Gene expression profiling: metatranscriptomics

Abstract

Metatranscriptomics has been developed to help understand how communities respond to changes in their environment. Metagenomic studies provided a snapshot of the genetic composition of the community at any given time. However, short-timescale studies investigating the response of communities to rapid environmental changes (e.g. pollution events or diurnal light availability) require analysis of changes in the abundance and composition of the active fraction of the community. Metatranscriptomics enables researchers to investigate the actively transcribed ribosomal and messenger RNA from a community. It has been applied to environments as diverse as soil and seawater. This chapter outlines sampling protocols and RNA extraction techniques from these two ecosystems, as well as details a method to enrich mRNA in the extracted nucleic acid. Also, a section is dedicated for outlining a bioinformatic procedure for the analysis of metatranscriptomic datasets.