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Local features determine Ty3 targeting frequency at RNA polymerase III transcription start sites

Retroelement integration into host genomes affects chromosome structure and function. A goal of a considerable number of investigations is to elucidate features influencing insertion site selection. The Saccharomyces cerevisiae Ty3 retrotransposon inserts proximal to the transcription start sites (T...

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Autores principales: Patterson, Kurt, Shavarebi, Farbod, Magnan, Christophe, Chang, Ivan, Qi, Xiaojie, Baldi, Pierre, Bilanchone, Virginia, Sandmeyer, Suzanne B.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory Press 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6673722/
https://www.ncbi.nlm.nih.gov/pubmed/31249062
http://dx.doi.org/10.1101/gr.240861.118
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author Patterson, Kurt
Shavarebi, Farbod
Magnan, Christophe
Chang, Ivan
Qi, Xiaojie
Baldi, Pierre
Bilanchone, Virginia
Sandmeyer, Suzanne B.
author_facet Patterson, Kurt
Shavarebi, Farbod
Magnan, Christophe
Chang, Ivan
Qi, Xiaojie
Baldi, Pierre
Bilanchone, Virginia
Sandmeyer, Suzanne B.
author_sort Patterson, Kurt
collection PubMed
description Retroelement integration into host genomes affects chromosome structure and function. A goal of a considerable number of investigations is to elucidate features influencing insertion site selection. The Saccharomyces cerevisiae Ty3 retrotransposon inserts proximal to the transcription start sites (TSS) of genes transcribed by RNA polymerase III (RNAP3). In this study, differential patterns of insertion were profiled genome-wide using a random barcode-tagged Ty3. Saturation transposition showed that tRNA genes (tDNAs) are targeted at widely different frequencies even within isoacceptor families. Ectopic expression of Ty3 integrase (IN) showed that it localized to targets independent of other Ty3 proteins and cDNA. IN, RNAP3, and transcription factor Brf1 were enriched at tDNA targets with high frequencies of transposition. To examine potential effects of cis-acting DNA features on transposition, targeting was tested on high-copy plasmids with restricted amounts of 5′ flanking sequence plus tDNA. Relative activity of targets was reconstituted in these constructions. Weighting of genomic insertions according to frequency identified an A/T-rich sequence followed by C as the dominant site of strand transfer. This site lies immediately adjacent to the adenines previously implicated in the RNAP3 TSS motif (CAA). In silico DNA structural analysis upstream of this motif showed that targets with elevated DNA curvature coincide with reduced integration. We propose that integration mediated by the Ty3 intasome complex (IN and cDNA) is subject to inputs from a combination of host factor occupancy and insertion site architecture, and that this results in the wide range of Ty3 targeting frequencies.
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spelling pubmed-66737222019-08-14 Local features determine Ty3 targeting frequency at RNA polymerase III transcription start sites Patterson, Kurt Shavarebi, Farbod Magnan, Christophe Chang, Ivan Qi, Xiaojie Baldi, Pierre Bilanchone, Virginia Sandmeyer, Suzanne B. Genome Res Research Retroelement integration into host genomes affects chromosome structure and function. A goal of a considerable number of investigations is to elucidate features influencing insertion site selection. The Saccharomyces cerevisiae Ty3 retrotransposon inserts proximal to the transcription start sites (TSS) of genes transcribed by RNA polymerase III (RNAP3). In this study, differential patterns of insertion were profiled genome-wide using a random barcode-tagged Ty3. Saturation transposition showed that tRNA genes (tDNAs) are targeted at widely different frequencies even within isoacceptor families. Ectopic expression of Ty3 integrase (IN) showed that it localized to targets independent of other Ty3 proteins and cDNA. IN, RNAP3, and transcription factor Brf1 were enriched at tDNA targets with high frequencies of transposition. To examine potential effects of cis-acting DNA features on transposition, targeting was tested on high-copy plasmids with restricted amounts of 5′ flanking sequence plus tDNA. Relative activity of targets was reconstituted in these constructions. Weighting of genomic insertions according to frequency identified an A/T-rich sequence followed by C as the dominant site of strand transfer. This site lies immediately adjacent to the adenines previously implicated in the RNAP3 TSS motif (CAA). In silico DNA structural analysis upstream of this motif showed that targets with elevated DNA curvature coincide with reduced integration. We propose that integration mediated by the Ty3 intasome complex (IN and cDNA) is subject to inputs from a combination of host factor occupancy and insertion site architecture, and that this results in the wide range of Ty3 targeting frequencies. Cold Spring Harbor Laboratory Press 2019-08 /pmc/articles/PMC6673722/ /pubmed/31249062 http://dx.doi.org/10.1101/gr.240861.118 Text en © 2019 Patterson et al.; Published by Cold Spring Harbor Laboratory Press http://creativecommons.org/licenses/by-nc/4.0/ This article, published in Genome Research, is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.
spellingShingle Research
Patterson, Kurt
Shavarebi, Farbod
Magnan, Christophe
Chang, Ivan
Qi, Xiaojie
Baldi, Pierre
Bilanchone, Virginia
Sandmeyer, Suzanne B.
Local features determine Ty3 targeting frequency at RNA polymerase III transcription start sites
title Local features determine Ty3 targeting frequency at RNA polymerase III transcription start sites
title_full Local features determine Ty3 targeting frequency at RNA polymerase III transcription start sites
title_fullStr Local features determine Ty3 targeting frequency at RNA polymerase III transcription start sites
title_full_unstemmed Local features determine Ty3 targeting frequency at RNA polymerase III transcription start sites
title_short Local features determine Ty3 targeting frequency at RNA polymerase III transcription start sites
title_sort local features determine ty3 targeting frequency at rna polymerase iii transcription start sites
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6673722/
https://www.ncbi.nlm.nih.gov/pubmed/31249062
http://dx.doi.org/10.1101/gr.240861.118
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