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Roles of transposable elements in the regulation of mammalian transcription
Open accessAbstract
Transposable elements (TEs) comprise about half of the mammalian genome. TEs often contain sequences capable of recruiting the host transcription machinery, which they use to express their own products and promote transposition. However, the regulatory sequences carried by TEs may affect host transcription long after the TEs have lost the ability to transpose. Recent advances in genome analysis and engineering have facilitated systematic interrogation of the regulatory activities of TEs. In this Review, we discuss diverse mechanisms by which TEs contribute to transcription regulation. Notably, TEs can donate enhancer and promoter sequences that influence the expression of host genes, modify 3D chromatin architecture and give rise to novel regulatory genes, including non-coding RNAs and transcription factors. We discuss how TEs spur regulatory evolution and facilitate the emergence of genetic novelties in mammalian physiology and development. By virtue of their repetitive and interspersed nature, TEs offer unique opportunities to dissect the effects of mutation and genomic context on the function and evolution of cis-regulatory elements. We argue that TE-centric studies hold the key to unlocking general principles of transcription regulation and evolution.
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“Contrary to the exogenous infectious agents discussed above, transposable elements are endogenous mobile genetic elements that can move and integrate into different locations within the genome [117,118].”
From What would it take to prove that a chronic infection is a causal agent in Alzheimer’s disease? (2025) · cites this paper as [117]
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“Although this study is focused on identifying CREs, there are other non-coding regulatory mechanisms that could alter gene expression in AD including microRNAs (miRNAs),90 long non-coding RNAs (lncRNAs),91 transposable elements,92 etc., that are not assessed.”
From Single nucleus multiomics identifies ZEB1 and MAFB as candidate regulators of Alzheimer’s disease-specific cis-regulatory elements (2023) · cites this paper as [92]
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Cites
Initial sequencing and analysis of the human genome
International Human Genome Sequencing Consortium, Whitehead Institute for Biomedical Research, C. F. G. R., Lander, E. S., Linton, L. M., Birren, B., Nusbaum, C., Zody, M. C., Baldwin, J., Devon, K., Dewar, K., et al. (2001) · Nature · doi:10.1038/35057062 · Cited by 24,216
Tissue-based map of the human proteome
Uhlén, M., Fagerberg, L., Hallström, B. M., Lindskog, C., Oksvold, P., Mardinoglu, A., Sivertsson, Å., Kampf, C., Sjöstedt, E., Asplund, A., et al. (2015) · Science · doi:10.1126/science.1260419 · Cited by 15,286
Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome
Lieberman-Aiden, E., van Berkum, N. L., Williams, L., Imakaev, M., Ragoczy, T., Telling, A., Amit, I., Lajoie, B. R., Sabo, P. J., Dorschner, M. O., et al. (2009) · Science · doi:10.1126/science.1181369 · Cited by 8,898
Topological domains in mammalian genomes identified by analysis of chromatin interactions
Dixon, J. R., Selvaraj, S., Yue, F., Kim, A., Li, Y., Shen, Y., Hu, M., Liu, J. S., & Ren, B. (2012) · Nature · doi:10.1038/nature11082 · Cited by 6,829
Coming of age: ten years of next-generation sequencing technologies
Goodwin, S., McPherson, J. D., & McCombie, W. R. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2016.49 · Cited by 4,352
Schizophrenia risk from complex variation of complement component 4
Sekar, A., Bialas, A. R., de Rivera, H., Davis, A., Hammond, T. R., Kamitaki, N., Tooley, K., Presumey, J., Baum, M., Van Doren, V., et al. (2016) · Nature · doi:10.1038/nature16549 · Cited by 2,394
Expanded encyclopaedias of DNA elements in the human and mouse genomes
The ENCODE Project Consortium, Abascal, F., Acosta, R., Addleman, N. J., Adrian, J., Afzal, V., Ai, R., Aken, B., Akiyama, J. A., Jammal, O. A., et al. (2020) · Nature · doi:10.1038/s41586-020-2493-4 · Cited by 2,378
An integrated map of structural variation in 2,504 human genomes
Sudmant, P. H., Rausch, T., Gardner, E. J., Handsaker, R. E., Abyzov, A., Huddleston, J., Zhang, Y., Ye, K., Jun, G., Hsi-Yang Fritz, M., et al. (2015) · Nature · doi:10.1038/nature15394 · Cited by 2,354
The diverse roles of DNA methylation in mammalian development and disease
Greenberg, M., & Bourc’his, D. (2019) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-019-0159-6 · Cited by 2,272
Gene Regulation for Higher Cells: A Theory
Britten, R. J., & Davidson, E. H. (1969) · Science · doi:10.1126/science.165.3891.349 · Cited by 2,078
Chiappinelli, K. B., Strissel, P. L., Desrichard, A., Li, H., Henke, C., Akman, B., Hein, A., Rote, N. S., Cope, L. M., Snyder, A., et al. (2015) · Cell · doi:10.1016/j.cell.2015.07.011 · Cited by 2,022
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
