Muller-F used to be the sex chromosome before Muller-A took over

Beatriz Vicoso and Doris Bachtrog have a very interesting paper showing that the Drosophila 4th (dot) chromosome is homologous to the sex chromosome of more basally branching Diptera.  It seems that, early in Drosophilid evolution, Muller-A took over the role of the sex chromosome from Muller-F.  They also have an interesting discussion of how such takeovers could occur.

How do different HOX genes control different sets of target genes?

This is actually an old mystery because the DNA-binding specificities of different HOX proteins, determined using biochemical approaches, are remarkably similar.  How can they regulate different genes if they all bind the same site?  Well, it looks like they don’t all bind the same sites.  This paper in EMBO Journal shows that different HOX proteins associate with different genomic regions in vivo.  How they end up there is still not understood, but presumably it depends on the specific interactions between the HOX proteins and other TFs that DO recognize different DNA sequences.  This is a very intriguing paper – take a look.

A modified RAD-seq technique

A new paper in Nature Methods describes a simplified approach for generating and assembling RAD libraries.  From the paper:

“Here we describe a streamlined and flexible approach for RAD genotyping, called 2b-RAD for its use of type IIB restriction enzymes. These enzymes (for example, BsaXI and AlfI) cleave genomic DNA upstream and downstream of the target site, producing tags of uniform length that are ideally suited for sequencing on existing next-generation platforms.”

Check it out.