beyond the north-eastern US, toinclude78particip beyond north-eastern the with The University Chicago of stimulated the expansion ofthisinitially regional meeting silico, invitro, invivo Keywords MA,USA. Woods Hole, in (MBL) Laboratory Biological Marine Elements: Genetic “Mobile conference, atarecent gap of diverse MGEs. Experimental andcomputational scientists came together to bridgethis * Phoebe A.Rice† and Irina R.Arkhipova* Elements: Genetic Mobile This article is protected Allrights bycopyright. reserved. 10.1111/mec.13543 of Record.versiondifferences and article Please between the cite this Version this as doi: through the copyediting, typesetting, pagination for publication accepted This articlehasbeen M ANDVIEWS NEWS Article type:Meeting Review : 15-Jan-2016 Date Accepted : 30-Nov-2015 Date Received of information provided by them, of informationprovided thefieldinto anew catapulted technology have applicati clever biotechnology inunderstanding thedeta advances steady of stream forherinsightf Prize a Nobel awarded was finally was firstdescri ofMGEs Theexistence revol steam inthelate1970sfollowing technical gather onMGEsbegan to atfirst,work (McClintock 1950,1953).Although appreciated poorly E- 1-773-702-0439; Rice; fax Irina Correspondence: Arkhipova; 1-508-457- fax traditional genomic studies, andalimited number ofexperimentalmodels amenablemore to discovery TE fast-paced between agap currently is there However, evolution. and function, organization, are and most of components universal represent (TEs), elements transposable called also (MGEs), elements genetic Mobile 60637, USA Biology,TheUnivers Biochemistry andMolecular Biological Laboratory,7Woods MA02543, MBL Street, Hole, Josephine Bay Paul Center forComparati Josephine BayPaulCenter

Accepted Article EETING R : transposable elements, : transposableelements, EVIEW in vitro

and ” held recent onSeptember (Fig. 1).The affiliation 3-5,2015 ofthe MBL in vivo in in silico, In Silico, InVitro,Vivo In mail: [email protected] mail: [email protected] ons for them. Most recently, revolutions inDNAsequencing revolutions ons forthem.Mostrecently, studies of structural, mechanistic, and regulatory properties properties regulatory and mechanistic, structural, of studies permeated much of the meeting ofthe much permeated stimulated byexponential growth of comparative ve Molecular Biology and Evolution, Marine ve MolecularBiologyandEvolution, and undergone full peer review buthasnot been review undergone fullpeer and bed by Barbara McClintock inthe1950s McClintock Barbara bed by chapter. These new technologies, and the flood andthe newtechnologies, These chapter. and proofreading process, which may lead to utions inmolecularbiology, utions andMcClintock ul work in 1983. The following decades saw a saw decades ul workin1983.Thefollowing 4727; E-mail:iarkhipova ity ofChicago,929E.57thStreet,IL intimately involved innearly allaspects of , transposition,genom ants from 14 states and 3 Canadian provinces. 3 Canadianprovinces. ants from14statesand ils of how such elements can move as well as canmoveaswell ils ofhowsuchelements

