RNA-guided DNA assembly

Angeleska, Aleksandra; Jonoska, Nataša; Saito, Masahico; Landweber, Laura F.

doi:10.1016/j.jtbi.2007.06.007

Cited by 49 publications

(55 citation statements)

References 29 publications

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“…Point mutations introduced by an injected RNA copy of a chromosome (Nowacki et al 2008) and, in the related ciliate Stylonychia lemnae, substitutions in the telomeric sequence, can be passed to chromosomal telomeres and persist through multiple asexual generations (Fuhrmann et al 2016). This suggests the long RNAs produced during conjugation may act as templates, as originally proposed in Prescott et al (2003) and Angeleska et al (2007), to guide rearrangement of genome segments during nuclear development (Fig. 1).…”

Section: Introductionmentioning

confidence: 62%

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

Lindblad

Bracht

Williams

et al. 2017

RNA

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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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Section: Introductionmentioning

confidence: 62%

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

Lindblad

Bracht

Williams

et al. 2017

RNA

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“…Some of them belong to computer science: models based on rewriting systems, permutations, strings, graphs, and formal languages, invariants results, computability results, etc., see, e.g., [29], while others, such as template-based DNA recombination, belong to theoretical and experimental biology, see, e.g., [34] and [5].…”

Section: Introductionmentioning

confidence: 99%

Computational Nature of Gene Assembly in Ciliates

Brijder

Daley

Harju

et al. 2012

Handbook of Natural Computing

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“…Various theoretical models have been proposed in order to model the genetic unscrambling processes in ciliate organisms: the reversible guided recombination model, [10,9], based on binary inter-and intra-molecular DNA recombination operations; the ld, hi, dlad model, [8,7,14], based on three unary intra-molecular DNA recombination operations; the template-guided recombination (TGR) model, [13], where a DNA molecule from the old macronucleus conducts inter-molecular DNA recombination process serving as a template; the RNA-guided DNA assembly model, [1], experimentally confirmed in [11], where either double-stranded RNA or single-stranded RNA act as templates. This paper proposes two improvements of the descriptional complexity (size of template language, size of alphabet) of the template-guided recombination model as studied by Daley and McQuillan [2].…”

Section: Introductionmentioning

confidence: 99%

Ciliate Gene Unscrambling with Fewer Templates

Kari¹,

Rahman²

2010

Electron. Proc. Theor. Comput. Sci.

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Abstract. One of the theoretical models proposed for the mechanism of gene unscrambling in some species of ciliates is the template-guided recombination (TGR) system by Prescott, Ehrenfeucht and Rozenberg which has been generalized by Daley and McQuillan from a formal language theory perspective. In this paper, we propose a refinement of this model that generates regular languages using the iterated TGR system with a finite initial language and a finite set of templates, using fewer templates and a smaller alphabet compared to that of the Daley-McQuillan model. To achieve Turing completeness using only finite components, i.e., a finite initial language and a finite set of templates, we also propose an extension of the contextual template-guided recombination system (CTGR system) by Daley and McQuillan, by adding an extra control called permitting contexts on the usage of templates.

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RNA-guided DNA assembly

Cited by 49 publications

References 29 publications

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

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

Computational Nature of Gene Assembly in Ciliates

Ciliate Gene Unscrambling with Fewer Templates

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