title: The human transcriptome map reveals extremes in gene density, intron length, GC content, and repeat pattern for domains of highly and weakly expressed genes.
abstract: The chromosomal gene expression profiles established by the Human Transcriptome Map (HTM) revealed a clustering of highly expressed genes in about 30 domains, called ridges. To physically characterize ridges, we constructed a new HTM based on the draft human genome sequence (HTMseq). Expression of 25,003 genes can be analyzed online in a multitude of tissues (http://bioinfo.amc.uva.nl/HTMseq). Ridges are found to be very gene-dense domains with a high GC content, a high SINE repeat density, and a low LINE repeat density. Genes in ridges have significantly shorter introns than genes outside of ridges. The HTMseq also identifies a significant clustering of weakly expressed genes in domains with fully opposite characteristics (antiridges). Both types of domains are open to tissue-specific expression regulation, but the maximal expression levels in ridges are considerably higher than in antiridges. Ridges are therefore an integral part of a higher order structure in the genome related to transcriptional regulation.
authors.affiliation: Department of Human Genetics, Academic Medical Center, University of Amsterdam, 1100DE Amsterdam, The Netherlands. R.Versteeg@AMC.UVA.NL
authors.forename: Rogier
authors.initials: R
authors.lastname: Versteeg
authors.forename: Barbera D C
authors.initials: BD
authors.lastname: van Schaik
authors.forename: Marinus F
authors.initials: MF
authors.lastname: van Batenburg
authors.forename: Marco
authors.initials: M
authors.lastname: Roos
authors.forename: Ramin
authors.initials: R
authors.lastname: Monajemi
authors.forename: Huib
authors.initials: H
authors.lastname: Caron
authors.forename: Harmen J
authors.initials: HJ
authors.lastname: Bussemaker
authors.forename: Antoine H C
authors.initials: AH
authors.lastname: van Kampen
mesh_terms: D001482:Base Composition; D003062:Codon; D019295:Computational Biology / Q000379:methods; D020862:GC Rich Sequence / Q000235:genetics*; D005786:Gene Expression Regulation; D005796:Genes; D006801:Humans; D007438:Introns; D005810:Multigene Family; D009928:Organ Specificity / Q000235:genetics; D020161:Physical Chromosome Mapping; D012091:Repetitive Sequences, Nucleic Acid; D020086:Short Interspersed Nucleotide Elements; D014158:Transcription, Genetic
chemical_list: D003062:Codon