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The Feschotte Lab
Eccles Institute of Human Genetics
15 North 2030 East
Salt Lake City, UT 84112
Office: Rm. 6150
Office: (801) 858-6061
Secrets of Snakes - Python and Cobra Genomes
Analyses of the first two snake genome sequences published in PNAS. Feschotte lab contributed to transposon analysis of the Burmese python genome, as part of a consortium led by Todd Castoe.
Python genome paper is here.
New Pritham-Feschotte group picture!
We closed 2013 with this group picture taken right here in the mighty Wasatch foothills. Click to enlarge. From left to right: Ellen Pritham, Ed Chuong, Jainy Thomas, Mauro Ortiz, Julia Carleton (roton), John McCormick, Ray Malfavon-Borja, Clay Carey (roton), Aurelie Kapusta, Xiaoyu Zhuo, Peng Wei (roton), CF.
Mauro Ortiz visits us from Brazil
We are very pleased to host Mauro de Freitas Ortiz, a visiting graduate student from the Federal University of Rio Grande do Sul in Brazil. Mauro is carrying his dissertation under the mentorship of Dr. Elgion Loreto, who has been studying the evolutionary genetics of Drosophila transposable elements for more than two decades with a strong focus on horizontal transfer. Mauro was awarded a fellowship from the Brazilian government to train for nine months in the lab. He is carrying a systematic assessment of the rate of horizontal transposon transfer in various mammal lineages.
Julia and Clay rotate in the lab
This month we welcome two new MB rotation students in the lab:
Julia Carleton, who grew up and studied in Portland, Oregon. Julia's rotation project is to annotate DNA transposons in Biomphalaria glabrata, a freshwater snail that is an intermediate host for Schistosoma parasitic trematodes. Almost nothing is known about mobile elements in molluscs so we are curious to see what lurks in this genome. This work is part of a large collaborative effort led by Pat Minx at The Genome Institute of Wash U.
Clay Carey comes from Humboldt, California. During this rotation, Clay will contribute to another transposon annotation project: that of the micronuclear (germline) genome of the model ciliate Tetrahymena thermophila. This genome project is led by Bob Coyne at the J. Craig Venter Institute. A unique feat of ciliates is that their single cell harbor two nuclei: a micronucleus (MIC) which is a transcriptionally silenced "sexual" germline genome, and a macronucleus (MAC) which is a derived, simplified, and edited version of the MIC that serves all somatic cellular functions. All transposon sequences are thought to be removed from the MIC during its transition to MAC. However only the MIC genome has been analyzed thus far, so we don't actually know much about the amount and type of transposons hiding in the MIC. Surely Clay's work will tell us a lot more soon!
Clay is also a talented nature photographer, make sure to take a peek at his amazing photos here.
Keystone symposium 'Mobile Genetic Elements and Genome Evolution'
Together with Nancy Craig and Henry Levin, I am co-organizing a Keystone Symposium on Mobile Genetic Elements and Genome Evolution in Santa Fe, New Mexico, March 9-14, 2014.
This international meeting will draw speakers and participants studying a wide range of organisms, systems, and questions.
The list of invited speakers can be found here. There will also be many short talks selected upon abstract, two special workshops (themes to be determined based on abstracts) and of course poster sessions.
Deadline for Abstract submission is Dec 9, 2013.
Deadline for Discounted Registration is Jan 8, 2014.
Congrats Xiaoyu on the paper and cover in JVI !
Xiaoyu Zhuo's paper on bat endogenous retroviruses is now published in the Journal of Virology.
He then moved up north to do his graduate work with Julie Baker at Stanford on regulatory genomics in the placenta.
His PhD work culminated in the publication this year of a spectacular paper in Nature Genetics on endogenous retroviruses functioning as lineage-specific placenta enhancers. More here on the theme.
Needless to say, we are delighted to have Ed joining forces with us and the Elde lab for a new ambitious project on the role of endogenous retroviruses in the evolution of the immune system.
After an heroic rotation in the lab this Spring, we are delighted to announce John McCormick has decided to join us for his PhD research.
John will be developing zebrafish as a model to investigate the short-term and long-term impact of transposable elements on organism function and evolution.
More about John here.
TEs & lncRNAs : our paper's out in PLOS Genetics
On April 25, 2013 PLOS Genetics publishes our paper entitled " Transposable Elements Are Major Contributors to the Origin, Diversification, and Regulation of Vertebrate Long Noncoding RNAs".
One of the most startling discoveries of vertebrate genomics is the realization that genes encoding functional non-coding RNAs are likely to outnumber those encoding proteins. Currently ~10,000 lncRNA genes are annotated in the human genome and their regulatory functions are being revealed at a very fast pace. By contrast we know almost nothing about their evolution. Where do lncRNAs come from? How do they emerge and diversify?
In this study, we provide evidence that transposable elements are major components of lncRNAs. While TEs are seldom seen in protein-coding transcripts, they are ubiquitous and make up a substantial fraction of mature lncRNA transcripts (~30% in human). Many TE families are enriched within and in the vicinity of lncRNA genes, where they frequently contribute to their transcriptional regulation. These are predominantly endogenous retroviruses, as shown in purple in the wordle above.
