The FSHD region on human chromosome 4q35 contains potential coding regions among pseudogenes and a high density of repeat elements.
The distal end of chromosome 4q contains the locus involved in facioscapulohumeral muscular dystrophy (FSHD1). Specific genomic deletions within a tandem DNA repeat (D4Z4) are associated with the disease status, but no causal genes have yet been discovered. In a systematic search for genes, a 161-kb stretch of genomic DNA proximal to D4Z4 was sequenced, analyzed for homologies, and subjected to gene prediction programs. A major fraction (45%) of the subtelomeric region is composed of repeat sequences attributable mainly to LINE-1 elements. Apart from the previously identified FRG1 and TUB4q sequences, several additional potential coding regions were identified by analyzing the sequence with exon prediction programs. So far, we have been unable to demonstrate transcripts by RT-PCR or cDNA library hybridization. However, several retrotransposed pseudogenes were identified. The high density of pseudogenes and repeat elements is consistent with the subtelomeric location of this region and explains why previous transcript identification studies have been problematic.
van Geel
M
M
Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, New York 14263, USA.
Heather
L J
LJ
Lyle
R
R
Hewitt
J E
JE
Frants
R R
RR
de Jong
P J
PJ
D002894:Chromosomes, Human, Pair 4; D019295:Computational Biology; D005091:Exons; D015870:Gene Expression; D006801:Humans; D007438:Introns; D008969:Molecular Sequence Data; D020391:Muscular Dystrophy, Facioscapulohumeral / Q000235:genetics*; D011544:Pseudogenes; D012091:Repetitive Sequences, Nucleic Acid; D017422:Sequence Analysis, DNA