title: Short-read sequencing technologies for transcriptional analyses.
abstract: The technological advances in DNA sequencing over the past five years have changed our approaches to gene expression analysis, fundamentally altering the basic methods used and in most cases driving a shift from hybridization-based approaches to sequencing-based approaches. Quantitative, tag-based studies of gene expression were one of the earliest applications of these next-generation technologies, but the tremendous depth of sequencing facilitates de novo transcript discovery, which replaces traditional expressed sequence tag (EST) sequencing. In addition, these technologies have created new opportunities for understanding the generation, stability, and decay of RNA and the impacts of chromatin differences on gene expression. As we review the impact of these methods on plant biology, we also mention published studies from animal systems when the methods are broadly applicable. We can anticipate that the published work over the past few years is a harbinger of much broader studies that are yet to be published and are sure to further advance our understanding of plant genomes in a field changing at a dizzying pace.
authors: Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711, USA.
authors: Stacey A
authors: SA
authors: Simon
authors: Jixian
authors: J
authors: Zhai
authors: Raja Sekhar
authors: RS
authors: Nandety
authors: Kevin P
authors: KP
authors: McCormick
authors: Jia
authors: J
authors: Zeng
authors: Diego
authors: D
authors: Mejia
authors: Blake C
authors: BC
authors: Meyers
mesh_terms: D018744:DNA, Plant / Q000235:genetics; D044127:Epigenesis, Genetic; D020224:Expressed Sequence Tags; D012333:RNA, Messenger / Q000235:genetics; D014158:Transcription, Genetic
chemical_list: D018744:DNA, Plant; D012333:RNA, Messenger