The Feschotte Lab
Department of Biology
Life Science Building
Arlington, TX 76019
Office: B08 / Lab: B02
what's new [archives - page 1]
Welcome to our newest addition, Dr. Aurelie Kapusta, now a postdoc in the lab.
Aurelie did her graduate work in the lab of Mireille Betermier at the CNRS unit CGM in Gif-sur-Yvette, France. She worked on the crazy and fascinating genome gymnastics of the ciliate Paramecium (note the species is called Paramecium tetraurelia, though I am not sure it was named after Aurelie). Check out her latest paper here.
And watch out as Aurelie is also an avid Aikido fighter!
Fairwell to Clement and Sarah
Kudos to Clement Gilbert (left on pic) and Sarah Schaack (right), two superb ex-postdocs in the lab, who have now secured faculty positions.
Clement will join the CNRS unit 'Ecology, Evolution, Symbiosis' at the University of Poitiers, France (his hometown!) where he will work closely with Richard Cordaux, another excellent past collaborator.
Congrats to both et bonne chance pour la suite!
Earlier this year the lab moved to the Engineering and Research Building. The ERB is a brand new state-of-the-art building housing research labs from the College of Engineering and the College of Science.
Our lab and offices are located on the 4th floor of the building alongside several of our close colleagues in the Genome Biology Group, including Pritham, Demuth, Betran labs on the 4th floor and Christensen, Roner and Hurdle labs on the 3rd floor.
Note: while office and lab locations are new, our mailing address remains the same.
Genomic fossils of Hepatitis B-like virus in finch genome
Clement's latest paleovirology effort is published on September 28 in PLoS Biology.
Some highlights from the press:
Science/AAAS: Ancient Virus Found Hiding Out in Finch Genome (by Cassandra Wilyard)
MSNBC/LiveScience: Ancient viruses lurk in songbird's DNA (by Wynne Parry)
Scientific American: Ancient "Fossil" Virus Shows Infection to Be Millions of Years Old (by Katherine Harmon)
The Guardian (Science Blog Punctuated Equilibrium): Fossil virus leaves evolutionary footprints in songbird DNA (by Grrlscientist)
UTA Press Release (by Traci Peterson)
The newest addition to the lab is Xiaoyu Zhuo.
Xiaoyu grew up in Southern China and obtained his B.S. and M.S from Wuhan University. There he studied RNA splicing under the mentorship of Dr. Yi Zhang and Dr. Xiang-Dong Fu. He then worked for a pharmaceutical company for 3 years in the field of drug discovery.
So Xiaoyu is already an accomplished scientist and we are delighted to have him join the lab as a PhD student!
Review article 'Promiscuous DNA: horizontal transfer of transposable elements and why it matters for eukaryotic evolution' published in the September issue of Trends in Ecology and Evolution.
Congrats to Sarah and Clement!
Our Nature paper evaluated as 'must read' by Faculty of 1000 - twice!
Read evaluation by Joachim Kurtz from the University of Muenster, Germany
Read evaluation by Andrea Schorn and Rob Martienssen from Cold Spring Harbor Laboratory, NY, USA
Bloodsucking parasites and mammalian hosts share transposons! Space Invaders strike again.
The parasites include the triatomine Rhodnius prolixus or kissing bug (pic on the left by Erwin Huebner), an insect that feeds on the blood of a variety of mammals, including humans, and is responsible for the transmission of trypanosomes causing Chagas disease. We found that the bug genome harbors four families of DNA transposons that are nearly identical to those found in several vertebrates and include the particularly promiscuous transposon that we previously baptised 'Space Invaders' or SPIN.
We also detected the SPIN transposons in the genome of the great pond snail Lymnaea stagnalis, a species that act as an intermediate host for a number of trematodes or flukes that must complete their cycle in vertebrates, including some of those invaded by SPIN.
We conclude that host-parasite interactions must have facilitated the horizontal transfer of transposons across these widely diverged animals. Given the tremendous impact that transposon invasions can have on the structure and function of genomes, we argue that the passage of transposons across species boundaries has been a previously underappreciated force influencing animal evolution.
Congrats to Clement and Sarah for their outstanding contribution to this work!
Nature Editor's summary
Paleovirology: the past (and future) of viruses buried in the genome
A collection of clips and articles from the general press featuring work from our lab and many others, in the emerging area of 'paleovirology'. This is the study of the ancient history of viruses through the analysis of viral DNA sequences fossilized in the genome of their host species.
Such viral fossils are deposited in the genome when virus DNA integrates into the chromosome of the host reproductive germ cells and becomes subsequenty inherited from parent to offspring, becoming what scientists call 'endogenous viruses'.
