Strategy for the analysis of tissue-specific methylation changes without physical isolation
One common experimental hurdle that arises when explore patterns of cytosine methylation is the generation of data derived from a single specific tissue, often arduous to isolate from a heterogeneous biospecimen. Here we show a new strategy for exploring environment- or mutation-caused changes in ce...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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Taylor & Francis Group
2019-01-01
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| Series: | Epigenetics |
| Subjects: | |
| Online Access: | http://dx.doi.org/10.1080/15592294.2019.1565589 |
| _version_ | 1797678926790656000 |
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| author | Cecilia C. Beyrne Rodrigo M. González Norberto D. Iusem |
| author_facet | Cecilia C. Beyrne Rodrigo M. González Norberto D. Iusem |
| author_sort | Cecilia C. Beyrne |
| collection | DOAJ |
| description | One common experimental hurdle that arises when explore patterns of cytosine methylation is the generation of data derived from a single specific tissue, often arduous to isolate from a heterogeneous biospecimen. Here we show a new strategy for exploring environment- or mutation-caused changes in cell type- or tissue-specific methylation landscapes, which requires neither transgenic reporter cell lines nor physical separation. This approach takes advantage of a known distinct methylation signature existing in only one of the tissues within an organ under a particular condition. From the information on such compared published methylomes, one can design a set of PCR primers that specifically amplify bisulfite-converted DNA of two nearby genomic regions of interest, thus allowing for tissue-specific DNA methylation data. To validate the performance of the approach, we designed primers able to amplify a portion of a gene in the context of root biology: the Arabidopsis homeotic gene Glabra-2 (Gl2), expressed only in epidermis during cell differentiation. We found that the extent of methylated cytosines appears remarkably different when root epidermis-specific primers were used vs. non-specific ones under three genetic backgrounds involving mutations in genes also associated with the establishment of cell identity. Although the genetic or environmental perturbations to be studied might modify methylation in the primer-annealing zone, leading to a possible misinterpretation of the data, the strategy presented here can become a useful first round screening tool to detect differences in tissue-specific epigenetic status under new conditions. |
| first_indexed | 2024-03-11T23:06:59Z |
| format | Article |
| id | doaj.art-ed34576513e847feb9d186dfd693670d |
| institution | Directory Open Access Journal |
| issn | 1559-2294 1559-2308 |
| language | English |
| last_indexed | 2024-03-11T23:06:59Z |
| publishDate | 2019-01-01 |
| publisher | Taylor & Francis Group |
| record_format | Article |
| series | Epigenetics |
| spelling | doaj.art-ed34576513e847feb9d186dfd693670d2023-09-21T13:09:21ZengTaylor & Francis GroupEpigenetics1559-22941559-23082019-01-01141415110.1080/15592294.2019.15655891565589Strategy for the analysis of tissue-specific methylation changes without physical isolationCecilia C. Beyrne0Rodrigo M. González1Norberto D. Iusem2Biología Molecular y Neurociencias (IFIByNE); CONICETBiología Molecular y Neurociencias (IFIByNE); CONICETBiología Molecular y Neurociencias (IFIByNE); CONICETOne common experimental hurdle that arises when explore patterns of cytosine methylation is the generation of data derived from a single specific tissue, often arduous to isolate from a heterogeneous biospecimen. Here we show a new strategy for exploring environment- or mutation-caused changes in cell type- or tissue-specific methylation landscapes, which requires neither transgenic reporter cell lines nor physical separation. This approach takes advantage of a known distinct methylation signature existing in only one of the tissues within an organ under a particular condition. From the information on such compared published methylomes, one can design a set of PCR primers that specifically amplify bisulfite-converted DNA of two nearby genomic regions of interest, thus allowing for tissue-specific DNA methylation data. To validate the performance of the approach, we designed primers able to amplify a portion of a gene in the context of root biology: the Arabidopsis homeotic gene Glabra-2 (Gl2), expressed only in epidermis during cell differentiation. We found that the extent of methylated cytosines appears remarkably different when root epidermis-specific primers were used vs. non-specific ones under three genetic backgrounds involving mutations in genes also associated with the establishment of cell identity. Although the genetic or environmental perturbations to be studied might modify methylation in the primer-annealing zone, leading to a possible misinterpretation of the data, the strategy presented here can become a useful first round screening tool to detect differences in tissue-specific epigenetic status under new conditions.http://dx.doi.org/10.1080/15592294.2019.1565589dna methylationtissue-specificarabidopsisroot epidermisbisulfite techniqueglabra2 |
| spellingShingle | Cecilia C. Beyrne Rodrigo M. González Norberto D. Iusem Strategy for the analysis of tissue-specific methylation changes without physical isolation Epigenetics dna methylation tissue-specific arabidopsis root epidermis bisulfite technique glabra2 |
| title | Strategy for the analysis of tissue-specific methylation changes without physical isolation |
| title_full | Strategy for the analysis of tissue-specific methylation changes without physical isolation |
| title_fullStr | Strategy for the analysis of tissue-specific methylation changes without physical isolation |
| title_full_unstemmed | Strategy for the analysis of tissue-specific methylation changes without physical isolation |
| title_short | Strategy for the analysis of tissue-specific methylation changes without physical isolation |
| title_sort | strategy for the analysis of tissue specific methylation changes without physical isolation |
| topic | dna methylation tissue-specific arabidopsis root epidermis bisulfite technique glabra2 |
| url | http://dx.doi.org/10.1080/15592294.2019.1565589 |
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