Surveying entamoeba histolytica transcriptome using massively parallel cDNA sequencing

Massively parallel cDNA sequencing, known as RNA-Seq, is a recently developed approach to interrogate transcriptomes. Its rapid and ongoing development promises to revolutionize transcriptomics over the next decade. In this chapter, we first review the transcriptome research of Entamoeba histolytica during the past 25 years in retrospect: From cDNA library screening in the 1980s to the latest RNA- Seq analyses. Then, we share our experiences on applying RNA-Seq to the Entamoeba transcriptome, aiming to provide useful caveats and tips. Next, we summarize the results of our latest RNA-Seq analyses of E. histolytica, including identification of unannotated transcripts, revision of existing gene models, reconstruction of alternative isoforms, and quantification of stochastic noise in splicing and polyadenylation. Finally, we outline a number of advanced applications of RNA-Seq that could potentially be applied to E. histolytica, hoping to shed light on the future directions of Entamoeba transcriptomics.