Virtual northern analysis of the human genome

Evan H. Hurowitz, Iddo Drori, Victoria C. Stodden, David L. Donoho, Patrick O. Brown

Research output: Contribution to journalArticle

Abstract

Background. We applied the Virtual Northern technique to human brain mRNA to systematically measure human mRNA transcript lengths on a genome-wide scale. Methodology/Principal Findings. We used separation by gel electrophoresis followed by hybridization to cDNA microarrays to measure 8,774 mRNA transcript lengths representing at least 6,238 genes at high (>90%) confidence. By comparing these transcript lengths to the Refseq and H-Invitational full-length cDNA databases, we found that nearly half of our measurements appeared to represent novel transcript variants. Comparison of length measurements determined by hybridization to different cDNAs derived from the same gene identified clones that potentially correspond to alternative transcript variants. We observed a close linear relationship between ORF and mRNA lengths in human mRNAs, identical in form to the relationship we had previously identified in yeast. Some functional classes of protein are encoded by mRNAs whose untranslated regions (UTRs) tend to be longer or shorter than average; these functional classes were similar in both human and yeast. Conclusions/Significance. Human transcript diversity is extensive and largely unannotated. Our length dataset can be used as a new criterion for judging the completeness of cDNAs and annotating mRNA sequences. Similar relationships between the lengths of the UTRs in human and yeast mRNAs and the functions of the proteins they encode suggest that UTR sequences serve an important regulatory role among eukaryotes.

Original languageEnglish (US)
Article numbere460
JournalPloS one
Volume2
Issue number5
DOIs
StatePublished - May 23 2007
Externally publishedYes

Fingerprint

Human Genome
Genes
Messenger RNA
genome
Untranslated Regions
Complementary DNA
Yeast
Yeasts
yeasts
hybridization
Microarrays
Oligonucleotide Array Sequence Analysis
Electrophoresis
Eukaryota
gel electrophoresis
Open Reading Frames
eukaryotic cells
open reading frames
Brain
Proteins

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)

Cite this

Hurowitz, E. H., Drori, I., Stodden, V. C., Donoho, D. L., & Brown, P. O. (2007). Virtual northern analysis of the human genome. PloS one, 2(5), [e460]. https://doi.org/10.1371/journal.pone.0000460

Virtual northern analysis of the human genome. / Hurowitz, Evan H.; Drori, Iddo; Stodden, Victoria C.; Donoho, David L.; Brown, Patrick O.

In: PloS one, Vol. 2, No. 5, e460, 23.05.2007.

Research output: Contribution to journalArticle

Hurowitz, EH, Drori, I, Stodden, VC, Donoho, DL & Brown, PO 2007, 'Virtual northern analysis of the human genome', PloS one, vol. 2, no. 5, e460. https://doi.org/10.1371/journal.pone.0000460
Hurowitz, Evan H. ; Drori, Iddo ; Stodden, Victoria C. ; Donoho, David L. ; Brown, Patrick O. / Virtual northern analysis of the human genome. In: PloS one. 2007 ; Vol. 2, No. 5.
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