Read more about what these fossils can tell us about the past and perhaps also the future of viruses, including some of our deadliest enemies:
Hunting fossil viruses in human DNA, by Carl Zimmer. The New York Times - January 11, 2010
A new breed of viral invasion, by Bob Grant. The Scientist - January 6, 2010
Bornavirus genes found in human DNA, by Tina Saey. Science News - January 6, 2010
Meet your viral ancestors, by Ed Yong. Not Exactly Rocket Science - January 6, 2010
Un nouvel ancetre viral de l'homme, by Stephane Foucart. Le Monde - January 8, 2010
Un nouvel heritage viral dans le genome de l'homme et d'autres mammiferes, by Les Echos via Agence France Presse - January 6, 2010
Genomic fossils in lemurs shed light on origin and evolution of HIV, Science Daily - March 24, 2009
Darwin's surprise, by Michael Specter, The New Yorker - December 3, 2007 (oldies but goodies)
Genomic fossils reveal germline infiltrations of lentivirus in lemurs
In a paper to appear in PLoS Genetics on March 20, we report that a retrovirus called pSIV, related to HIV and primate lentiviruses, has become stably integrated into the genome of several lemurs around 4.2 Million years ago. These are the first endogenous lentiviruses discovered in primates.
The gray mouse lemur Microcebus murinus represents one of two prosimian lineages infected by pSIV.
(Photo credit: David Haring, Duke Lemur Center)
We show that the germline infiltration of pSIV occurred in parallel in two different lineages of lemurs endemic to Madagascar. Based on 'fossil' sequences collected from different lemur species, we reconstructed computationally an apparently intact and complete DNA sequence for an ancestral prosimian lentivirus. These findings should allow future functional analysis of the extinct virus and advance our understanding of the biology and origin of lentiviruses, including HIV.
Space Invaders: more intergalactic tales!
On Feb 10, our SPIN paper was evaluated as 'must read' 'by Faculty of 1000 member Debashish Battacharya (with C-X Chan). Their evalutation can be read here.
The story was also featured in the February Issue of Natural History, the magazine of the American Museum of Natural History.
The Guardian (UK) also highlighted the study in a mildly provocative article entitled "Charles Darwin was wrong about the tree of life". Darwin's sketch of the tree of life is shown on the right.
Lastly, at the invitation of a new open-access journal called Communicative and Integrative Biology. we wrote our own commentary on the study (they call this an 'addendum'). Our addendum gives a few more speculations on how the SPIN invasion could have happened.
Space Invaders have landed!
Our Space Invaders (SPIN) story is getting some nice coverage, both from the specialized and mainstream press. It was really interesting to follow the reaction of people to the Invaders landing around the world. As might be expected the news came with a healthy dose of speculations and some inevitable distortions. Below I have selected some of the most interesting news stories. For the best or the worst.
The New Scientist (USA): 'Space invader' DNA infiltrated mammalian genomes.
GenomeWeb Daily News (USA): Researchers Find Evidence for Horizontal Gene Transfer in Mammals, Reptiles
The Philadephia Inquirer (USA): Study finds DNA crosses species boundaries
The Australian Life Scientist (Australia): Space Invaders transfer horizontally in mammals
Not Exactly Rocket Science (Scienceblog by Ed Yong): Space Invader DNA jumps across species
Softpedia: DNA used viruses to switch species (with a BIG maybe)
Globo.com (Brazil, in portugese): 'Mamíferos e outros bichos são transgênicos naturais, mostra estudo'
Beware the invasion!
In a new paper in press for PNAS, we show that a DNA transposon family dubbed SPACE INVADERS (or SPIN) has independently invaded the genome of seven tetrapod species, including species from 5 mammalian orders, via horizontal transfer (HT).
Horizontal or lateral gene transfer is the transmission of genetic material between repoductively isolated species (as opposed to vertical inheritance from parent to offspring). HT is common and central to the evolution of bacteria, but it has been scarcely reported among eukaryotes.
Our study provides the first unequivocal evidence for the HT of a DNA transposon into distant vertebrates, including African clawed frog, anole lizard, and 5 divergent mammals (bushbaby, tenrec, bat, opossum and murine rodent). We show that these germline infiltrations occured around the same evolutionary time (15-46 Myr ago) and spawned some of the largest bursts of DNA transposon activity ever recorded in any species lineage. For example, about 100,000 SPIN copies are fixed in the tenrec genome!
The mechanism via which SPIN were able to infiltrate the germline of these species (or their ancestors) is unknown, but we think that viruses may have acted as intermediate vectors. Regardless, the data strongly suggest that HT has played an important role in sculpting the genomes of mammals and other tetrapods.
