1
|
Mohanan NK, Shaji F, Koshre GR, Laishram RS. Alternative polyadenylation: An enigma of transcript length variation in health and disease. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 13:e1692. [PMID: 34581021 DOI: 10.1002/wrna.1692] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 06/16/2021] [Accepted: 08/24/2021] [Indexed: 12/19/2022]
Abstract
Alternative polyadenylation (APA) is a molecular mechanism during a pre-mRNA processing that involves usage of more than one polyadenylation site (PA-site) generating transcripts of varying length from a single gene. The location of a PA-site affects transcript length and coding potential of an mRNA contributing to both mRNA and protein diversification. This variation in the transcript length affects mRNA stability and translation, mRNA subcellular and tissue localization, and protein function. APA is now considered as an important regulatory mechanism in the pathophysiology of human diseases. An important consequence of the changes in the length of 3'-untranslated region (UTR) from disease-induced APA is altered protein expression. Yet, the relationship between 3'-UTR length and protein expression remains a paradox in a majority of diseases. Here, we review occurrence of APA, mechanism of PA-site selection, and consequences of transcript length variation in different diseases. Emerging evidence reveals coordinated involvement of core RNA processing factors including poly(A) polymerases in the PA-site selection in diseases-associated APAs. Targeting such APA regulators will be therapeutically significant in combating drug resistance in cancer and other complex diseases. This article is categorized under: RNA Processing > 3' End Processing RNA in Disease and Development > RNA in Disease Translation > Regulation.
Collapse
Affiliation(s)
- Neeraja K Mohanan
- Cardiovascular and Diabetes Biology Group, Rajiv Gandhi Centre for Biotechnology, Trivandrum, India
- Manipal Academy of Higher Education, Manipal, India
| | - Feba Shaji
- Cardiovascular and Diabetes Biology Group, Rajiv Gandhi Centre for Biotechnology, Trivandrum, India
- Regional Centre for Biotechnology, Faridabad, India
| | - Ganesh R Koshre
- Cardiovascular and Diabetes Biology Group, Rajiv Gandhi Centre for Biotechnology, Trivandrum, India
- Manipal Academy of Higher Education, Manipal, India
| | - Rakesh S Laishram
- Cardiovascular and Diabetes Biology Group, Rajiv Gandhi Centre for Biotechnology, Trivandrum, India
| |
Collapse
|
2
|
Behlmann AM, Goyal NA, Yang X, Chen PH, Ankala A. A Hemizygous Deletion Within the PGK1 Gene in Males with PGK1 Deficiency. JIMD Rep 2018; 45:105-110. [PMID: 30570712 PMCID: PMC6336546 DOI: 10.1007/8904_2018_147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 08/24/2018] [Accepted: 09/25/2018] [Indexed: 02/05/2023] Open
Abstract
Phosphoglycerate kinase-1 (PGK1) deficiency is a rare X-linked disorder caused by pathogenic variants in the PGK1 gene. Complete loss-of-function variants have not been reported in this gene, indicating that residual enzyme function is critical for viability in males. Therefore, copy number variants (CNVs) that include single exon or multiple exon deletions or duplications are generally not expected in individuals with PGK1 deficiency. Here we describe a 64-year-old male presenting with a family history (three additional affected males) and a personal history of childhood-onset metabolic myopathy that involves episodes of muscle pain, stiffness after activity, exercise intolerance, and myoglobinuria after exertion. Biochemical analysis on a muscle biopsy indicated significantly reduced activity (15% compared to normal) for phosphoglycerate kinase (PGK1), a glycolytic enzyme encoded by PGK1. A diagnosis of PGK1 deficiency was established by molecular analysis which detected an approximately 886 kb deletion involving the polyadenylation site in the 3'UTR of the PGK1 gene. RNA analysis showed significantly reduced PGK1 transcript levels (30% compared to normal). This is the first deletion reported in the PGK1 gene and is the first pathogenic variant involving the 3'UTR polyadenylation site of this gene. Our report emphasizes the role of 3'UTR variants in human disorders and underscores the need for exploring noncoding regions of disease-associated genes when seeking a molecular diagnosis.
