo.org/upload/pdf/gi-2019-17-1-e9.pdffirst intronminor allele frequencypromoterrare allele |
| spellingShingle | Shin-Sang Jo Sun Shim Choi Enrichment of rare alleles within epigenetic chromatin marks in the first intron Genomics & Informatics first intron minor allele frequency promoter rare allele |
| title | Enrichment of rare alleles within epigenetic chromatin marks in the first intron |
| title_full | Enrichment of rare alleles within epigenetic chromatin marks in the first intron |
| title_fullStr | Enrichment of rare alleles within epigenetic chromatin marks in the first intron |
| title_full_unstemmed | Enrichment of rare alleles within epigenetic chromatin marks in the first intron |
| title_short | Enrichment of rare alleles within epigenetic chromatin marks in the first intron |
| title_sort | enrichment of rare alleles within epigenetic chromatin marks in the first intron |
| topic | first intron minor allele frequency promoter rare allele |
| url | http://genominfo.org/upload/pdf/gi-2019-17-1-e9.pdf |
| work_keys_str_mv | AT shinsangjo enrichmentofrarealleleswithinepigeneticchromatinmarksinthefirstintron AT sunshimchoi enrichmentofrarealleleswithinepigeneticchromatinmarksinthefirstintron |