Cohesin Loss Eliminates All Loop Domains
Rao, S. S. P., Huang, S.-C., Glenn St Hilaire, B., Engreitz, J. M., Perez, E. M., Kieffer-Kwon, K.-R., Sanborn, A. L., Johnstone, S. E., Bascom, G. D., Bochkov, I. D., et al. (2017) · Cell · doi:10.1016/j.cell.2017.09.026 · Cited by 1,883
Nora, E. P., Goloborodko, A., Valton, A.-L., Gibcus, J. H., Uebersohn, A., Abdennur, N., Dekker, J., Mirny, L. A., & Bruneau, B. G. (2017) · Cell · doi:10.1016/j.cell.2017.05.004 · Cited by 1,709
Roulois, D., Loo Yau, H., Singhania, R., Wang, Y., Danesh, A., Shen, S. Y., Han, H., Liang, G., Jones, P. A., Pugh, T. J., et al. (2015) · Cell · doi:10.1016/j.cell.2015.07.056 · Cited by 1,527
Regulatory activities of transposable elements: from conflicts to benefits
Chuong, E. B., Elde, N. C., & Feschotte, C. (2017) · Nature Reviews Genetics · doi:10.1038/nrg.2016.139 · Cited by 1,489
Self-citationThe next generation of CRISPR–Cas technologies and applications
Pickar-Oliver, A., & Gersbach, C. A. (2019) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-019-0131-5 · Cited by 1,459
Transposable elements and the evolution of regulatory networks
Feschotte, C. (2008) · Nature Reviews Genetics · doi:10.1038/nrg2337 · Cited by 1,379
Self-citationPIWI-interacting RNAs: small RNAs with big functions
Özata, D. M., Gainetdinov, I. V., Zoch, A., O’Carroll, D., & Zamore, P. D. (2018) · Nature Reviews Genetics · doi:10.1038/s41576-018-0073-3 · Cited by 1,196
Organization and function of the 3D genome
Bonev, B., & Cavalli, G. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2016.112 · Cited by 1,174
Organizational principles of 3D genome architecture
Rowley, M. J., & Corces, V. G. (2018) · Nature Reviews Genetics · doi:10.1038/s41576-018-0060-8 · Cited by 1,171
Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq
Arnold, C. D., Gerlach, D., Stelzer, C., Boryń, Ł. M., Rath, M., & Stark, A. (2013) · Science · doi:10.1126/science.1232542 · Cited by 1,125
Activity-by-contact model of enhancer–promoter regulation from thousands of CRISPR perturbations
Fulco, C. P., Nasser, J., Jones, T. R., Munson, G., Bergman, D. T., Subramanian, V., Grossman, S. R., Anyoha, R., Doughty, B. R., Patwardhan, T. A., et al. (2019) · Nature Genetics · doi:10.1038/s41588-019-0538-0 · Cited by 1,111
Long-range enhancer–promoter contacts in gene expression control
Schoenfelder, S., & Fraser, P. (2019) · Nature Reviews Genetics · doi:10.1038/s41576-019-0128-0 · Cited by 1,102
Regulatory evolution of innate immunity through co-option of endogenous retroviruses
Chuong, E. B., Elde, N. C., & Feschotte, C. (2016) · Science · doi:10.1126/science.aad5497 · Cited by 1,008
Self-citationMapping long-range promoter contacts in human cells with high-resolution capture Hi-C
Mifsud, B., Tavares-Cadete, F., Young, A. N., Sugar, R., Schoenfelder, S., Ferreira, L., Wingett, S. W., Andrews, S., Grey, W., Ewels, P. A., et al. (2015) · Nature Genetics · doi:10.1038/ng.3286 · Cited by 990
Embryonic stem cell potency fluctuates with endogenous retrovirus activity
Macfarlan, T. S., Gifford, W. D., Driscoll, S., Lettieri, K., Rowe, H. M., Bonanomi, D., Firth, A., Singer, O., Trono, D., & Pfaff, S. L. (2012) · Nature · doi:10.1038/nature11244 · Cited by 981
Ever-Changing Landscapes: Transcriptional Enhancers in Development and Evolution
Long, H. K., Prescott, S. L., & Wysocka, J. (2016) · Cell · doi:10.1016/j.cell.2016.09.018 · Cited by 945
Self-citationEnhancer Evolution across 20 Mammalian Species
Villar, D., Berthelot, C., Aldridge, S., Rayner, T. F., Lukk, M., Pignatelli, M., Park, T. J., Deaville, R., Erichsen, J. T., Jasinska, A. J., et al. (2015) · Cell · doi:10.1016/j.cell.2015.01.006 · Cited by 825
The regulated retrotransposon transcriptome of mammalian cells
Faulkner, G. J., Kimura, Y., Daub, C. O., Wani, S., Plessy, C., Irvine, K. M., Schroder, K., Cloonan, N., Steptoe, A. L., Lassmann, T., et al. (2009) · Nature Genetics · doi:10.1038/ng.368 · Cited by 819
Wang, Y., Xu, Z., Jiang, J., Xu, C., Kang, J., Xiao, L., Wu, M., Xiong, J., Guo, X., & Liu, H. (2013) · Developmental Cell · doi:10.1016/j.devcel.2013.03.002 · Cited by 795
Transposable elements have rewired the core regulatory network of human embryonic stem cells
Kunarso, G., Chia, N., Jeyakani, J., Hwang, C., Lu, X., Chan, Y.-S., Ng, H., & Bourque, G. (2010) · Nature Genetics · doi:10.1038/ng.600 · Cited by 777
Evolution of genetic redundancy
Nowak, M. A., Boerlijst, M. C., Cooke, J., & Smith, J. M. (1997) · Nature · doi:10.1038/40618 · Cited by 760
The role of 3D genome organization in development and cell differentiation
Zheng, H., & Xie, W. (2019) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-019-0132-4 · Cited by 742
Hendrickson, P. G., Dorais, J., Grow, E. J., Whiddon, J. L., Lim, J.-W., Wike, C. L., Weaver, B. D., Pflueger, C., Emery, B. R., Wilcox, A. L., et al. (2017) · Nature Genetics · doi:10.1038/ng.3844 · Cited by 731
Retrotransposons regulate host genes in mouse oocytes and preimplantation embryos
Peaston, A. E., Evsikov, A. V., Graber, J. H., de Vries, W. N., Holbrook, A. E., Solter, D., & Knowles, B. B. (2004) · Developmental Cell · doi:10.1016/j.devcel.2004.09.004 · Cited by 710
