Different transcriptional responses by the CRISPRa system in distinct types of heterochromatin in Drosophila melanogaster
Abstract Transcription factors (TFs) activate gene expression by binding to elements close to promoters or enhancers. Some TFs can bind to heterochromatic regions to initiate gene activation, suggesting that if a TF is able to bind to any type of heterochromatin, it can activate transcription. To in...
| Main Authors: | , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Nature Portfolio
2022-07-01
|
| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-022-15944-7 |
| _version_ | 1811224075063787520 |
|---|---|
| author | Andrea Ortega-Yáñez Samantha Cruz-Ruiz Martha Vázquez Mario Zurita |
| author_facet | Andrea Ortega-Yáñez Samantha Cruz-Ruiz Martha Vázquez Mario Zurita |
| author_sort | Andrea Ortega-Yáñez |
| collection | DOAJ |
| description | Abstract Transcription factors (TFs) activate gene expression by binding to elements close to promoters or enhancers. Some TFs can bind to heterochromatic regions to initiate gene activation, suggesting that if a TF is able to bind to any type of heterochromatin, it can activate transcription. To investigate this possibility, we used the CRISPRa system based on dCas9-VPR as an artificial TF in Drosophila. dCas9-VPR was targeted to the TAHRE telomeric element, an example of constitutive heterochromatin, and to promoters and enhancers of the HOX Ultrabithorax (Ubx) and Sex Combs Reduced (Scr) genes in the context of facultative heterochromatin. dCas9-VPR robustly activated TAHRE transcription, showing that although this element is heterochromatic, dCas9-VPR was sufficient to activate its expression. In the case of HOX gene promoters, although Polycomb complexes epigenetically silence these genes, both were ectopically activated. When the artificial TF was directed to enhancers, we found that the expression pattern was different compared to the effect on the promoters. In the case of the Scr upstream enhancer, dCas9-VPR activated the gene ectopically but with less expressivity; however, ectopic activation also occurred in different cells. In the case of the bxI enhancer located in the third intron of Ubx, the presence of dCas9-VPR is capable of increasing transcription initiation while simultaneously blocking transcription elongation, generating a lack of functional phenotype. Our results show that CRISPRa system is able to activate transcription in any type of heterochromatin; nevertheless, its effect on transcription is subject to the intrinsic characteristics of each gene or regulatory element. |
| first_indexed | 2024-04-12T08:42:45Z |
| format | Article |
| id | doaj.art-6d61f3554d2244ea96bf52c866c7091c |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-04-12T08:42:45Z |
| publishDate | 2022-07-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-6d61f3554d2244ea96bf52c866c7091c2022-12-22T03:39:48ZengNature PortfolioScientific Reports2045-23222022-07-0112111310.1038/s41598-022-15944-7Different transcriptional responses by the CRISPRa system in distinct types of heterochromatin in Drosophila melanogasterAndrea Ortega-Yáñez0Samantha Cruz-Ruiz1Martha Vázquez2Mario Zurita3Departamento de Genética del Desarrollo Y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de MéxicoDepartamento de Genética del Desarrollo Y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de MéxicoDepartamento de Genética del Desarrollo Y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de MéxicoDepartamento de Genética del Desarrollo Y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de MéxicoAbstract Transcription factors (TFs) activate gene expression by binding to elements close to promoters or enhancers. Some TFs can bind to heterochromatic regions to initiate gene activation, suggesting that if a TF is able to bind to any type of heterochromatin, it can activate transcription. To investigate this possibility, we used the CRISPRa system based on dCas9-VPR as an artificial TF in Drosophila. dCas9-VPR was targeted to the TAHRE telomeric element, an example of constitutive heterochromatin, and to promoters and enhancers of the HOX Ultrabithorax (Ubx) and Sex Combs Reduced (Scr) genes in the context of facultative heterochromatin. dCas9-VPR robustly activated TAHRE transcription, showing that although this element is heterochromatic, dCas9-VPR was sufficient to activate its expression. In the case of HOX gene promoters, although Polycomb complexes epigenetically silence these genes, both were ectopically activated. When the artificial TF was directed to enhancers, we found that the expression pattern was different compared to the effect on the promoters. In the case of the Scr upstream enhancer, dCas9-VPR activated the gene ectopically but with less expressivity; however, ectopic activation also occurred in different cells. In the case of the bxI enhancer located in the third intron of Ubx, the presence of dCas9-VPR is capable of increasing transcription initiation while simultaneously blocking transcription elongation, generating a lack of functional phenotype. Our results show that CRISPRa system is able to activate transcription in any type of heterochromatin; nevertheless, its effect on transcription is subject to the intrinsic characteristics of each gene or regulatory element.https://doi.org/10.1038/s41598-022-15944-7 |
| spellingShingle | Andrea Ortega-Yáñez Samantha Cruz-Ruiz Martha Vázquez Mario Zurita Different transcriptional responses by the CRISPRa system in distinct types of heterochromatin in Drosophila melanogaster Scientific Reports |
| title | Different transcriptional responses by the CRISPRa system in distinct types of heterochromatin in Drosophila melanogaster |
| title_full | Different transcriptional responses by the CRISPRa system in distinct types of heterochromatin in Drosophila melanogaster |
| title_fullStr | Different transcriptional responses by the CRISPRa system in distinct types of heterochromatin in Drosophila melanogaster |
| title_full_unstemmed | Different transcriptional responses by the CRISPRa system in distinct types of heterochromatin in Drosophila melanogaster |
| title_short | Different transcriptional responses by the CRISPRa system in distinct types of heterochromatin in Drosophila melanogaster |
| title_sort | different transcriptional responses by the crispra system in distinct types of heterochromatin in drosophila melanogaster |
| url | https://doi.org/10.1038/s41598-022-15944-7 |
| work_keys_str_mv | AT andreaortegayanez differenttranscriptionalresponsesbythecrisprasystemindistincttypesofheterochromatinindrosophilamelanogaster AT samanthacruzruiz differenttranscriptionalresponsesbythecrisprasystemindistincttypesofheterochromatinindrosophilamelanogaster AT marthavazquez differenttranscriptionalresponsesbythecrisprasystemindistincttypesofheterochromatinindrosophilamelanogaster AT mariozurita differenttranscriptionalresponsesbythecrisprasystemindistincttypesofheterochromatinindrosophilamelanogaster |