in silico, invitro, invivo USA; †Department of USA; †Department “ : ics, bioinformatics ics, @mbl.edu; Phoebe ,” heldatthe in assemble highlygenomic similar output ofwhichwasvali our own V(D)J recombinationsystem andmi our ownV(D)J inteinsspreadby Many mobileintronsand theyhave process: break repair Connecticut) presented a comput a Connecticut) presented assembly data for next-generation cloud computingBaseSpace environment fromIl data, whichrepetitive can beproblematic for highly sequences. rawsequence the analyzing correctly is TEidentification concomitant and assembly genome workshop ledby abioinformatics offered Amother lode ofnewinsights lurkswithinthe and ever-expanding entirely MGEs new be a daunting task. To facilitate data processingas well as database utilization, the meeting thoseoutsideofthe butfor sequence databases, this astransposases, toact recombinases known (Kim structure domain catalytic 2015) andDyda, (Hickman ends intoatarget DNA i Cas1proteincan purified casposon evidence that “casposons” (Krupovic systems also acquisition inCRISPR are spacer andKoonin,2015). (Krupovic transposon ancestors Eugene Koonin someMG ofevolution, course During the thatallowthehostorgaadaptive immunity systems partofanorganism anintegral are where they backbone. change totheprotein when they doevolve torecognize different targets, theycan do sowithvery little structural effortsonthemost theirrecognition concentrate bioinformatics, bioche of target specificity thecomparative examined perse. sequence particular DNA to have the ability torecognize the conserved coding for protein region sequencesa than It istheref process. repair locus during the thatthey havenot hostgene relatives of)their Novikova conditions ( This article is protected Allrights bycopyright. reserved. Accepted which typicallydiscovery toolfornovelrepeats Articlewhen itwouldbe detrimental tothe cell (Callahan describedexamples ofinteins where splicin thusavoiding interf proteins aftertranslation, thehostcantolerate thought that ofasparasites ad protein domains)couldprovide In keeping withMcClintock’s original suggestion that MGEscan regulatory have roles, by one theme ofthe meeting was the interactions be Marlene Belfort Marlene et al et e.g . 2015). . 2015). . redox state and temperature), and can t and andtemperature), state . redox (NCBI/NIH), making splendid use of (NCBI/NIH), splendiduse making (SUNY at Albany) described howmobile intronsand inteins at (self-splicing Albany) described (SUNY mistry, and crystallography, showing that homing endonucleases showingmistry, endonucleases crystallography, thathoming and et al dated by repeat alignment to PacBio long reads. The pipeline can pipeline reads. The long PacBio to alignment repeat by dated . 2014). a “homing endonuclease” a “homing activity endonuclease” th et al et ational repeat identification identification ational repeat Barry Stoddard repeats directly from raw shotgun reads, and can be used as a usedas and canbe reads, rawshotgun from directly repeats and downstream applications. and downstream aptive features to their hosts. Inteins have generally been been Inteins generally have hosts. their to features aptive . 2013; Nuñez . 2013;Nuñez Alison Hickman Vladimir Kapitonov ore perhaps more important for homing endonucleases homing endonucleases moreimportantfor ore perhaps g onpar isdependent crobial CRISPR/Cas systemscrobial evolvedfrom erence withhostfunction. erence . Striking examples of this can befoundin ofthiscan . Striking examples homing endonucleases with acombination of with endonucleases homing yet invaded, and are then copied intothenew copied yet then invaded, andare conserved in a set of transposons termed transposons inasetof conserved because they splice themselves outoftheirhost themselves they splice because informatics field, exploiting those resources can field,exploiting can thoseresources informatics fail to assemble from such short reads. short reads. toassemblefromsuch fail represents a new family of DNA transposase. DNA transposase. of family anew represents conserved nucleotides of each codon,butthat ofeach nucleotides conserved tween MGEs and their hosts. Thekeynote talk and theirhosts. tween MGEs lumina, which permits hassle-free workflows workflows whichpermitshassle-free lumina, Es have become “domesticated” to the point point the to “domesticated” become Es have (Fred Hutchinson Cancer Research Center) Research Center) HutchinsonCancer (Fred exploitingdouble strand theirhostorganism’s ndeed catalyze integration ofpairedCasposon integration ndeed catalyze et al et . As Cas1 proteins have a very different avery different . AsCas1proteinshave nisms the flexibility to react to new attacks. react tonew nisms theflexibility to et al et The Cas1 proteins that are required for arerequired TheCas1proteinsthat (NIDDK/NIH) presented thefirst presented (NIDDK/NIH) hus inhibittheirhostproteins’function genomic databases, . 2011;Topilina . 2014) from any of theother . 2014)fromany of

