The team found many diverse kinds of RNAs transcribed from distinct regions of the genome, creating a complex pool of overlapping transcription. While the team validated many known protein-coding transcripts that contribute to this complex pool, they also discovered that:
Seventy-five percent of all of the RNA that were exclusively found in the nucleus had not been previously detected.
Any single base in the genome can be transcribed into several different transcripts with different, but overlapping sequences. Often, transcripts from one strand of DNA can share parts of their sequence with overlapping transcripts from the same strand or even from the opposite strand (antisense).
Transcripts missing a run of adenosine nucleotides (non-polyA) at the tail-end were twice as common as the more well-studied RNAs that have this sequence. Most transcripts derived from the sparsely transcribed regions between centers of dense transcription are non-polyA transcripts.
This study focused on an in depth scan of 10 chromosomes; however, Affymetrix has developed tiling microarrays that cover all human chromosomes. GeneChip tiling microarrays have been used by Gingeras and his collaborators, as well as the NHGRI publicly funded ENCODE project, to study the human genome in an unbiased fashion -- including regions that have historically been termed coding and non-coding.
Affymetrix is now beginning to commercialize tiling microarrays to give the research community the ability to perform these types of unbiased studies as well. By focusing research beyond the parts of the genome that have been traditionally studied, scientists hope to discover new drug targets, new biomarkers, and a better understanding of disease mechanism.
This project has been funded in whole or in part with Federal Funds from the National Cancer Institute,