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Olivucci G, Iovino E, Innella G, Turchetti D, Pippucci T, Magini P. Long read sequencing on its way to the routine diagnostics of genetic diseases. Front Genet 2024; 15:1374860. [PMID: 38510277 PMCID: PMC10951082 DOI: 10.3389/fgene.2024.1374860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 02/26/2024] [Indexed: 03/22/2024] Open
Abstract
The clinical application of technological progress in the identification of DNA alterations has always led to improvements of diagnostic yields in genetic medicine. At chromosome side, from cytogenetic techniques evaluating number and gross structural defects to genomic microarrays detecting cryptic copy number variants, and at molecular level, from Sanger method studying the nucleotide sequence of single genes to the high-throughput next-generation sequencing (NGS) technologies, resolution and sensitivity progressively increased expanding considerably the range of detectable DNA anomalies and alongside of Mendelian disorders with known genetic causes. However, particular genomic regions (i.e., repetitive and GC-rich sequences) are inefficiently analyzed by standard genetic tests, still relying on laborious, time-consuming and low-sensitive approaches (i.e., southern-blot for repeat expansion or long-PCR for genes with highly homologous pseudogenes), accounting for at least part of the patients with undiagnosed genetic disorders. Third generation sequencing, generating long reads with improved mappability, is more suitable for the detection of structural alterations and defects in hardly accessible genomic regions. Although recently implemented and not yet clinically available, long read sequencing (LRS) technologies have already shown their potential in genetic medicine research that might greatly impact on diagnostic yield and reporting times, through their translation to clinical settings. The main investigated LRS application concerns the identification of structural variants and repeat expansions, probably because techniques for their detection have not evolved as rapidly as those dedicated to single nucleotide variants (SNV) identification: gold standard analyses are karyotyping and microarrays for balanced and unbalanced chromosome rearrangements, respectively, and southern blot and repeat-primed PCR for the amplification and sizing of expanded alleles, impaired by limited resolution and sensitivity that have not been significantly improved by the advent of NGS. Nevertheless, more recently, with the increased accuracy provided by the latest product releases, LRS has been tested also for SNV detection, especially in genes with highly homologous pseudogenes and for haplotype reconstruction to assess the parental origin of alleles with de novo pathogenic variants. We provide a review of relevant recent scientific papers exploring LRS potential in the diagnosis of genetic diseases and its potential future applications in routine genetic testing.
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Affiliation(s)
- Giulia Olivucci
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
- Department of Surgical and Oncological Sciences, University of Palermo, Palermo, Italy
| | - Emanuela Iovino
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Giovanni Innella
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy
- Medical Genetics Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Daniela Turchetti
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy
- Medical Genetics Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Tommaso Pippucci
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Pamela Magini
- Medical Genetics Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
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Wang R, Helbig I, Edmondson AC, Lin L, Xing Y. Splicing defects in rare diseases: transcriptomics and machine learning strategies towards genetic diagnosis. Brief Bioinform 2023; 24:bbad284. [PMID: 37580177 PMCID: PMC10516351 DOI: 10.1093/bib/bbad284] [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: 03/14/2023] [Revised: 07/10/2023] [Accepted: 07/20/2023] [Indexed: 08/16/2023] Open
Abstract
Genomic variants affecting pre-messenger RNA splicing and its regulation are known to underlie many rare genetic diseases. However, common workflows for genetic diagnosis and clinical variant interpretation frequently overlook splice-altering variants. To better serve patient populations and advance biomedical knowledge, it has become increasingly important to develop and refine approaches for detecting and interpreting pathogenic splicing variants. In this review, we will summarize a few recent developments and challenges in using RNA sequencing technologies for rare disease investigation. Moreover, we will discuss how recent computational splicing prediction tools have emerged as complementary approaches for revealing disease-causing variants underlying splicing defects. We speculate that continuous improvements to sequencing technologies and predictive modeling will not only expand our understanding of splicing regulation but also bring us closer to filling the diagnostic gap for rare disease patients.
