Figure 7.

Evidence for transcription and RNA stability in LMCEs. A complete representation of the positions and analysis of MCEs within all 46 megabases analyzed is available via custom tracks in the UCSC Genome Browser [26] through supplemental data. (a) A view depicting a transcribed LMCE identified by both DoTS and tiling array data upstream from EXOC4(.84) is shown. The LMCE is shown by the red track towards the top and is highly conserved to zebra and puffer fish, whereas DoTS transcripts from clustered mRNA and EST sequences is shown as the next brown track below, and evidence for significant transcription by tiling array data is shown by blue bars on the next track down. (b) Expression patterns of LMCEs across tissues were compared with patterns obtained for RT-PCR products generated by priming at exons upstream and downstream of the LMCE. The PCR products were visualized by gel electrophoresis to show similar patterns of expression to the nearby genes. Shown are elements upstream from CAST(.694), downstream from RAB3C(.306) in the neighboring PDE4D gene, and in an internal intron of NBEA(.708). (c) A view depicting a LMCE with significant stable RNA secondary structure spanning alternatively spliced exons of SNAP25(.159) is shown along with the optimal minimum free energy RNA structure. Intronic portion of this LMCE are also highly conserved to zebra and puffer fish. DoTS, Database of Transcribed Sequences; EST, expressed sequence tag; LMCE, large most conserved element; RT-PCR, reverse transcription polymerase chain reaction.