pipeline called REPdenovo,the pipeline called (NCBI/NIH). Thefirstissuein (NCBI/NIH). Chandrasen Soans ticular environmental Chong Chu at cleaves copies of (or close (or copiesof at cleaves et al et However, Dr.Belfort However, described howboth . 2014,2015; (University of offeredthe copepods, freshwater crustaceans with many experi withmany crustaceans copepods, freshwater structure. complex a ofMGEfamilies large variety with TElandscape anunusual shaped apparently asexual bdelloid rotifers, small aquatic invertebrates inwhich potent silencing mechanisms (Arriagada (Arriagada mission, severala In withMBL’s keeping element, genetic mobile aretrovirus-like with associated is that clams affecting cancer copepods. clams, rotifers,and junction resolvases (Mukha junction resolvases(Mukha domain,whichshowsan restriction endonuclease-like from of theR2Bm atArlington) combined ofTexas (University This article is protected Allrights bycopyright. reserved. Acceptedorganism (Sun “recyc andpresumably ofsomaticcells genomes early development, billionsofbasegenome) ofthe TEs(>50% total pairs are of deleted fromthe a dramatic undergo eggs. These andexternal size Kleckner2014). and (Gladyshev duplexes homology DNA between a newmechan tounderstanding repeats may lead unusualability organism’s described howthat to Gladyshev previous than greater systems iseven within ourownmicrobiome,and In commonmodelor looking beyond themost and the ofChicago, University Laboratory, The other genomicrearrangements Article2015). (Kapitonov andKoonin, subunitstoasingle recombinase RAG2 V(D)J and RAG1 ofvertebrate origins the trace to wasable way, he In this encoded. were proteins thenlooks for pa proteins withrelateddomains, for databases the by searches MGEs, beexploited to likely domains catalytic of alignments 2015 andDyda (Hickman another andtoRNaseH and re transposases DNA of“classical” domains toexploi approach Adifferent catalytic the –forinstance, contexts different in repeatedly domains catalytic certain exploited mobile elementsbeginni of types for new search (Jin analyses expression differential during generated of mapping toimproverecovery calledTEtrans package inasoftware Laboratory) repetitiveaddressed sequences by was and deletions infruitflies(Rahman The existence ofmultiple genomic same sequences forthe orsimilar species provides a to exploiting MGEecology utilizing hislab’s database, new transposoninsertions of TIDAL, ofMGEs. new windowontheecology (Harvard University), working with the filamentous fungus fungus withthefilamentous working University), (Harvard et al et et al et . 2014; Metzger . 2014; . 2015). Grace Wyngaard Grace et al et can be found. For example, example, For can befound. Michael Metzger Michael nd superfamilies, including novel nd superfamilies, TE-derived transcripts in large transcriptomic datasets inlarge transcripts transcriptomic TE-derived et al et . 2013). . 2013). Eugene Koonin Bombyx mori et al et . 2015). ly suspected (Koonin and Krupovic 2015). (KooninandKrupovic2015). suspected ly ting the databases, presented by (James Madison University) introduced the audience to to audience the introduced University) Madison (James Ying Jin Ying Nelson Lau Nelson . 2015). The problemofma . 2015). in silico Irina Arkhipova Irina transposon found in echinoderms and oysters andoysters foundinechinoderms transposon tterns in the larger genomic context wherethose genomic context tterns inthelarger and MBL) described thevariet described MBL) troviral integrases are closely related to one to closely related are integrases troviral ng with known catalytic modules. Evolutionhas ng withknowncatalytic generate mutationsi generate to reveal noncanonical catalytic residues inthe residues catalytic torevealnoncanonical led” as a nutritional source forthedeveloping asanutritionalsource led” ism for the direct recognition of sequence ofsequence forthedirect recognition ism (Columbia University) atypically low overall transposon contentbuta transposon lowoverall atypically cripts, which deals with ambiguous short-read whichdealswithambiguous short-read cripts, quatic systems were described, including including described, were quatic systems genomic pruning: at a predetermined stage of stage genomicat apredetermined pruning: ). Dr. Kapitonov thus begins with sequence ). Dr.Kapitonovthusbegins withsequence explained that the variety of CRISPR/Cas of CRISPR/Cas variety the that explained (Brandeis University) described his approach describedhisapproach University) (Brandeis mentally convenient features suchassmall features mentally convenient Molly Hammell modeling with ganisms, an amazing variety of MGEsand anamazingganisms, variety et al et intriguing similarity structural toHolliday

