Paper on deletions of hunchback binding sites in eve covered by Global medical discovery

Arnar Pálsson, 14/10/2014

Our recent paper on deletion polymorphism in the eve stripe 3+7 enhancer was covered by the Global medical discovery website.

Palsson A, Wesolowska N, Reynisdóttir S, Ludwig MZ, Kreitman M (2014) Naturally Occurring Deletions of Hunchback Binding Sites in the Even-Skipped Stripe 3+7 Enhancer. PLoS ONE 9(5): e91924. doi:10.1371/journal.pone.0091924

Transcription factors (TF) bind to specific DNA sequence to regulate expression of genes. Evolutionary studies of enhancers show that some TF binding sites are well conserved while others are less constrained. The regulatory elements of the even-skipped (eve) gene in Drosophila are a textbook example of regulatory function, as specific activating and repressing TFs bind to specific binding sites and control the spatio-temporal expression of the gene. These enhancers are also a textbook example of TF binding site “turn-over” and compensatory evolution within regulatory elements.

In this study we examine natural sequence polymorphism in characterized enhancers in Drosophila melanogaster, and find the TF binding sites to be preserved by selection. Curiously we find two exceptions, both in the same enhancer of eve (that forms stripes 3 and 7 in the embryo). Both mutations are large deletions (larger than 45 bp) and both remove conserved binding sites for the same transcription factor. Hunchback is an important developmental regulator that affects expression of eve in the embryo. Both deletions are at high frequency in fly populations, and thus do not seem to be harmful for the flies. By analogy one might say that a tree is struck twice by lighting, but doesnt catch fire.

The most puzzling result of this study is that both Hb binding sites are conserved and the two deletions removing them are at up to 35% frequency in the population.

Furthermore, one of the Hb sites was not noticed earlier, because the Drosophila reference genome is homozygous for the deletion allele.

We postulate that coevolution between Hb function and its target sequences best explains the data. In other words, this could reflect compensatory evolution of cis and trans factors, that is developmental system drift in the gene regulatory network controlling stripe formation in fruitfly embryos.

Transcriptional dynamics of a conserved gene expression network

Arnar Pálsson, 25/09/2014

The charr group had one paper accepted in BMC EvoDevo last week. The title is:

Ehsan P Ahi, Kalina H Kapralova, Arnar Palsson, Valerie H Maier, Johannes Gudbrandsson, Sigurdur S Snorrason, Zophonias O Jonsson and Sigridur R Franzdottir Transcriptional dynamics of a conserved gene expression network associated with benthic-limnetic craniofacial divergence in Arctic charr. Abstract to follow.

(Icelandic) Stefnumót skilvirkni og breytileika – snertiflötur þroskunar og þróunar

Arnar Pálsson, 17/09/2014

A review article in Icelandic about the interface of development and evolution, published in the Icelandic Naturalist (Natturufraedingurinn).

(Icelandic) Ritfregn: Tilviljun og nauðsyn

Arnar Pálsson, 17/09/2014

Book review about, the translation of Chance and necessity by Jacques Monod, published in the Icelandic Naturalist (Natturufraedingurinn).

A talk at the Evolution and Ecology center at the University of Oslo

Arnar Pálsson, 01/09/2014

This past Friday (August 29th. 2014) I enjoyed the great fortune of visiting the Center for Ecological and Evolutionary Synthesis at the University of Oslo. A colleague from the Chicago years, Lee Hsiang Liow was our host.

The title of our talk was “On rapid and repeated evolution via transcriptional cooption and decay” and the abstract reads like:

The function and evolution of gene regulatory mechanisms and networks has implications for development, diseases and ecology. In this talk I will describe our work on transcriptional evolution, drawing on studies in two systems. I will outline population genetic, morphometric and transcriptomic analyses of parallel evolution of recently evolved dwarfism and associated phenotypes in Arctic charr (Salvelinus alpinus). Secondly I will focus on naturally occuring deletions of transcription factor bindings sites in characterized enhancers of the even-skipped gene in Drosophila melanogaster. Lastly I will outline musings about general principles of evolution by gene recruitment and transcriptional decay, and predictions that follow.

The talk summarized the Arctic charr work that we participate in and two projects on regulatory evolution. I got great questions and had wonderful conversations while in Oslo. Hopefully I can visit again soon.

