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Meeting Report: Mobile Genetic Elements and Genome Plasticity 2018 John M Abrams et al. Mobile DNA (2018) 9:21 https://doi.org/10.1186/s13100-018-0126-3 MEETING REPORT Open Access Meeting report: mobile genetic elements and genome plasticity 2018 John M. Abrams1, Irina R. Arkhipova2, Marlene Belfort3, Jef D. Boeke4, M. Joan Curcio5, Geoffrey J. Faulkner6, John L. Goodier7, Ruth Lehmann8 and Henry L. Levin9* Abstract The Mobile Genetic Elements and Genome Plasticity conference was hosted by Keystone Symposia in Santa Fe, NM USA, February 11–15, 2018. The organizers were Marlene Belfort, Evan Eichler, Henry Levin and Lynne Maquat. The goal of this conference was to bring together scientists from around the world to discuss the function of transposable elements and their impact on host species. Central themes of the meeting included recent innovations in genome analysis and the role of mobile DNA in disease and evolution. The conference included 200 scientists who participated in poster presentations, short talks selected from abstracts, and invited talks. A total of 58 talks were organized into eight sessions and two workshops. The topics varied from mechanisms of mobilization, to the structure of genomes and their defense strategies to protect against transposable elements. Introduction variation. The TEs and hosts discussed at the meeting in- Transposable elements (TEs) constitute a major portion cluded a range of systems such as eubacteria, protists, of genomes, particularly in eukaryotes, and by causing plants, fungi, and animals. The keynote address was given mutations, rearrangements, and duplications, they have by one of the leaders in developing groundbreaking appli- a dramatic impact on genome content. In addition to cations of clustered regularly interspaced short palin- the importance of TE-mediated mutations that result in dromic repeat (CRISPR). disease, there is increasing significance in the role TEs play in shaping expression of regulatory networks. Re- cent discoveries regarding the function of TEs motivated Keynote address Keystone Symposia to host the conference on Mobile Keynote Speaker, Feng Zhang (MIT, USA), launched the Genetic Elements and Genome Plasticity in Santa Fe, meeting with a bang. Zhang is well known for develop- NM, USA, February 11 through February 15th. Topics ing powerful molecular technologies. He spoke about discussed at the conference often relied on advances in mining microbial diversity of CRISPR-Cas systems. After DNA sequencing and in the analysis of highly repetitive using zinc finger and TALE endonucleases to perform genomes. The presentations described the potent impact genome editing, his lab turned to CRISPR because of its of TEs on genetic variation and introduced mechanisms versatility, efficiency and specificity. First, they made a responsible for structural variation in the evolution of Cas9 enzyme available from Staphylococcus aureus primate genomes. Other talks described the discovery of (SaCas9), whose gene is more than 1 kb shorter than the cellular systems that inhibit TE activity, adding new original S. pyogenes Cas9 homolog. The shorter SaCas9 insight to the evolutionary arms race between mobile is better accommodated by adeno-associated virus DNA elements and their hosts. Also included was new (AAV) vectors. They packaged SaCas9 and guide RNA evidence of TE activity in neurons and cancer cells. The into AAV to target the DNA of Pask9, a cholesterol conference established relationships between scientists regulatory gene in mammalian cells, to yield significant working on TE biology, genome evolution, and structural decreases in cholesterol levels. In collaboration with the Koonin lab, Zhang explored * Correspondence: [email protected] CRISPR diversity in different bacterial systems, leading 9Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA to the discovery of the Cas13 RNA targeting system. Full list of author information is available at the end of the article Cas13 has a curious collateral activity that degrades © The Author(s). 