Interspersed repetitive sequences articles within Nature Communications

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  • Article
    | Open Access

    It has been suggested that transposable elements (TE) play a role in tumourigenesis, but the associated mechanisms remain unclear. Here, the authors show, using colorectal cancer data and Bayesian Networks, that TEs can mediate the effect of expression quantitative trait loci and contribute to the regulation of cancer-related genes.

    • Nikolaos M. R. Lykoskoufis
    • , Evarist Planet
    •  & Emmanouil T. Dermitzakis

  • Article
    | Open Access

    Pachytene Piwi-interacting RNAs (piRNAs) expressed in mammalian germ lines are abundant, but their evolution and function are not fully understood. Here, the authors find that pachytene piRNA loci are hotspots of structural variation, which underlies rapid piRNA birth, divergence, and loss.

    • Yu H. Sun
    • , Hongxiao Cui
    •  & Xin Zhiguo Li

  • Article
    | Open Access

    The human genome harbors more than 4.5 million transposable element (TE)-derived insertions, the result of recurrent waves of invasion and internal propagation. Here they show that TEs belonging to evolutionarily recent subfamilies go on to regulate later stages of human embryonic development, notably conditioning the expression of genes involved in gastrulation and early organogenesis.

    • Julien Pontis
    • , Cyril Pulver
    •  & Didier Trono

  • Article
    | Open Access

    Transposable element insertion polymorphisms (TIPs) are a potential source of large effect alleles. Here, the authors use genome resequencing data for 602 tomato accessions together with transcriptomic and extensive phenotypic information to investigate the contribution of TIPs to tomato diversity.

    • Marisol Domínguez
    • , Elise Dugas
    •  & Leandro Quadrana

  • Article
    | Open Access

    Transposable elements are a potential source of transcriptional regulators, but how these sequences contribute to oncogenesis remains poorly understood. Here, the authors identify endogenous retroviruses (ERVs) with acute myeloid leukemia (AML)-associated enhancer chromatin signatures, and provide evidence that ERV activation provides an additional layer of gene regulation in AML.

    • Özgen Deniz
    • , Mamataz Ahmed
    •  & Miguel R. Branco

  • Article
    | Open Access

    Transposable elements (TE) make up a large component of the human genome and have been shown to contribute to human diseases. Here, Hormozdiari et al. estimate the contribution of TEs to the heritability of 41 complex traits and diseases and find enrichment of SINEs in blood traits.

    • Farhad Hormozdiari
    • , Bryce van de Geijn
    •  & Alkes L. Price

  • Article
    | Open Access

    Transposable elements (TE) are the dominant constituent of plant genomes. Here the authors develop a tool to analyze TE insertion sites in 3000 rice genomes and provide evidence for recent TE activity during cultivation and that external, rather than genetic, stimuli trigger most activations.

    • Marie-Christine Carpentier
    • , Ernandes Manfroi
    •  & Olivier Panaud

  • Article
    | Open Access

    Tarsiers occupy a key node between strepsirrhines and anthropoids in the primate phylogeny. Here, Warren and colleagues present the genome of Tarsius syrichta, including a survey of transposable elements, an unusual mitochondrial insertion, and evidence for positive gene selection.

    • Jürgen Schmitz
    • , Angela Noll
    •  & Wesley C. Warren

  • Article |

    The neocortex is a mammalian-specific structure that is responsible for higher functions but details of how it evolved are lacking. Here the authors show that the transposable element family MER130 is highly enriched among the enhancers in the developing mouse neocortex, suggesting a role in the evolution of this structure.

    • James H. Notwell
    • , Tisha Chung
    •  & Gill Bejerano

  • Article |

    Recombination-based tools for generating targeted mutations in Mycobacterium tuberculosislack efficiency. Here the authors present a CRISPR interference approach that is able to efficiently repress the expression of target genes in mycobacteria, in a rapid and cost-effective manner.

    • Eira Choudhary
    • , Preeti Thakur
    •  & Nisheeth Agarwal

  • Article |

    Retrotransposons replicate via a copy-paste mechanism involving a cytoplasmic intermediate. Guo et al.report that autophagy can suppress genetic variation by degrading cytoplasmic retrotransposon RNA, suggesting additional means by which autophagy may influence tumorigenesis.

    • Huishan Guo
    • , Maneka Chitiprolu
    •  & Derrick Gibbings

  • Article |

    The Hoppel transposable element mediates heterochromatin formation in Drosophila. Here Savva et al. report that the RNA-editing enzyme, ADAR, edits a long double-stranded RNA generated by the Hoppeltransposon, thereby regulating heterochromatin formation and gene expression.

    • Yiannis A. Savva
    • , James E. C. Jepson
    •  & Robert A. Reenan

  • Article |

    SINEs are retrotransposons that insert exact copies of themselves into genomes. Using a marked copy of a SINE, Yadavet al. show that the sequences of newly transposed SINEs are a combination of marked and existing SINEs, suggesting a mechanism for the formation of mosaic SINEs.

    • Vijay Pal Yadav
    • , Prabhat Kumar Mandal
    •  & Sudha Bhattacharya

  • Article |

    APOBEC3 is a DNA editing enzyme that is important for antiviral responses. In this study, Carmi and colleagues show that APOBEC3 editing of retrotransposon sequences in mammalian genomes is widespread, with implications for the evolution of retrotransposons.

    • Shai Carmi
    • , George M. Church
    •  & Erez Y. Levanon

  • Article
    | Open Access

    Zebra finches are passerine birds, but their phylogenetic relationship with non-passerine birds remains controversial. By examining retroposon insertion loci in avian genomes, the authors reveal that parrots are the closest relatives of passerines, which may have implications for understanding the evolution of birdsong.

    • Alexander Suh
    • , Martin Paus
    •  & Jürgen Schmitz

  • Article |

    Microvesicles containing RNA are released from tumour cells. Here, the authors show that microvesicles released from tumour cells in culture have amplified levels of thec-Myconcogene, which is also found in the cell of origin, suggesting that microvesicles could be used as biomarkers.

    • Leonora Balaj
    • , Ryan Lessard
    •  & Johan Skog

  • Article |

    Insertion sequences are transposable elements that are found in the genomes of many bacteria. Here, the authors identify an enhancer element that results in a high frequency of excision of insertion elements, and suggest that the excision enhancer element coevolved with the insertion sequences.

    • Masahiro Kusumoto
    • , Tadasuke Ooka
    •  & Tetsuya Hayashi

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