title: A versatile reporter system for CRISPR-mediated chromosomal rearrangements.
abstract: Although chromosomal deletions and inversions are important in cancer, conventional methods for detecting DNA rearrangements require laborious indirect assays. Here we develop fluorescent reporters to rapidly quantify CRISPR/Cas9-mediated deletions and inversions. We find that inversion depends on the non-homologous end-joining enzyme LIG4. We also engineer deletions and inversions for a 50 kb Pten genomic region in mouse liver. We discover diverse yet sequence-specific indels at the rearrangement fusion sites. Moreover, we detect Cas9 cleavage at the fourth nucleotide on the non-complementary strand, leading to staggered instead of blunt DNA breaks. These reporters allow mechanisms of chromosomal rearrangements to be investigated.
authors.affiliation: Department of Bioinformatics, School of Life Science and Technology, Tongji University, Shanghai, P. R. China. xlccalyx@gmail.com.
authors.forename: Yingxiang
authors.initials: Y
authors.lastname: Li
authors.affiliation: RNA Therapeutics Institute and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, 01605, USA. Angela.Park@umassmed.edu.
authors.forename: Angela I
authors.initials: AI
authors.lastname: Park
authors.affiliation: RNA Therapeutics Institute and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, 01605, USA. Haiwei.Mou@umassmed.edu.
authors.forename: Haiwei
authors.initials: H
authors.lastname: Mou
authors.affiliation: RNA Therapeutics Institute and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, 01605, USA. Cansu.Colpan@umassmed.edu.
authors.forename: Cansu
authors.initials: C
authors.lastname: Colpan
authors.affiliation: RNA Therapeutics Institute and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, 01605, USA. Aizhan.Bizhanova@umassmed.edu.
authors.forename: Aizhan
authors.initials: A
authors.lastname: Bizhanova
authors.affiliation: David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA. egarren@gmail.com.
authors.forename: Elliot
authors.initials: E
authors.lastname: Akama-Garren
authors.affiliation: David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA. nsjoshi@MIT.EDU.
authors.forename: Nik
authors.initials: N
authors.lastname: Joshi
authors.affiliation: Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Medical School, Minneapolis, MN, 55455, USA. hendr064@umn.edu.
authors.forename: Eric A
authors.initials: EA
authors.lastname: Hendrickson
authors.affiliation: Abramson Family Cancer Research Institute, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19104, USA. dfeldser@upenn.edu.
authors.forename: David
authors.initials: D
authors.lastname: Feldser
authors.affiliation: David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA. haoyin@mit.edu.
authors.forename: Hao
authors.initials: H
authors.lastname: Yin
authors.affiliation: David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA. dgander@mit.edu.|Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA. dgander@mit.edu.|Harvard-MIT Division of Health Sciences & Technology, Cambridge, MA, 02139, USA. dgander@mit.edu.|Institute of Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA. dgander@mit.edu.
authors.forename: Daniel G
authors.initials: DG
authors.lastname: Anderson
authors.affiliation: David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA. tjacks@mit.edu.
authors.forename: Tyler
authors.initials: T
authors.lastname: Jacks
authors.affiliation: Department of Bioinformatics, School of Life Science and Technology, Tongji University, Shanghai, P. R. China. Zhiping.Weng@umassmed.edu.|Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, 01605, USA. Zhiping.Weng@umassmed.edu.
authors.forename: Zhiping
authors.initials: Z
authors.lastname: Weng
authors.affiliation: RNA Therapeutics Institute and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, 01605, USA. Wen.Xue@umassmed.edu.
authors.forename: Wen
authors.initials: W
authors.lastname: Xue
mesh_terms: D000818:Animals; D064113:CRISPR-Cas Systems; D002872:Chromosome Deletion; D007446:Chromosome Inversion; D064112:Clustered Regularly Interspaced Short Palindromic Repeats; D005260:Female; D015321:Gene Rearrangement; D023281:Genomics / Q000379:methods; D057809:HEK293 Cells; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D054643:INDEL Mutation; D008099:Liver / Q000378:metabolism; D051379:Mice; D008815:Mice, Inbred Strains; D010957:Plasmids