Transposable elements and the epigenetic regulation of the genome

Transposable elements: targets for early nutritional effects on epigenetic gene regulation

Waterland, R. A., & Jirtle, R. L. (2003) · Molecular and Cellular Biology · doi:10.1128/mcb.23.15.5293-5300.2003 · Cited by 2,019 · see citing works

Epigenetic inheritance at the agouti locus in the mouse

Morgan, H. D., Sutherland, H. G. E., Martin, D. I. K., & Whitelaw, E. (1999) · Nature Genetics · doi:10.1038/15490 · Cited by 1,476 · see citing works

Evidence for a <i>piwi</i> -Dependent RNA Silencing of the <i>gypsy</i> Endogenous Retrovirus by the <i>Drosophila melanogaster flamenco</i> Gene

Sarot, E., Payen-Groschêne, G., Bucheton, A., & Pélisson, A. (2004) · Genetics · doi:10.1534/genetics.166.3.1313 · Cited by 251 · see citing works

Position-effect variegation and the genetic dissection of chromatin regulation in Drosophila

Schotta, G., Ebert, A., Dorn, R., & Reuter, G. (2003) · Seminars in Cell &amp; Developmental Biology · doi:10.1016/s1084-9521(02)00138-6 · Cited by 213 · see citing works

DNA methylation landscapes: Provocative insights from epigenomics

Suzuki, M. M., & Bird, A. (2008) · Nature Reviews Genetics · doi:10.1038/nrg2341 · Cited by 3,039 · see citing works

Environmental epigenomics and disease susceptibility

Jirtle, R. L., & Skinner, M. K. (2007) · Nature Reviews Genetics · doi:10.1038/nrg2045 · Cited by 2,492 · see citing works

Transgenerational epigenetic inheritance: myths and mechanisms

Heard, E., & Martienssen, R. A. (2014) · Cell · doi:10.1016/j.cell.2014.02.045 · Cited by 1,864 · see citing works

The Piwi-piRNA Pathway Provides an Adaptive Defense in the Transposon Arms Race

Aravin, A. A., Hannon, G. J., & Brennecke, J. (2007) · Science · doi:10.1126/science.1146484 · Cited by 1,096 · see citing works

Global Analysis of mRNA Localization Reveals a Prominent Role in Organizing Cellular Architecture and Function

Lécuyer, E., Yoshida, H., Parthasarathy, N., Alm, C., Babak, T., Cerovina, T., Hughes, T. R., Tomancak, P., & Krause, H. M. (2007) · Cell · doi:10.1016/j.cell.2007.08.003 · Cited by 967 · see citing works

Landscape of Somatic Retrotransposition in Human Cancers

Lee, E., Iskow, R., Yang, L., Gokcumen, O., Haseley, P., Luquette, L. J., Lohr, J. G., Harris, C. C., Ding, L., Wilson, R. K., et al. (2012) · Science · doi:10.1126/science.1222077 · Cited by 762 · see citing works

Dynamic interactions between transposable elements and their hosts

Levin, H. L., & Moran, J. V. (2011) · Nature Reviews Genetics · doi:10.1038/nrg3030 · Cited by 621 · see citing works

Transposable elements reveal a stem cell-specific class of long noncoding RNAs

Kelley, D., & Rinn, J. (2012) · Genome Biology · doi:10.1186/gb-2012-13-11-r107 · Cited by 531 · see citing works

The Aging Epigenome

Booth, L. N., & Brunet, A. (2016) · Molecular Cell · doi:10.1016/j.molcel.2016.05.013 · Cited by 499 · see citing works

Heterochromatin: Guardian of the Genome

Janssen, A., Colmenares, S. U., & Karpen, G. H. (2018) · Annual Review of Cell and Developmental Biology · doi:10.1146/annurev-cellbio-100617-062653 · Cited by 500 · see citing works

