Characterization of transcriptional enhancers in the chicken genome using CRISPR-mediated activation
DNA regulatory elements intricately control when, where, and how genes are activated. Therefore, understanding the function of these elements could unveil the complexity of the genetic regulation network. Genome-wide significant variants are predominantly found in non-coding regions of DNA, so compr...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2023-10-01
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| Series: | Frontiers in Genome Editing |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fgeed.2023.1269115/full |
| _version_ | 1797649923414425600 |
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| author | Jeong Hoon Han Hong Jo Lee Tae Hyun Kim Tae Hyun Kim |
| author_facet | Jeong Hoon Han Hong Jo Lee Tae Hyun Kim Tae Hyun Kim |
| author_sort | Jeong Hoon Han |
| collection | DOAJ |
| description | DNA regulatory elements intricately control when, where, and how genes are activated. Therefore, understanding the function of these elements could unveil the complexity of the genetic regulation network. Genome-wide significant variants are predominantly found in non-coding regions of DNA, so comprehending the predicted functional regulatory elements is crucial for understanding the biological context of these genomic markers, which can be incorporated into breeding programs. The emergence of CRISPR technology has provided a powerful tool for studying non-coding regulatory elements in genomes. In this study, we leveraged epigenetic data from the Functional Annotation of Animal Genomes project to identify promoter and putative enhancer regions associated with three genes (HBBA, IRF7, and PPARG) in the chicken genome. To identify the enhancer regions, we designed guide RNAs targeting the promoter and candidate enhancer regions and utilized CRISPR activation (CRISPRa) with dCas9-p300 and dCas9-VPR as transcriptional activators in chicken DF-1 cells. By comparing the expression levels of target genes between the promoter activation and the co-activation of the promoter and putative enhancers, we were able to identify functional enhancers that exhibited augmented upregulation. In conclusion, our findings demonstrate the remarkable efficiency of CRISPRa in precisely manipulating the expression of endogenous genes by targeting regulatory elements in the chicken genome, highlighting its potential for functional validation of non-coding regions. |
| first_indexed | 2024-03-11T15:54:07Z |
| format | Article |
| id | doaj.art-8e8890569db54568bda7c6a1d962b0f6 |
| institution | Directory Open Access Journal |
| issn | 2673-3439 |
| language | English |
| last_indexed | 2024-03-11T15:54:07Z |
| publishDate | 2023-10-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genome Editing |
| spelling | doaj.art-8e8890569db54568bda7c6a1d962b0f62023-10-25T11:45:10ZengFrontiers Media S.A.Frontiers in Genome Editing2673-34392023-10-01510.3389/fgeed.2023.12691151269115Characterization of transcriptional enhancers in the chicken genome using CRISPR-mediated activationJeong Hoon Han0Hong Jo Lee1Tae Hyun Kim2Tae Hyun Kim3Department of Animal Science, The Pennsylvania State University, University Park, PA, United StatesDivision of Animal Sciences, University of Missouri, Columbia, MO, United StatesDepartment of Animal Science, The Pennsylvania State University, University Park, PA, United StatesThe Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, United StatesDNA regulatory elements intricately control when, where, and how genes are activated. Therefore, understanding the function of these elements could unveil the complexity of the genetic regulation network. Genome-wide significant variants are predominantly found in non-coding regions of DNA, so comprehending the predicted functional regulatory elements is crucial for understanding the biological context of these genomic markers, which can be incorporated into breeding programs. The emergence of CRISPR technology has provided a powerful tool for studying non-coding regulatory elements in genomes. In this study, we leveraged epigenetic data from the Functional Annotation of Animal Genomes project to identify promoter and putative enhancer regions associated with three genes (HBBA, IRF7, and PPARG) in the chicken genome. To identify the enhancer regions, we designed guide RNAs targeting the promoter and candidate enhancer regions and utilized CRISPR activation (CRISPRa) with dCas9-p300 and dCas9-VPR as transcriptional activators in chicken DF-1 cells. By comparing the expression levels of target genes between the promoter activation and the co-activation of the promoter and putative enhancers, we were able to identify functional enhancers that exhibited augmented upregulation. In conclusion, our findings demonstrate the remarkable efficiency of CRISPRa in precisely manipulating the expression of endogenous genes by targeting regulatory elements in the chicken genome, highlighting its potential for functional validation of non-coding regions.https://www.frontiersin.org/articles/10.3389/fgeed.2023.1269115/fullchickenCRISPR activationenhancerFAANGpromoterregulatory elements |
| spellingShingle | Jeong Hoon Han Hong Jo Lee Tae Hyun Kim Tae Hyun Kim Characterization of transcriptional enhancers in the chicken genome using CRISPR-mediated activation Frontiers in Genome Editing chicken CRISPR activation enhancer FAANG promoter regulatory elements |
| title | Characterization of transcriptional enhancers in the chicken genome using CRISPR-mediated activation |
| title_full | Characterization of transcriptional enhancers in the chicken genome using CRISPR-mediated activation |
| title_fullStr | Characterization of transcriptional enhancers in the chicken genome using CRISPR-mediated activation |
| title_full_unstemmed | Characterization of transcriptional enhancers in the chicken genome using CRISPR-mediated activation |
| title_short | Characterization of transcriptional enhancers in the chicken genome using CRISPR-mediated activation |
| title_sort | characterization of transcriptional enhancers in the chicken genome using crispr mediated activation |
| topic | chicken CRISPR activation enhancer FAANG promoter regulatory elements |
| url | https://www.frontiersin.org/articles/10.3389/fgeed.2023.1269115/full |
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