Abstract:
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.
Registro:
Documento: |
Artículo
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Título: | Strategy for the analysis of tissue-specific methylation changes without physical isolation |
Autor: | Beyrne, C.C.; González, R.M.; Iusem, N.D. |
Filiación: | Instituto de Fisiología, Biología Molecular y Neurociencias (IFIByNE); CONICET, Buenos Aires, Argentina Departamento de Fisiología, Biología Molecular y Celular (FBMC); Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
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Palabras clave: | 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 |
Año: | 2019
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Volumen: | 14
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Número: | 1
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Página de inicio: | 41
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Página de fin: | 51
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DOI: |
http://dx.doi.org/10.1080/15592294.2019.1565589 |
Título revista: | Epigenetics
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Título revista abreviado: | Epigenetics
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ISSN: | 15592294
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CAS: | bisulfite, 15181-46-1, 7631-90-5, 7773-03-7; cytosine, 71-30-7
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Registro: | https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_15592294_v14_n1_p41_Beyrne |
Referencias:
- Jeltsch, A., Beyond Watson and Crick: DNA methylation and molecular enzymology of DNA methyltransferases (2002) ChemBioChem, 3
- Burggren, W.W., Crews, D., Epigenetics in comparative biology: why we should pay attention (2014) Integr Comp Biol, 54, pp. 7-20
- Fang, J., Schneider, B., Laser microdissection: a sample preparation technique for plant micrometabolic profiling (2014) Phytochem Anal, 25, pp. 307-313
- Iyer-Pascuzzi, A.S., Benfey, P.N., Fluorescence-activated cell sorting in plant developmental biology, , In: Hennig L, Köhler C, editors. Plant developmental biology. Methods molecular biology (Methods and protocols). 655. Totowa (NJ): Humana Press; 2010. p. 313–319
- Deal, R.B., Henikoff, S., The INTACT method for cell typeg-specific gene expression and chromatin profiling in Arabidopsis thaliana (2011) Nat Protoc, 6, pp. 56-68
- Endo, M., Shimizu, H., Araki, T., Rapid and simple isolation of vascular, epidermal and mesophyll cells from plant leaf tissue (2016) Nat Protoc, 11, pp. 1388-1395
- Svozil, J., Gruissem, W., Baerenfaller, K., Meselect–A rapid and effective method for the separation of the main leaf tissue types (2016) Front Plant Sci, 7
- van Beijnum, J.R., Rousch, M., Castermans, K., Isolation of endothelial cells from fresh tissues (2008) Nat Protoc, 3, pp. 1085-1091
- Frommer, M., McDonald, L.E., Millar, D.S., A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands (1992) Proc Natl Acad Sci
- Capra, E., Toschi, P., Del Corvo, M.D., Genome-wide epigenetic characterization of tissues from three germ layers isolated from sheep fetuses (2017) Front Genet, 8
- Kundaje, A., Meuleman, W., Ernst, J., Integrative analysis of 111 reference human epigenomes (2015) Nature, 518, pp. 317-330
- Sánchez-Martín, F.J., Lindquist, D.M., Landero-Figueroa, J., Sex- and tissue-specific methylome changes in brains of mice perinatally exposed to lead (2015) Neurotoxicology, 46, pp. 92-100
- Song, Q., Decato, B., Hong, E.E., A reference methylome database and analysis pipeline to facilitate integrative and comparative epigenomics (2013) PLoS One, 8
- Di Cristina, M., Sessa, G., Dolan, L., The Arabidopsis Athb-10 (GLABRA2) is an HD-Zip protein required for regulation of root hair development (1996) Plant J, 10, pp. 393-402