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Affiliation(s)
- Robert Wang
- Center for Computational and Genomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Genomics and Computational Biology Graduate Program, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ingo Helbig
- The Epilepsy NeuroGenetics Initiative, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Neurology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Andrew C Edmondson
- Center for Computational and Genomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pediatrics, Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Lan Lin
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Yi Xing
- Center for Computational and Genomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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3
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Zhang Z, Bae B, Cuddleston WH, Miura P. Coordination of alternative splicing and alternative polyadenylation revealed by targeted long read sequencing. Nat Commun 2023; 14:5506. [PMID: 37679364 PMCID: PMC10484994 DOI: 10.1038/s41467-023-41207-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 08/25/2023] [Indexed: 09/09/2023] Open
Abstract
Nervous system development is associated with extensive regulation of alternative splicing (AS) and alternative polyadenylation (APA). AS and APA have been extensively studied in isolation, but little is known about how these processes are coordinated. Here, the coordination of cassette exon (CE) splicing and APA in Drosophila was investigated using a targeted long-read sequencing approach we call Pull-a-Long-Seq (PL-Seq). This cost-effective method uses cDNA pulldown and Nanopore sequencing combined with an analysis pipeline to quantify inclusion of alternative exons in connection with alternative 3' ends. Using PL-Seq, we identified genes that exhibit significant differences in CE splicing depending on connectivity to short versus long 3'UTRs. Genomic long 3'UTR deletion was found to alter upstream CE splicing in short 3'UTR isoforms and ELAV loss differentially affected CE splicing depending on connectivity to alternative 3'UTRs. This work highlights the importance of considering connectivity to alternative 3'UTRs when monitoring AS events.
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Affiliation(s)
- Zhiping Zhang
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington, CT, USA
- Department of Biology, University of Nevada, Reno, Reno, NV, USA
| | - Bongmin Bae
- Department of Biology, University of Nevada, Reno, Reno, NV, USA
| | | | - Pedro Miura
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington, CT, USA.
- Department of Biology, University of Nevada, Reno, Reno, NV, USA.
- Institute for System Genomics, University of Connecticut, Storrs, CT, USA.
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Mastrorosa FK, Miller DE, Eichler EE. Applications of long-read sequencing to Mendelian genetics. Genome Med 2023; 15:42. [PMID: 37316925 DOI: 10.1186/s13073-023-01194-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 05/18/2023] [Indexed: 06/16/2023] Open
Abstract
Advances in clinical genetic testing, including the introduction of exome sequencing, have uncovered the molecular etiology for many rare and previously unsolved genetic disorders, yet more than half of individuals with a suspected genetic disorder remain unsolved after complete clinical evaluation. A precise genetic diagnosis may guide clinical treatment plans, allow families to make informed care decisions, and permit individuals to participate in N-of-1 trials; thus, there is high interest in developing new tools and techniques to increase the solve rate. Long-read sequencing (LRS) is a promising technology for both increasing the solve rate and decreasing the amount of time required to make a precise genetic diagnosis. Here, we summarize current LRS technologies, give examples of how they have been used to evaluate complex genetic variation and identify missing variants, and discuss future clinical applications of LRS. As costs continue to decrease, LRS will find additional utility in the clinical space fundamentally changing how pathological variants are discovered and eventually acting as a single-data source that can be interrogated multiple times for clinical service.
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Affiliation(s)
| | - Danny E Miller
- Division of Genetic Medicine, Department of Pediatrics, University of Washington and Seattle Children's Hospital, Seattle, WA, 98195, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA, 98195, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, 98195, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA.
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Zhang Z, Bae B, Cuddleston WH, Miura P. Coordination of Alternative Splicing and Alternative Polyadenylation revealed by Targeted Long-Read Sequencing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.23.533999. [PMID: 36993601 PMCID: PMC10055423 DOI: 10.1101/2023.03.23.533999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Nervous system development is associated with extensive regulation of alternative splicing (AS) and alternative polyadenylation (APA). AS and APA have been extensively studied in isolation, but little is known about how these processes are coordinated. Here, the coordination of cassette exon (CE) splicing and APA in Drosophila was investigated using a targeted long-read sequencing approach we call Pull-a-Long-Seq (PL-Seq). This cost-effective method uses cDNA pulldown and Nanopore sequencing combined with an analysis pipeline to resolve the connectivity of alternative exons to alternative 3' ends. Using PL-Seq, we identified genes that exhibit significant differences in CE splicing depending on connectivity to short versus long 3'UTRs. Genomic long 3'UTR deletion was found to alter upstream CE splicing in short 3'UTR isoforms and ELAV loss differentially affected CE splicing depending on connectivity to alternative 3'UTRs. This work highlights the importance of considering connectivity to alternative 3'UTRs when monitoring AS events.