. 2015). Jack Gilbert (MBL) focused her talk on hertalk (MBL)focused retroelements of exceptionally ofexceptionally retroelements pping RNA-seq datato pping in vitro Aruna Govindaraju Aruna nduced by DNA sequence sequence by DNA nduced (ColdSpring Harbor Vladimir Kapitonov Neurospora crassa Neurospora (Argonne National National (Argonne described a described contagious y of mobile elements elements y ofmobile biochemicalstudies Eugene Steamer

, , isto

genome. genome. withnon-autonomousAl elements, whichtogether mostprominentforcesshaping the DNAtransposonsandphages represent While In retroelements. over by e inmanygenomes, prokaryotic that supportDNAreplication. forhelicases common asis ring ahexameric forms it showing that latter, the of structure crystal encoded thatcarries by the MGE methicillin resistance inStaphylococci. She also presented the homologies betweenreplication the initiator /helicase SaPIs ofthe conservedand a protein This article is protected Allrights bycopyright. reserved. Drosophila, inwhich eukaryotic MGEswere initially discovered, to offer continues rich genomic of comparing environments landscapes fixation regional integration and ofsophi thepower State University) demonstrated as retrotransposons. intragenomically line andnowspread have which retroviruses (ERVs), Computationalstudiesuncovered differe retrotransposon biology. translocations. engaged in,leading interactions thatthey are 53BP1, retrotransposon-containing locishow Rocha eviden finding lymphomas telomerase, lacking mechanisms toch other recombination-based Morrish to be critical retrotransposition fortheir 3’-termini the at poly(A)-tracts to transcriptase) experimentally Alu pairby highlighted by (Dartmouth College), respectively. Mother penchant forrecycling Nature’s basic machinery was entities were described by and themechanism inunderstanding advances of the meeting Another recurring was theme the between interplay ofMGEs the world In th and thatofvirusesbacteriophages. naturally occurring fixed and polymorphic insertion sites. and polymorphic insertion fixed naturally occurring of fraction LINEs,Inaddition to asizeable transcripts inmultiple tissues, andgenes. effectively ofover expression human a drives thousand promot antisense by its mediated on adjacent transf facilitated by can alsobe genomes.Horizont orprophage the integrated SaPI from aredistant that genes ofchromosomal transfer horizontal the trigger can ofSaPIs presence (Chen and theirhelperphages between theSaPIs hislab’s University) described strains. new to horizontally transferred SaPIs efficiently the SaPI hijackedtopackage are (SaPIs), Accepted fly Thefruit meeting. the at prominently featured werealso organisms model Traditional Article (New York University) (New reported that, inth (University of Toledo) explored therela Toledo) explored of (University John Moran Phoebe Rice Phoebe (University of Michigan) explained the extraordinary success of the L1- the of success extraordinary the explained Michigan) of (University Steve Criscione Steve particular, mammalian Andrew Lang demonstratingaffinity the (University of Chicago), who found (through whofound(through (University ofChicago), recent advances in understanding the regulatory interplay theregulatoryunderstanding interplay in advances recent ukaryotes genome re-shaping an re-shaping genome ukaryotes abandoned their infectious lifestyles upon entering the germ the uponentering infectious lifestyles abandoned their er agents andLang(Mercer 2014; Lang ex vivo in cis (Memorial University) (Memorial and (Brown University) presented evidence of L1 impact L1 impact of evidence presented University) (Brown mammaliangenomesis of ERVs in mouse and human genomes by genomes by of ERVsinmouseandhuman integration sites intissue culture cells to those of e case oftheStaphyloccocal case e romosome end maintena to more frequent invol frequent to more and an increase in the amount of chromosomal intheamountofchromosomal an increase ce consistent withmultiple ce mechanisms. evolution of these domesticated phage-like ofthesedomesticated evolution of both L1 and Alu elements, whichturnedout L1Alu elements, both of and nt complementing aspects of mammalian ofmammalian nt complementing aspects et al tive contribution of L1 and retrotransposition tive contributionof genomes are densely populated by LINE by populated densely are genomes e absence of the DNA damage sensor protein sensorprotein damage theDNA absenceof e in trans sticated statisticalanal u repeats make up about one-thirdofourown upabout u repeatsmake er, which gives rise to numerous alternative alternative numerous gives to rise er, which al transfer of genetic material among bacteria bacteria genetic among material al transferof DNA rather than their own. Thistrickgets thantheir rather DNA . 2015). He also described howthe . 2015).Healsodescribed of L1-encoded ORF2 (reverse