Stay tuned for more SPIN and beware the invasion!
Our research on bat transposons featured on the cover of Genome Research
The photograph shows the Greater Mouse-eared Bat (Myotis myotis), a member of the vespertilionid bat family and a close relative of the Little Brown Bat (Myotis lucifugus).
Bats constitute more than 20% of extant mammalian species and the Vespertilionidae is the most diverse family with about 300 species distributed worldwide. Concomitantly to their diversification over the past 35 million years, vespertilionid bats have experienced successive waves of genome invasion by diverse DNA transposons, mobile genetic elements that use a cut-and-paste mechanism of transposition (schematized at the bottom of the cover). The level of recent DNA transposon activity reflected in the genome of M. lucifugus is unprecedented among mammals and at least one family still appears to be in the midst of its expansion in natural populations.
The pdf of the paper is here.
Transposable Elements and the Evolution of Regulatory Networks
An article [pdf] published in the May issue of Nature Reviews Genetics where I revisit and attempt to merge several influential theories, put forward during the 60s and 70s by some of the pioneers in genome exploration, in support of the idea that TEs play a central role in eukaryotic gene regulation.
The first idea is that interspersed DNA repeats, which derive from the activity of TEs, can provide the raw material for the assembly of regulatory networks by virtue of their ability to disperse and integrate cis-regulatory elements throughout the genome. This hypothesis was first elaborated by Roy Britten and Eric Davidson in their influential '69 Science paper "Gene regulation in higher cells: a theory".
The second inspiration is the concept of evolutionary 'tinkering', as proposed by Francois Jacob in 1977 (Science 196:1161), which postulates that regulatory evolution proceeds mainly by rearrangement and re-utilization of pre-existing forms and material. This is also reminiscent of the concept of 'exaptation', first introduced by Gould and Vrba in 1982, which refers to the co-option, of a functional character or structure for a new function. It is now clear that exaptation of TEs is common occurence and that the process, together with movement and chromosomal rearrangements mediated by TEs, contributes to the rewiring and tinkering of regulatory networks.
The third and most provocative concept pertains to Barbara McClintock's definition of TEs as 'controlling elements' that can directly influence the regulation of host genes located in their vicinity. A growing amount of data supports the view that TEs are often incorporated into the regulatory apparatus of adjacent genes, and frequently exert their effect on gene expression via epigenetic modifications. In addition, there is now direct evidence that TE-encoded proteins (e.g. transposase) are occasionally recycled into trans-acting regulators, such as transcription factors (one example drawn from our research).
Bat genome recently invaded by diverse DNA transposons
The level of DNA transposon activty observed over the past 35 Myr of vespertilionid bat evolution is unprecedented in mammals. We show that this activity has been continuous, but has involved distinct waves of amplification of diverse families, some of which have never been reported in any vertebrate species. Most likely these elements have infiltrated the genome horizontally from exogeneous sources. We identified at least one transposon family that seems to be in the midst of its expansion in natural populations.
Together with our previous report of massive Helitron activity in the M. lucifugus lineage, this new study further emphasizes that the genomes of vespertilionid bats harbor a very distinctive transposon landscape than other mammals. The reason(s) for this remains a mystery that we are now gearing up to resolve. Bats rock.
Faculty of 1000 highlights two of our recent papers
On Jan 11, Faculty of 1000 member Manyuan Long, from the University of Chicago, evaluated as 'must read' our paper in Science on transposase-derived transcription factors in Arabidopsis. His evalutation can be read here.
On Jan 24, Faculty of 1000 member Vish Nene, from the Institute for Genome Sciences in Baltimore, evaluated as 'recommended' our paper in GENE on Mavericks, a new class of transposable elements related to DNA viruses. His evaluation is here.Thanks to these two outstanding scientists for their interests in our research. It brings the number of our F1000-evaluated papers to seven.
ILLUMINATING TRANSPOSONS! Domesticated transposases modulate plant light responses
The work establishes that two Arabidopsis proteins, FHY3 and FAR1, entirely derived from Mutator-like transposases, are transcription factors that directly bind to and activate a network of genes involved in light signaling. Genetic analysis shows that the domesticated transposases are required for the plant's response to far-red light and that both proteins have partially redundant function and DNA targets in Arabidopsis. Moreover, FHY3 and FAR1 have separable DNA-binding and transcriptional activation domains that are highly conserved in Mutator-like transposases, suggesting that their transcription factor activity has been inherited from the ancestral transposase and that Mutator-like transposases can be readily recycled into transcription factors.