DNA methylation: The nuts and bolts of repression
Miranda, T. B., & Jones, P. A. (2007) · Journal of Cellular Physiology · doi:10.1002/jcp.21224 · Cited by 701
Kapusta, A., Kronenberg, Z., Lynch, V. J., Zhuo, X., Ramsay, L., Bourque, G., Yandell, M., & Feschotte, C. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003470 · Cited by 687
Self-citationA Field Guide to Eukaryotic Transposable Elements
Wells, J. N., & Feschotte, C. (2020) · Annual Review of Genetics · doi:10.1146/annurev-genet-040620-022145 · Cited by 686
Self-citationA Unique Gene Regulatory Network Resets the Human Germline Epigenome for Development
Tang, W. W. C., Dietmann, S., Irie, N., Leitch, H. G., Floros, V. I., Bradshaw, C. R., Hackett, J. A., Chinnery, P. F., & Surani, M. A. (2015) · Cell · doi:10.1016/j.cell.2015.04.053 · Cited by 670
Roles for retrotransposon insertions in human disease
Hancks, D. C., & Kazazian, H. H. (2016) · Mobile DNA · doi:10.1186/s13100-016-0065-9 · Cited by 670
Intrinsic retroviral reactivation in human preimplantation embryos and pluripotent cells
Grow, E. J., Flynn, R. A., Chavez, S. L., Bayless, N. L., Wossidlo, M., Wesche, D. J., Martin, L., Ware, C. B., Blish, C. A., Chang, H. Y., et al. (2015) · Nature · doi:10.1038/nature14308 · Cited by 666
Self-citationEnhancer redundancy provides phenotypic robustness in mammalian development
Osterwalder, M., Barozzi, I., Tissières, V., Fukuda-Yuzawa, Y., Mannion, B. J., Afzal, S. Y., Lee, E. A., Zhu, Y., Plajzer-Frick, I., Pickle, C. S., et al. (2018) · Nature · doi:10.1038/nature25461 · Cited by 642
Duboule, D. (1994) · Development · doi:10.1242/dev.1994.supplement.135 · Cited by 634
KRAB zinc-finger proteins contribute to the evolution of gene regulatory networks
Imbeault, M., Helleboid, P.-Y., & Trono, D. (2017) · Nature · doi:10.1038/nature21683 · Cited by 623
Schmidt, D., Schwalie, P. C., Wilson, M. D., Ballester, B., Gonçalves, Â., Kutter, C., Brown, G. D., Marshall, A., Flicek, P., & Odom, D. T. (2012) · Cell · doi:10.1016/j.cell.2011.11.058 · Cited by 620
A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens
Gasperini, M., Hill, A. J., McFaline-Figueroa, J. L., Martin, B., Kim, S., Zhang, M. D., Jackson, D., Leith, A., Schreiber, J., Noble, W. S., et al. (2019) · Cell · doi:10.1016/j.cell.2018.11.029 · Cited by 613
DNA methylation dynamics of the human preimplantation embryo
Smith, Z. D., Chan, M. M., Humm, K. C., Karnik, R., Mekhoubad, S., Regev, A., Eggan, K. C., & Meissner, A. (2014) · Nature · doi:10.1038/nature13581 · Cited by 600
Evolution of the mammalian transcription factor binding repertoire via transposable elementsPreprint
Bourque, G., Leong, B., Vega, V. B., Chen, X., Lee, Y. L., Srinivasan, K. G., Chew, J.-L., Ruan, Y., Wei, C., Ng, H., et al. (2008) · Genome Research · doi:10.1101/gr.080663.108 · Cited by 579
Transposable elements in cancer
Burns, K. H. (2017) · Nature Reviews Cancer · doi:10.1038/nrc.2017.35 · Cited by 572
A LINE1-Nucleolin Partnership Regulates Early Development and ESC Identity
Percharde, M., Lin, C.-J., Yin, Y., Guan, J., Peixoto, G. A., Bulut-Karslıoğlu, A., Biechele, S., Huang, B., Shen, X., & Ramalho‐Santos, M. (2018) · Cell · doi:10.1016/j.cell.2018.05.043 · Cited by 570
Regulation of Gene Expression: Possible Role of Repetitive Sequences
Davidson, E. H., & Britten, R. J. (1979) · Science · doi:10.1126/science.451548 · Cited by 568
Karimi, M. M., Goyal, P., Maksakova, I. A., Bilenky, M., Leung, D., Tang, J. X., Shinkai, Y., Mager, D. L., Jones, S., Hirst, M., et al. (2011) · Cell Stem Cell · doi:10.1016/j.stem.2011.04.004 · Cited by 535
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
Widespread contribution of transposable elements to the innovation of gene regulatory networks
Sundaram, V., Cheng, Y., Ma, Z., Li, D., Xing, X., Edge, P., Snyder, M. P., & Wang, T. (2014) · Genome Research · doi:10.1101/gr.168872.113 · Cited by 529
Phenotypic robustness conferred by apparently redundant transcriptional enhancers
Frankel, N., Davis, G. K., Vargas, D., Wang, S., Payre, F., & Stern, D. L. (2010) · Nature · doi:10.1038/nature09158 · Cited by 510
An evolutionary arms race between KRAB zinc-finger genes ZNF91/93 and SVA/L1 retrotransposons
Jacobs, F. M. J., Greenberg, D., Nguyen, N., Haeussler, M., Ewing, A. D., Katzman, S., Paten, B., Salama, S. R., & Haussler, D. (2014) · Nature · doi:10.1038/nature13760 · Cited by 506
Regulation of transposable elements by DNA modifications
Deniz, Ö., Frost, J. M., & Branco, M. R. (2019) · Nature Reviews Genetics · doi:10.1038/s41576-019-0106-6 · Cited by 500
Human endogenous retrovirus-K contributes to motor neuron disease
Li, W., Lee, M.-H., Henderson, L., Tyagi, R., Bachani, M., Steiner, J., Campanac, E., Hoffman, D. A., von Geldern, G., Johnson, K., et al. (2015) · Science Translational Medicine · doi:10.1126/scitranslmed.aac8201 · Cited by 482
Human Alu RNA Is a Modular Transacting Repressor of mRNA Transcription during Heat Shock
