title: Feature co-localization landscape of the human genome.
abstract: Although feature co-localizations could serve as useful guide-posts to genome architecture, a comprehensive and quantitative feature co-localization map of the human genome has been lacking. Herein we show that, in contrast to the conventional bipartite division of genomic sequences into genic and inter-genic regions, pairwise co-localizations of forty-two genomic features in the twenty-two autosomes based on 50-kb to 2,000-kb sequence windows indicate a tripartite zonal architecture comprising Genic zones enriched with gene-related features and Alu-elements; Proximal zones enriched with MIR- and L2-elements, transcription-factor-binding-sites (TFBSs), and conserved-indels (CIDs); and Distal zones enriched with L1-elements. Co-localizations between single-nucleotide-polymorphisms (SNPs) and copy-number-variations (CNVs) reveal a fraction of sequence windows displaying steeply enhanced levels of SNPs, CNVs and recombination rates that point to active adaptive evolution in such pathways as immune response, sensory perceptions, and cognition. The strongest positive co-localization observed between TFBSs and CIDs suggests a regulatory role of CIDs in cooperation with TFBSs. The positive co-localizations of cancer somatic CNVs (CNVT) with all Proximal zone and most Genic zone features, in contrast to the distinctly more restricted co-localizations exhibited by germline CNVs (CNVG), reveal disparate distributions of CNVTs and CNVGs indicative of dissimilarity in their underlying mechanisms.
authors: Division of Life Science, Applied Genomics Center and Center for Statistical Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong.
authors: Siu-Kin
authors: SK
authors: Ng
authors: Division of Life Science, Applied Genomics Center and Center for Statistical Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong.
authors: Taobo
authors: T
authors: Hu
authors: Division of Life Science, Applied Genomics Center and Center for Statistical Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong.
authors: Xi
authors: X
authors: Long
authors: Division of Life Science, Applied Genomics Center and Center for Statistical Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong.
authors: Cheuk-Hin
authors: CH
authors: Chan
authors: Division of Life Science, Applied Genomics Center and Center for Statistical Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong.
authors: Shui-Ying
authors: SY
authors: Tsang
authors: Division of Life Science, Applied Genomics Center and Center for Statistical Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong.
authors: Hong
authors: H
authors: Xue
mesh_terms: D002874:Chromosome Mapping; D004251:DNA Transposable Elements; D021901:DNA, Intergenic / Q000235:genetics*; D015894:Genome, Human; D006801:Humans; D035683:MicroRNAs / Q000235:genetics; D020641:Polymorphism, Single Nucleotide; D020218:Response Elements
chemical_list: D004251:DNA Transposable Elements; D021901:DNA, Intergenic; D035683:MicroRNAs