A universal molecular control for DNA, mRNA and protein expression
Abstract The expression of genes encompasses their transcription into mRNA followed by translation into protein. In recent years, next-generation sequencing and mass spectrometry methods have profiled DNA, RNA and protein abundance in cells. However, there are currently no reference standards that a...
| Main Authors: | , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2024-03-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-024-46456-9 |
| _version_ | 1797247214327693312 |
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| author | Helen M. Gunter Scott E. Youlten Andre L. M. Reis Tim McCubbin Bindu Swapna Madala Ted Wong Igor Stevanovski Arcadi Cipponi Ira W. Deveson Nadia S. Santini Sarah Kummerfeld Peter I. Croucher Esteban Marcellin Tim R. Mercer |
| author_facet | Helen M. Gunter Scott E. Youlten Andre L. M. Reis Tim McCubbin Bindu Swapna Madala Ted Wong Igor Stevanovski Arcadi Cipponi Ira W. Deveson Nadia S. Santini Sarah Kummerfeld Peter I. Croucher Esteban Marcellin Tim R. Mercer |
| author_sort | Helen M. Gunter |
| collection | DOAJ |
| description | Abstract The expression of genes encompasses their transcription into mRNA followed by translation into protein. In recent years, next-generation sequencing and mass spectrometry methods have profiled DNA, RNA and protein abundance in cells. However, there are currently no reference standards that are compatible across these genomic, transcriptomic and proteomic methods, and provide an integrated measure of gene expression. Here, we use synthetic biology principles to engineer a multi-omics control, termed pREF, that can act as a universal molecular standard for next-generation sequencing and mass spectrometry methods. The pREF sequence encodes 21 synthetic genes that can be in vitro transcribed into spike-in mRNA controls, and in vitro translated to generate matched protein controls. The synthetic genes provide qualitative controls that can measure sensitivity and quantitative accuracy of DNA, RNA and peptide detection. We demonstrate the use of pREF in metagenome DNA sequencing and RNA sequencing experiments and evaluate the quantification of proteins using mass spectrometry. Unlike previous spike-in controls, pREF can be independently propagated and the synthetic mRNA and protein controls can be sustainably prepared by recipient laboratories using common molecular biology techniques. Together, this provides a universal synthetic standard able to integrate genomic, transcriptomic and proteomic methods. |
| first_indexed | 2024-04-24T19:55:08Z |
| format | Article |
| id | doaj.art-9596d107d6324684931ffa09eb32bdd9 |
| institution | Directory Open Access Journal |
| issn | 2041-1723 |
| language | English |
| last_indexed | 2024-04-24T19:55:08Z |
| publishDate | 2024-03-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj.art-9596d107d6324684931ffa09eb32bdd92024-03-24T12:25:36ZengNature PortfolioNature Communications2041-17232024-03-0115111310.1038/s41467-024-46456-9A universal molecular control for DNA, mRNA and protein expressionHelen M. Gunter0Scott E. Youlten1Andre L. M. Reis2Tim McCubbin3Bindu Swapna Madala4Ted Wong5Igor Stevanovski6Arcadi Cipponi7Ira W. Deveson8Nadia S. Santini9Sarah Kummerfeld10Peter I. Croucher11Esteban Marcellin12Tim R. Mercer13Australian Institute of Bioengineering and Nanotechnology, The University of QueenslandDepartment of Genetics, Yale University School of MedicineGenomics and Inherited Disease Program, Garvan Institute of Medical ResearchAustralian Institute of Bioengineering and Nanotechnology, The University of QueenslandGarvan Institute of Medical ResearchGarvan Institute of Medical ResearchGenomics and Inherited Disease Program, Garvan Institute of Medical ResearchGarvan Institute of Medical ResearchGenomics and Inherited Disease Program, Garvan Institute of Medical ResearchCentro Nacional de Investigación Disciplinaria en Conservación y Mejoramiento de Ecosistemas Forestales, INIFAPGarvan Institute of Medical ResearchGarvan Institute of Medical ResearchAustralian Institute of Bioengineering and Nanotechnology, The University of QueenslandAustralian Institute of Bioengineering and Nanotechnology, The University of QueenslandAbstract The expression of genes encompasses their transcription into mRNA followed by translation into protein. In recent years, next-generation sequencing and mass spectrometry methods have profiled DNA, RNA and protein abundance in cells. However, there are currently no reference standards that are compatible across these genomic, transcriptomic and proteomic methods, and provide an integrated measure of gene expression. Here, we use synthetic biology principles to engineer a multi-omics control, termed pREF, that can act as a universal molecular standard for next-generation sequencing and mass spectrometry methods. The pREF sequence encodes 21 synthetic genes that can be in vitro transcribed into spike-in mRNA controls, and in vitro translated to generate matched protein controls. The synthetic genes provide qualitative controls that can measure sensitivity and quantitative accuracy of DNA, RNA and peptide detection. We demonstrate the use of pREF in metagenome DNA sequencing and RNA sequencing experiments and evaluate the quantification of proteins using mass spectrometry. Unlike previous spike-in controls, pREF can be independently propagated and the synthetic mRNA and protein controls can be sustainably prepared by recipient laboratories using common molecular biology techniques. Together, this provides a universal synthetic standard able to integrate genomic, transcriptomic and proteomic methods.https://doi.org/10.1038/s41467-024-46456-9 |
| spellingShingle | Helen M. Gunter Scott E. Youlten Andre L. M. Reis Tim McCubbin Bindu Swapna Madala Ted Wong Igor Stevanovski Arcadi Cipponi Ira W. Deveson Nadia S. Santini Sarah Kummerfeld Peter I. Croucher Esteban Marcellin Tim R. Mercer A universal molecular control for DNA, mRNA and protein expression Nature Communications |
| title | A universal molecular control for DNA, mRNA and protein expression |
| title_full | A universal molecular control for DNA, mRNA and protein expression |
| title_fullStr | A universal molecular control for DNA, mRNA and protein expression |
| title_full_unstemmed | A universal molecular control for DNA, mRNA and protein expression |
| title_short | A universal molecular control for DNA, mRNA and protein expression |
| title_sort | universal molecular control for dna mrna and protein expression |
| url | https://doi.org/10.1038/s41467-024-46456-9 |
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