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It is now possible to perform whole-genome shotgun sequencing as well as capture of specific genomic regions for extinct organisms. However, targeted resequencing of large parts of nuclear genomes has yet to be demonstrated for ancient DNA. Here we show that hybridization capture on microarrays can successfully recover more than a megabase of target regions from Neandertal DNA even in the presence of approximately 99.8% microbial DNA. Using this approach, we have sequenced approximately 14,000 protein-coding positions inferred to have changed on the human lineage since the last common ancestor shared with chimpanzees. By generating the sequence of one Neandertal and 50 present-day humans at these positions, we have identified 88 amino acid substitutions that have become fixed in humans since our divergence from the Neandertals.
Assignment of the human gene (GLCLC) that encodes the heavy or catalytic subunit of gamma-glutamylcysteine synthetase (glutamate-cysteine ligase; EC 18.104.22.168) to human chromosome 6 was accomplished by hybridization to Southern blotted somatic cell hybrid DNA. This assignment was confirmed by PCR from somatic cell hybrid DNAs.
The bovine endothelial nitric oxide synthase gene plus 2.9 kilobases of 5'-flanking sequence has been isolated and characterized. The gene spans 20 kilobases and contains 26 exons and 25 introns. Two transcription start sites have been determined by primer extension analysis which are located 170 and 240 base pairs upstream, respectively, from the methionine translational initiation codon. Evidence supporting the upstream boundary region for transcriptional initiation was also obtained by reverse transcription-polymerase chain reaction. The 5'-flanking region lacks a typical TATA box but contains numerous putative transcription factor binding sites. These include consensus sequences for an AP-1 site, an NF-1 site, a tumor necrosis factor responsive element, two sterol regulatory elements, 3 acute-phase response element, two sterol regulatory elements, 3 acute-phase response elements, 6 GATA motifs, 16 CACCC boxes, 5 Sp1 sites, 15 estrogen half-palindromic motifs, and 9 fluid shear stress-responsive elements. The isolated gene promoter directs basal transcription of a luciferase reporter gene when transiently transfected into bovine aortic endothelial cells. High sequence homology of the promoter region to the human endothelial nitric oxide synthase gene promoter (75% nucleotide identity in 1.6 kilobases of 5'-flanking sequence) suggests evolutionary conservation of transcriptional regulation. Isolation and characterization of the bovine endothelial nitric oxide synthase gene should facilitate further investigation of mechanisms by which gene expression is regulated.