Mariner, P. D., Walters, R. D., Espinoza, C. A., Drullinger, L. F., Wagner, S. D., Kugel, J. F., & Goodrich, J. A. (2008) · Molecular Cell · doi:10.1016/j.molcel.2007.12.013 · Cited by 479
Primate-specific endogenous retrovirus-driven transcription defines naive-like stem cells
Wang, J., Xie, G., Singh, M., Ghanbarian, A. T., Raskó, T., Szvetnik, A., Cai, H., Besser, D., Prigione, A., Fuchs, N. V., et al. (2014) · Nature · doi:10.1038/nature13804 · Cited by 455
Neomorphic agouti mutations in obese yellow mice
Duhl, D. M. J., Vrieling, H., Miller, K. A., Wolff, G. L., & Barsh, G. S. (1994) · Nature Genetics · doi:10.1038/ng0994-59 · Cited by 448
The retrovirus HERVH is a long noncoding RNA required for human embryonic stem cell identity
Lu, X., Sachs, F., Ramsay, L., Jacques, P., Göke, J., Bourque, G., & Ng, H. (2014) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2799 · Cited by 437
Restricting retrotransposons: a review
Goodier, J. L. (2016) · Mobile DNA · doi:10.1186/s13100-016-0070-z · Cited by 436
Lynch, V. J., Leclerc, R. D., May, G. E., & Wagner, G. P. (2011) · Nature Genetics · doi:10.1038/ng.917 · Cited by 434
Endogenous retroviruses function as species-specific enhancer elements in the placenta
Chuong, E. B., Rumi, M. A. K., Soares, M. J., & Baker, J. C. (2013) · Nature Genetics · doi:10.1038/ng.2553 · Cited by 429
Jachowicz, J. W., Bing, X., Pontabry, J., Bošković, A., Rando, O. J., & Torres‐Padilla, M. (2017) · Nature Genetics · doi:10.1038/ng.3945 · Cited by 423
Measuring and interpreting transposable element expression
Lanciano, S., & Cristofari, G. (2020) · Nature Reviews Genetics · doi:10.1038/s41576-020-0251-y · Cited by 415
Abundant contribution of short tandem repeats to gene expression variation in humans
Gymrek, M., Willems, T., Guilmatre, A., Zeng, H., Markus, B., Georgiev, S., Daly, M. J., Price, A. L., Pritchard, J. K., Sharp, A. J., et al. (2016) · Nature Genetics · doi:10.1038/ng.3461 · Cited by 410
Wang, T., Zeng, J., Lowe, C. B., Sellers, R. G., Salama, S. R., Yang, M., Burgess, S. M., Brachmann, R. K., & Haussler, D. H. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0703637104 · Cited by 406
Transposable elements drive widespread expression of oncogenes in human cancers
Jang, H. J., Shah, N. M., Du, A. Y., Dailey, Z. Z., Pehrsson, E. C., Godoy, P. M., Zhang, D., Li, D., Xing, X., Kim, S., et al. (2019) · Nature Genetics · doi:10.1038/s41588-019-0373-3 · Cited by 403
Zhang, Y., Li, T., Preißl, S., Amaral, M. L., Grinstein, J. D., Farah, E. N., Destici, E., Qiu, Y., Hu, R., Lee, A. Y., et al. (2019) · Nature Genetics · doi:10.1038/s41588-019-0479-7 · Cited by 384
Göke, J., Lu, X., Chan, Y.-S., Ng, H., Ly, L.-H., Sachs, F., & Szczerbinska, I. (2015) · Cell stem cell · doi:10.1016/j.stem.2015.01.005 · Cited by 378
Selective silencing of euchromatic L1s revealed by genome-wide screens for L1 regulators
Liu, N., Lee, C. H., Swigut, T., Grow, E. J., Gu, B., Bassik, M. C., & Wysocka, J. (2017) · Nature · doi:10.1038/nature25179 · Cited by 376
Self-citationTransposable elements in human genetic disease
Payer, L. M., & Burns, K. H. (2019) · Nature Reviews Genetics · doi:10.1038/s41576-019-0165-8 · Cited by 366
Enhancer Divergence and cis-Regulatory Evolution in the Human and Chimp Neural Crest
Prescott, S. L., Srinivasan, R., Marchetto, M. C., Grishina, I., Narvaiza, I., Selleri, L., Gage, F. H., Swigut, T., & Wysocka, J. (2015) · Cell · doi:10.1016/j.cell.2015.08.036 · Cited by 364
Self-citationThe Majority of Primate-Specific Regulatory Sequences Are Derived from Transposable Elements
Jacques, P., Jeyakani, J., & Bourque, G. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003504 · Cited by 360
Insertional polymorphisms of full-length endogenous retroviruses in humans
Turner, G., Barbulescu, M., Su, M., Jensen-Seaman, M. I., Kidd, K. K., & Lenz, J. (2001) · Current Biology · doi:10.1016/s0960-9822(01)00455-9 · Cited by 358
Retrotransposons as epigenetic mediators of phenotypic variation in mammals
Whitelaw, E., & Martin, D. I. K. (2001) · Nature Genetics · doi:10.1038/86850 · Cited by 353
DNMT and HDAC inhibitors induce cryptic transcription start sites encoded in long terminal repeats
Brocks, D., Schmidt, C. R., Daskalakis, M., Jang, H. S., Shah, N. M., Li, D., Li, J., Zhang, B., Hou, Y., Laudato, S., et al. (2017) · Nature Genetics · doi:10.1038/ng.3889 · Cited by 339
The RIDL hypothesis: transposable elements as functional domains of long noncoding RNAs
Johnson, R., & Guigó, R. (2014) · RNA · doi:10.1261/rna.044560.114 · Cited by 324
Flemr, M., Malı́k, R., Franke, V., Nejepinska, J., Sedláček, R., Vlahoviček, K., & Svoboda, P. (2013) · Cell · doi:10.1016/j.cell.2013.10.001 · Cited by 320
Suboptimization of developmental enhancers
Farley, E. K., Olson, K. M., Zhang, W., Brandt, A. J., Rokhsar, D. S., & Levine, M. S. (2015) · Science · doi:10.1126/science.aac6948 · Cited by 319
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
Fort, A., Hashimoto, K., Yamada, D., Salimullah, M., Keya, C. A., Saxena, A., Bonetti, A., Voineagu, I., Bertin, N., Kratz, A., et al. (2014) · Nature Genetics · doi:10.1038/ng.2965 · Cited by 314