Collapse
Affiliation(s)
- Andrea Medrano Behlmann
- grid.189967.80000 0001 0941 6502Department of Human Genetics, Emory University School of Medicine, Atlanta, GA USA
| | - Namita A. Goyal
- grid.266093.80000 0001 0668 7243Department of Neurology, University of California, Irvine, CA USA
| | - Xiaoyu Yang
- grid.189967.80000 0001 0941 6502Department of Cell Biology, Emory University School of Medicine, Atlanta, GA USA
| | - Ping H. Chen
- grid.189967.80000 0001 0941 6502Department of Cell Biology, Emory University School of Medicine, Atlanta, GA USA
| | - Arunkanth Ankala
- grid.189967.80000 0001 0941 6502Department of Human Genetics, Emory University School of Medicine, Atlanta, GA USA ,EGL Genetic Diagnostics LLC, Tucker, GA USA
| |
Collapse
|
3
|
Surapolchai P, Sirachainan N, So CC, Hongeng S, Pakakasama S, Anurathapan U, Chuansumrit A. Curative Stem Cell Transplantation for Severe Hb H Disease Manifesting From Early Infancy: Phenotypic and Genotypic Analyses. Hemoglobin 2015; 40:70-3. [PMID: 26575104 DOI: 10.3109/03630269.2015.1105815] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Most people with Hb H disease live normal lives; however, a minority of cases requires lifelong regular transfusions. An atypical form of nondeletional Hb H disease was reported in a Thai boy, characterized by severe persistent hemolytic anemia since the age of 2 months. Molecular diagnosis revealed the apparent compound heterozygosity for the Southeast Asian (- -(SEA)) and α2 polyadenylation (polyA) signal (AATAAA>AATA- -) deletions. The proband was successfully treated with allogeneic hematopoietic stem cell transplantation (HSCT). Accurate phenotypic and genotypic diagnosis in atypically severe Hb H disease is helpful for the understanding of its pathophysiology, the institution of appropriate management, and provision of genetic counseling and prenatal diagnosis. Hematopoietic stem cell transplantation is a potentially curative treatment option for this severe α-thalassemia (α-thal) syndrome.
Collapse
Affiliation(s)
- Pacharapan Surapolchai
- a Department of Pediatrics , Faculty of Medicine, Thammasat University , Pathumthani , Thailand
| | - Nongnuch Sirachainan
- b Department of Pediatrics , Faculty of Medicine, Ramathibodi Hospital, Mahidol University , Bangkok , Thailand
| | - Chi-Chiu So
- c Department of Pathology , Li Ka Shing Faculty of Medicine, Queen Mary Hospital, The University of Hong Kong , Hong Kong SAR , People's Republic of China
| | - Suradej Hongeng
- b Department of Pediatrics , Faculty of Medicine, Ramathibodi Hospital, Mahidol University , Bangkok , Thailand
| | - Samart Pakakasama
- b Department of Pediatrics , Faculty of Medicine, Ramathibodi Hospital, Mahidol University , Bangkok , Thailand
| | - Usanarat Anurathapan
- b Department of Pediatrics , Faculty of Medicine, Ramathibodi Hospital, Mahidol University , Bangkok , Thailand
| | - Ampaiwan Chuansumrit
- b Department of Pediatrics , Faculty of Medicine, Ramathibodi Hospital, Mahidol University , Bangkok , Thailand
| |
Collapse
|
4
|
Deshpande P, Kamalanathan N, Sampath E, George B, Shaji RV, Edison ES. Characterization of Clinical and Laboratory Profiles of the Deletional α2-Globin Gene Polyadenylation Signal Sequence (AATAAA > AATA- -) in an Indian Population. Hemoglobin 2015; 39:415-8. [PMID: 26365411 DOI: 10.3109/03630269.2015.1079785] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
α-Thalassemia (α-thal) is characterized by large deletions involving the variable regions of α2 and/or α1 genes. Nondeletional mutations and polyadenylation (polyA) signal sequence motif mutations are less common. In this retrospective study, we describe a fragment length analysis-based polymerase chain reaction (PCR) assay for screening the T(Indian) (AATAAA > AATA- -; HBA2: c.*93_*94delAA) polyA signal deletion along with its clinical and laboratory presentation in 21 patients. Most of the patients were diagnosed in early adulthood with a clinical presentation ranging from asymptomatic in the heterozygous state to severe Hb H disease with a prominent hemolytic component in the homozygous state. On genetic analysis, 14 patients were found to be homozygotes, five were compound heterozygotes and two were heterozygotes. Thus, the T(Indian) polyA signal deletion is common in the Indian population and should be screened for in patients with nondeletional α-thal mutations.