NSF has posted a press release [here] that covers mostly the physiological insights of the study. I'll post more on the evolutionary aspects whenever I have a decent lapse of time to update the quiescent Mobile DNA blog.
The pic [high-resolution] shows micrographs of Arabidopsis roots expressing fusion GFP-FHY3 proteins. The artists have superimposed computational models showing FHY3 protein (in green) binding to DNA (in gray). (Credit: Pelkie, Daniel Ripoll, and Rongcheng Lin)
PDF of the paper.
TAMED TWICE! Convergent Domestication of Transposases into Centromere-binding Proteins in Yeast and Mammals
In this paper, which appeared in Advance Access for MBE on Oct 16, we show that two different sources of pogo-like transposases were recruited independently in the lineages of fission yeast and mammals to become centromere-binding proteins with important, albeit probably distinct chromosomal functions for their hosts. This is what we call 'convergent transposase domestication'. Congrats to Claudio and Don for their equally outstanding contribution to this study. Double congrats to Don for his first paper! The preprint is here.
Chromosome art by Alisa Poh [buy it].
Welcome Qi, Stephanie and John and farewell Claudio!
With each new semester comes the addition of new members in the lab and the regretted departure of some others. This Fall, we are welcoming Qi Wang, a new PhD student coming from China (pic on the right) as well as two new undergrads, Stephanie Ethofer and John McCormick.
Meanwhile, we wish good luck to Claudio Casola, which has just joined the lab of Matt Hahn at Indiana University as a postdoc. Claudio leaves a great record of research accomplishments in the lab and his enthusiasm will stick with us forever. GRANDE!
Faculty of 1000 evaluates our paper on human DNA transposons
June 2007 - Faculty of 1000 member and eminent evolutionary biologist Deborah Charlesworth evaluated our paper on the evolution of human DNA transposons. The paper, recently published in Genome Research, was evaluated as 'Recommended' and as 'Tech Advance'. This is the fifth paper co-authored by CF that is evaluated by F1000.
Read the evaluation here.
PIF-like transposons and derived genes in Drosophila
In this new paper, we show that members of the PIF superfamily of DNA transposons are present, diverse and sometimes abundant in Drosophila species. Perhaps even more unexpectedly, we also found that this type of elements have been a reccurent source of new 'host' genes, recycling transposase and other coding sequences into novel functional proteins throughout Drosophila evolution. We speculate that these proteins are now functioning as transcription factors in the flies.
The paper appeared online June 7, 2007 in MBE and the pre-print is here.
Congrats Claudio and co.!
On the road...
Two exciting conferences that we will be attending this summer:
June 2-8: FASEB Summer Research Conference on 'Mobile Elements in Mammalian Genomes' in Tucson, AZ [program]
July 11-13: AGA Annual Symposium 'Mechanisms of Genome Evolution' in Bloomington, IN [program]
Two NIH grants awarded!
Our research on human DNA transposons is now funded by a NIH/NIGMS R01 grant (abstract). In addition, we also received funding from NIH/NIAID for our collaborative research with Jessica Kissinger and Ellen Pritham on TEs and other repeats in apicomplexan genomes (abstract).
Evolutionary history of human DNA transposons: intense activity in the primate lineage
John's first paper is now in press for Genome Research -- congrats John!
Contrary to the long-standing view that human DNA transposons are ancient molecular fossils, we show that nearly 100,000 human DNA transposons were integrated during primate evolution, but prior to the emergence of New World Monkeys, about 40 Myr ago. The picture on the left shows a galago, a primate that lacks many of the DNA transposons present in human.
The paper appeared online March 5, 2007 and the final PDF is here.
An explosive amplification of rolling-circle transposons in bats!
A collaborative work with Ellen Pritham. In press for PNAS,
Bats constitute more than 20% of extant mammalian species and the vesper bats are the most successful group with about 300 species distributed worldwide. Concomitantly to their early diversification, about 30 million years ago, some vesper bats experienced a massive colonization of their genomes by rolling-circle transposons (or Helitrons). These elements now make up at least 3% of the genome of the little brown bat and they have been involved in the movement and duplication of host genes. This is the first report of rolling-circle transposons in mammals.
The paper appeard online January 30, 2007 and the PDF is here.
Comparative genomics of Drosophila retrogenes
A collaborative work with the Betran lab.
In press for Genome Biology [open access]
The evolutionary history of 97 functional retrogenes identified in D. melanogaster was reconstructed using the wealth of data provided by the genome sequences of 12 additional Drosophila species. This analysis reveals that functional retrogenes originate at a constant rate of about 0.5 gene per Myr during the Drosophila radiation.