Volatile evolution of long noncoding RNA repertoires: mechanisms and biological implications
Kapusta, A., & Feschotte, C. (2014) · Trends in Genetics · doi:10.1016/j.tig.2014.08.004 · Cited by 306
Self-citationThe relationship between genome structure and function
Oudelaar, A. M., & Higgs, D. R. (2021) · Nature Reviews Genetics · doi:10.1038/s41576-020-00303-x · Cited by 304
CTCF: making the right connectionsPreprint
Ghirlando, R., & Felsenfeld, G. (2016) · Genes & Development · doi:10.1101/gad.277863.116 · Cited by 302
Host–transposon interactions: conflict, cooperation, and cooptionPreprint
Cosby, R. L., Chang, N., & Feschotte, C. (2019) · Genes & Development · doi:10.1101/gad.327312.119 · Cited by 300
Self-citationPontis, J., Planet, E., Offner, S., Turelli, P., Duc, J., Coudray, A., Theunissen, T. W., Jaenisch, R., & Trono, D. (2019) · Cell stem cell · doi:10.1016/j.stem.2019.03.012 · Cited by 294
The SINE-encoded mouse B2 RNA represses mRNA transcription in response to heat shock
Allen, T. A., Kaenel, S. V., Goodrich, J. A., & Kugel, J. F. (2004) · Nature Structural & Molecular Biology · doi:10.1038/nsmb813 · Cited by 293
Endogenous retroviruses and neighboring genes are coordinately repressed by LSD1/KDM1APreprint
Macfarlan, T. S., Gifford, W. D., Agarwal, S., Driscoll, S. P., Lettieri, K., Wang, J., Andrews, S. E., Franco, L., Rosenfeld, M. G., Ren, B., et al. (2011) · Genes & Development · doi:10.1101/gad.2008511 · Cited by 288
Transposable Element Domestication As an Adaptation to Evolutionary Conflicts
Jangam, D., Feschotte, C., & Betrán, E. (2017) · Trends in Genetics · doi:10.1016/j.tig.2017.07.011 · Cited by 287
Self-citationTransposable elements are the primary source of novelty in primate gene regulationPreprint
Trizzino, M., Park, Y., Beltrame, M. H., Aracena, K. A., Mika, K. M., Çalışkan, M., Perry, G. H., Lynch, V. J., & Brown, C. D. (2017) · Genome Research · doi:10.1101/gr.218149.116 · Cited by 286
Ting, C.-N., Rosenberg, M. P., Snow, C., Samuelson, L. C., & Meisler, M. H. (1992) · Genes & Development · doi:10.1101/gad.6.8.1457 · Cited by 284
Mechanisms and Functions of Chromosome Compartmentalization
Hildebrand, E. M., & Dekker, J. (2020) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2020.01.002 · Cited by 284
Molecular mechanisms driving transcriptional stress responses
Vihervaara, A., Duarte, F. M., & Lis, J. T. (2018) · Nature Reviews Genetics · doi:10.1038/s41576-018-0001-6 · Cited by 283
Molecular basis of immune evasion by the Delta and Kappa SARS-CoV-2 variants
McCallum, M., Walls, A. C., Sprouse, K. R., Bowen, J. E., Rosen, L. E., Dang, H. V., Marco, A. D., Franko, N., Tilles, S. W., Logue, J. K., et al. (2021) · Science · doi:10.1126/science.abl8506 · Cited by 280
Developmentally Regulated Activation of a SINE B2 Repeat as a Domain Boundary in Organogenesis
Lunyak, V. V., Préfontaine, G. G., Núñez, E., Cramer, T., Ju, B., Ohgi, K. A., Hutt, K. R., Roy, R., García-Díaz, Á., Zhu, X., et al. (2007) · Science · doi:10.1126/science.1140871 · Cited by 279
Histone H3 lysine 9 trimethylation and HP1γ favor inclusion of alternative exons
Saint-André, V., Batsché, E., Rachez, C., & Muchardt, C. (2011) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1995 · Cited by 278
Molecular basis and biological function of variability in spatial genome organization
Finn, E. H., & Misteli, T. (2019) · Science · doi:10.1126/science.aaw9498 · Cited by 278
A graph neural network model to estimate cell-wise metabolic flux using single-cell RNA-seq dataPreprint
Alghamdi, N., Chang, W., Dang, P., Lu, X., Wan, C., Gampala, S., Huang, Z., Wang, J., Ma, Q., Zang, Y., et al. (2021) · Genome Research · doi:10.1101/gr.271205.120 · Cited by 271
B2 RNA binds directly to RNA polymerase II to repress transcript synthesis
Espinoza, C. A., Allen, T. A., Hieb, A. R., Kugel, J. F., & Goodrich, J. A. (2004) · Nature Structural & Molecular Biology · doi:10.1038/nsmb812 · Cited by 266
Ohnuki, M., Tanabe, K., Sutou, K., Teramoto, I., Sawamura, Y., Narita, M., Nakamura, M., Tokunaga, Y., Nakamura, M., Watanabe, A., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1413299111 · Cited by 265
Endogenous retroviral promoter exaptation in human cancer
Babaian, A., & Mager, D. L. (2016) · Mobile DNA · doi:10.1186/s13100-016-0080-x · Cited by 261
Xie, M., Hong, C., Zhang, B., Lowdon, R. F., Xing, X., Li, D., Zhou, X., Lee, H. J., Maire, C. L., Ligon, K. L., et al. (2013) · Nature Genetics · doi:10.1038/ng.2649 · Cited by 260
Birth of a chimeric primate gene by capture of the transposase gene from a mobile element
Cordaux, R., Udit, S., Batzer, M. A., & Feschotte, C. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0601161103 · Cited by 258
Self-citationLynch, V. J., Nnamani, M. C., Kapusta, A., Brayer, K. J., Plaza, S. L., Mazur, E. C., Emera, D., Sheikh, S. Z., Grützner, F., Bauersachs, S., et al. (2015) · Cell Reports · doi:10.1016/j.celrep.2014.12.052 · Cited by 255
Self-citationTransposable elements as a potent source of diverse cis -regulatory sequences in mammalian genomes
