<p>This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</p> <p>The aryl hydrocarbon receptor nuclear translocator (<italic>ARNT</italic>) and cathepsin K 
(<italic>CTSK</italic>) genes lie in a tandem head-to-tail arrangement on human chromosome 1. The two
genes are in extremely close proximity; the usual <italic>CTSK</italic> transcription start site is
less than 1.4 kb downstream of the end of the longest reported <italic>ARNT</italic> transcript.
By generating an RT-PCR product that overlaps both the 3′ end of <italic>ARNT</italic> and
the 5′ end of <italic>CTSK</italic>, we show that <italic>ARNT</italic> transcripts may extend through the
<italic>ARNT</italic>–<italic>CTSK</italic> intergenic region and progress into the <italic>CTSK</italic> gene. 
Furthermore, by using quantitative RT-PCR from several tissues to detect the <italic>ARNT</italic> expression
signature in <italic>CTSK</italic> introns, we show that <italic>ARNT</italic> transcripts can read through into
<italic>CTSK</italic> as far as <italic>CTSK</italic> intron 3, extending approximately 3.7 kb downstream of the
end of the longest previously described <italic>ARNT</italic> mRNA. Given that <italic>ARNT</italic> and 
<italic>CTSK</italic> are expressed in an overlapping range of tissues, <italic>ARNT</italic> read-through may have a
negative impact on <italic>CTSK</italic> transcript levels by interfering with <italic>CTSK</italic> expression.
We also present evidence for novel <italic>CTSK</italic> transcripts following sequence analysis
of <italic>CTSK</italic>-derived ESTs and RT-PCR products. These transcripts show alternate 5′
splicing and or 5′ extension and are sometimes initiated from a cryptic alternative
promoter which is upstream of the known <italic>CTSK</italic> promoter and possibly in the 3′
UTR of <italic>ARNT</italic>.</p>
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Comp Funct Genomics. 2005 Jul-Aug; 6(5-6):268-276