(Doucet (Doucet Kateryna Makova Richard Novick d remodeling has been taken taken hasbeen d remodeling et al et derived from endogenous vement inchromosomal vement Migun ShakyaMigun nce in mouse B-cell B-cell mouse in nce . 2015). ysis methodstouncover pathogenicity islands in silico in et al et (New York (NewYork (Pennsylvania (Pennsylvania Tammy Tammy . 2015). Recent . 2015).Recent approaches) approaches)

Pedro the mammalian genome, and the mammaliangenome, competition betweenLINE retrotransposon subfamilie Neretti (Venner sites integration available or enzymes common for e.g. resources, ecological models Ofnote,applicationsof forshared competing areoccasionally which community, genome the of asmembers existence co- ontheir and focuses mini-ecosystem, a as genome the views ofTEs ecology Molecular their catalytic andhighlighting function complexity the ofancestral relationships. telomerases, and itsmaturase domain tospliceoso theII similaritywhich revealed intron, ofitsreverse transcriptase catalyticdomain toeukaryotic Belfort Marlene in conjunctionwithbiochemistry alsohighli was analyze spatial distribution of TEs along distributionof TEsalong analyze spatial how itdoesitsjob(Shi structures thathelpexplain This article is protected Allrights bycopyright. reserved. that targets replication forks. (Fricker families several from MGEs prokaryotic by targeted also forksare Replication apparatustowa proteins thatsteerthetransposition Tn7 and Peters2014).Transposon pombe Schizosaccharomyces retrotranspositionyeast intermediates in cellsyeast, mother withage. The fission ofTy1 accumulation ofpreferential evidence and provided aging, study to system a model impact reproduction. asymmetric occurring thenormally counteract budding yeast polebodies(thefunc assembly sitesandspindle of ease the in advantage yeasts anunmatched provide eukaryotes, Ofunicellular Joan Curcio by employed approaches experimental combining ofhTDP-43. effects neurodegenerative betwee critical connection and tomakea humanTDP-43proteinimpli toexpress Laboratory) transcripts (Yu populations. and foridentification quantitation(conTExt) oftandemly across sequences repeated natural segr formation andchromosome theinvolvement (Cornell University)emphasized roles opportunities forinvestigating their Accepted (Jacobs LTRby retrotransposons explan providing an barrier, used aspolarfork is protein Sap1 forkswhen replication arrested to aretargeted elements Tf1 retrotransposable Articlereinforces transcriptional silencing acomponent introducedPanoramix, Laboratory) muta other by down-regulated anditscontrolof formation, heterochromatin a Drosophilahi dSETDB1,connections between (Brown University) used models derived from ecological communities to reveal reveal to communities ecological from derived usedmodels University) (Brown (Wadsworth Center) reported thestable Center)reported (Wadsworth Prashanth Rangan Saccharomyces cerevisiae Saccharomyces et al et reported a high-resolution cryo-EM struct ahigh-resolution cryo-EM reported . 2015). The fruit fly was also used by also was . 2015).Thefruitfly Patrick Maxwell Patrick , was used by , wasusedby Brent Saylor Joe Peters tions that derepress TEs. tions thatderepress egation, and also introduced a new computational framework framework computational introduced anew andalso egation, (RNA Institute, SUNY at Albany) reported fascinating fascinating Institute, (RNA reported SUNY atAlbany) et al et via is an interesting example that is aninteresting example . 2015). recruitment ofgeneral silencing machinery tonascent (Rensselaer Polytechnic Institute) uses budding yeastInstitute)uses budding as Polytechnic (Rensselaer n endogenous retrotra n endogenous (Cornell University) presented a series ofTnsE aseries presented University) (Cornell , arguing that Ty1 nucleocapsid assembly may , arguing nucleocapsid thatTy1 the chromosomes of different species. species. ofdifferent the chromosomes in fundamental cellu in fundamental Jake Jacobs Jake (University of Guelph) applied ecological methodsto ecological applied (University ofGuelph) Wnt signaling,Wnt which isinturnindependently ation for universal avoida ation foruniversal centrosome inheritance and couldnegatively and inheritance centrosome tional equivalentsofth stone H3K9 methyltransferase required for for required H3K9methyltransferase stone ghted in other presentations. In ghted particular, inotherpresentations. of the Piwi complex inDrosophilawhich of thePiwicomplex to TE analysis are currently gaining ground.gaining currently are toTEanalysis mal PRP8proteins,providing into newinsights of TEsandsatelliterepe geneticists, biochemists, rds different with TnsE being targets, the one et al et cated in several neurodegenerative disorders, disorders, neurodegenerative several in cated association between Ty1 retrotransposon associationbetween s at specific times duringevolution of the . 2015). The value of structural biology of structuralbiology . 2015).Thevalue Yang Yu Yang (RutgersUniversity) todemonstrate that