Sundaram, V., & Wysocka, J. (2020) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2019.0347 · Cited by 253
Self-citationGellersen, B., Kempf, R., Telgmann, R., & DiMattia, G. E. (1994) · Molecular Endocrinology · doi:10.1210/mend.8.3.8015553 · Cited by 249
Computational tools to unmask transposable elements
Goerner-Potvin, P., & Bourque, G. (2018) · Nature Reviews Genetics · doi:10.1038/s41576-018-0050-x · Cited by 243
Shadow Enhancers Are Pervasive Features of Developmental Regulatory Networks
Cannavò, E., Khoueiry, P., Garfield, D. A., Geeleher, P., Zichner, T., Gustafson, E. H., Ciglar, L., Korbel, J. O., & Furlong, E. E. M. (2016) · Current Biology · doi:10.1016/j.cub.2015.11.034 · Cited by 235
Many Human Genes Are Transcribed from the Antisense Promoter of L1 Retrotransposon
Nigumann, P., Redik, K., Mätlik, K., & Speek, M. (2002) · Genomics · doi:10.1006/geno.2002.6758 · Cited by 229
Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells
Barakat, T. S., Halbritter, F., Zhang, M., Rendeiro, A. F., Perenthaler, E., Bock, C., & Chambers, I. (2018) · Cell stem cell · doi:10.1016/j.stem.2018.06.014 · Cited by 227
The HUSH complex cooperates with TRIM28 to repress young retrotransposons and new genes
Robbez-Masson, L., Tie, C. H. C., Conde, L., Tunbak, H., Husovsky, C., Tchasovnikarova, I. A., Timms, R. T., Herrero, J., Lehner, P. J., & Rowe, H. M. (2018) · Genome Research · doi:10.1101/gr.228171.117 · Cited by 221
He, J., Babarinde, I. A., Sun, L., Xu, S., Chen, R., Shi, J., Wei, Y., Li, Y., Ma, G., Zhuang, Q., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-21808-x · Cited by 205
Regulatory Landscaping: How Enhancer-Promoter Communication Is Sculpted in 3D
Robson, M. I., Ringel, A. R., & Mundlos, S. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.05.032 · Cited by 203
Hell and High Water: Practice-Relevant Adaptation Science
Moss, R. H., Meehl, G. A., Lemos, M. C., Smith, J. B., Arnold, J. R., Arnott, J. C., Béhar, D., Brasseur, G. P., Broomell, S. B., Busalacchi, A. J., et al. (2013) · Science · doi:10.1126/science.1239569 · Cited by 201
Fuentes, D., Swigut, T., & Wysocka, J. (2018) · eLife · doi:10.7554/elife.35989 · Cited by 198
Self-citationPossible involvement of SINEs in mammalian-specific brain formation
Sasaki, T., Nishihara, H., Hirakawa, M., Fujimura, K., Tanaka, M., Kokubo, N., Kimura-Yoshida, C., Matsuo, I., Sumiyama, K., Saitou, N., et al. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0709398105 · Cited by 195
Silver, M. J., Kessler, N. J., Hennig, B. J., Domínguez-Salas, P., Laritsky, E., Baker, M. S., Coarfa, C., Hernández‐Vargas, H., Castelino, J. M., Routledge, M. N., et al. (2015) · Genome biology · doi:10.1186/s13059-015-0660-y · Cited by 188
The road ahead in genetics and genomics
McGuire, A. L., Gabriel, S., Tishkoff, S. A., Wonkam, A., Chakravarti, A., Furlong, E. E. M., Treutlein, B., Meissner, A., Chang, H. Y., López-Bigas, N., et al. (2020) · Nature Reviews Genetics · doi:10.1038/s41576-020-0272-6 · Cited by 188
Durruthy-Durruthy, J., Sebastiano, V., Wossidlo, M., Cepeda, D. A., Cui, J., Grow, E. J., Davila, J., Mall, M., Wong, W. H., Wysocka, J., et al. (2015) · Nature Genetics · doi:10.1038/ng.3449 · Cited by 186
Self-citationErratum: Organization and function of the 3D genome
Bonev, B., & Cavalli, G. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2016.147 · Cited by 184
Ito, J., Sugimoto, R., Nakaoka, H., YAMADA, S., Kimura, T., Hayano, T., & Inoue, I. (2017) · PLoS Genetics · doi:10.1371/journal.pgen.1006883 · Cited by 181
Kazachenka, A., Bertozzi, T. M., Sjoberg-Herrera, M. K., Walker, N., Gardner, J., Gunning, R., Pahita, E., Adams, S., Adams, D., & Ferguson-Smith, A. C. (2018) · Cell · doi:10.1016/j.cell.2018.09.043 · Cited by 181
Harmston, N., Ing‐Simmons, E., Tan, G., Perry, M., Merkenschlager, M., & Lenhard, B. (2017) · Nature Communications · doi:10.1038/s41467-017-00524-5 · Cited by 175
Recurrent evolution of vertebrate transcription factors by transposase capture
Cosby, R. L., Judd, J., Zhang, R., Zhong, A., Garry, N., Pritham, E. J., & Feschotte, C. (2021) · Science · doi:10.1126/science.abc6405 · Cited by 173
Self-citationLoss of Extreme Long-Range Enhancers in Human Neural Crest Drives a Craniofacial Disorder
Long, H. K., Osterwalder, M., Welsh, I. C., Hansen, K. L., Davies, J. O. J., Liu, Y. E., Koska, M., Adams, A. T., Aho, R., Arora, N., et al. (2020) · Cell stem cell · doi:10.1016/j.stem.2020.09.001 · Cited by 166
Self-citationThe HUSH complex is a gatekeeper of type I interferon through epigenetic regulation of LINE-1s
Tunbak, H., Enriquez-Gasca, R., Tie, C. H. C., Gould, P. A., Mlcochova, P., Gupta, R. K., Fernandes, L., Holt, J., van der Veen, A. G., Giampazolias, E., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-19170-5 · Cited by 162
Kaaij, L. J. T., Mohn, F., van der Weide, R. H., de Wit, E., & Bühler, M. (2019) · Cell · doi:10.1016/j.cell.2019.08.007 · Cited by 161
Bruno, M., Mahgoub, M., & Macfarlan, T. S. (2019) · Annual Review of Genetics · doi:10.1146/annurev-genet-112618-043717 · Cited by 160
The developmental hourglass model: a predictor of the basic body plan?
