Beyond the Identification of Transcribed Sequences:
Functional, Evolutionary and Expression Analysis
12th International Workshop
October 25-28, 2002
Washington, DC

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Large Scale Transcriptional Activity Observed in Chromosomes 21 and 22

Thomas Gingeras
Affymetrix, Santa Clara, CA 95051 USA
Telephone: 408-731-5069
Fax: 408-481-0422

Large-Scale Transcriptional Activity Observed in Chromosomes 21 and 22. Thomas R. Gingeras, Affymetrix, Inc. Santa Clara, Ca, 95051. The draft sequences of the human chromosomes 21 and 22 currently indicate that there are approximately 786 well-characterized Ensembl genes (v7.29a). Recently, we described a collection of empirically derived maps identifying active areas of RNA transcription on these chromosomes using cytosolic poly A+ RNA obtained from 11 human cell lines. (Kapranov, P., et al. 2002 Science 296:916). These unbiased maps were created using oligonucleotide arrays containing 25- mer probes spaced on average every 35 base pairs along these chromosomes. When compared to the sequence annotations available for these chromosomes it is noted that as much as an order of magnitude more of the genomic sequence is used for transcription than envisioned by the predicted and characterized exons. Specifically, 9.7% (98,231) of the total number of probes used to interrogate these chromosomes detected transcripts in at least 5 of the 11 cell lines ( with estimated false positive rate of ~5%). Of these interrogating probes 2.6%, 24.9% and 72.7% were positioned within exonic, intronic and intergenic regions, respectively. Of the total number of probes used, only 11% detected transcripts within an annotated exon. The remaining positive probes (~89%) were located in intronic and intergenic regions and approximately half of these were >300 base pairs away from the nearest annotation. Validation of these data has focused on 30 distinct regions along both chromosomes, situated well away from any annotations. Copies of cDNA for these regions could be found in NCI supplied cDNA library ( from Dr. L. Hong ) made from cytosolic polyA+ RNA of a single cell line, HepG2. Given that we have ~60% verification rate from a single cell line, provides additional confidence that these novel transcripts will be joined by an increasing number as we scale up the verification effort. Additional information concerning the location of these novel transcripts and the conservation to non-human genomic sequences will be presented.

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