Lisa Krug ure of a self-splicing bacterial group group bacterial a self-splicing ure of lar processes. lar processes. nsposon activation and nsposon activation encodes different accessory differentaccessory encodes (ColdSpring Harbor (ColdSpring Harbor e centrosome) inthe centrosome) e nce of coding sequences sequences ofcoding nce ats inheterochromatin ats andcellbiologists. et al et Daniel Barbash Daniel . 2009). Nicola

Repbase, the database of of Repbase, thedatabase ofth founder Dr.Jerzybasis by Jurka, thelate A word cloud representation of aggregate talk ofaggregate Awordcloud representation researchers. needs suchaforum that evident particularly al R21AI117593(P.R.) R01GM101989 and NIH and byGM111917 (I.A.), authors’ laboratories Research inthe meeting, financial supportofthe Illumi ofChicago, thankTheUniversity We Acknowledgements come. Itother. isexactly thiskindofinteraction that thisconferenceyears intends inthe topromote to regular within oneanother's beingnecessarily workingThus, investigators ondifferen naturally. do elements mobile that something -- andrestructuring engineering genome to approaches studies have the tobring potential newtoolsintothe existing genetic facilitating toolbox, new In genomes. annotation oflarge eukaryotes, previously escaped which tothe detection due difficulties inassembly and assemblyand analysis are nowpermitting discovery large of genetic entities movable in long-read in advances recent Themost gene transfer. horizontal of capable DNA bacterial genomics became methods incomparative thatwe TE-host cellIndeed, interactions. itisthrough th clearly illustratesgenomic inTEstudies, the importance of and context the generalemphasis on 2006-2012 by the conference “Genomic impact of “Genomic impactof conference 2006-2012 by the e components. Forgenomic novel unappreciated genomiccom elements inknown sequence automated genome annotation pipelin to aims specifically which forum a regular for need the highlighted meeting the Overall, identification ofinteresting new targetsfor ex the accelerate orderto in researchers TE andcomputational experimental bring together their collaborations and/ordrive responde participants half oftheconference graduate stude and postdocs, faculty, as between com between opportunities fordirectinteractions meetingallowedsubmitted abstracts, talks ustoselect half from provided ofthe unmatched and the of scale compact relatively The history ofTEresearch. rich its to venuedue as anexcellent This article is protected Allrights bycopyright. reserved. drew Cold Spring Harborin2013, Its theirhosts. interplay predec TEsand between mobile studying researchers together bringing of value the demonstrated Theconference andcomputational experimental LifeBacteria, of – domains DNA indifferent Summary