Irie, N., & Kuratani, S. (2014) · Development · doi:10.1242/dev.107318 · Cited by 157
The Human Long Interspersed Element-1 Retrotransposon: An Emerging Biomarker of Neoplasia
Ardeljan, D., Taylor, M. S., Ting, D. T., & Burns, K. H. (2017) · Clinical Chemistry · doi:10.1373/clinchem.2016.257444 · Cited by 152
Lee, S., Oshige, M., Durant, S. T., Rasila, K. K., Williamson, E. A., Ramsey, H. E., Corwin, L. K., Nickoloff, J. A., & Hromas, R. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0503676102 · Cited by 150
Todd, C. D., Deniz, Ö., Taylor, D., & Branco, M. R. (2019) · eLife · doi:10.7554/elife.44344 · Cited by 148
Unfixed Endogenous Retroviral Insertions in the Human Population
Marchi, E., Kanapin, A. A., Magiorkinis, G., & Belshaw, R. D. (2014) · Journal of Virology · doi:10.1128/jvi.00919-14 · Cited by 144
Transposable elements generate regulatory novelty in a tissue-specific fashion
Trizzino, M., Kapusta, A., & Brown, C. D. (2018) · BMC Genomics · doi:10.1186/s12864-018-4850-3 · Cited by 141
Structural variants caused by Alu insertions are associated with risks for many human diseases
Payer, L. M., Steranka, J. P., Yang, W. R., Kryatova, M. S., Medabalimi, S., Ardeljan, D., Liu, C., Boeke, J. D., Avramopoulos, D., & Burns, K. H. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1704117114 · Cited by 140
DUX-miR-344-ZMYM2-Mediated Activation of MERVL LTRs Induces a Totipotent 2C-like State
Yang, F., Huang, X., Zang, R., Chen, J., Fidalgo, M., Sánchez-Priego, C., Yang, J., Caichen, A., Ma, F., Macfarlan, T. S., et al. (2020) · Cell stem cell · doi:10.1016/j.stem.2020.01.004 · Cited by 140
L1 Antisense Promoter Drives Tissue‐Specific Transcriptionof Human Genes
Mätlik, K., Redik, K., & Speek, M. (2006) · BioMed Research International · doi:10.1155/jbb/2006/71753 · Cited by 133
A-MYB (MYBL1) transcription factor is a master regulator of male meiosis
Bolcun‐Filas, E., Bannister, L., Barash, A., Schimenti, K. J., Hartford, S. A., Eppig, J. J., Handel, M. A., Shen, L., & Schimenti, J. C. (2011) · Development · doi:10.1242/dev.067645 · Cited by 132
MIR retrotransposon sequences provide insulators to the human genome
Wang, J., Vicente‐García, C., Seruggia, D., Moltó, E., Fernández‐Miñán, A., Neto, A., Lee, E., Gómez-Skármeta, J. L., Montoliu, L., Lunyak, V. V., et al. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1507253112 · Cited by 128
Berwaer, M., MARTIAL, J. A., & Davis, J. R. (1994) · Molecular Endocrinology · doi:10.1210/mend.8.5.8058071 · Cited by 127
Diseases of the nERVous system: retrotransposon activity in neurodegenerative disease
Tam, O. H., Ostrow, L. W., & Hammell, M. (2019) · Mobile DNA · doi:10.1186/s13100-019-0176-1 · Cited by 127
A mouse-specific retrotransposon drives a conserved Cdk2ap1 isoform essential for development
Modzelewski, A. J., Shao, W., Chen, J., Lee, A., Qi, X., Noon, M., Tjokro, K., Sales, G., Biton, A., Anand, A., et al. (2021) · Cell · doi:10.1016/j.cell.2021.09.021 · Cited by 120
The 3D folding of metazoan genomes correlates with the association of similar repetitive elements
Cournac, A., Koszul, R., & Mozziconacci, J. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv1292 · Cited by 118
Prolactin in man: a tale of two promoters
Gerlo, S., Davis, J. R., Mager, D. L., & Kooijman, R. (2006) · BioEssays · doi:10.1002/bies.20468 · Cited by 117
Chromatin topology, condensates and gene regulation: shifting paradigms or just a phase?
Mir, M., Bickmore, W. A., Furlong, E. E. M., & Narlikar, G. J. (2019) · Development · doi:10.1242/dev.182766 · Cited by 113
The epigenomic landscape of transposable elements across normal human development and anatomy
Pehrsson, E. C., Choudhary, M. N. K., Sundaram, V., & Wang, T. (2019) · Nature Communications · doi:10.1038/s41467-019-13555-x · Cited by 111
TFs for TEs: the transcription factor repertoire of mammalian transposable elementsPreprint
Hermant, C., & Torres‐Padilla, M. (2021) · Genes & Development · doi:10.1101/gad.344473.120 · Cited by 111
Emera, D., Casola, C., Lynch, V. J., Wildman, D. E., Agnew, D., & Wagner, G. P. (2011) · Molecular Biology and Evolution · doi:10.1093/molbev/msr189 · Cited by 110
Co-opted transposons help perpetuate conserved higher-order chromosomal structures
Choudhary, M. N. K., Friedman, R. Z., Wang, J. T., Jang, H. J., Zhuo, X., & Wang, T. (2020) · Genome biology · doi:10.1186/s13059-019-1916-8 · Cited by 110
Transposable elements: Self‐seekers of the germline, team‐players of the soma
Haig, D. (2016) · BioEssays · doi:10.1002/bies.201600125 · Cited by 107
Nimble and Ready to Mingle: Transposon Outbursts of Early Development
Rodriguez‐Terrones, D., & Torres‐Padilla, M. (2018) · Trends in Genetics · doi:10.1016/j.tig.2018.06.006 · Cited by 106
Zscan4c activates endogenous retrovirus MERVL and cleavage embryo genes
Zhang, W., Chen, F., Chen, R., Xie, D., Yang, J., Zhao, X. J., Guo, R., Zhang, Y., Shen, Y., Göke, J., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz594 · Cited by 106
A family of transposable elements co-opted into developmental enhancers in the mouse neocortex
Notwell, J. H., Chung, T. R., Heavner, W. E., & Bejerano, G. (2015) · Nature Communications · doi:10.1038/ncomms7644 · Cited by 104
Sun, X., Wang, X., Tang, Z., Grivainis, M., Kahler, D. J., Yun, C., Mita, P., Fenyö, D., & Boeke, J. D. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1722565115 · Cited by 98
Genome-wide characterization of human L1 antisense promoter-driven transcripts
Criscione, S. W., Theodosakis, N., Micevic, G., Cornish, T. C., Burns, K. H., Neretti, N., & Rodić, N. (2016) · BMC Genomics · doi:10.1186/s12864-016-2800-5 · Cited by 96
Destabilization of B2 RNA by EZH2 Activates the Stress Response
Zovoilis, A., Cifuentes‐Rojas, C., Chu, H.-P. C., Hernandez, A. J., & Lee, J. T. (2016) · Cell · doi:10.1016/j.cell.2016.11.041 · Cited by 95
