DNA methylation dynamics at transposable elements in mammals DOI
Natasha Jansz

Essays in Biochemistry, Journal Year: 2019, Volume and Issue: 63(6), P. 677 - 689

Published: Oct. 11, 2019

Transposable elements dominate the mammalian genome, but their contribution to genetic and epigenetic regulation has been largely overlooked. This was in part due technical limitations, which made study of repetitive sequences at single copy resolution difficult. The advancement next-generation sequencing assays last decade greatly enhanced our understanding transposable element function. In some instances, specific are thought have co-opted into regulatory roles during both mouse human development, while disease such potential can contribute malignancy. DNA methylation is arguably best characterised regulator activity. associated with repression, acts limit genotoxic potential. developmental contexts, erasure a burst expression. Developmental enables transposon activation, ensuring survival propagation throughout host also allows access encoded within elements. Here I discuss elements, describing its function dynamic murine development.

Language: Английский

A Field Guide to Eukaryotic Transposable Elements DOI Open Access
Jonathan N. Wells, Cédric Feschotte

Annual Review of Genetics, Journal Year: 2020, Volume and Issue: 54(1), P. 539 - 561

Published: Sept. 21, 2020

Transposable elements (TEs) are mobile DNA sequences that propagate within genomes. Through diverse invasion strategies, TEs have come to occupy a substantial fraction of nearly all eukaryotic genomes, and they represent major source genetic variation novelty. Here we review the defining features each group explore their evolutionary origins relationships. We discuss how unique biology different influences propagation distribution across Environmental factors acting at level host species further modulate activity, diversification, fate TEs, producing dramatic in TE content observed eukaryotes. argue cataloging diversity dissecting idiosyncratic behavior individual crucial expanding our comprehension impact on genomes evolution species.

Language: Английский

Citations

448
The role of retrotransposable elements in ageing and age-associated diseases DOI
Vera Gorbunova, Andrei Seluanov, Paolo Mita

et al.

Nature, Journal Year: 2021, Volume and Issue: 596(7870), P. 43 - 53

Published: Aug. 4, 2021

Language: Английский

Citations

309
Roles of transposable elements in the regulation of mammalian transcription DOI
Raquel Fueyo, Julius Judd, Cédric Feschotte

et al.

Nature Reviews Molecular Cell Biology, Journal Year: 2022, Volume and Issue: 23(7), P. 481 - 497

Published: Feb. 28, 2022

Language: Английский

Citations

268
Transposable elements shape the evolution of mammalian development DOI
Anna D. Senft, Todd S. Macfarlan

Nature Reviews Genetics, Journal Year: 2021, Volume and Issue: 22(11), P. 691 - 711

Published: Aug. 5, 2021

Language: Английский

Citations

209
Endogenous retroviruses in the origins and treatment of cancer DOI Creative Commons
Natasha Jansz, Geoffrey J. Faulkner

Genome biology, Journal Year: 2021, Volume and Issue: 22(1)

Published: May 10, 2021

Abstract Endogenous retroviruses (ERVs) are emerging as promising therapeutic targets in cancer. As remnants of ancient retroviral infections, ERV-derived regulatory elements coordinate expression from gene networks, including those underpinning embryogenesis and immune cell function. ERV activation can promote an interferon response, a phenomenon termed viral mimicry. Although is associated with cancer, provisionally autoimmune neurodegenerative diseases, ERV-mediated inflammation being explored way to sensitize tumors immunotherapy. Here we review co-option development innate immunity, the aberrant contribution ERVs tumorigenesis, wider biomedical potential therapies directed at ERVs.

Language: Английский

Citations

117
The chromatin remodeler DDM1 prevents transposon mobility through deposition of histone variant H2A.W DOI
Akihisa Osakabe, Bhagyshree Jamge, Elin Axelsson

et al.

Nature Cell Biology, Journal Year: 2021, Volume and Issue: 23(4), P. 391 - 400

Published: April 1, 2021

Language: Английский

Citations

108
Taming transposable elements in vertebrates: from epigenetic silencing to domestication DOI
Miguel Vasconcelos Almeida, Grégoire Vernaz, Audrey L. K. Putman

et al.

Trends in Genetics, Journal Year: 2022, Volume and Issue: 38(6), P. 529 - 553

Published: March 17, 2022

Language: Английский

Citations

102
Stage-specific H3K9me3 occupancy ensures retrotransposon silencing in human pre-implantation embryos DOI Creative Commons
Ruimin Xu, Sen Li, Qiu Wu

et al.

Cell stem cell, Journal Year: 2022, Volume and Issue: 29(7), P. 1051 - 1066.e8

Published: July 1, 2022

Language: Английский

Citations

73
Earl Grey: A Fully Automated User-Friendly Transposable Element Annotation and Analysis Pipeline DOI Creative Commons
Tobias Baril, James D. Galbraith, Alexander Hayward

et al.

Molecular Biology and Evolution, Journal Year: 2024, Volume and Issue: 41(4)

Published: April 1, 2024

Transposable elements (TEs) are major components of eukaryotic genomes and implicated in a range evolutionary processes. Yet, TE annotation characterization remain challenging, particularly for nonspecialists, since existing pipelines typically complicated to install, run, extract data from. Current methods automated also subject issues that reduce overall quality, (i) fragmented overlapping annotations, leading erroneous estimates count coverage, (ii) repeat models represented by short sections total length, with poor capture 5' 3' ends. To address these issues, we present Earl Grey, fully pipeline designed user-friendly curation TEs genome assemblies. Using nine simulated an Drosophila melanogaster, show Grey outperforms current widely used methodologies ameliorating the mentioned above while scoring highly benchmarking classification being robust across genomic contexts. provides comprehensive toolkit researchers paper-ready summary figures outputs standard formats compatible other bioinformatics tools. has modular format, great scope inclusion additional modules focused on further quality control tailored analyses future releases.

Language: Английский

Citations

57
Non-retroviral Endogenous Viral Element Limits Cognate Virus Replication in Aedes aegypti Ovaries DOI Creative Commons
Yasutsugu Suzuki, Artem Baidaliuk, Pascal Miesen

et al.

Current Biology, Journal Year: 2020, Volume and Issue: 30(18), P. 3495 - 3506.e6

Published: July 16, 2020

Endogenous viral elements (EVEs) are sequences integrated in host genomes. A large number of non-retroviral EVEs was recently detected Aedes mosquito genomes, leading to the hypothesis that may control exogenous infections by closely related viruses. Here, we experimentally investigated role an EVE naturally found aegypti populations and derived from widespread insect-specific virus, cell-fusing agent virus (CFAV). Using CRISPR-Cas9 genome editing, created Ae. line lacking CFAV EVE. Absence resulted increased replication ovaries, possibly modulating vertical transmission virus. Viral controlled targeting RNA EVE-derived P-element-induced wimpy testis-interacting RNAs (piRNAs). Our results provide evidence antiviral piRNAs produced presence a occurring its cognate demonstrating functional link between immunity natural insect-virus interaction.

Language: Английский

Citations

115