Kopp Lab

An evolutionary & developmental biology lab

Month: January 2012

Genetic control of body/organ size

In the last few years, there has been a lot of work (finally!) on how the size of developing organs is controlled.  An animal has to have the correct proportions, so every organ needs to coordinate with every other organs and decide how fast to grow and when to stop growing.  Several pathways have been shown to be required for this coordination.  Now, this paper shows that one of the ways growth is coordinated is through the regulation of tRNA synthesis:

Drosophila RNA polymerase III repressor Maf1 controls body size and developmental timing by modulating tRNAiMet synthesis and systemic insulin signaling

How is this relevant to evolution?  Body size and organ proportions (allometry) are among the fastest evolving morphological traits, but we know virtually nothing about how that happens.  Similarly, sexual size dimorphism is very common, but we don’t know how it is accomplished and how in changes in evolution.  Hopefully, better knowledge of the molecular genetics of size control will stimulate more work on the evolution of size and allometry.

A mechanism for environmental sex determination?

Here’s a really cool paper:

DNA Methylation of the Gonadal Aromatase (cyp19a) Promoter Is Involved in Temperature-Dependent Sex Ratio Shifts in the European Sea Bass

They show that temperature-dependent sex determination (or rather, in this case, trans-differentiation) is mediated by the methylation of the aromatase promoter.  An obvious question is whether the environmentally driven methylation of the promoters of genes involved in sexual differentiation could be a general mechanism in species with environmental sex determination.  I am sure lots of people will be asking this soon, at least in vertebrates.

Does anyone known a dipteran with temperature-dependent sex determination?  Can’t think of one right now.

Genomic analysis of parallel adaptation in sticklebacks

Here is the story that Felicity Jones talked about last year:

A Genome-wide SNP Genotyping Array Reveals Patterns of Global and Repeated Species-Pair Divergence in Sticklebacks

Most of it is probably not “real” convergence from the genetic point of view, but the result of parallel selective sweeps acting on the same standing variation.  It’s a really nice systematic analysis.

New collection of attP-based reporter vectors for enhancer bashing

This might be useful for enhancer analysis, if our current vectors misbehave for some reason:

Drosophila Reporter Vectors Compatible with ΦC31 Integrase Transgenesis Techniques and Their Use to Generate New Notch Reporter Fly Lines

They have GFP, mCherry, and YFP versions.  The polylinker is smallish though – a common problem.  The promoter is hsp70.

Comparative analysis of ChIP data

If you are thinking of doing a comparative ChIP study in different species, genotypes, or cell types, take a look at this paper:

A computational pipeline for comparative ChIP-seq analyses

It deals specifically with the issues and solutions for comparative analysis, which most ChIP papers do not address.

Power tools for gene expression and clonal analysis in Drosophila

Here is a nice review paper in the last issue of Nature Methods:

Power tools for gene expression and clonal analysis in Drosophila

It will give you a good introduction to the recent developments in Drosophila transgenic techniques, but the main emphasis is on clonal analysis techniques.

Lots of other good stuff in this issue of Nature Methods, including several papers on the use of gene-editing nucleases.

Gene-editing nucleases

Making sequencing libraries from picogram amounts of template

Here is a couple of recent papers on transposome-mediated construction of sequencing libraries:

Transposase mediated construction of RNA-seq libraries

Preparation of high-quality next-generation sequencing libraries from picogram quantities of target DNA

Transposase-based methods are much more efficient than the traditional fragmentation/end-repair/tailing/ligation approach.  With fewer enzymatic and purification steps, template losses are greatly reduced and small-volume handling is easier, allowing you to use a lot less template.  I think there is already at least one transposome-based kit for making sequencing libraries, and I am sure more are coming in the near future.

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