Epigenetic mechanisms in neurological disease

Jakovcevski, M., & Akbarian, S. (2012) · Nature Medicine · doi:10.1038/nm.2828 · Cited by 450 · see citing works

The role of DNA damage and repair in aging through the prism of Koch-like criteria

Moskalev, A. A., Shaposhnikov, M. V., Plyusnina, E. N., Zhavoronkov, A., Budovsky, A., Yanai, H., & Fraifeld, V. E. (2013) · Ageing Research Reviews · doi:10.1016/j.arr.2012.02.001 · Cited by 387 · see citing works

LTR-Retrotransposon Control by tRNA-Derived Small RNAs

Schorn, A. J., Gutbrod, M. J., LeBlanc, C., & Martienssen, R. (2017) · Cell · doi:10.1016/j.cell.2017.06.013 · Cited by 366 · see citing works

Endogenous retroviral LTRs as promoters for human genes: A critical assessment

Cohen, C. J., Lock, W. M., & Mager, D. L. (2009) · Gene · doi:10.1016/j.gene.2009.06.020 · Cited by 314 · see citing works

Pathogenic tau-induced piRNA depletion promotes neuronal death through transposable element dysregulation in neurodegenerative tauopathies

Sun, W., Samimi, H., Gamez, M., Zare, H., & Frost, B. (2018) · Nature Neuroscience · doi:10.1038/s41593-018-0194-1 · Cited by 315 · see citing works

Coevolution between transposable elements and recombination

Kent, T. V., Uzunović, J., & Wright, S. I. (2017) · Philosophical Transactions of the Royal Society B: Biological Sciences · doi:10.1098/rstb.2016.0458 · Cited by 312 · see citing works

Daddy Issues: Paternal Effects on Phenotype

Rando, O. J. (2012) · Cell · doi:10.1016/j.cell.2012.10.020 · Cited by 292 · see citing works

Epigenetic changes during aging and their reprogramming potential

Kane, A. E., & Sinclair, D. A. (2019) · Critical Reviews in Biochemistry and Molecular Biology · doi:10.1080/10409238.2019.1570075 · Cited by 283 · see citing works

A Transcriptome-wide RNAi Screen in the Drosophila Ovary Reveals Factors of the Germline piRNA Pathway

Czech, B., Preall, J. B., McGinn, J., & Hannon, G. J. (2013) · Molecular Cell · doi:10.1016/j.molcel.2013.04.007 · Cited by 269 · see citing works

Evolutionally dynamic L1 regulation in embryonic stem cells

Castro-Diaz, N., Ecco, G., Coluccio, A., Kapopoulou, A., Yazdanpanah, B., Friedli, M., Duc, J., Jang, S. M., Turelli, P., & Trono, D. (2014) · Genes &amp; Development · doi:10.1101/gad.241661.114 · Cited by 225 · see citing works

EPIGENETIC VARIATION IN ASEXUALLY REPRODUCING ORGANISMS: SPECIAL SECTION

Verhoeven, K. J. F., & Preite, V. (2014) · Evolution · doi:10.1111/evo.12320 · Cited by 216 · see citing works

Chromatin-modifying genetic interventions suppress age-associated transposable element activation and extend life span in <i>Drosophila</i>

Wood, J. G., Jones, B. C., Jiang, N., Chang, C., Hosier, S., Wickremesinghe, P., Garcia, M., Hartnett, D. A., Burhenn, L., Neretti, N., et al. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1604621113 · Cited by 214 · see citing works

Retrotransposon activation contributes to neurodegeneration in a Drosophila TDP-43 model of ALS

Krug, L., Chatterjee, N., Borges-Monroy, R., Hearn, S., Liao, W.-W., Morrill, K., Prazak, L., Rozhkov, N., Theodorou, D., Hammell, M., et al. (2017) · PLOS Genetics · doi:10.1371/journal.pgen.1006635 · Cited by 201 · see citing works

Pan-cancer analysis identifies tumor-specific antigens derived from transposable elements