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Affiliation(s)
- Zhiping Zhang
- Department of Biology, University of Nevada, Reno, Reno, NV, USA
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT, USA
| | - Bongmin Bae
- Department of Biology, University of Nevada, Reno, Reno, NV, USA
| | | | - Pedro Miura
- Department of Biology, University of Nevada, Reno, Reno, NV, USA
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT, USA
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Application of Long-Read Nanopore Sequencing to the Search for Mutations in Hypertrophic Cardiomyopathy. Int J Mol Sci 2022; 23:ijms232415845. [PMID: 36555486 PMCID: PMC9779642 DOI: 10.3390/ijms232415845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 12/10/2022] [Accepted: 12/10/2022] [Indexed: 12/15/2022] Open
Abstract
Increasing evidence suggests that both coding and non-coding regions of sarcomeric protein genes can contribute to hypertrophic cardiomyopathy (HCM). Here, we introduce an experimental workflow (tested on four patients) for complete sequencing of the most common HCM genes (MYBPC3, MYH7, TPM1, TNNT2, and TNNI3) via long-range PCR, Oxford Nanopore Technology (ONT) sequencing, and bioinformatic analysis. We applied Illumina and Sanger sequencing to validate the results, FastQC, Qualimap, and MultiQC for quality evaluations, MiniMap2 to align data, Clair3 to call and phase variants, and Annovar's tools and CADD to assess pathogenicity of variants. We could not amplify the region encompassing exons 6-12 of MYBPC3. A higher sequencing error rate was observed with ONT (6.86-6.92%) than with Illumina technology (1.14-1.35%), mostly for small indels. Pathogenic variant p.Gln1233Ter and benign polymorphism p.Arg326Gln in MYBPC3 in a heterozygous state were found in one patient. We demonstrated the ability of ONT to phase single-nucleotide variants, enabling direct haplotype determination for genes TNNT2 and TPM1. These findings highlight the importance of long-range PCR efficiency, as well as lower accuracy of variant calling by ONT than by Illumina technology; these differences should be clarified prior to clinical application of the ONT method.
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Marwaha S, Knowles JW, Ashley EA. A guide for the diagnosis of rare and undiagnosed disease: beyond the exome. Genome Med 2022; 14:23. [PMID: 35220969 PMCID: PMC8883622 DOI: 10.1186/s13073-022-01026-w] [Citation(s) in RCA: 83] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 02/10/2022] [Indexed: 02/07/2023] Open
Abstract
AbstractRare diseases affect 30 million people in the USA and more than 300–400 million worldwide, often causing chronic illness, disability, and premature death. Traditional diagnostic techniques rely heavily on heuristic approaches, coupling clinical experience from prior rare disease presentations with the medical literature. A large number of rare disease patients remain undiagnosed for years and many even die without an accurate diagnosis. In recent years, gene panels, microarrays, and exome sequencing have helped to identify the molecular cause of such rare and undiagnosed diseases. These technologies have allowed diagnoses for a sizable proportion (25–35%) of undiagnosed patients, often with actionable findings. However, a large proportion of these patients remain undiagnosed. In this review, we focus on technologies that can be adopted if exome sequencing is unrevealing. We discuss the benefits of sequencing the whole genome and the additional benefit that may be offered by long-read technology, pan-genome reference, transcriptomics, metabolomics, proteomics, and methyl profiling. We highlight computational methods to help identify regionally distant patients with similar phenotypes or similar genetic mutations. Finally, we describe approaches to automate and accelerate genomic analysis. The strategies discussed here are intended to serve as a guide for clinicians and researchers in the next steps when encountering patients with non-diagnostic exomes.
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Schwäbe FV, Peter EK, Taft MH, Manstein DJ. Assessment of the Contribution of a Thermodynamic and Mechanical Destabilization of Myosin-Binding Protein C Domain C2 to the Pathomechanism of Hypertrophic Cardiomyopathy-Causing Double Mutation MYBPC3Δ25bp/D389V. Int J Mol Sci 2021; 22:ijms222111949. [PMID: 34769381 PMCID: PMC8584774 DOI: 10.3390/ijms222111949] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 10/31/2021] [Accepted: 11/02/2021] [Indexed: 01/01/2023] Open
Abstract
Mutations in the gene encoding cardiac myosin-binding protein-C (MyBPC), a thick filament assembly protein that stabilizes sarcomeric structure and regulates cardiac function, are a common cause for the development of hypertrophic cardiomyopathy. About 10% of carriers of the Δ25bp variant of MYBPC3, which is common in individuals from South Asia, are also carriers of the D389V variant on the same allele. Compared with noncarriers and those with MYBPC3Δ25bp alone, indicators for the development of hypertrophic cardiomyopathy occur with increased frequency in MYBPC3Δ25bp/D389V carriers. Residue D389 lies in the IgI-like C2 domain that is part of the N-terminal region of MyBPC. To probe the effects of mutation D389V on structure, thermostability, and protein–protein interactions, we produced and characterized wild-type and mutant constructs corresponding to the isolated 10 kDa C2 domain and a 52 kDa N-terminal fragment that includes subdomains C0 to C2. Our results show marked reductions in the melting temperatures of D389V mutant constructs. Interactions of construct C0–C2 D389V with the cardiac isoforms of myosin-2 and actin remain unchanged. Molecular dynamics simulations reveal changes in the stiffness and conformer dynamics of domain C2 caused by mutation D389V. Our results suggest a pathomechanism for the development of HCM based on the toxic buildup of misfolded protein in young MYBPC3Δ25bp/D389V carriers that is supplanted and enhanced by C-zone haploinsufficiency at older ages.
