Especially at TSSs located in CpG islands, one finds transcripts starting from many different nearby sites covering tens and sometimes hundreds of nucleotides.
In contrast to OsRap2.6, PAL transcripts peaked at 1 hr after chitin treatment and PBZ1 transcripts started to increase at 3 hr after chitin treatment.
This identifies how many transcription start sites (TSS) are used in each gene and groups transcripts from that gene by their TSS.
Second, one or two major transcripts are most often observed, which would suggest either that only one or two major transcription start sites exist, or that if many transcription start sites are utilised then these are either very close together or else only one or two give rise to a major stable transcript.
Ribosome profiling in mouse embryonic stem cells (Ingolia et al. 2011) indicates that for many transcripts multiple translation starts may be used, primarily additional AUG sites, but also near-cognate codons.
Our analysis of transcript 5' ends suggests that transcription initiation and transcript processing in Anabaena is often complex, and that many transcripts have long 5' UTRs with unclear transcriptional start sites or processing sites.
Further work would be needed to assess whether LNA-mediated template-switching could be preferable for digital expression profiling starting from partially degraded RNA samples, where the cap structure of many transcripts has been lost.
Our comparative analysis of detection sensitivity with material from clinical samples revealed that even with the usage of 30 times less starting material (50 ng vs 1.5 micrograms) Exon arrays could detect as many transcripts above background as in RNA-seq.
Many transcripts associated with the pericarp and photosynthesis decline steadily from the start of the sampling (1_4, 2_4, 3_4); however others maintain a more constant level of expression throughout the developmental series (1_3, 2_3).
Photographs, memorabilia and original documents accompany many transcripts.
