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Dvorak P, Hlavac V, Hanicinec V, Rao BH, Soucek P. Genes divided according to the relative position of the longest intron show increased representation in different KEGG pathways. BMC Genomics 2024; 25:649. [PMID: 38943073 PMCID: PMC11214234 DOI: 10.1186/s12864-024-10558-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 06/24/2024] [Indexed: 07/01/2024] Open
Abstract
Despite the fact that introns mean an energy and time burden for eukaryotic cells, they play an irreplaceable role in the diversification and regulation of protein production. As a common feature of eukaryotic genomes, it has been reported that in protein-coding genes, the longest intron is usually one of the first introns. The goal of our work was to find a possible difference in the biological function of genes that fulfill this common feature compared to genes that do not. Data on the lengths of all introns in genes were extracted from the genomes of six vertebrates (human, mouse, koala, chicken, zebrafish and fugu) and two other model organisms (nematode worm and arabidopsis). We showed that more than 40% of protein-coding genes have the relative position of the longest intron located in the second or third tertile of all introns. Genes divided according to the relative position of the longest intron were found to be significantly increased in different KEGG pathways. Genes with the longest intron in the first tertile predominate in a range of pathways for amino acid and lipid metabolism, various signaling, cell junctions or ABC transporters. Genes with the longest intron in the second or third tertile show increased representation in pathways associated with the formation and function of the spliceosome and ribosomes. In the two groups of genes defined in this way, we further demonstrated the difference in the length of the longest introns and the distribution of their absolute positions. We also pointed out other characteristics, namely the positive correlation between the length of the longest intron and the sum of the lengths of all other introns in the gene and the preservation of the exact same absolute and relative position of the longest intron between orthologous genes.
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Affiliation(s)
- Pavel Dvorak
- Department of Biology, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 76, 32300, Pilsen, Czech Republic.
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 76, 32300, Pilsen, Czech Republic.
- Institute of Medical Genetics, University Hospital Pilsen, Dr. Edvarda Benese 13, 30599, Pilsen, Czech Republic.
| | - Viktor Hlavac
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 76, 32300, Pilsen, Czech Republic
- Toxicogenomics Unit, National Institute of Public Health, Srobarova 48, 10042, Prague, Czech Republic
| | - Vojtech Hanicinec
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 76, 32300, Pilsen, Czech Republic
| | - Bhavana Hemantha Rao
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 76, 32300, Pilsen, Czech Republic
| | - Pavel Soucek
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 76, 32300, Pilsen, Czech Republic
- Toxicogenomics Unit, National Institute of Public Health, Srobarova 48, 10042, Prague, Czech Republic
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Farris J, Khanna C, Smadbeck JB, Johnson SH, Bothun E, Kaplan T, Hoffman F, Polonis K, Oliver G, Reis LM, Semina EV, Rust L, Hoppman NL, Vasmatzis G, Marcou CA, Schimmenti LA, Klee EW. Complex balanced intrachromosomal rearrangement involving PITX2 identified as a cause of Axenfeld-Rieger Syndrome. Am J Med Genet A 2024; 194:e63542. [PMID: 38234180 PMCID: PMC11003841 DOI: 10.1002/ajmg.a.63542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 12/15/2023] [Accepted: 01/07/2024] [Indexed: 01/19/2024]
Abstract
Axenfeld-Rieger Syndrome (ARS) type 1 is a rare autosomal dominant condition characterized by anterior chamber anomalies, umbilical defects, dental hypoplasia, and craniofacial anomalies, with Meckel's diverticulum in some individuals. Here, we describe a clinically ascertained female of childbearing age with ARS for whom clinical targeted sequencing and deletion/duplication analysis followed by clinical exome and genome sequencing resulted in no pathogenic variants or variants of unknown significance in PITX2 or FOXC1. Advanced bioinformatic analysis of the genome data identified a complex, balanced rearrangement disrupting PITX2. This case is the first reported intrachromosomal rearrangement leading to ARS, illustrating that for patients with compelling clinical phenotypes but negative genomic testing, additional bioinformatic analysis are essential to identify subtle genomic abnormalities in target genes.
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Affiliation(s)
- Joseph Farris
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Cheryl Khanna
- Department of Ophthalmology, Mayo Clinic, Rochester, Minnesota, USA
| | - James B Smadbeck
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Sarah H Johnson
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Erick Bothun
- Department of Ophthalmology, Mayo Clinic, Rochester, Minnesota, USA
| | - Tyler Kaplan
- Department of Ophthalmology, Mayo Clinic, Rochester, Minnesota, USA
| | - Francis Hoffman
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Katarzyna Polonis
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Gavin Oliver
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Linda M Reis
- Department of Pediatrics and Children's Research Institute, Medical College of Wisconsin and Children's Wisconsin, Milwaukee, Wisconsin, USA
| | - Elena V Semina
- Department of Pediatrics and Children's Research Institute, Medical College of Wisconsin and Children's Wisconsin, Milwaukee, Wisconsin, USA
- Department of Ophthalmology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Laura Rust
- Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota, USA
| | - Nicole L Hoppman
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - George Vasmatzis
- Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota, USA
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota, USA
| | - Cherisse A Marcou
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Lisa A Schimmenti
- Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota, USA
| | - Eric W Klee
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota, USA
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