Revealing truths about non-coding transcripts

Comparisons between human and mouse genomes have releaved more than the expected number of conserved sequences, many of which lie far from annotated exons. Moreover, previous studies have

indicated that there is much more transcriptional activity in the genome than can be accounted for by current genome annotation. Wanting to explore the transcriptome and perhaps discover the

missing transcripts, Cawley and Bekiranov et al. used a combination of high-density oligonucleotide arrays and chromatin immunoprecipitation to look for the binding sites of three

well-known transcription factors: cMyc, Sp1 and p53. Their search, which was carried out in two cell lines, was restricted to the non-repeat genomic sequences of chromosomes 21 and 22.

Their results were unexpected — the number of transcription-factor binding sites was very large (ranging from 1,600 for p53 to 25,000 for cMyc, extrapolated to the whole genome) and their

distribution was surprising. Only 22% of these sites lie within the 5′ termini of protein-coding genes, whereas 36% lie within or near the 3′ termini of protein-coding genes, indicating that

they are distal regulatory elements or promoters for ncRNAs.

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