Collapse
Affiliation(s)
- Prashant Deshpande
- a Department of Haematology , Christian Medical College , Vellore , Tamil Nadu , India
| | | | - Eswari Sampath
- a Department of Haematology , Christian Medical College , Vellore , Tamil Nadu , India
| | - Biju George
- a Department of Haematology , Christian Medical College , Vellore , Tamil Nadu , India
| | - Ramachandran V Shaji
- a Department of Haematology , Christian Medical College , Vellore , Tamil Nadu , India
| | - Eunice S Edison
- a Department of Haematology , Christian Medical College , Vellore , Tamil Nadu , India
| |
Collapse
|
5
|
Londin ER, Adijanto J, Philp N, Novelli A, Vitale E, Perria C, Serra G, Alesi V, Surrey S, Fortina P. Donor splice-site mutation in CUL4B is likely cause of X-linked intellectual disability. Am J Med Genet A 2014; 164A:2294-9. [PMID: 24898194 DOI: 10.1002/ajmg.a.36629] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Accepted: 05/14/2014] [Indexed: 12/21/2022]
Abstract
X-linked intellectual disability is the most common form of cognitive disability in males. Syndromic intellectual disability encompasses cognitive deficits with other medical and behavioral manifestations. Recently, a large family with a novel form of syndromic X-linked intellectual disability was characterized. Eight of 24 members of the family are male and had cognitive dysfunction, short stature, aphasia, skeletal abnormalities, and minor anomalies. To identify the causative gene(s), we performed exome sequencing in three affected boys, both parents, and an unaffected sister. We identified a haplotype consisting of eight variants located in cis within the linkage region that segregated with affected members in the family. Of these variants, two were novel. The first was at the splice-donor site of intron 7 (c.974+1G>T) in the cullin-RING ubiquitin ligase (E3) gene, CUL4B. This variant is predicted to result in failure to splice and remove intron 7 from the primary transcript. The second variant mapped to the 3'-UTR region of the KAISO gene (c.1127T>G). Sanger sequencing validated the variants in these relatives as well as in three affected males and five carriers. The KAISO gene variant was predicted to create a binding site for the microRNAs miR-4999 and miR-4774; however, luciferase expression assays failed to validate increased targeting of these miRNAs to the variant 3'-UTR. This SNP may affect 3'-UTR structure leading to decreased mRNA stability. Our results suggest that the intellectual disability phenotype in this family is caused by aberrant splicing and removal of intron 7 from CUL4B gene primary transcript.
