Structural and functional analysis of the human Y-box binding protein (YB-1) gene promoter

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Abstract
We have isolated three overlapping genomic clones containing the 5′ portion of the human YB-1 gene. These clones span ∼25 kb of contiguous DNA containing 10 kb of 5′ flanking sequence and 15 kb of the gene. The nucleotide sequence of the first exon and of 2000 upstream base pairs (bp) was determined. The first exon is unusually large and contains a 166 bp coding sequence and a 331 bp untranslated region. CpG sequences cover the 5′-end of the YB-1 gene including its first exon and intron as well as the upstream regions. The GC content around the first exon is ∼70% and a CpG-free region was located in the untranslated sequence. The segment preceding the major transcription initiation site does not contain a TATA box, CCAAT box and the binding sequence for known transcription factors. A transient expression assay using the chloramphenicol acetyltransferase (CAT) gene showed that the sequence from +24 to +281 was critical for CAT expression. Fluorescence in situ hybridization demonstrated the chromosomal locus of YB-1 gene on chromosome 1p34. Polymerase chain reaction analysis on other genomic phage DNAs showed that several clones were derived from pseudogenes.