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Thousands of RNA-cached copies of whole chromosomes are present in the ciliate Oxytricha during development

The ciliate Oxytricha trifallax maintains two genomes: a germline genome that is active only during sexual conjugation and a transcriptionally active, somatic genome that derives from the germline via extensive sequence reduction and rearrangement. Previously, we found that long noncoding (lnc) RNA...

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Detalles Bibliográficos
Autores principales: Lindblad, Kelsi A., Bracht, John R., Williams, April E., Landweber, Laura F.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory Press 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5513065/
https://www.ncbi.nlm.nih.gov/pubmed/28450531
http://dx.doi.org/10.1261/rna.058511.116
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author Lindblad, Kelsi A.
Bracht, John R.
Williams, April E.
Landweber, Laura F.
author_facet Lindblad, Kelsi A.
Bracht, John R.
Williams, April E.
Landweber, Laura F.
author_sort Lindblad, Kelsi A.
collection PubMed
description The ciliate Oxytricha trifallax maintains two genomes: a germline genome that is active only during sexual conjugation and a transcriptionally active, somatic genome that derives from the germline via extensive sequence reduction and rearrangement. Previously, we found that long noncoding (lnc) RNA “templates”—telomere-containing, RNA-cached copies of mature chromosomes—provide the information to program the rearrangement process. Here we used a modified RNA-seq approach to conduct the first genome-wide search for endogenous, telomere-to-telomere RNA transcripts. We find that during development, Oxytricha produces long noncoding RNA copies for over 10,000 of its 16,000 somatic chromosomes, consistent with a model in which Oxytricha transmits an RNA-cached copy of its somatic genome to the sexual progeny. Both the primary sequence and expression profile of a somatic chromosome influence the temporal distribution and abundance of individual template RNAs. This suggests that Oxytricha may undergo multiple rounds of DNA rearrangement during development. These observations implicate a complex set of thousands of long RNA molecules in the wiring and maintenance of a highly elaborate somatic genome architecture.
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spelling pubmed-55130652017-08-02 Thousands of RNA-cached copies of whole chromosomes are present in the ciliate Oxytricha during development Lindblad, Kelsi A. Bracht, John R. Williams, April E. Landweber, Laura F. RNA Article The ciliate Oxytricha trifallax maintains two genomes: a germline genome that is active only during sexual conjugation and a transcriptionally active, somatic genome that derives from the germline via extensive sequence reduction and rearrangement. Previously, we found that long noncoding (lnc) RNA “templates”—telomere-containing, RNA-cached copies of mature chromosomes—provide the information to program the rearrangement process. Here we used a modified RNA-seq approach to conduct the first genome-wide search for endogenous, telomere-to-telomere RNA transcripts. We find that during development, Oxytricha produces long noncoding RNA copies for over 10,000 of its 16,000 somatic chromosomes, consistent with a model in which Oxytricha transmits an RNA-cached copy of its somatic genome to the sexual progeny. Both the primary sequence and expression profile of a somatic chromosome influence the temporal distribution and abundance of individual template RNAs. This suggests that Oxytricha may undergo multiple rounds of DNA rearrangement during development. These observations implicate a complex set of thousands of long RNA molecules in the wiring and maintenance of a highly elaborate somatic genome architecture. Cold Spring Harbor Laboratory Press 2017-08 /pmc/articles/PMC5513065/ /pubmed/28450531 http://dx.doi.org/10.1261/rna.058511.116 Text en © 2017 Lindblad et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society http://creativecommons.org/licenses/by/4.0/ This article, published in RNA, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
Lindblad, Kelsi A.
Bracht, John R.
Williams, April E.
Landweber, Laura F.
Thousands of RNA-cached copies of whole chromosomes are present in the ciliate Oxytricha during development
title Thousands of RNA-cached copies of whole chromosomes are present in the ciliate Oxytricha during development
title_full Thousands of RNA-cached copies of whole chromosomes are present in the ciliate Oxytricha during development
title_fullStr Thousands of RNA-cached copies of whole chromosomes are present in the ciliate Oxytricha during development
title_full_unstemmed Thousands of RNA-cached copies of whole chromosomes are present in the ciliate Oxytricha during development
title_short Thousands of RNA-cached copies of whole chromosomes are present in the ciliate Oxytricha during development
title_sort thousands of rna-cached copies of whole chromosomes are present in the ciliate oxytricha during development
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5513065/
https://www.ncbi.nlm.nih.gov/pubmed/28450531
http://dx.doi.org/10.1261/rna.058511.116
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