(Icelandic) Hver var Thomas Morgan og hvert var hans framlag til erfðafræðinnar?

Arnar Pálsson, 21/08/2014

Sorry, this entry is only available in Icelandic.

Politics, not science, at center of debate

Arnar Pálsson, 20/08/2014

In 2005, while a post doc at the University of Chicago I read a op-ed piece by John Angus Campbell and Stephen Meyer in USA Today titled Evolution: Debate it.

I felt sufficiently outraged by their argument to send a letter to the paper, here printed in full. I would like to thank my friend Kelli Birdsall for reminding me of this letter.

Politics, not science, at center of debate

Commentary writers John Angus Campbell and Stephen Meyer argue for a scientific debate regarding the evolution-intelligent design controversy. While I agree the issue needs to be discussed, the debate has not been and never will be scientific (“How should schools handle evolution? Debate it,” The Forum, Monday).

The writers’ argument displays a basic misunderstanding about how the scientific process yields understanding of the material world. Scientific knowledge is gathered by evaluating logically coherent, testable hypotheses by careful and repeated experiments or comparisons. The process operates very much like a detective does: Possibilities are evaluated and eliminated if disproved. But because intelligent design does not make predictions that can be evaluated scientifically, i.e. are not testable, there is no scientific controversy. A real scientific debate on evolution would unfold in peer-reviewed journals because scientists like very much to prove each other wrong.

Instead, the current debate is social and political in nature. Politicians are exploiting many Christians’ religious convictions for political gain. But, however popular such politicians are in polls or elections, they cannot alter the fundamental discoveries of science — such as gravity, or the fact that life on this planet has shared ancestry and continues to evolve.

This confusion about the scientific process is a severe handicap to our society and calls for reform of the science curriculum. We should teach the scientific method and the testable scientific theories that we have been unable to refute — meaning Charles Darwin’s theory of evolution, and not intelligent design.

Arnar Palsson, Ph.D., Chicago

Science web – human genome

Arnar Pálsson, 19/08/2014

Sorry, this entry is only available in Icelandic.

Naturally occurring deletions of Hunchback binding sites in the even-skipped stripe 3+7 enhancer

Arnar Pálsson, 24/04/2014

Our manuscript on deletion variations in regulatory elements was published in Plos One.

Naturally occurring deletions of Hunchback binding sites in the even-skipped stripe 3+7 enhancer

Arnar Palsson, Natalia Wesolowska, Sigrún Reynisdóttir, Michael Z. Ludwig and Martin Kreitman

Faculty of Life and Environmental Sciences, University of Iceland, Reykjavik, Iceland.

Institute of Biology, University of Iceland, Reykjavik, Iceland

Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA.

Changes in regulatory DNA contribute to phenotypic differences within and between taxa. Comparative studies show that many transcription factor binding sites (TFBS) are conserved between species and functional studies reveal that some mutations segregating within species alter TFBS function. Single base and insertions/deletion polymorphism are rare in characterized regulatory elements in Drosophila melanogaster. Experimentally defined TFBS are nearly devoid of segregating mutations and evolutionarily conserved. For instance, 8 of 11 Hunchback binding sites in the stripe 3+7 enhancer of even-skipped are conserved between D. melanogaster and Drosophila virilis. Oddly, we found a 72 bp deletion that removes one of those binding sites (Hb8), segregating within D. melanogaster. Furthermore, a 45 bp deletion polymorphism in the spacer between the stripe 3+7 and stripe 2 enhancers, removes another predicted Hunchback site. These two deletions are separated by ~250 bp, sit on distinct haplotypes, and segregate at appreciable frequency. The Hb8del is at 5 to 35% frequency in the new world, but also has cosmopolitan distribution. There is depletion of sequence variation on the Hb8del carrying haplotype. Quantitative genetic tests indicate that Hb8del affects developmental time, but not viability of offspring. The Eve expression pattern differs between inbred lines, but the stripe 3 and 7 boundaries are seemingly not affected by the Hb8del. The deletions of those two Hb binding sites in the eve regulatory elements do not appear to be deleterious to D. melanogaster. The data reveal segregating variation for a characterized TFBS, which may reflect evolutionary turnover due to drift or co-evolution.

Figure 1 of the manuscript illustrates the main findings.

About the academic point system at the University of Iceland

Arnar Pálsson, 31/03/2014

Sorry, this entry is only available in Icelandic.