The human transcriptome map reveals extremes in gene density, intron length, GC content, and repeat pattern for domains of highly and weakly expressed genes.
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.
Versteeg
Rogier
R
Department of Human Genetics, Academic Medical Center, University of Amsterdam, 1100DE Amsterdam, The Netherlands. R.Versteeg@AMC.UVA.NL
van Schaik
Barbera D C
BD
van Batenburg
Marinus F
MF
Roos
Marco
M
Monajemi
Ramin
R
Caron
Huib
H
Bussemaker
Harmen J
HJ
van Kampen
Antoine H C
AH
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
D003062:Codon