Accepted 2009;Arkhipova . 2007;Jurka Article eukaryotic TEs (Jurka eukaryotic TEs(Jurka addition toproviding biology, intogenome newinsights MGE and Bill Reznikoff for critical reading of the manuscript. of critical reading for and Bill Reznikoff approaches to achieve deeper understanding of the complex complex ofthe understanding deeper toachieve approaches et al et research in new directions. directions. new in research 75 participants from11states a 75participants is supported by NSF MCB-1121334 and NIHby R01 and is supported NSF MCB-1121334 . 2012), which was organized . 2012),whichwasorganized es withessentialinformati ponents and on the properties of hitherto of andontheproperties ponents d that the meeting helped them forge new forge new the meeting them helped d that na Inc., and Integrated DNA Technologies for to include bothprokaryo to include perimentation, andto perimentation, Archaea and Eukarya – as well asintegrating –aswell and Eukarya Archaea e Genetic Information Rese e Genetic orbits, could benefit most from meeting each couldbenefitmostfrom orbits, et al et e advances e advances of genome assembly and analysis nts. Importantly, one- inapost-meeting survey, nts. essor, the regional mobile DNA meeting heldin DNA meeting theregionalmobile essor, putational andexperiment ukaryotic TEs, such a forum wasprovidedin forum ukaryotic TEs,sucha t systems and with different perspectives,not systems andwithdifferent t eukaryotic transposable elements” (Batzer elements”(Batzer eukaryotic transposable aware of the prevalence of large segments of segments oflarge prevalence ofthe aware . 2005). The current meeting made it made meeting . 2005).Thecurrent and poster abstracts is given in Fig. 2. It Fig. isgiven 2. poster abstracts in and

on thefunctionally important nd 7 countries, and also served andalsoserved nd 7countries, in Asilomar on a triannual in Asilomaronatriannual provide designers of provide designers tic and eukaryoticand tic TE arch Institute andof arch al scientists,aswell et et This article is protected Allrights bycopyright. reserved. Lipkin WI, ReinischC,Street Goff SP Muttray J, Sherry AF, MJ, G,Metzger Arriagada References Jurka J, KapitonovVV, Pavlicek A,Klonowski J, Jurka Kapitonov VV, Koonin EV (2015) Evolutionof Kapitonov VV,Koonin Impact (2009)"Genomic ofEukaryo J Jurka Callahan BP, Topilina NI, Stanger MJ, Van Roey P, Stanger VanRoeyCallahan BP, TopilinaNI, MJ, MoranJV. J, Jurka PL, Batzer MA,Deininger Feschotte BrosiusIR, J, MA, Batzer Arkhipova Gladyshev E, Kleckner N (2014) Direct reco N (2014)Direct E,Kleckner Gladyshev (2014)Vulnerabilitieson JE Fricker AD,Peters for isrequired tract poly(A) Miyoshi (2015)A3' Liu Wilusz Y, Moran JV JE, T, Doucet AJ, Brow RamG,PenadésJR, Chen J, Krupovic M1, Makarova KS, Forterre P, Prangi KS, Forterre Krupovic M1,Makarova (2015)Evolutionofadaptiv Koonin EV,KrupovicM L, M,Huynh ThiYen KimJS Kim TY,Shin Hickman AB, Dyda F (2015b) Mechanisms of DNA transposition. MechanismsofDNA F (2015b) Dyda Hickman AB, Cas1proteinfrom casposon-encoded The F. (2015a) Dyda Hickman AB, Jin Y,TamOH,Paniagua E,HammellM(2015) Jin S,Ci Cranz-Mileva Rosado-Lugo JZ, JD, Jacobs (2014) Activationoftranscri neoplastic hemocytes of the mollusk neoplastic hemocytes ofthe California, February 6-10, 2009. California, February 6-10, Update, a database eukaryotic of repetitive elements. Gene ofeu impact "Genomic meeting the to dedicated elements. transposable ofeukaryotic impact Genomic 14180. from the same transposon. from thesametransposon. LINE-1 retrotransposition. genes. of unlinkedchromosomal Struct MolBiol competent intein trap a caught and withfunctional redox evolutionary in implications. immunity. DNAtransposons ofself-synthesizing superfamily combined withinnate immune systems. Commun DNA in elements. mobile Archaeoglobus fulgidus 10587. boonei Accepted31 transposable indifferential analysis elements expression datasets. ofRNA-seq guid replication forks Arrested MDNA3-0034-2014. Article , 3593-3599.

