Methods of massive parallel reporter assays for investigation of enhancers
The correct deployment of genetic programs for development and differentiation relies on finely coordinated regulation of specific gene sets. Genomic regulatory elements play an exceptional role in this process. There are few types of gene regulatory elements, including promoters, enhancers, insulat...
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Siberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and Breeders
2021-06-01
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| Series: | Вавиловский журнал генетики и селекции |
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| Online Access: | https://vavilov.elpub.ru/jour/article/view/3018 |
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| author | S. E. Romanov D. A. Kalashnikova P. P. Laktionov |
| author_facet | S. E. Romanov D. A. Kalashnikova P. P. Laktionov |
| author_sort | S. E. Romanov |
| collection | DOAJ |
| description | The correct deployment of genetic programs for development and differentiation relies on finely coordinated regulation of specific gene sets. Genomic regulatory elements play an exceptional role in this process. There are few types of gene regulatory elements, including promoters, enhancers, insulators and silencers. Alterations of gene regulatory elements may cause various pathologies, including cancer, congenital disorders and autoimmune diseases. The development of high-throughput genomic assays has made it possible to significantly accelerate the accumulation of information about the characteristic epigenetic properties of regulatory elements. In combination with high-throughput studies focused on the genome-wide distribution of epigenetic marks, regulatory proteins and the spatial structure of chromatin, this significantly expands the understanding of the principles of epigenetic regulation of genes and allows potential regulatory elements to be searched for in silico. However, common experimental approaches used to study the local characteristics of chromatin have a number of technical limitations that may reduce the reliability of computational identification of genomic regulatory sequences. Taking into account the variability of the functions of epigenetic determinants and complex multicomponent regulation of genomic elements activity, their functional verification is often required. A plethora of methods have been developed to study the functional role of regulatory elements on the genome scale. Common experimental approaches for in silico identification of regulatory elements and their inherent technical limitations will be described. The present review is focused on original high-throughput methods of enhancer activity reporter analysis that are currently used to validate predicted regulatory elements and to perform de novo searches. The methods described allow assessing the functional role of the nucleotide sequence of a regulatory element, to determine its exact boundaries and to assess the influence of the local state of chromatin on the activity of enhancers and gene expression. These approaches have contributed substantially to the understanding of the fundamental principles of gene regulation. |
| format | Article |
| id | doaj-art-013c0d6e95c24ef2b880031a3933f469 |
| institution | Kabale University |
| issn | 2500-3259 |
| language | English |
| publishDate | 2021-06-01 |
| publisher | Siberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and Breeders |
| record_format | Article |
| series | Вавиловский журнал генетики и селекции |
| spelling | doaj-art-013c0d6e95c24ef2b880031a3933f4692025-02-01T09:58:10ZengSiberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and BreedersВавиловский журнал генетики и селекции2500-32592021-06-0125334435510.18699/VJ21.0381165Methods of massive parallel reporter assays for investigation of enhancersS. E. Romanov0D. A. Kalashnikova1P. P. Laktionov2Novosibirsk State University; Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of SciencesNovosibirsk State University; Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of SciencesNovosibirsk State University; Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of SciencesThe correct deployment of genetic programs for development and differentiation relies on finely coordinated regulation of specific gene sets. Genomic regulatory elements play an exceptional role in this process. There are few types of gene regulatory elements, including promoters, enhancers, insulators and silencers. Alterations of gene regulatory elements may cause various pathologies, including cancer, congenital disorders and autoimmune diseases. The development of high-throughput genomic assays has made it possible to significantly accelerate the accumulation of information about the characteristic epigenetic properties of regulatory elements. In combination with high-throughput studies focused on the genome-wide distribution of epigenetic marks, regulatory proteins and the spatial structure of chromatin, this significantly expands the understanding of the principles of epigenetic regulation of genes and allows potential regulatory elements to be searched for in silico. However, common experimental approaches used to study the local characteristics of chromatin have a number of technical limitations that may reduce the reliability of computational identification of genomic regulatory sequences. Taking into account the variability of the functions of epigenetic determinants and complex multicomponent regulation of genomic elements activity, their functional verification is often required. A plethora of methods have been developed to study the functional role of regulatory elements on the genome scale. Common experimental approaches for in silico identification of regulatory elements and their inherent technical limitations will be described. The present review is focused on original high-throughput methods of enhancer activity reporter analysis that are currently used to validate predicted regulatory elements and to perform de novo searches. The methods described allow assessing the functional role of the nucleotide sequence of a regulatory element, to determine its exact boundaries and to assess the influence of the local state of chromatin on the activity of enhancers and gene expression. These approaches have contributed substantially to the understanding of the fundamental principles of gene regulation.https://vavilov.elpub.ru/jour/article/view/3018gene regulatory elementsenhancersmassive parallel assays |
| spellingShingle | S. E. Romanov D. A. Kalashnikova P. P. Laktionov Methods of massive parallel reporter assays for investigation of enhancers Вавиловский журнал генетики и селекции gene regulatory elements enhancers massive parallel assays |
| title | Methods of massive parallel reporter assays for investigation of enhancers |
| title_full | Methods of massive parallel reporter assays for investigation of enhancers |
| title_fullStr | Methods of massive parallel reporter assays for investigation of enhancers |
| title_full_unstemmed | Methods of massive parallel reporter assays for investigation of enhancers |
| title_short | Methods of massive parallel reporter assays for investigation of enhancers |
| title_sort | methods of massive parallel reporter assays for investigation of enhancers |
| topic | gene regulatory elements enhancers massive parallel assays |
| url | https://vavilov.elpub.ru/jour/article/view/3018 |
| work_keys_str_mv | AT seromanov methodsofmassiveparallelreporterassaysforinvestigationofenhancers AT dakalashnikova methodsofmassiveparallelreporterassaysforinvestigationofenhancers AT pplaktionov methodsofmassiveparallelreporterassaysforinvestigationofenhancers |