title: Assessing long-distance RNA sequence connectivity via RNA-templated DNA-DNA ligation.
abstract: Many RNAs, including pre-mRNAs and long non-coding RNAs, can be thousands of nucleotides long and undergo complex post-transcriptional processing. Multiple sites of alternative splicing within a single gene exponentially increase the number of possible spliced isoforms, with most human genes currently estimated to express at least ten. To understand the mechanisms underlying these complex isoform expression patterns, methods are needed that faithfully maintain long-range exon connectivity information in individual RNA molecules. In this study, we describe SeqZip, a methodology that uses RNA-templated DNA-DNA ligation to retain and compress connectivity between distant sequences within single RNA molecules. Using this assay, we test proposed coordination between distant sites of alternative exon utilization in mouse Fn1, and we characterize the extraordinary exon diversity of Drosophila melanogaster Dscam1.
authors: RNA Therapeutics Institute, Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, United States.
authors: Christian K
authors: CK
authors: Roy
authors: Institute for Systems Genomics, Department of Genetics and Developmental Biology, University of Connecticut Health Center, Farmington, United States.
authors: Sara
authors: S
authors: Olson
authors: Institute for Systems Genomics, Department of Genetics and Developmental Biology, University of Connecticut Health Center, Farmington, United States.
authors: Brenton R
authors: BR
authors: Graveley
authors: RNA Therapeutics Institute, Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, United States.
authors: Phillip D
authors: PD
authors: Zamore
authors: RNA Therapeutics Institute, Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, United States.
authors: Melissa J
authors: MJ
authors: Moore
mesh_terms: D017398:Alternative Splicing; D000818:Animals; D001681:Biological Assay; D015815:Cell Adhesion Molecules; D004247:DNA / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D029721:Drosophila Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D004331:Drosophila melanogaster / Q000235:genetics / Q000254:growth & development / Q000378:metabolism; D004625:Embryo, Nonmammalian; D005091:Exons; D005353:Fibronectins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D014644:Genetic Variation; D006801:Humans; D051379:Mice; D019006:Neural Cell Adhesion Molecules / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D009693:Nucleic Acid Hybridization; D020033:Protein Isoforms / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D017393:RNA Editing; D012322:RNA Precursors / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D062085:RNA, Long Noncoding / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism
chemical_list: D015815:Cell Adhesion Molecules; D029721:Drosophila Proteins; C491736:Dscam1 protein, Drosophila; D005353:Fibronectins; D019006:Neural Cell Adhesion Molecules; D020033:Protein Isoforms; D012322:RNA Precursors; D062085:RNA, Long Noncoding; D004247:DNA
keywords: D. melanogaster; Dscam1; RNA-templated; alternative splicing; chromosomes; fibronectin; genes; isoform; ligation; mouse