Cargando…

Analysis of Escherichia coli RNase E and RNase III activity in vivo using tiling microarrays

Tiling microarrays have proven to be a valuable tool for gaining insights into the transcriptomes of microbial organisms grown under various nutritional or stress conditions. Here, we describe the use of such an array, constructed at the level of 20 nt resolution for the Escherichia coli MG1655 geno...

Descripción completa

Detalles Bibliográficos
Autores principales: Stead, Mark B., Marshburn, Sarah, Mohanty, Bijoy K., Mitra, Joydeep, Castillo, Lourdes Peňa, Ray, Debashish, van Bakel, Harm, Hughes, Timothy R., Kushner, Sidney R.
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2011
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3082872/
https://www.ncbi.nlm.nih.gov/pubmed/21149258
http://dx.doi.org/10.1093/nar/gkq1242
_version_ 1782202343060668416
author Stead, Mark B.
Marshburn, Sarah
Mohanty, Bijoy K.
Mitra, Joydeep
Castillo, Lourdes Peňa
Ray, Debashish
van Bakel, Harm
Hughes, Timothy R.
Kushner, Sidney R.
author_facet Stead, Mark B.
Marshburn, Sarah
Mohanty, Bijoy K.
Mitra, Joydeep
Castillo, Lourdes Peňa
Ray, Debashish
van Bakel, Harm
Hughes, Timothy R.
Kushner, Sidney R.
author_sort Stead, Mark B.
collection PubMed
description Tiling microarrays have proven to be a valuable tool for gaining insights into the transcriptomes of microbial organisms grown under various nutritional or stress conditions. Here, we describe the use of such an array, constructed at the level of 20 nt resolution for the Escherichia coli MG1655 genome, to observe genome-wide changes in the steady-state RNA levels in mutants defective in either RNase E or RNase III. The array data were validated by comparison to previously published results for a variety of specific transcripts as well as independent northern analysis of additional mRNAs and sRNAs. In the absence of RNase E, 60% of the annotated coding sequences showed either increases or decreases in their steady-state levels. In contrast, only 12% of the coding sequences were affected in the absence of RNase III. Unexpectedly, many coding sequences showed decreased abundance in the RNase E mutant, while more than half of the annotated sRNAs showed changes in abundance. Furthermore, the steady-state levels of many transcripts showed overlapping effects of both ribonucleases. Data are also presented demonstrating how the arrays were used to identify potential new genes, RNase III cleavage sites and the direct or indirect control of specific biological pathways.
format Text
id pubmed-3082872
institution National Center for Biotechnology Information
language English
publishDate 2011
publisher Oxford University Press
record_format MEDLINE/PubMed
spelling pubmed-30828722011-04-27 Analysis of Escherichia coli RNase E and RNase III activity in vivo using tiling microarrays Stead, Mark B. Marshburn, Sarah Mohanty, Bijoy K. Mitra, Joydeep Castillo, Lourdes Peňa Ray, Debashish van Bakel, Harm Hughes, Timothy R. Kushner, Sidney R. Nucleic Acids Res Genomics Tiling microarrays have proven to be a valuable tool for gaining insights into the transcriptomes of microbial organisms grown under various nutritional or stress conditions. Here, we describe the use of such an array, constructed at the level of 20 nt resolution for the Escherichia coli MG1655 genome, to observe genome-wide changes in the steady-state RNA levels in mutants defective in either RNase E or RNase III. The array data were validated by comparison to previously published results for a variety of specific transcripts as well as independent northern analysis of additional mRNAs and sRNAs. In the absence of RNase E, 60% of the annotated coding sequences showed either increases or decreases in their steady-state levels. In contrast, only 12% of the coding sequences were affected in the absence of RNase III. Unexpectedly, many coding sequences showed decreased abundance in the RNase E mutant, while more than half of the annotated sRNAs showed changes in abundance. Furthermore, the steady-state levels of many transcripts showed overlapping effects of both ribonucleases. Data are also presented demonstrating how the arrays were used to identify potential new genes, RNase III cleavage sites and the direct or indirect control of specific biological pathways. Oxford University Press 2011-04 2010-12-11 /pmc/articles/PMC3082872/ /pubmed/21149258 http://dx.doi.org/10.1093/nar/gkq1242 Text en © The Author(s) 2010. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/2.5 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Genomics
Stead, Mark B.
Marshburn, Sarah
Mohanty, Bijoy K.
Mitra, Joydeep
Castillo, Lourdes Peňa
Ray, Debashish
van Bakel, Harm
Hughes, Timothy R.
Kushner, Sidney R.
Analysis of Escherichia coli RNase E and RNase III activity in vivo using tiling microarrays
title Analysis of Escherichia coli RNase E and RNase III activity in vivo using tiling microarrays
title_full Analysis of Escherichia coli RNase E and RNase III activity in vivo using tiling microarrays
title_fullStr Analysis of Escherichia coli RNase E and RNase III activity in vivo using tiling microarrays
title_full_unstemmed Analysis of Escherichia coli RNase E and RNase III activity in vivo using tiling microarrays
title_short Analysis of Escherichia coli RNase E and RNase III activity in vivo using tiling microarrays
title_sort analysis of escherichia coli rnase e and rnase iii activity in vivo using tiling microarrays
topic Genomics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3082872/
https://www.ncbi.nlm.nih.gov/pubmed/21149258
http://dx.doi.org/10.1093/nar/gkq1242
work_keys_str_mv AT steadmarkb analysisofescherichiacolirnaseeandrnaseiiiactivityinvivousingtilingmicroarrays
AT marshburnsarah analysisofescherichiacolirnaseeandrnaseiiiactivityinvivousingtilingmicroarrays
AT mohantybijoyk analysisofescherichiacolirnaseeandrnaseiiiactivityinvivousingtilingmicroarrays
AT mitrajoydeep analysisofescherichiacolirnaseeandrnaseiiiactivityinvivousingtilingmicroarrays
AT castillolourdespena analysisofescherichiacolirnaseeandrnaseiiiactivityinvivousingtilingmicroarrays
AT raydebashish analysisofescherichiacolirnaseeandrnaseiiiactivityinvivousingtilingmicroarrays
AT vanbakelharm analysisofescherichiacolirnaseeandrnaseiiiactivityinvivousingtilingmicroarrays
AT hughestimothyr analysisofescherichiacolirnaseeandrnaseiiiactivityinvivousingtilingmicroarrays
AT kushnersidneyr analysisofescherichiacolirnaseeandrnaseiiiactivityinvivousingtilingmicroarrays