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Affiliation(s)
- Frederic V. Schwäbe
- Fritz Hartmann Centre for Medical Research, Institute for Biophysical Chemistry, Hannover Medical School, Carl Neuberg Str. 1, D-30625 Hannover, Germany; (F.V.S.); (E.K.P.); (M.H.T.)
| | - Emanuel K. Peter
- Fritz Hartmann Centre for Medical Research, Institute for Biophysical Chemistry, Hannover Medical School, Carl Neuberg Str. 1, D-30625 Hannover, Germany; (F.V.S.); (E.K.P.); (M.H.T.)
| | - Manuel H. Taft
- Fritz Hartmann Centre for Medical Research, Institute for Biophysical Chemistry, Hannover Medical School, Carl Neuberg Str. 1, D-30625 Hannover, Germany; (F.V.S.); (E.K.P.); (M.H.T.)
| | - Dietmar J. Manstein
- Fritz Hartmann Centre for Medical Research, Institute for Biophysical Chemistry, Hannover Medical School, Carl Neuberg Str. 1, D-30625 Hannover, Germany; (F.V.S.); (E.K.P.); (M.H.T.)
- Division for Structural Biochemistry, Hannover Medical School, Carl Neuberg Str. 1, D-30625 Hannover, Germany
- Correspondence:
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Holliday M, Singer ES, Ross SB, Lim S, Lal S, Ingles J, Semsarian C, Bagnall RD. Transcriptome Sequencing of Patients With Hypertrophic Cardiomyopathy Reveals Novel Splice-Altering Variants in MYBPC3. CIRCULATION-GENOMIC AND PRECISION MEDICINE 2021; 14:e003202. [PMID: 33657327 DOI: 10.1161/circgen.120.003202] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
BACKGROUND Transcriptome sequencing can improve genetic diagnosis of Mendelian diseases but requires access to tissue expressing disease-relevant transcripts. We explored genetic testing of hypertrophic cardiomyopathy using transcriptome sequencing of patient-specific human induced pluripotent stem cell derived cardiomyocytes (hiPSC-CMs). We also explored whether antisense oligonucleotides (AOs) could inhibit aberrant mRNA splicing in hiPSC-CMs. METHODS We derived hiPSC-CMs from patients with hypertrophic cardiomyopathy due to MYBPC3 splice-gain variants, or an unresolved genetic cause. We used transcriptome sequencing of hiPSC-CM RNA to identify pathogenic splicing and used AOs to inhibit this splicing. RESULTS Transcriptome sequencing of hiPSC-CMs confirmed aberrant splicing in 2 people with previously identified MYBPC3 splice-gain variants (c.1090+453C>T and c.1224-52G>A). In a patient with an unresolved genetic cause of hypertrophic cardiomyopathy following genome sequencing, transcriptome sequencing of hiPSC-CMs revealed diverse cryptic exon splicing due to an MYBPC3 c.1928-569G>T variant, and this was confirmed in cardiac tissue from an affected sibling. Antisense oligonucleotide treatment demonstrated almost complete inhibition of cryptic exon splicing in one patient-specific hiPSC-CM line. CONCLUSIONS Transcriptome sequencing of patient specific hiPSC-CMs solved a previously undiagnosed genetic cause of hypertrophic cardiomyopathy and may be a useful adjunct approach to genetic testing. Antisense oligonucleotide inhibition of cryptic exon splicing is a potential future personalized therapeutic option.
