ArticleCell2014
The architecture of a scrambled genome reveals massive levels of genomic rearrangement during development.
Article in Cell, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 100 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
100 citing papers in PubMed, 181 citations in OpenAlex.
- The mechanistic and evolutionary diversity of programmed DNA elimination.Nature reviews. Genetics · 2026Review
- The tiny germline chromosomes of Paramecium aurelia have an exceptionally high recombination rate and are capped by a new class of Helitrons.BMC biology · 2026Article
- A developmental condensin I complex assists the Paramecium PiggyMac domesticated transposase during programmed DNA elimination.Nucleic acids research · 2026Article
- A PIWI protein-dependent DNA N6-adenine methylation pathway inbioRxiv : the preprint server for biology · 2026Article
- Differentiated molecular defense strategies and survival trade-offs in the marine ciliateFrontiers in microbiology · 2026Article
- Soma-derived 30-nt small RNAs are coupled with chromosome breakage and precisely target nontransposon DNA against elimination inScience advances · 2025Article
- How and when organisms edit their own genomes.Nature genetics · 2025Review
- Relaxed DNA substrate specificity of transposases involved in programmed genome rearrangement.Nucleic acids research · 2025Article
- The PIWI-interacting protein Gtsf1 controls the selective degradation of small RNAs in Paramecium.Nucleic acids research · 2025Article
- Widespread 3D genome reorganization precedes programmed DNA rearrangement inbioRxiv : the preprint server for biology · 2025Article
- Genes and proteins expressed at different life cycle stages in the model protist Euplotes vannus revealed by both transcriptomic and proteomic approaches.Science China. Life sciences · 2025Article
- GTSF1 is required for transposon silencing in the unicellular eukaryote Paramecium tetraurelia.Nucleic acids research · 2024Article
- Diverse Genome Structures among Eukaryotes May Have Arisen in Response to Genetic Conflict.Genome biology and evolution · 2024Review
- Nuclear dualism without extensive DNA elimination in the ciliateProceedings of the National Academy of Sciences of the United States of America · 2024Article
- Application of RNA interference and protein localization to investigate housekeeping and developmentally regulated genes in the emerging model protozoan Paramecium caudatum.Communications biology · 2024Article
- From germline genome to highly fragmented somatic genome: genome-wide DNA rearrangement during the sexual process in ciliated protists.Marine life science & technology · 2024Article
- Somatic genome architecture and molecular evolution are decoupled in "young" linage-specific gene families in ciliates.PloS one · 2024Article
- Programmed chromosome fragmentation in ciliated protozoa: multiple means to chromosome ends.Microbiology and molecular biology reviews : MMBR · 2023Review
- SDRAP for annotating scrambled or rearranged genomes.NAR genomics and bioinformatics · 2023Article
- Genome-wide identification of ATP-binding cassette transporter B subfamily, focusing on its structure, evolution and rearrangement in ciliates.Open biology · 2023Article
40 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
12 authors at 6 institutions in 2 countries.
Funding
Abstract
Programmed DNA rearrangements in the single-celled eukaryote Oxytricha trifallax completely rewire its germline into a somatic nucleus during development. This elaborate, RNA-mediated pathway eliminates noncoding DNA sequences that interrupt gene loci and reorganizes the remaining fragments by inversions and permutations to produce functional genes. Here, we report the Oxytricha germline genome and compare it to the somatic genome to present a global view of its massive scale of genome rearrangements. The remarkably encrypted genome architecture contains >3,500 scrambled genes, as well as >800 predicted germline-limited genes expressed, and some posttranslationally modified, during genome rearrangements. Gene segments for different somatic loci often interweave with each other. Single gene segments can contribute to multiple, distinct somatic loci. Terminal precursor segments from neighboring somatic loci map extremely close to each other, often overlapping. This genome assembly provides a draft of a scrambled genome and a powerful model for studies of genome rearrangement.
Indexed as
Identifiers
What OpenQuestion holds
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.