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...
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2019
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| Acceso en línea: | https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_15592294_v14_n1_p41_Beyrne http://hdl.handle.net/20.500.12110/paper_15592294_v14_n1_p41_Beyrne |
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paper:paper_15592294_v14_n1_p41_Beyrne2025-07-30T18:59:21Z Strategy for the analysis of tissue-specific methylation changes without physical isolation Arabidopsis bisulfite technique DNA methylation Glabra2 root epidermis tissue-specific bisulfite cytosine genomic DNA Arabidopsis Article cell differentiation DNA extraction DNA methylation DNA sequence epigenetics gene gene expression gene mutation Glabra 2 gene microscopy molecular cloning phenotype photoperiodicity polymerase chain reaction root hair tissue specificity 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. © 2019, © 2019 Informa UK Limited, trading as Taylor & Francis Group. 2019 https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_15592294_v14_n1_p41_Beyrne http://hdl.handle.net/20.500.12110/paper_15592294_v14_n1_p41_Beyrne |
| institution |
Universidad de Buenos Aires |
| institution_str |
I-28 |
| repository_str |
R-134 |
| collection |
Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA) |
| topic |
Arabidopsis bisulfite technique DNA methylation Glabra2 root epidermis tissue-specific bisulfite cytosine genomic DNA Arabidopsis Article cell differentiation DNA extraction DNA methylation DNA sequence epigenetics gene gene expression gene mutation Glabra 2 gene microscopy molecular cloning phenotype photoperiodicity polymerase chain reaction root hair tissue specificity |
| spellingShingle |
Arabidopsis bisulfite technique DNA methylation Glabra2 root epidermis tissue-specific bisulfite cytosine genomic DNA Arabidopsis Article cell differentiation DNA extraction DNA methylation DNA sequence epigenetics gene gene expression gene mutation Glabra 2 gene microscopy molecular cloning phenotype photoperiodicity polymerase chain reaction root hair tissue specificity Strategy for the analysis of tissue-specific methylation changes without physical isolation |
| topic_facet |
Arabidopsis bisulfite technique DNA methylation Glabra2 root epidermis tissue-specific bisulfite cytosine genomic DNA Arabidopsis Article cell differentiation DNA extraction DNA methylation DNA sequence epigenetics gene gene expression gene mutation Glabra 2 gene microscopy molecular cloning phenotype photoperiodicity polymerase chain reaction root hair tissue specificity |
| 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. © 2019, © 2019 Informa UK Limited, trading as Taylor & Francis Group. |
| title |
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_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_sort |
strategy for the analysis of tissue-specific methylation changes without physical isolation |
| publishDate |
2019 |
| url |
https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_15592294_v14_n1_p41_Beyrne http://hdl.handle.net/20.500.12110/paper_15592294_v14_n1_p41_Beyrne |
| _version_ |
1843124128908836864 |