Shah, N. M., Jang, H. J., Liang, Y., Maeng, J. H., Tzeng, S.-C., Wu, A., Basri, N. L., Qu, X., Fan, C., Li, A., et al. (2023) · Nature Genetics · doi:10.1038/s41588-023-01349-3 · Cited by 175 · see citing works

An RB-EZH2 Complex Mediates Silencing of Repetitive DNA Sequences

Ishak, C. A., Marshall, A. E., Passos, D. T., White, C. R., Kim, S. J., Cecchini, M. J., Ferwati, S., MacDonald, W. A., Howlett, C. J., Welch, I. D., et al. (2016) · Molecular Cell · doi:10.1016/j.molcel.2016.10.021 · Cited by 167 · see citing works

Epigenetic mechanisms in schizophrenia and other psychotic disorders: a systematic review of empirical human findings

Smigielski, L., Jagannath, V., Rössler, W., Walitza, S., & Grünblatt, E. (2020) · Molecular Psychiatry · doi:10.1038/s41380-019-0601-3 · Cited by 168 · see citing works

Molecular Architecture of the Mos1 Paired-End Complex: The Structural Basis of DNA Transposition in a Eukaryote

Richardson, J. M., Colloms, S. D., Finnegan, D. J., & Walkinshaw, M. D. (2009) · Cell · doi:10.1016/j.cell.2009.07.012 · Cited by 145 · see citing works

Common themes in siRNA-mediated epigenetic silencing pathways

Verdel, A., Vavasseur, A., Le Gorrec, M., & Touat-Todeschini, L. (2009) · The International Journal of Developmental Biology · doi:10.1387/ijdb.082691av · Cited by 135 · see citing works

A somatic piRNA pathway in the Drosophila fat body ensures metabolic homeostasis and normal lifespan

Jones, B. C., Wood, J. G., Chang, C., Tam, A. D., Franklin, M. J., Siegel, E. R., & Helfand, S. L. (2016) · Nature Communications · doi:10.1038/ncomms13856 · Cited by 130 · see citing works

Onco-exaptation of an endogenous retroviral LTR drives IRF5 expression in Hodgkin lymphoma

Babaian, A., Romanish, M. T., Gagnier, L., Kuo, L. Y., Karimi, M. M., Steidl, C., & Mager, D. L. (2016) · Oncogene · doi:10.1038/onc.2015.308 · Cited by 121 · see citing works

Confining euchromatin/heterochromatin territory: <i>jumonji</i> crosses the line

Tamaru, H. (2010) · Genes &amp; Development · doi:10.1101/gad.1941010 · Cited by 118 · see citing works

Repetitive element transcripts are elevated in the brain of C9orf72 ALS/FTLD patients

Prudencio, M., Gonzales, P. K., Cook, C. N., Gendron, T. F., Daughrity, L. M., Song, Y., Ebbert, M. T. W., van Blitterswijk, M., Zhang, Y.-J., Jansen-West, K., et al. (2017) · Human Molecular Genetics · doi:10.1093/hmg/ddx233 · Cited by 122 · see citing works

FBXO44 promotes DNA replication-coupled repetitive element silencing in cancer cells

Shen, J. Z., Qiu, Z., Wu, Q., Finlay, D., Garcia, G., Sun, D., Rantala, J., Barshop, W., Hope, J. L., Gimple, R. C., et al. (2021) · Cell · doi:10.1016/j.cell.2020.11.042 · Cited by 113 · see citing works

Somaclonal Variation—Advantage or Disadvantage in Micropropagation of the Medicinal Plants

Duta-Cornescu, G., Constantin, N., Pojoga, D.-M., Nicuta, D., & Simon-Gruita, A. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms24010838 · Cited by 108 · see citing works

Transposon-triggered innate immune response confers cancer resistance to the blind mole rat

