Odorant receptors (ORs) constitute one of the largest gene families in mammalian genomes. Odorant receptor genes are expressed in olfactory sensory neurons (OSN), with each OSN stably expressing a single OR protein (from a single allele). How exactly this is achieved is largely unresolved (and fascinating). How do cells chose which OR is going to be expressed ? How do they make sure that only this OR is expressed (which may means that other ORs have to be repressed). In a recent Cell paper (pointed out to me by Yoav), Ryba, Belluscio and colleagues present new exciting data about the underlying mechanisms. In mouse, transgenic odorant receptor genes cannot be expressed in olfactory neurons, when directly under the control of OR promoters. The authors hypothesize that this is due to interactions between regulatory sequences in OR coding regions, and regulatory sequences in OR promoters. So they tried to eliminate this interaction by separating OR promoters from coding sequences. They placed an OR coding sequence under the control of an artificial promoter (TetO), activable by TTA. The TTA-coding gene is itself placed under the control of an OR promoter. Using this system, they managed to express the OR in a good fraction of neurons. In turn, this allowed them to observe that the expressed OR suppresses expression of endogenous ORs. Likewise, TetO-OR expression appears suppressed in neurons where an endogenous OR is expressed. The authors conclude that regulatory sequences in OR coding regions are mediating the inhibition. Identifying these sequences and what binds to them is therefore the next step … it is unclear whether sequence conservation can help, as it appears that the ~1kb OR coding sequences are highly variable.
Determining nucleosome positions using Solexa sequencing March 9, 2008
In this amazing Cell paper, Keji Zhao and his colleagues used Solexa sequencing to create genome-wide maps of nucleosome positions in resting and activated human T cells. They digested DNA with micrococcal nuclease, then gel-purified ~150bp fragments (DNA fragments wrapped around nucleosomes are ~147bp-long) and ran their sample through the Solexa pipeline. The Solexa technology allows the 5′ and 3′ ends (~25bp) of these fragments to be sequenced, and these reads are then mapped onto the human genome.
The resolution of the results they got provides some fascinating insights into chromatin structure and regulation, and the link with gene expression. They detected 8 phased nucleosomes surrounding the TSS of expressed genes, but only right upstream (+1) of the TSS of non-expressed genes. The 5′ end of +1 nucleosomes peaked at +40bp for expressed genes, but +10bp for non-expressed genes. Nucleosome levels at -1 were lower than -2 and +1 for both expressed and non-expressed genes, suggesting that all core promoters are nucleosome-depleted. -1 levels of induced genes do not appear to change upon T cell activation, however increases in -1 levels were observed for repressed genes (-1 nucleosome levels appear inversely correlated to RNA Pol occupancy, also measured by ChIP-seq). The lists goes on and on.
While the authors focus their paper on nucleosome patterns surrounding the TSS, to me, nucleosome patterns in the rest of the genome would be more intriguing. What kind of nucleosome patterns are found in gene deserts ? in recombination hotspots ? in ultra-conserved sequenced ? they present anecdotal evidence that enhancer regions need to be nucleosome-free, in order for regulatory elements to be able to recruit transcription factors. It would be interesting to see if this is a general feature of enhancers (which would then allow to predict where they are in the genome).
