Bicistronic and fused monocistronic transcripts are derived from adjacent loci in the Arabidopsis genome

  1. JYOTHI THIMMAPURAM1,
  2. HUI DUAN2,
  3. LEI LIU1, and
  4. MARY A. SCHULER2
  1. 1Bioinformatics Unit, W.M. Keck Center for Functional Genomics and 2Department of Cell and Structural Biology, University of Illinois, Urbana, Illinois 61801, USA

Abstract

Comparisons of full-length cDNAs and genomic DNAs available for Arabidopsis thaliana described here indicate that some adjacent loci are transcribed into extremely long RNAs spanning two annotated genes. Once expressed, some of these transcripts are post-transcriptionally spliced within their coding and intergenic sequences to generate bicistronic transcripts containing two complete open reading frames. Others are spliced to generate monocistronic transcripts coding for fusion proteins with sequences derived from both loci. RT-PCR of several P450 transcripts in this collection indicates that these extended transcripts exist side by side with shorter monocistronic transcripts derived from the individual loci in each pair. The existence of these unusual transcripts highlights variations in the processes of transcription and splicing that could not possibly have been predicted in the algorithms used for genome annotation and splice site predictions.

Keywords

Footnotes

  • 1 In two cases, both transcripts are RIKEN clones (RAFL07-15-G11 equivalent to RAFL05-14-C13; RAFL09-44-D01 equivalent to RAFL09-70-M08). In four cases, the two transcripts are RIKEN and non-RIKEN clones (RAFL09-60-B14 equivalent to AV528973 and AV523321 and AV530163 and AV524280; RAFL11-13-C20 equivalent to AY084340; RAFL15-09-A22 equivalent to AY087549; RAFL16-01-C03 equivalent to AV529139 and AV523459).

  • 2 RAFL06-69-H17, RAFL14-80-M23, RAFL16-69-P16, RAFL21-17-J10.

  • 3 Functions annotated for 13 combined loci are extended and the same as one or both of the previously annotated functions for RAFL06-69-H17, RAFL06-10-K24, RAFL07-12-J11, RAFL07-15-F13, RAFL07-15-G11, RAFL09-56-O16, RAFL19-84-B16, RAFL21-17-J10, RAFL05-02-O09, RAFL08-08-P22, RAFL09-60-B14, RAFL16-73-D01, and RAFL16-69-P16.

  • 4 Functional annotations have now been made for five combined loci including RAFL08-17-N09 (nicastrin precursor), RAFL09-16-G02 (pyrrolodone carboxyl peptidase-like protein), RAFL15-41-F10 (ribulose-1,5-bisphosphate carboxylase large subunit N-methyltransferase), RAFL09-24-E16 (ZW18 protein), RAFL09-85-I15 (single-strand DNA endonuclease 1).

  • Article and publication are at http://www.rnajournal.org/cgi/doi/10.1261/rna.7114505.

    • Accepted November 18, 2004.
    • Received June 24, 2004.
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