A tiling microarray for global analysis of chloroplast genome expression in cucumber and other plants

Plastids are small organelles equipped with their own genomes (plastomes). Although these organelles are involved in numerous plant metabolic pathways, current knowledge about the transcriptional activity of plastomes is limited. To solve this problem, we constructed a plastid tiling microarray (Pla...

Full description

Bibliographic Details
Main Authors:	Żmieńko, Agnieszka, Guzowska-Nowowiejska, Magdalena, Urbaniak, Radosław, Pląder, Wojciech, Formanowicz, Piotr, Figlerowicz, Marek
Format:	Online
Language:	English
Published:	BioMed Central 2011
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3195753/

id	pubmed-3195753
recordtype	oai_dc
spelling	pubmed-31957532011-10-19 A tiling microarray for global analysis of chloroplast genome expression in cucumber and other plants Żmieńko, Agnieszka Guzowska-Nowowiejska, Magdalena Urbaniak, Radosław Pląder, Wojciech Formanowicz, Piotr Figlerowicz, Marek Methodology Plastids are small organelles equipped with their own genomes (plastomes). Although these organelles are involved in numerous plant metabolic pathways, current knowledge about the transcriptional activity of plastomes is limited. To solve this problem, we constructed a plastid tiling microarray (PlasTi-microarray) consisting of 1629 oligonucleotide probes. The oligonucleotides were designed based on the cucumber chloroplast genomic sequence and targeted both strands of the plastome in a non-contiguous arrangement. Up to 4 specific probes were designed for each gene/exon, and the intergenic regions were covered regularly, with 70-nt intervals. We also developed a protocol for direct chemical labeling and hybridization of as little as 2 micrograms of chloroplast RNA. We used this protocol for profiling the expression of the cucumber chloroplast plastome on the PlasTi-microarray. Owing to the high sequence similarity of plant plastomes, the newly constructed microarray can be used to study plants other than cucumber. Comparative hybridization of chloroplast transcriptomes from cucumber, Arabidopsis, tomato and spinach showed that the PlasTi-microarray is highly versatile. BioMed Central 2011-09-28 /pmc/articles/PMC3195753/ /pubmed/21952044 http://dx.doi.org/10.1186/1746-4811-7-29 Text en Copyright ©2011 Żmieńko et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Żmieńko, Agnieszka Guzowska-Nowowiejska, Magdalena Urbaniak, Radosław Pląder, Wojciech Formanowicz, Piotr Figlerowicz, Marek
spellingShingle	Żmieńko, Agnieszka Guzowska-Nowowiejska, Magdalena Urbaniak, Radosław Pląder, Wojciech Formanowicz, Piotr Figlerowicz, Marek A tiling microarray for global analysis of chloroplast genome expression in cucumber and other plants
author_facet	Żmieńko, Agnieszka Guzowska-Nowowiejska, Magdalena Urbaniak, Radosław Pląder, Wojciech Formanowicz, Piotr Figlerowicz, Marek
author_sort	Żmieńko, Agnieszka
title	A tiling microarray for global analysis of chloroplast genome expression in cucumber and other plants
title_short	A tiling microarray for global analysis of chloroplast genome expression in cucumber and other plants
title_full	A tiling microarray for global analysis of chloroplast genome expression in cucumber and other plants
title_fullStr	A tiling microarray for global analysis of chloroplast genome expression in cucumber and other plants
title_full_unstemmed	A tiling microarray for global analysis of chloroplast genome expression in cucumber and other plants
title_sort	tiling microarray for global analysis of chloroplast genome expression in cucumber and other plants
description	Plastids are small organelles equipped with their own genomes (plastomes). Although these organelles are involved in numerous plant metabolic pathways, current knowledge about the transcriptional activity of plastomes is limited. To solve this problem, we constructed a plastid tiling microarray (PlasTi-microarray) consisting of 1629 oligonucleotide probes. The oligonucleotides were designed based on the cucumber chloroplast genomic sequence and targeted both strands of the plastome in a non-contiguous arrangement. Up to 4 specific probes were designed for each gene/exon, and the intergenic regions were covered regularly, with 70-nt intervals. We also developed a protocol for direct chemical labeling and hybridization of as little as 2 micrograms of chloroplast RNA. We used this protocol for profiling the expression of the cucumber chloroplast plastome on the PlasTi-microarray. Owing to the high sequence similarity of plant plastomes, the newly constructed microarray can be used to study plants other than cucumber. Comparative hybridization of chloroplast transcriptomes from cucumber, Arabidopsis, tomato and spinach showed that the PlasTi-microarray is highly versatile.
publisher	BioMed Central
publishDate	2011
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3195753/
_version_	1611481748556742656

A tiling microarray for global analysis of chloroplast genome expression in cucumber and other plants

Similar Items