Kopp Lab

An evolutionary & developmental biology lab

Month: November 2011

New and improved one-hybrid screens

Several papers in Nature Methods describe high-throughput yeast one-hybrid screens and their integration with ChIP to characterize transcriptional networks:

Exciting times: bountiful data to facilitate studies of cis-regulatory control

Automated protein-DNA interaction screening of Drosophila regulatory elements

Enhanced yeast one-hybrid assays for high-throughput gene-centered regulatory network mapping

Yeast one-hybrid assays for gene-centered human gene regulatory network mapping

The joys and pitfalls of kits

Here’s a perspective on the use of kits in molecular biology that I agree wholeheartedly with:

Training the kit generation

You guys know my anti-kit bias. They are great, and they save a lot of time and troubleshooting, but you REALLY have to understand how they work!

Worms getting some real evolution and ecology!

It always bugged me that so little was known about the evolutionary and ecological context of the C. elegans model system.  Why haven’t these worms become a model of speciation or ecological adaptation?  Compared to Drosophila, evolutionary biologists were slow to take them up.  The situation has been getting much better recently, with some really good evo-devo and evolutionary genetics studies coming out in the last few year.  Now, this paper should really expand the scope and power of comparative studies:

A phylogeny and molecular barcodes for Caenorhabditis, with numerous new species from rotting fruits

It describes a field survey of Caenorhabditis population and characterization of lots of new species – their phylogeny, reproductive isolation, phenotypic differences, etc.  This should be really exciting for worm people and even, vicariously, for me.

Another mite genome

The genome of the spider mite, Tetranychus, is finally published:

The genome of Tetranychus urticae reveals herbivorous pest adaptations

We now have three complete mite genomes.  With these plus Daphnia (and more chelicerates, crustaceans, and myriapods on the way), it will be easier to look at the evolution of insect-specific features.  Have fun!

Shadow enhancers

As we think about the evolution of enhancers that their role in the evolution of phenotypes, defining the boundaries of the functionally and evolutionarily relevant CREs is one important question (see previous post).  Another question/danger/caveat is the potential presence of redundant enhancers contributing to gene expression in the same tissue or organ – the so-called shadow enhancers.  In such cases, evolution can modify any or all of these enhancers to change the phenotype.  The danger is that any enhancer you identify, even if it is behaving as you expect, may only be telling you part of the story.

In this paper, Scott Barolo, an enhancer-bashing enthusiast and guru, gives a nice overview of shadow enhancers:

Shadow enhancers: Frequently asked questions about distributed cis-regulatory information and enhancer redundancy

Check it out.

What exactly is an enhancer, and where are its boundaries?

Check out this paper in PLoS Genetics:

Consequences of Eukaryotic Enhancer Architecture for Gene Expression Dynamics, Development, and Fitness

After more than 10 years, Michael Ludwig and his colleagues are still squeezing new insights out of the eve stripe 2 enhancer. Here, they show that sequences flanking the experimentally defined minimal enhancer contribute to the fine-tuning and robustness of gene expression. This helps explain Ryan Bickel’s results that we published last year (Composite Effects of Polymorphisms near Multiple Regulatory Elements Create a Major-Effect QTL). Using a population-genetic approach, Ryan showed that the sequence differences responsible for intraspecific phenotypic variation mapped to regions flanking the known functional elements of the bab locus – enhancer, PRE, and promoter – but not inside these regions.

Aside from the pure scientific knowledge it brings, this paper raises interesting practical questions.  In our search for well-defined minimal enhancers, where should we stop before we go too far? Evolutionary action may well take place outside of the minimal regions sufficient to drive expression in reporter assays. Striking the right balance between functional characterization and evolutionary relevance may be difficult in some cases.

Scientific writing

Andrew Moore has an interesting editorial in the last issue of Bioessays:

The long sentence: A disservice to science in the Internet age

I cannot say that I agree with it 100%. I myself tend to favor longer sentences, as I feel that some subtlety of meaning and intonation can get lost when a long sentence is cut up.  And there should be some room for scientese in science.  But there’s no doubt that clarity is the first and foremost duty of a writer. There–I used “but” to start my sentence! Andrew Moore would be proud.

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