Collapse
Affiliation(s)
- Eric R Londin
- Computational Medicine Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | | | | | | | | | | | | | | | | | | |
Collapse
|
6
|
Bowman M, Oldridge M, Archer C, O'Rourke A, McParland J, Brekelmans R, Seller A, Lester T. Gross deletions in TCOF1 are a cause of Treacher-Collins-Franceschetti syndrome. Eur J Hum Genet 2012; 20:769-77. [PMID: 22317976 DOI: 10.1038/ejhg.2012.2] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Treacher-Collins-Franceschetti syndrome (TCS) is an autosomal dominant craniofacial disorder characterised by midface hypoplasia, micrognathia, downslanting palpebral fissures, eyelid colobomata, and ear deformities that often lead to conductive deafness. A total of 182 patients with signs consistent with a diagnosis of TCS were screened by DNA sequence and dosage analysis of the TCOF1 gene. In all, 92 cases were found to have a pathogenic mutation by sequencing and 5 to have a partial gene deletion. A further case had a novel in-frame deletion in the alternatively spliced exon 6A of uncertain pathogenicity. The majority of the pathogenic sequence changes were found to predict premature protein termination, however, four novel missense changes in the LIS1 homology motif at the 5' end of the gene were identified. The partial gene deletions of different sizes represent ~5.2% of all the pathogenic TCOF1 mutations identified, indicating that gene rearrangements account for a significant proportion of TCS cases. This is the first report of gene rearrangements resulting in TCS. These findings expand the TCOF1 mutation spectrum indicating that dosage analysis should be performed together with sequence analysis, a strategy that is predicted to have a sensitivity of 71% for patients in whom TCS is strongly suspected.
Collapse
Affiliation(s)
- Michael Bowman
- Clinical Molecular Genetics Laboratory, Churchill Hospital, Oxford, UK
| | | | | | | | | | | | | | | |
Collapse
|
7
|
Hellani A, Fadel E, El-Sadadi S, El-Sweilam H, El-Dawood A, Abu-Amero KK. Molecular spectrum of alpha-thalassemia mutations in microcytic hypochromic anemia patients from Saudi Arabia. Genet Test Mol Biomarkers 2009; 13:219-21. [PMID: 19371220 DOI: 10.1089/gtmb.2008.0123] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
AIM To describe the molecular spectrum of alpha-thalassemia molecular defects in a population sample of Saudi Arabian patients from the eastern province. METHODS DNA was extracted from 41 patients suffering from microcytic, hypochromic anemia. We screened the alpha-globin gene for deletional and nondeletional mutations. RESULTS Besides the common Rightward alpha(-3.7) (64%), polyA mutation (AATAAA to AATAAG) was found (41%). The risk of developing hemoglobin H (HBH) disease in case of homozygous polyA inheritance highlights the importance of detecting such mutation. CONCLUSION The high prevalence of polyA mutation and the lack of any clue in discerning such alpha-thalassemia defect by routine complete blood count (CBC) necessitate a strict molecular screening of all cases presenting with hypochromic microcytic anemia.
Collapse
Affiliation(s)
- Ali Hellani
- PGD Laboratory and Hematology Department, Saad Specialist Hospital, Al-Khobar, Saudi Arabia
| | | | | | | | | | | |
Collapse
|
8
|
Bhattacharya G, Sarkar AA, Banerjee D, Chandra S, Das M, Dasgupta UB. Polymerase Chain Reaction-Based Search for Two α-Globin Gene Mutations in India. Hemoglobin 2009; 32:485-90. [DOI: 10.1080/03630260802341620] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
9
|
Abstract
Protein synthesis is often regulated at the level of initiation of translation, making it a critical step. This regulation occurs by both the cis-regulatory elements, which are located in the 5'- and 3'-UTRs (untranslated regions), and trans-acting factors. A breakdown in this regulation machinery can perturb cellular metabolism, leading to various physiological abnormalities. The highly structured UTRs, along with features such as GC-richness, upstream open reading frames and internal ribosome entry sites, significantly influence the rate of translation of mRNAs. In this review, we discuss how changes in the cis-regulatory sequences of the UTRs, for example, point mutations and truncations, influence expression of specific genes at the level of translation. Such modifications may tilt the physiological balance from healthy to diseased states, resulting in conditions such as hereditary thrombocythaemia, breast cancer, fragile X syndrome, bipolar affective disorder and Alzheimer's disease. This information tends to establish the crucial role of UTRs, perhaps as much as that of coding sequences, in health and disease.
Collapse
|