In the human genome alone, we found that TEs contribute ~30,000 unique sites for transcription initiation, splicing, or polyadenylation of lncRNAs, highlighting the pervasive involvement of TEs in the biogenesis of lncRNAs. These global trends are recapitulated in several well-studied lncRNAs with established functions. Finally we show that a subset of TEs embedded in lncRNAs are subject to RNA editing and are predicted to form secondary structures important for lncRNA function.
These results highlight yet another way mobile genetic elements have influenced genome evolution and shaped a crucial layer of cellular and developmental regulation.
Congrats to Aurelie and all coauthors!
Welcome to Aditi Rambani, who is joining us for a few months to work on bat genome evolution.
Aditi graduated with a Master's from Brigham Young University where she worked on cotton genomics in Josh Udall lab. Her research involved a comparative analysis of the transcriptome and DNA methylome of diploid and tetraploid cotton genomes.
After this interlude in the lab, Aditi will return to plant genomics as a PhD student at the University of Tennessee.
Cedric joins PLOS Genetics board and F1000
Cedric is now an Associate Editor for PLOS Genetics.
First F1000 recommendation is here.
Follow to be alerted of the next recommendation.
Welcome to Dr. Ray Malfavon-Borja, a new postdoctoral associate in the lab!
Ray joins us after graduating with a PhD in Genome Sciences from the University of Washington. For his dissertation, Ray worked with Harmit Malik and Michael Emerman to identify novel retroviral restriction factors in primates. See his recent PNAS paper here.
Ray was born and raised in Southern California, and is a self-proclaimed 'GuaMexican'. Outside the lab, and depending on the season, there are two places where one is most likely to encounter Ray: here or here. And yes Ray also likes to sneak into refrigerators.
piggyBat: first active mammalian DNA transposon
piggyBat elements have colonized very recently the genome of Myotis lucifugus. A canonical autonomous copy extracted from the genome is capable of transposition in human, bat, and yeast cells.
piggyBat is distantly related to piggyBac, another active transposon family from a moth originally discovered because it had jumped from its lepidopteran host cell into a baculovirus. Naughty transposons. Since then piggyBac has been shown to be active in a wide range of species when experimentally introduced and is widely used for gene tagging and genome engineering (for example).
How did piggyBat enter the bat genome to begin with is unknown. But I am willing to bet it's been acquired from a moth or another insect which these bats devour in enormous quantity (a single Myotis bat eats its own body weight in insects every day). But that's another story...
Anyway we're excited because piggyBat is the first naturally active DNA transposon family identified in a mammal. This system offers an unprecedented opportunity to study the mechanism, regulation, and genomic consequences of cut-and-paste transposition in a mammalian host.
Della rotates in the lab
Welcome to Della Fixsen, 1st year MB PhD student, who rotates in the lab for six weeks to take a closer look at the life cycle of human endogenous retroviruses.
Della is also a serious rock climber [watch]
Space Invader Transposon Resurrected
Nancy Craig and her group at Johns Hopkins University resurrected an active SPIN transposon that jumps at high frequency in human cells in culture.
The reactivated element brings a new potent addition to the transposon toolbox for genome engineering.
June 2012: we've moved to Utah!
I am accepting applications for PhD students and postdocs. See ad to follow soon for more information. If you are interested, do not hesitate to email me.
Useful info on the Bioscience/Molecular Biology PhD Programs at the U.
Top ten reasons to live (and study) in Utah.
Our research on the front page of "Le Monde.fr"
Read a very nice interview of Clement Gilbert (now working here) exploring the exciting new field of paleovirology for the top French newspaper "Le Monde". This was conducted by Pierre Barthelemy for his excellent blog, Passeur de Sciences, and appeared on the homepage of LeMonde.fr on May 28, 2012.
Endogenous viruses for Nature Reviews Genetics
Published in the April 2012 issue of Nature Reviews Genetics:
Endogenous viruses: insights into viral evolution and impact on host biology
Cedric Feschotte & Clement Gilbert
The Beauty of Reptilian Genomes
This magnificient creature on the left is a copperhead.
Copperheads are very common around Arlington. I found this fortunate, but not everybody agrees. Anyhow, this month we co-authored three papers that illustrate how fascinating these and other reptiles are when it comes to their genomes too. On this I hope everybody will agree.
The first paper, spearheaded by Todd Castoe and David Pollock at the University of Colorado Health Sciences Center, uses next-gen sequencing to carry out a comparative analysis of the repetitive DNA landscape of two celebrated snakes, the copperhead and the Burmese python. The two species display striking differences in repeat content, with the copperhead genome having two-fold higher density of TEs and much higher levels of TE-derived transcripts, despite having a smaller genome. How this might relate to differences in morphology and physiology between these two group of snakes is an interesting question awaiting further investigation.
The second paper reports the result of a large-scale screen to detect SPIN transposons in non-avian reptiles conducted by postdoc Clement Gilbert and a bunch of talented undergrads. We found that SPIN was introduced horizontally no less than 15 times in various lineages of squamates (lizards, snakes, including copperhead). In contrast, we found no traces of SPIN in crocodiles and turtles. These data triples the number of SPIN horizontal transfers known in animals and confirms a previously hypothesized transoceanic movement of the transposon.
The third paper summarizes the effort of the recently established Snake Genomics Consortium to produce a whole genome sequence for the Burmese python, led by Todd and David. A first draft of the genome assembly was released earlier this year. We are glad to participate in this exciting endeavor and look forward to getting involved in more genomic explorations of the reptile world.