Biophysical Society Thematic Meeting| Santa Cruz 2018

Genome Biophysics: Integrating Genomics and Biophysics to Understand Structural and Functional Aspects of Genomes

Thursday Speaker Abstracts

Thermostable Group II Intron Reverse Transcriptases (TGIRTs) and Their Use in RNA- seq Alan M. Lambowitz 1 1 University of Texas at Austin, , Austin, Texas, United States Group II intron reverse transcriptases (RTs) are ancient enzymes that are evolutionary ancestors of retroviral RTs and have novel biochemical properties advantageous for RNA-seq and other biotechnological applications. These properties include higher fidelity and processivity than retroviral RTs, and a novel template-switching activity that enables seamless attachment of RNA-seq adapters to nucleic acid templates without RNA tailing or ligation, enabling RNA-seq library construction from small amounts of starting material. Thermostable group II intron RTs (TGIRTs) from bacterial thermophiles combine these properties with the ability to reverse transcribe at high temperatures, which help melt out impeding RNA secondary structures. We have used TGIRTs to develop new RNA-seq methods (TGIRT-seq), which enable: (i) quantitative profiling of protein-coding and long ncRNAs in the same RNA-seq as tRNAs and other small ncRNAs; (ii) give full-length, end-to-end reads of tRNAs and other structured small ncRNAs; and (iii) enable high-throughput mapping of post-transcriptional modifications by distinctive patterns of misincorporation. Validation of TGIRT-seq using fragmented human reference RNAs with ERCC spike-ins demonstrated advantages compared to the widely used TruSeq v3 method, including better quantitation, higher strand-specificity, less bias, more uniform 5’- to 3’-gene coverage, and detection of more splice junctions, particularly near the 5’ ends of genes, even from fragmented RNAs. The ability of TGIRT-seq to construct comprehensive RNA-seq libraries from small amounts of RNA is useful for analyzing extracellular RNAs in human plasma and exosomes, with potential liquid biopsy applications. A crystal structure of a full-length TGIRT bound to template-primer substrate and incoming dNTP identified novel structural features that contribute to its beneficial properties, revealed a close evolutionary relationship between group II intron RTs and RNA-dependent RNA polymerases, and indicated that retroviral RTs are degenerate enzymes that have lost regions and active-site features that contribute to the high processivity and fidelity of group II intron RTs.

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