DNA methylation and gene expression regulation associated with vascularization in Sorghum bicolor

Turco, G. M., Kajala, K., Kunde-Ramamoorthy, G., Ngan, C. Y., Olson, A., Deshphande, S., Tolkunov, D., Waring, B., Stelpflug, S., Klein, P., Schmutz, J., Kaeppler, S., Ware, D., Wei, C. L., Etchells, J. P., Brady, S. M. (2017) DNA methylation and gene expression regulation associated with vascularization in Sorghum bicolor. New Phytol, 214 (3). pp. 1213-1229. ISSN 0028-646x

URL: https://www.ncbi.nlm.nih.gov/pubmed/28186631
DOI: 10.1111/nph.14448

Abstract

Plant secondary cell walls constitute the majority of plant biomass. They are predominantly found in xylem cells, which are derived from vascular initials during vascularization. Little is known about these processes in grass species despite their emerging importance as biomass feedstocks. The targeted biofuel crop Sorghum bicolor has a sequenced and well-annotated genome, making it an ideal monocot model for addressing vascularization and biomass deposition. Here we generated tissue-specific transcriptome and DNA methylome data from sorghum shoots, roots and developing root vascular and nonvascular tissues. Many genes associated with vascular development in other species show enriched expression in developing vasculature. However, several transcription factor families varied in vascular expression in sorghum compared with Arabidopsis and maize. Furthermore, differential expression of genes associated with DNA methylation were identified between vascular and nonvascular tissues, implying that changes in DNA methylation are a feature of sorghum root vascularization, which we confirmed using tissue-specific DNA methylome data. Roots treated with a DNA methylation inhibitor also showed a significant decrease in root length. Tissues and organs can be discriminated based on their genomic methylation patterns and methylation context. Consequently, tissue-specific changes in DNA methylation are part of the normal developmental process.

Item Type: Paper
Uncontrolled Keywords: biofuel cell type-specific epigenetics sorghum (Sorghum bicolor) transcriptome
Subjects: bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > DNA methylation
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > epigenetics
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > epigenetics

bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > genes, structure and function > gene expression
organism description > plant
CSHL Authors:
Communities: CSHL labs > Ware lab
Depositing User: Matt Covey
Date Deposited: 16 Feb 2017 17:31
Last Modified: 07 Sep 2017 16:32
Related URLs:
Dataset ID:
URI: http://repository.cshl.edu/id/eprint/34130

Actions (login required)

Administrator's edit/view item Administrator's edit/view item
CSHL HomeAbout CSHLResearchEducationNews & FeaturesCampus & Public EventsCareersGiving