Transcription termination and chimeric RNA formation controlled by Arabidopsis thaliana FPA and DICER-LIKE 1. Sequencing of A. thaliana transcriptome with Direct RNA sequencing by Helicos

Alternative cleavage and polyadenylation influences the coding and regulatory potential of mRNA and where transcription termination occurs. Although widespread, few regulators of this process are known. The Arabidopsis thaliana protein FPA is a rare example of a trans-acting regulator of poly(A) site choice. Analysing fpa mutants therefore provides the opportunity to reveal generic consequences of disrupting this process. Here we show that specific chimeric RNAs formed between the exons of otherwise separate genes are a striking consequence of loss of FPA function. We also found that defective termination at specific loci in fpa mutants was shared with dicer-like (dcl)1 or dcl4 mutants, leading us to alternative explanations for some silencing roles of these proteins. We relate our findings to the impact that altered patterns of 3’ end formation can have on gene and genome organization.