Closing the gaps on human chromosome 19 revealed genes with a high density of repetitive tandemly arrayed elements.
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 approximately 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.
Leem
Sun-Hee
SH
Laboratory of Biosystems and Cancer, Center for Cancer Research, National Cancer Institute (NCI, NIH), Bethesda, Maryland 20892, USA.
Kouprina
Natalay
N
Grimwood
Jane
J
Kim
Jung-Hyun
JH
Mullokandov
Michael
M
Yoon
Young-Ho
YH
Chae
Ji-Youn
JY
Morgan
Jenna
J
Lucas
Susan
S
Richardson
Paul
P
Detter
Chris
C
Glavina
Tijana
T
Rubin
Eddy
E
Barrett
J Carl
JC
Larionov
Vladimir
V
D020087:Alu Elements / Q000235:genetics*; D000818:Animals; D002874:Chromosome Mapping / Q000379:methods*; D002888:Chromosomes, Human, Pair 19 / Q000235:genetics*; D003001:Cloning, Molecular / Q000379:methods*; D006224:Cricetinae; D022041:Euchromatin / Q000235:genetics; D005796:Genes / Q000235:genetics*; D015894:Genome, Human; D016045:Human Genome Project; D006801:Humans; D006822:Hybrid Cells; D008969:Molecular Sequence Data; D017422:Sequence Analysis, DNA / Q000379:methods
D022041:Euchromatin