1
|
Ryczek N, Łyś A, Makałowska I. The Functional Meaning of 5'UTR in Protein-Coding Genes. Int J Mol Sci 2023; 24:ijms24032976. [PMID: 36769304 PMCID: PMC9917990 DOI: 10.3390/ijms24032976] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/20/2023] [Accepted: 01/26/2023] [Indexed: 02/05/2023] Open
Abstract
As it is well known, messenger RNA has many regulatory regions along its sequence length. One of them is the 5' untranslated region (5'UTR), which itself contains many regulatory elements such as upstream ORFs (uORFs), internal ribosome entry sites (IRESs), microRNA binding sites, and structural components involved in the regulation of mRNA stability, pre-mRNA splicing, and translation initiation. Activation of the alternative, more upstream transcription start site leads to an extension of 5'UTR. One of the consequences of 5'UTRs extension may be head-to-head gene overlap. This review describes elements in 5'UTR of protein-coding transcripts and the functional significance of protein-coding genes 5' overlap with implications for transcription, translation, and disease.
Collapse
|
2
|
Mapping gene and gene pathways associated with coronary artery disease: a CARDIoGRAM exome and multi-ancestry UK biobank analysis. Sci Rep 2021; 11:16461. [PMID: 34385509 PMCID: PMC8361107 DOI: 10.1038/s41598-021-95637-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Accepted: 07/28/2021] [Indexed: 02/07/2023] Open
Abstract
Coronary artery disease (CAD) genome-wide association studies typically focus on single nucleotide variants (SNVs), and many potentially associated SNVs fail to reach the GWAS significance threshold. We performed gene and pathway-based association (GBA) tests on publicly available Coronary ARtery DIsease Genome wide Replication and Meta-analysis consortium Exome (n = 120,575) and multi ancestry pan UK Biobank study (n = 442,574) summary data using versatile gene-based association study (VEGAS2) and Multi-marker analysis of genomic annotation (MAGMA) to identify novel genes and pathways associated with CAD. We included only exonic SNVs and excluded regulatory regions. VEGAS2 and MAGMA ranked genes and pathways based on aggregated SNV test statistics. We used Bonferroni corrected gene and pathway significance threshold at 3.0 × 10-6 and 1.0 × 10-5, respectively. We also report the top one percent of ranked genes and pathways. We identified 17 top enriched genes with four genes (PCSK9, FAM177, LPL, ARGEF26), reaching statistical significance (p ≤ 3.0 × 10-6) using both GBA tests in two GWAS studies. In addition, our analyses identified ten genes (DUSP13, KCNJ11, CD300LF/RAB37, SLCO1B1, LRRFIP1, QSER1, UBR2, MOB3C, MST1R, and ABCC8) with previously unreported associations with CAD, although none of the single SNV associations within the genes were genome-wide significant. Among the top 1% non-lipid pathways, we detected pathways regulating coagulation, inflammation, neuronal aging, and wound healing.
Collapse
|
3
|
Rosikiewicz W, Sikora J, Skrzypczak T, Kubiak MR, Makałowska I. Promoter switching in response to changing environment and elevated expression of protein-coding genes overlapping at their 5' ends. Sci Rep 2021; 11:8984. [PMID: 33903630 PMCID: PMC8076222 DOI: 10.1038/s41598-021-87970-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 04/07/2021] [Indexed: 11/09/2022] Open
Abstract
Despite the number of studies focused on sense-antisense transcription, the key question of whether such organization evolved as a regulator of gene expression or if this is only a byproduct of other regulatory processes has not been elucidated to date. In this study, protein-coding sense-antisense gene pairs were analyzed with a particular focus on pairs overlapping at their 5' ends. Analyses were performed in 73 human transcription start site libraries. The results of our studies showed that the overlap between genes is not a stable feature and depends on which TSSs are utilized in a given cell type. An analysis of gene expression did not confirm that overlap between genes causes downregulation of their expression. This observation contradicts earlier findings. In addition, we showed that the switch from one promoter to another, leading to genes overlap, may occur in response to changing environment of a cell or tissue. We also demonstrated that in transfected and cancerous cells genes overlap is observed more often in comparison with normal tissues. Moreover, utilization of overlapping promoters depends on particular state of a cell and, at least in some groups of genes, is not merely coincidental.
Collapse
Affiliation(s)
- Wojciech Rosikiewicz
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jarosław Sikora
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Tomasz Skrzypczak
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
- Center for Advanced Technology, Adam Mickiewicz University, Poznań, Poland
| | - Magdalena R Kubiak
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Izabela Makałowska
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland.