2018 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Abrams et al. Mobile DNA (2018) 9:21 Page 2 of 10 RNA non-specifically once the CRISPR Cas13 system reported on a comparative insertion site profiling of the has recognized the RNA target. In a clever design, this TEs Sleeping Beauty and piggyBac as well as gammare- collateral effect of Cas13 was harnessed to cleave re- troviral and lentiviral vectors. Unlike the other genetic porter RNA and release signal (e.g. fluorescence), to pro- elements in this study, Sleeping Beauty appears to lack a vide rapid DNA or RNA detection with high sensitivity preference for gene sequences, suggesting a potential for and specificity. This specific high-sensitivity enzymatic enhanced safety in a clinical context. reporter unlocking (SHERLOCK) system has applica- Josh Dubnau (Stony Brook University, USA) described tions in pathogen detection, both viral (Zika and Den- TDP-43, an RNA and DNA binding protein that forms gue) and bacterial, in DNA genotyping and in mutation cytoplasmic inclusions in the vast majority of both fa- detection in tumors, and has been adapted for use in the milial and sporadic cases of amyotrophic lateral sclerosis field. The method can be multiplexed for the simultan- (ALS). Using a Drosophila TDP-43 over-expression eous detection of different nucleic acids. In a second ap- model, Dubnau has recapitulated characteristics of plication, catalytically inactive Cas13 was used to direct TDP-43-linked disease including protein aggregation adenosine-to-inosine deamination by ADAR2, to edit and locomotor impairment. Such expression results in transcripts in mammalian cells with damaging muta- loss of siRNA silencing and de-repression of both LINE tions. The sophisticated combination of technologies and long terminat repeat (LTR) families of retrotranspo- made the talk a tour de force! sable elements (RTEs). The RTE activity contributes to the degenerative phenotypes in these flies. Dubnau Mechanisms and results of genome editing established that TDP-43 toxicity in glial cells involves a (Laura Landweber, session chair) fundamental non-cell autonomous mechanism leading Mitchell O’Connell (University of Rochester, USA) de- to programmed cell death of both glial cells and adjacent scribed his work understanding the molecular mecha- neurons. Similar to the human endogenous retrovirus K nisms of Cas13 that protects a range of bacterial species (HERV-K), which is expressed in the cortex of some from TEs. Specifically, he described biochemical and ALS subjects, the gypsy RTE retains a functional env gene, structural data that showed Cas13 contains two distinct which provides the potential for non-cell autonomous RNA-nuclease modalities: one nuclease activity required transfer to adjacent neurons. In co-culture experiments, to cleave foreign phage mRNA and the other activity re- Dubnau found that gypsy elements are indeed able to quired to generate mature guide-RNAs from long pre- transfer reporter expression. Dubnau’s findings raise the cursors. As described by Zhang, O’Connell also showed possibility that HERV-mediated movement between cells that these RNA activities can be utilized to create a sen- could contribute to the focal onset and spread of neurode- sitive RNA detection assay to measure RNA abundances generative disorders within the nervous system. within complex samples. O’Connell finished by describ- Laura Landweber (Columbia University, USA), intro- ing unpublished observations regarding the specificity by duced the ciliate Oxytricha trifallax, which undergoes which Cas13 binds and cleaves its RNA targets. massive DNA rearrangements that produce a highly frag- John Schiel (Horizon Discovery, USA) discussed pre- mented but functional somatic macronucleus from a com- cise genome repair with the CRISPR-Cas9 system using plex germline micronucleus. Landweber discussed how the homology-directed repair (HDR) pathway. The effi- this process eliminates nearly all noncoding DNA, includ- ciency of gene knock-in with the HDR pathway is much ing transposons, and rearranges over 225,000 short DNA lower when compared to gene knockout with the NHEJ segments to produce a second genome containing thou- pathway. Schiel compared different formats of repair sands of gene-sized “nanochromosomes.” She also showed templates, such as ssDNA and plasmid, to evaluate the data indicating that noncoding RNAs regulate the process ability of each repair template to knock-in EGFP at the of genome rearrangement, including millions of 27 nt piR- same position in the gene target, using the same syn- NAs that mark and protect the retained DNA segments. thetic guide RNA. Design and experimental conditions She finished by describing how maternally-inherited, long, of each template were evaluated to provide optimal rec- non-coding (lnc) RNAs also serve as templates for gen- ommendations for template and homology arm length. ome remodeling and RNA-guided DNA repair. Zoltan Ivics
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