Zhao, Y., Oreskovic, E., Zhang, Q., Lu, Q., Gilman, A., Lin, Y. S., He, J., Zheng, Z., Lu, J. Y., Lee, J., et al. (2021) · Nature Immunology · doi:10.1038/s41590-021-01027-8 · Cited by 99 · see citing works

High Genetic and Epigenetic Stability in Coffea arabica Plants Derived from Embryogenic Suspensions and Secondary Embryogenesis as Revealed by AFLP, MSAP and the Phenotypic Variation Rate

Bobadilla Landey, R., Cenci, A., Georget, F., Bertrand, B., Camayo, G., Dechamp, E., Herrera, J. C., Santoni, S., Lashermes, P., Simpson, J., et al. (2013) · PLoS ONE · doi:10.1371/journal.pone.0056372 · Cited by 95 · see citing works

Global and gene-specific DNA methylation across multiple tissues in early infancy: implications for children's health research

Armstrong, D. A., Lesseur, C., Conradt, E., Lester, B. M., & Marsit, C. J. (2014) · The FASEB Journal · doi:10.1096/fj.13-238402 · Cited by 89 · see citing works

Genomics of plant speciation

Bock, D. G., Cai, Z., Elphinstone, C., González-Segovia, E., Hirabayashi, K., Huang, K., Keais, G. L., Kim, A., Owens, G. L., & Rieseberg, L. H. (2023) · Plant Communications · doi:10.1016/j.xplc.2023.100599 · Cited by 84 · see citing works

A nucleosomal surface defines an integration hotspot for the <i>Saccharomyces cerevisiae</i> Ty1 retrotransposon

Baller, J. A., Gao, J., Stamenova, R., Curcio, M. J., & Voytas, D. F. (2012) · Genome Research · doi:10.1101/gr.129585.111 · Cited by 61 · see citing works

How Stress Facilitates Phenotypic Innovation Through Epigenetic Diversity

Srikant, T., & Drost, H.-G. (2021) · Frontiers in Plant Science · doi:10.3389/fpls.2020.606800 · Cited by 67 · see citing works

Transposon mobilization in the human fungal pathogen <i>Cryptococcus</i> is mutagenic during infection and promotes drug resistance in vitro

Gusa, A., Williams, J. D., Cho, J.-E., Averette, A. F., Sun, S., Shouse, E. M., Heitman, J., Alspaugh, J. A., & Jinks-Robertson, S. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2001451117 · Cited by 65 · see citing works

DNA methylation changes and TE activity induced in tissue cultures of barley (Hordeum vulgare L.)

Orłowska, R., Machczyńska, J., Oleszczuk, S., Zimny, J., & Bednarek, P. T. (2016) · Journal of Biological Research-Thessaloniki · doi:10.1186/s40709-016-0056-5 · Cited by 53 · see citing works

Rethinking quasispecies theory: from fittest type to cooperative consortia

Villarreal, L. P., & Witzany, G. (2013) · World Journal of Biological Chemistry · doi:10.4331/wjbc.v4.i4.79 · Cited by 49 · see citing works

The Role of Retrotransposons and Endogenous Retroviruses in Age-Dependent Neurodegenerative Disorders

Frost, B., & Dubnau, J. (2024) · Annual Review of Neuroscience · doi:10.1146/annurev-neuro-082823-020615 · Cited by 45 · see citing works

Mitotic Recombination and Adaptive Genomic Changes in Human Pathogenic Fungi

Gusa, A., & Jinks-Robertson, S. (2019) · Genes · doi:10.3390/genes10110901 · Cited by 38 · see citing works

What might retrotransposons teach us about aging?

Maxwell, P. H. (2016) · Current Genetics · doi:10.1007/s00294-015-0538-2 · Cited by 31 · see citing works

The pattern of R2 retrotransposon activity in natural populations of drosophila simulans reflects the dynamic nature of the rDNA locus

Zhou, J., & Eickbush, T. H. (2009) · PLoS Genetics · doi:10.1371/journal.pgen.1000386 · Cited by 30 · see citing works