Massively Parallel Reporter Assays for High-Throughput In Vivo Analysis of Cis-Regulatory Elements
The rapid improvement of descriptive genomic technologies has fueled a dramatic increase in hypothesized connections between cardiovascular gene expression and phenotypes. However, in vivo testing of these hypotheses has predominantly been relegated to slow, expensive, and linear generation of genet...
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| Format: | Article |
| Language: | English |
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MDPI AG
2023-03-01
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| Series: | Journal of Cardiovascular Development and Disease |
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| Online Access: | https://www.mdpi.com/2308-3425/10/4/144 |
| _version_ | 1797604946115297280 |
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| author | Yanjiang Zheng Nathan J. VanDusen |
| author_facet | Yanjiang Zheng Nathan J. VanDusen |
| author_sort | Yanjiang Zheng |
| collection | DOAJ |
| description | The rapid improvement of descriptive genomic technologies has fueled a dramatic increase in hypothesized connections between cardiovascular gene expression and phenotypes. However, in vivo testing of these hypotheses has predominantly been relegated to slow, expensive, and linear generation of genetically modified mice. In the study of genomic <i>cis</i>-regulatory elements, generation of mice featuring transgenic reporters or <i>cis</i>-regulatory element knockout remains the standard approach. While the data obtained is of high quality, the approach is insufficient to keep pace with candidate identification and therefore results in biases introduced during the selection of candidates for validation. However, recent advances across a range of disciplines are converging to enable functional genomic assays that can be conducted in a high-throughput manner. Here, we review one such method, massively parallel reporter assays (MPRAs), in which the activities of thousands of candidate genomic regulatory elements are simultaneously assessed via the next-generation sequencing of a barcoded reporter transcript. We discuss best practices for MPRA design and use, with a focus on practical considerations, and review how this emerging technology has been successfully deployed in vivo. Finally, we discuss how MPRAs are likely to evolve and be used in future cardiovascular research. |
| first_indexed | 2024-03-11T04:54:03Z |
| format | Article |
| id | doaj.art-6c797dbd123244c0bfc7fcd3649b81c1 |
| institution | Directory Open Access Journal |
| issn | 2308-3425 |
| language | English |
| last_indexed | 2024-03-11T04:54:03Z |
| publishDate | 2023-03-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Journal of Cardiovascular Development and Disease |
| spelling | doaj.art-6c797dbd123244c0bfc7fcd3649b81c12023-11-17T19:47:26ZengMDPI AGJournal of Cardiovascular Development and Disease2308-34252023-03-0110414410.3390/jcdd10040144Massively Parallel Reporter Assays for High-Throughput In Vivo Analysis of Cis-Regulatory ElementsYanjiang Zheng0Nathan J. VanDusen1Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu 610041, ChinaDepartment of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USAThe rapid improvement of descriptive genomic technologies has fueled a dramatic increase in hypothesized connections between cardiovascular gene expression and phenotypes. However, in vivo testing of these hypotheses has predominantly been relegated to slow, expensive, and linear generation of genetically modified mice. In the study of genomic <i>cis</i>-regulatory elements, generation of mice featuring transgenic reporters or <i>cis</i>-regulatory element knockout remains the standard approach. While the data obtained is of high quality, the approach is insufficient to keep pace with candidate identification and therefore results in biases introduced during the selection of candidates for validation. However, recent advances across a range of disciplines are converging to enable functional genomic assays that can be conducted in a high-throughput manner. Here, we review one such method, massively parallel reporter assays (MPRAs), in which the activities of thousands of candidate genomic regulatory elements are simultaneously assessed via the next-generation sequencing of a barcoded reporter transcript. We discuss best practices for MPRA design and use, with a focus on practical considerations, and review how this emerging technology has been successfully deployed in vivo. Finally, we discuss how MPRAs are likely to evolve and be used in future cardiovascular research.https://www.mdpi.com/2308-3425/10/4/144MPRAtranscriptional regulationfunctional genomicscardiovasculardevelopment |
| spellingShingle | Yanjiang Zheng Nathan J. VanDusen Massively Parallel Reporter Assays for High-Throughput In Vivo Analysis of Cis-Regulatory Elements Journal of Cardiovascular Development and Disease MPRA transcriptional regulation functional genomics cardiovascular development |
| title | Massively Parallel Reporter Assays for High-Throughput In Vivo Analysis of Cis-Regulatory Elements |
| title_full | Massively Parallel Reporter Assays for High-Throughput In Vivo Analysis of Cis-Regulatory Elements |
| title_fullStr | Massively Parallel Reporter Assays for High-Throughput In Vivo Analysis of Cis-Regulatory Elements |
| title_full_unstemmed | Massively Parallel Reporter Assays for High-Throughput In Vivo Analysis of Cis-Regulatory Elements |
| title_short | Massively Parallel Reporter Assays for High-Throughput In Vivo Analysis of Cis-Regulatory Elements |
| title_sort | massively parallel reporter assays for high throughput in vivo analysis of cis regulatory elements |
| topic | MPRA transcriptional regulation functional genomics cardiovascular development |
| url | https://www.mdpi.com/2308-3425/10/4/144 |
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