- Masucci, J.D., Rerie, W.G., Foreman, D.R., The homeobox gene GLABRA2 is required for position-dependent cell differentiation in the root epidermis of Arabidopsis thaliana (1996) Development, 122, pp. 1253-1260
- Dolan, L., Janmaat, K., Willemsen, V., Cellular organisation of the Arabidopsis thaliana root (1993) Development, 119, pp. 71-84
- Kawakatsu, T., Stuart, T., Valdes, M., Unique cell-type-specific patterns of DNA methylation in the root meristem (2016) Nat Plants, 2
- Lee, M.M., Schiefelbein, J., WEREWOLF, a MYB-related protein in Arabidopsis, is a position-dependent regulator of epidermal cell patterning (1999) Cell, 99, pp. 473-483
- Wada, T., Role of a positive regulator of root hair development, CAPRICE, in Arabidopsis root epidermal cell differentiation (2002) Development, 129, pp. 5409-5419. , http://dev.biologists.org/cgi/doi/10.1242/dev.00111, Available from
- Kirik, V., Simon, M., Huelskamp, M., The ENHANCER of TRY and CPC1 gene acts redundantly with TRIPTYCHON and CAPRICE in trichome and root hair cell patterning in Arabidopsis (2004) Dev Biol, 268, pp. 506-513
- Wojdacz, T.K., Hansen, L.L., Dobrovic, A., A new approach to primer design for the control of PCR bias in methylation studies (2008) BMC Res Notes, 1
- Wada, T., Tachibana, T., Shimura, Y., Epidermal cell differentiation in Arabidopsis determined by a Myb homolog, CPC (1997) Science, 277, pp. 1113-1116. , 80-
- Houseman, E.A., Kile, M.L., Christiani, D.C., Reference-free deconvolution of DNA methylation data and mediation by cell composition effects (2016) BMC Bioinformatics, 17
- Peng, Q., Ecker, J.R., Detection of allele-specific methylation through a generalized heterogeneous epigenome model (2012) Bioinformatics, 28, pp. i163-i171
- Doležel, J., Greilhuber, J., Suda, J., Flow cytometry with plants: an overview (2007) Flow cytometry with plant cells: analysis of genes, chromosomes and genomes, , https://onlinelibrary.wiley.com/doi/book/10.1002/9783527610921, In: Doležel J, Greilhuber J, Suda J, editors. Available from
- Bruex, A., Kainkaryam, R.M., Wieckowski, Y., A gene regulatory network for root epidermis cell differentiation in Arabidopsis (2012) PLoS Genet, 8
- Tirado-Magallanes, R., Rebbani, K., Lim, R., Whole genome DNA methylation: beyond genes silencing (2017) Oncotarget, 8
- Weigel, D., Glazebrook, J., (2002) Arabidopsis : a laboratory manual, , Cold Spring Harbor Laboratory Press,. Woodbury (NY
- González, R.M., Ricardi, M.M., Iusem, N.D., Epigenetic marks in an adaptive water stress-responsive gene in tomato roots under normal and drought conditions (2013) Epigenetics, 8, pp. 864-872
- Gruntman, E., Qi, Y., Slotkin, R.K., Kismeth: analyzer of plant methylation states through bisulfite sequencing (2008) BMC Bioinformatics, 9, p. 371
Citas:
---------- APA ----------
Beyrne, C.C., González, R.M. & Iusem, N.D.
(2019)
. Strategy for the analysis of tissue-specific methylation changes without physical isolation. Epigenetics, 14(1), 41-51.
http://dx.doi.org/10.1080/15592294.2019.1565589---------- CHICAGO ----------
Beyrne, C.C., González, R.M., Iusem, N.D.
"Strategy for the analysis of tissue-specific methylation changes without physical isolation"
. Epigenetics 14, no. 1
(2019) : 41-51.
http://dx.doi.org/10.1080/15592294.2019.1565589---------- MLA ----------
Beyrne, C.C., González, R.M., Iusem, N.D.
"Strategy for the analysis of tissue-specific methylation changes without physical isolation"
. Epigenetics, vol. 14, no. 1, 2019, pp. 41-51.
http://dx.doi.org/10.1080/15592294.2019.1565589---------- VANCOUVER ----------
Beyrne, C.C., González, R.M., Iusem, N.D. Strategy for the analysis of tissue-specific methylation changes without physical isolation. Epigenetics. 2019;14(1):41-51.
http://dx.doi.org/10.1080/15592294.2019.1565589