ArticlePloS one2008
The pathway to detangle a scrambled gene.
Article in PloS one, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
What it found
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Who cites it
23 citing papers in PubMed, 45 citations in OpenAlex.
- Widespread 3D genome reorganization precedes programmed DNA rearrangement inbioRxiv : the preprint server for biology · 2025Article
- Macronuclear development in ciliates, with a focus on nuclear architecture.The Journal of eukaryotic microbiology · 2022Review
- Review
- Programmed genome rearrangements in Oxytricha produce transcriptionally active extrachromosomal circular DNA.Nucleic acids research · 2019Article
- 27nt-RNAs guide histone variant deposition via 'RNA-induced DNA replication interference' and thus transmit parental genome partitioning in Stylonychia.Epigenetics & chromatin · 2018Article
- Russian Doll Genes and Complex Chromosome Rearrangements inG3 (Bethesda, Md.) · 2018Article
- Review
- Thousands of RNA-cached copies of whole chromosomes are present in the ciliateRNA (New York, N.Y.) · 2017Article
- Chromosome fusions triggered by noncoding RNA.RNA biology · 2017Article
- Recurring patterns among scrambled genes in the encrypted genome of the ciliate Oxytricha trifallax.Journal of theoretical biology · 2016Article
- RNA-template dependent de novo telomere addition.RNA biology · 2016Article
- Article
- Programmed Genome Rearrangements in the Ciliate Oxytricha.Microbiology spectrum · 2014Review
- Review
- Article
- Cytosine methylation and hydroxymethylation mark DNA for elimination in Oxytricha trifallax.Genome biology · 2012Article
- RNA-Mediated Epigenetic Programming of Genome Rearrangements.Annual review of genomics and human genetics · 2011Review
- RNA-dependent control of gene amplification.Proceedings of the National Academy of Sciences of the United States of America · 2010Article
- Alternative processing of scrambled genes generates protein diversity in the ciliate Chilodonella uncinata.Journal of experimental zoology. Part B, Molecular and developmental evolution · 2010Article
- The evolutionary history of histone H3 suggests a deep eukaryotic root of chromatin modifying mechanisms.BMC evolutionary biology · 2010Article
Corrections and comments
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Authors and funding
11 authors at 3 institutions in 3 countries.
Funding
Abstract
backgroundProgrammed DNA elimination and reorganization frequently occur during cellular differentiation. Development of the somatic macronucleus in some ciliates presents an extreme case, involving excision of internal eliminated sequences (IESs) that interrupt coding DNA segments (macronuclear destined sequences, MDSs), as well as removal of transposon-like elements and extensive genome fragmentation, leading to 98% genome reduction in Stylonychia lemnae. Approximately 20-30% of the genes are estimated to be scrambled in the germline micronucleus, with coding segment order permuted and present in either orientation on micronuclear chromosomes. Massive genome rearrangements are therefore critical for development. METHODOLOGY/PRINCIPAL
findingsTo understand the process of DNA deletion and reorganization during macronuclear development, we examined the population of DNA molecules during assembly of different scrambled genes in two related organisms in a developmental time-course by PCR. The data suggest that removal of conventional IESs usually occurs first, accompanied by a surprising level of error at this step. The complex events of inversion and translocation seem to occur after repair and excision of all conventional IESs and via multiple pathways. CONCLUSIONS/SIGNIFICANCE: This study reveals a temporal order of DNA rearrangements during the processing of a scrambled gene, with simpler events usually preceding more complex ones. The surprising observation of a hidden layer of errors, absent from the mature macronucleus but present during development, also underscores the need for repair or screening of incorrectly-assembled DNA molecules.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.