390 is a DNA integrase that generates target siteduplications. target thatgenerates isaDNAintegrase Neurospora crassa . , 1-2. , 1-2. 441 BMC Biol , 720-725. , 720-725. . 18 Annu RevGenet , 630-633. . 12 and characterization ofitsnucleolyticactivity. , 36. , Biol Direct Biol Mol Cell . ption andretrotranspositi Nat Commun e retrotransposon integration. integration. e retrotransposon n S,NovickRP (2015)Pathogeni Gene

48

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tic Transposable Elem tic Transposable ,103. ,103. gnition of homology between double helicesof gnition ofhomology between (2013) from Crystal ofCas1 structure 5 Mol Cell , 3509. (2007). Introduction(2007). forth C, Moran JV, Schmitz Schmitz (2012) J, MoranJV, Jurka J C, shvili D,KooninEV(2014)Casposons:anew shvili P, Kohany O,Walichi P, Kohany the lagging-strand temp the RAG1-RAG2locus: TEtranscripts: a package for including TEtranscripts: apackage ccaglione Zaratiegui M(2015) V, KM,Tournier karyotic transposable elements" at Asilomar. Asilomar. at elements" transposable karyotic Belfort M (2011) Structure of catalytically catalytically of Belfort M(2011)Structure at the origin of prokaryotic CRISPR-Cas CRISPR-Cas attheorigin prokaryotic of . e immunity tran from Proc NatlAcadSciUSA

57 Cytogenet GenomeRes on of a novel retroelement, on ofanovelretroelement, Mob DNA .

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ents", Pacific Grove, PacificGrove, ents", 3 Microbiol Spectr Microbiol Nucleic Acids Res Acids Nucleic city island-directed transfer transfer island-directed city , 19.

ewicz J (2005)Repbase J ewicz 349 late: opportunities for late: e Gene special issue Genespecial e Biochem BiophysRes Biochem both proteinscame both Aciduliprofundum Aciduliprofundum , 1549-1553. sposable elements

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Venner S, Feschotte C, Biémont Feschotte C, Venner S, Topilina NI,Green CM,Jayachandran P,KelleyDS, Stanger Piazza MJ, CL, Nayak S,Belfort M This article is protected Allrights bycopyright. reserved. (2012)Gene O, Beatty JT LangAS, Zhaxybayeva Luo MaJ, JinY, Y, PreallJB, Yu Y,GuJ, McClintock B (1950) The origin and be originMcClintock B (1950)The Mercer RG, Lang AS (2014) Identificationa Lang of RG, AS(2014) Mercer Induction ofinst McClintock B (1953) Metzger MJ, Reinisch C, Sherry J, GoffSP(2015) ReinischC,Sherry J, Metzger MJ, Shi Q, Straus MR, Caron JJ, WangShi Q,StrausMR,CaronJJ, H,Chung YS TV, Kapelinskaya EG, Mukha DV,Pasyukova Rahman R, Chirn GW, KanodiaA,Sytnikova Rahman R,ChirnGW, Wright PJ, NoeskeJ, Kranzusch JK, Nuñez P,Kelley DS,Morton Novikova O,Jayachandran Topilina NI, Novikova O, StangerBanava Topilina NI,Novikova O, M, HA, DB,Sun C,Wyngaard Wichman G,Walton stresses. (2015) SufB inteinof exchange. exchange. piRNA-dependent cotransc genome. community ofthe ecology capsulatus agent Rc gene transfer production ofthe 36 causes clams. leukemia insoft-shell Nucleic Acids Res Acids Nucleic Acids Res Res Tn7. element transposase heteromeric the for choice site target controls toggling across pervasive are landscapes transposon Unique Struct MolBiol acquis spacer mediates formation complex Nov 25.pii:msv271.[Epub aheadofprint] model fortransposition. of the AcceptedenvironmentalRadA activity switch of exte by copepod development. during genome somatic the from eliminated are sequences repetitive expanded, recently ArticleInteinclustering functional suggests im , 344-355. . 43 Drosophila melanogaster , 10734-10745. , Proc Natl Acad Sci USA Proc NatlAcad . Nat RevMicrobiol Nat . 43 BMC Microbiol , 6631-6648. , 6631-6648. . 21 . , 528-534. 43 , 10655-10672. , 10655-10672. Mycobacterium tuberculosis Mycobacterium BMC Genomics

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“Mobile Genetic Elements: “Mobile Genetic in silico,