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Affiliation(s)
- Mira Holliday
- Agnes Ginges Centre for Molecular Cardiology at Centenary Institute (M.H., E.S.S., S.B.R., S.L., J.I., C.S., R.D.B.), The University of Sydney
- Faculty of Medicine and Health (M.H., E.S.S., S.B.R., S.L., J.I., C.S., R.D.B.), The University of Sydney
| | - Emma S Singer
- Agnes Ginges Centre for Molecular Cardiology at Centenary Institute (M.H., E.S.S., S.B.R., S.L., J.I., C.S., R.D.B.), The University of Sydney
- Faculty of Medicine and Health (M.H., E.S.S., S.B.R., S.L., J.I., C.S., R.D.B.), The University of Sydney
| | - Samantha B Ross
- Agnes Ginges Centre for Molecular Cardiology at Centenary Institute (M.H., E.S.S., S.B.R., S.L., J.I., C.S., R.D.B.), The University of Sydney
- Faculty of Medicine and Health (M.H., E.S.S., S.B.R., S.L., J.I., C.S., R.D.B.), The University of Sydney
| | - Seakcheng Lim
- Agnes Ginges Centre for Molecular Cardiology at Centenary Institute (M.H., E.S.S., S.B.R., S.L., J.I., C.S., R.D.B.), The University of Sydney
| | - Sean Lal
- Faculty of Medicine and Health (M.H., E.S.S., S.B.R., S.L., J.I., C.S., R.D.B.), The University of Sydney
| | - Jodie Ingles
- Agnes Ginges Centre for Molecular Cardiology at Centenary Institute (M.H., E.S.S., S.B.R., S.L., J.I., C.S., R.D.B.), The University of Sydney
- Faculty of Medicine and Health (M.H., E.S.S., S.B.R., S.L., J.I., C.S., R.D.B.), The University of Sydney
- Department of Cardiology, Royal Prince Alfred Hospital, Sydney, NSW, Australia (J.I., C.S.)
| | - Christopher Semsarian
- Agnes Ginges Centre for Molecular Cardiology at Centenary Institute (M.H., E.S.S., S.B.R., S.L., J.I., C.S., R.D.B.), The University of Sydney
- Faculty of Medicine and Health (M.H., E.S.S., S.B.R., S.L., J.I., C.S., R.D.B.), The University of Sydney
- Department of Cardiology, Royal Prince Alfred Hospital, Sydney, NSW, Australia (J.I., C.S.)
| | - Richard D Bagnall
- Agnes Ginges Centre for Molecular Cardiology at Centenary Institute (M.H., E.S.S., S.B.R., S.L., J.I., C.S., R.D.B.), The University of Sydney
- Faculty of Medicine and Health (M.H., E.S.S., S.B.R., S.L., J.I., C.S., R.D.B.), The University of Sydney
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Zhou SY, Dong QL, Zhu KS, Gao L, Chen X, Xiang H. Long-read transcriptomic analysis of orb-weaving spider Araneus ventricosus indicates transcriptional diversity of spidroins. Int J Biol Macromol 2020; 168:395-402. [PMID: 33275979 DOI: 10.1016/j.ijbiomac.2020.11.182] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 08/31/2020] [Accepted: 11/26/2020] [Indexed: 12/01/2022]
Abstract
Spider silk, which is composed of diverse silk proteins (spidroin), is a kind of natural high-mass biomaterial with great potential. However, due to the complexity of both the structure and the composition of the spidroins in natural spider silk, application of this valuable biomass is still limited to date. There are diverse kinds of spider silk in the orb-weaving spider with different mechanical and structural characteristics. In order to systematically illustrate the landscape of all the different spidrons, here we chose Araneus ventricosus, an orb-weaving spider with superior silk mechanical features and genome information, to generate a long-read whole body transcriptome. We deciphered the repeat arrangements of each kind of spidroin, based on which we found that there are substantially transcriptional diversity of each spidroin gene. Some repeat motifs are not documented before. Specifically, we discovered novel full-lengh MaSp transcript as well as a relatively small full-length AcSp isoforms, which are potential promising materials for bioengineering of recombinant spidroin. Our study provided a batch of new spidron resources with detail sequential information. The finding of transcriptional diversity may provide cues in understanding of within-species variation of the mechanical properties of the natural spider silk and further molecular designing of recombinant spidroin.
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Affiliation(s)
- Shi-Yi Zhou
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Qing-Lin Dong
- State Key Laboratory of Molecular Engineering of Polymers, Laboratory of Advanced Materials and Department of Macromolecular Science, Fudan University, Shanghai 200433, China
| | - Ke-Sen Zhu
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Lei Gao
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China.
| | - Xin Chen
- State Key Laboratory of Molecular Engineering of Polymers, Laboratory of Advanced Materials and Department of Macromolecular Science, Fudan University, Shanghai 200433, China.
| | - Hui Xiang
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China.
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