Closing the Gaps on Human Chromosome 19 Revealed Genes With a High Density of Repetitive Tandemly Arrayed Elements (original) (raw)

  1. Sun-Hee Leem1,2,
  2. Natalay Kouprina1,
  3. Jane Grimwood3,
  4. Jung-Hyun Kim1,2,
  5. Michael Mullokandov1,
  6. Young-Ho Yoon1,2,
  7. Ji-Youn Chae1,2,
  8. Jenna Morgan4,
  9. Susan Lucas4,
  10. Paul Richardson4,
  11. Chris Detter4,
  12. Tijana Glavina4,
  13. Eddy Rubin4,
  14. J. Carl Barrett1, and
  15. Vladimir Larionov1,5
  16. 1 Laboratory of Biosystems and Cancer, Center for Cancer Research, National Cancer Institute (NCI, NIH), Bethesda, Maryland, 20892, USA
  17. 2 Department of Biology, Dong-A University, Busan 604-714, Korea
  18. 3 Department of Genetics, Stanford University School of Medicine, Stanford, California, 94305, USA
  19. 4 U.S. Department of Energy Joint Genome Institute, Walnut Creek, California, 94598, USA

Abstract

The reported human genome sequence includes about 400 gaps of unknown sequence that were not found in the bacterial artificial chromosome (BAC) and cosmid libraries used for sequencing of the genome. These missing sequences correspond to ∼1% of euchromatic regions of the human genome. Gap filling is a laborious process because it relies on analysis of random clones of numerous genomic BAC or cosmid libraries. In this work we demonstrate that closing the gaps can be accelerated by a selective recombinational capture of missing chromosomal segments in yeast. The use of both methodologies allowed us to close the four remaining gaps on the human chromosome 19. Analysis of the gap sequences revealed that they contain several abnormalities that could result in instability of the sequences in microbe hosts, including large blocks of micro- and minisatellites and a high density of_Alu_ repeats. Sequencing of the gap regions, in both BAC and YAC forms, allowed us to generate a complete sequence of four genes, including the neuronal cell signaling gene SCK1/SLI. The SCK1/SLI gene contains a record number of minisatellites, most of which are polymorphic and transmitted through meiosis following a Mendelian inheritance. In conclusion, the use of the alternative recombinational cloning system in yeast may greatly accelerate work on closing the remaining gaps in the human genome (as well as in other complex genomes) to achieve the goal of annotation of all human genes.

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