| |
Collapse
|
4
|
Wawrzyniak P, Sobolewska-Ruta A, Zaleski P, Łukasiewicz N, Kabaj P, Kierył P, Gościk A, Bierczyńska-Krzysik A, Baran P, Mazurkiewicz-Pisarek A, Płucienniczak A, Bartosik D. Molecular dissection of the replication system of plasmid pIGRK encoding two in-frame Rep proteins with antagonistic functions. BMC Microbiol 2019; 19:254. [PMID: 31722681 PMCID: PMC6854812 DOI: 10.1186/s12866-019-1595-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 09/10/2019] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Gene overlapping is a frequent phenomenon in microbial genomes. Excluding so-called "trivial overlapping", there are significant implications of such genetic arrangements, including regulation of gene expression and modification of protein activity. It is also postulated that, besides gene duplication, the appearance of overlapping genes (OGs) is one of the most important factors promoting a genome's novelty and evolution. OGs coding for in-frame proteins with different functions are a particularly interesting case. In this study we identified and characterized two in-frame proteins encoded by OGs on plasmid pIGRK from Klebsiella pneumoniae, a representative of the newly distinguished pHW126 plasmid family. RESULTS A single repR locus located within the replication system of plasmid pIGRK encodes, in the same frame, two functional polypeptides: a full-length RepR protein and a RepR' protein (with N-terminal truncation) translated from an internal START codon. Both proteins form homodimers, and interact with diverse DNA regions within the plasmid replication origin and repR promoter operator. Interestingly, RepR and RepR' have opposing functions - RepR is crucial for initiation of pIGRK replication, while RepR' is a negative regulator of this process. Nevertheless, both proteins act cooperatively as negative transcriptional regulators of their own expression. CONCLUSIONS Regulation of the initiation of pIGRK replication is a complex process in which a major role is played by two in-frame proteins with antagonistic functions. In-frame encoded Rep proteins are uncommon, having been described in only a few plasmids. This is the first description of such proteins in a plasmid of the pHW126 family.
Collapse
Affiliation(s)
- Paweł Wawrzyniak
- Bioengineering Department, Institute of Biotechnology and Antibiotics, Starościńska 5, 02-516 Warsaw, Poland
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Ilji Miecznikowa 1, 02-096 Warsaw, Poland
| | - Agnieszka Sobolewska-Ruta
- Bioengineering Department, Institute of Biotechnology and Antibiotics, Starościńska 5, 02-516 Warsaw, Poland
| | - Piotr Zaleski
- Bioengineering Department, Institute of Biotechnology and Antibiotics, Starościńska 5, 02-516 Warsaw, Poland
| | - Natalia Łukasiewicz
- Bioengineering Department, Institute of Biotechnology and Antibiotics, Starościńska 5, 02-516 Warsaw, Poland
| | - Paulina Kabaj
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Ilji Miecznikowa 1, 02-096 Warsaw, Poland
| | - Piotr Kierył
- Bioengineering Department, Institute of Biotechnology and Antibiotics, Starościńska 5, 02-516 Warsaw, Poland
| | - Agata Gościk
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Ilji Miecznikowa 1, 02-096 Warsaw, Poland
| | - Anna Bierczyńska-Krzysik
- Bioengineering Department, Institute of Biotechnology and Antibiotics, Starościńska 5, 02-516 Warsaw, Poland
| | - Piotr Baran
- Bioengineering Department, Institute of Biotechnology and Antibiotics, Starościńska 5, 02-516 Warsaw, Poland
| | - Anna Mazurkiewicz-Pisarek
- Bioengineering Department, Institute of Biotechnology and Antibiotics, Starościńska 5, 02-516 Warsaw, Poland
| | - Andrzej Płucienniczak
- Bioengineering Department, Institute of Biotechnology and Antibiotics, Starościńska 5, 02-516 Warsaw, Poland
| | - Dariusz Bartosik
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Ilji Miecznikowa 1, 02-096 Warsaw, Poland
| |
Collapse
|
5
|
Chen CH, Pan CY, Lin WC. Overlapping protein-coding genes in human genome and their coincidental expression in tissues. Sci Rep 2019; 9:13377. [PMID: 31527706 PMCID: PMC6746723 DOI: 10.1038/s41598-019-49802-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 08/29/2019] [Indexed: 01/23/2023] Open
Abstract
The completion of human genome sequences and the advancement of next-generation sequencing technologies have engendered a clear understanding of all human genes. Overlapping genes are usually observed in compact genomes, such as those of bacteria and viruses. Notably, overlapping protein-coding genes do exist in human genome sequences. Accordingly, we used the current Ensembl gene annotations to identify overlapping human protein-coding genes. We analysed 19,200 well-annotated protein-coding genes and determined that 4,951 protein-coding genes overlapped with their adjacent genes. Approximately a quarter of all human protein-coding genes were overlapping genes. We observed different clusters of overlapping protein-coding genes, ranging from two genes (paired overlapping genes) to 22 genes. We also divided the paired overlapping protein-coding gene groups into four subtypes. We found that the divergent overlapping gene subtype had a stronger expression association than did the subtypes of 5'-tandem overlapping and 3'-tandem overlapping genes. The majority of paired overlapping genes exhibited comparable coincidental tissue expression profiles; however, a few overlapping gene pairs displayed distinctive tissue expression association patterns. In summary, we have carefully examined the genomic features and distributions about human overlapping protein-coding genes and found coincidental expression in tissues for most overlapping protein-coding genes.
Collapse
Affiliation(s)
- Chao-Hsin Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan R.O.C
| | - Chao-Yu Pan
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan R.O.C.,Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan R.O.C
| | - Wen-Chang Lin
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan R.O.C.. .,Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan R.O.C..
| |
Collapse
|