Lynch, V. J., Brayer, K. J., Gellersen, B., & Wagner, G. P. (2009) · PLoS ONE · doi:10.1371/journal.pone.0006845 · Cited by 94
TET-dependent regulation of retrotransposable elements in mouse embryonic stem cells
de la Rica, L., Deniz, Ö., Cheng, K. C. L., Todd, C. D., Cruz, C., Houseley, J. M., & Branco, M. R. (2016) · Genome biology · doi:10.1186/s13059-016-1096-8 · Cited by 93
Dunn-Fletcher, C., Muglia, L. M., Pavličev, M., Wolf, G., Sun, M., Hu, Y., Huffman, E., Tumukuntala, S., Thiele, K., Mukherjee, A., et al. (2018) · PLoS Biology · doi:10.1371/journal.pbio.2006337 · Cited by 93
Ye, M., Goudot, C., Hoyler, T., Lemoine, B., Amigorena, S., & Zueva, E. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1912008117 · Cited by 92
Endogenous retroviruses drive species-specific germline transcriptomes in mammals
Sakashita, A., Maezawa, S., Takahashi, K., Alavattam, K. G., Yukawa, M., Hu, Y., Kojima, S., Parrish, N. F., Barski, A., Pavličev, M., et al. (2020) · Nature Structural & Molecular Biology · doi:10.1038/s41594-020-0487-4 · Cited by 92
Sgarbanti, M., Remoli, A. L., Marsili, G., Ridolfi, B., Borsetti, A., Perrotti, E., Orsatti, R., Ilari, R., Sernicola, L., Stellacci, E., et al. (2008) · Journal of Virology · doi:10.1128/jvi.00599-07 · Cited by 90
Long non-coding RNAs and transposable elements: A functional relationship
Fort, V., Khelifi, G., & Hussein, S. M. I. (2020) · Biochimica et Biophysica Acta (BBA) - Molecular Cell Research · doi:10.1016/j.bbamcr.2020.118837 · Cited by 89
A NEW VIABLE YELLOW MUTATION IN THE HOUSE MOUSE
DICKIES, M. M. (1962) · Journal of Heredity · doi:10.1093/oxfordjournals.jhered.a107129 · Cited by 88
Functional cis-regulatory modules encoded by mouse-specific endogenous retrovirus
Sundaram, V., Choudhary, M. N. K., Pehrsson, E. C., Xing, X., Fiore, C., Pandey, M., Maricque, B. B., Udawatta, M., Ngo, D., Chen, Y., et al. (2017) · Nature Communications · doi:10.1038/ncomms14550 · Cited by 88
Roles of Transposable Elements in the Different Layers of Gene Expression Regulation
Drongitis, D., Aniello, F., Fucci, L., & Donizetti, A. (2019) · International Journal of Molecular Sciences · doi:10.3390/ijms20225755 · Cited by 87
Transposable element-derived sequences in vertebrate development
Etchegaray, E., Naville, M., Volff, J., & Haftek-Terreau, Z. (2021) · Mobile DNA · doi:10.1186/s13100-020-00229-5 · Cited by 87
Emera, D., & Wagner, G. P. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1118566109 · Cited by 86
Suntsova, M., Gogvadze, E. V., Salozhin, S. V., Гайфуллин, Н., Eroshkin, F. M., Dmitriev, S. E., Martynova, N. Y., Kulikov, K., Malakhova, G., Тухбатова, Г. Р., et al. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1318172110 · Cited by 85
Turelli, P., Playfoot, C. J., Grun, D., Raclot, C., Pontis, J., Coudray, A., Thorball, C. W., Duc, J., Pankevich, E. V., Deplancke, B., et al. (2020) · Science Advances · doi:10.1126/sciadv.aba3200 · Cited by 85
Forces driving the three‐dimensional folding of eukaryotic genomes
Rada-Iglesias, Á., Grosveld, F. G., & Papantonis, A. (2018) · Molecular Systems Biology · doi:10.15252/msb.20188214 · Cited by 84
Simonti, C., Pavličev, M., & Capra, J. A. (2017) · Molecular Biology and Evolution · doi:10.1093/molbev/msx219 · Cited by 83
Tissue-specific usage of transposable element-derived promoters in mouse development
Miao, B., Fu, S., Lyu, C., Gontarz, P. M., Wang, T., & Zhang, B. (2020) · Genome biology · doi:10.1186/s13059-020-02164-3 · Cited by 82
Hide and seek: how chromatin-based pathways silence retroelements in the mammalian germline
Molaro, A., & Malik, H. S. (2016) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2015.12.001 · Cited by 80
Long-range function of an intergenic retrotransposon
Pi, W., Zhu, X., Wu, M., Wang, Y., Fulzele, S., Eroğlu, A., Ling, J., & Tuan, D. Y. H. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1004139107 · Cited by 79
Transposable elements drive reorganisation of 3D chromatin during early embryogenesisPreprint
Kruse, K., Díaz, N., Enriquez-Gasca, R., Gaume, X., Torres‐Padilla, M., & Vaquerizas, J. M. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/523712 · Cited by 79
Establishment of environmentally sensitive DNA methylation states in the very early human embryo
Kessler, N. J., Waterland, R. A., Prentice, A. M., & Silver, M. J. (2018) · Science Advances · doi:10.1126/sciadv.aat2624 · Cited by 78
Lowe, C. B., & Haussler, D. H. (2012) · PLoS ONE · doi:10.1371/journal.pone.0043128 · Cited by 77
Molecular basis of immune evasion by the delta and kappa SARS-CoV-2 variantsPreprint
McCallum, M., Walls, A. C., Sprouse, K. R., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.08.11.455956 · Cited by 74
Chang, N.-C., Rovira, Q., Wells, J. N., Feschotte, C., & Vaquerizas, J. M. (2022) · Genome Research · doi:10.1101/gr.275655.121 · Cited by 73
Self-citationThe evolutionary capacitor HSP90 buffers the regulatory effects of mammalian endogenous retroviruses
Hummel, B., Hansen, E. C., Yoveva, A., Aprile-Garcia, F., Hussong, R., & Sawarkar, R. (2017) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.3368 · Cited by 72
Breitling, R., & Gerber, J. (2000) · Development Genes and Evolution · doi:10.1007/s004270000106 · Cited by 69
MER41 Repeat Sequences Contain Inducible STAT1 Binding Sites
Schmid, C. D., & Bücher, P. (2010) · PLoS ONE · doi:10.1371/journal.pone.0011425 · Cited by 67
Ling, J., Pi, W., Bollag, R. J., Zeng, S., Keskintepe, M., Saliman, H., Krantz, S. B., Whitney, B., & Tuan, D. Y. H. (2002) · Journal of Virology · doi:10.1128/jvi.76.5.2410-2423.2002 · Cited by 67
Amylase gene structures in primates: retroposon insertions and promoter evolution
Samuelson, L. C., Phillips, R. S., & Swanberg, L. J. (1996) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a025637 · Cited by 64
Shao, W., & Wang, T. (2020) · Genome Research · doi:10.1101/gr.265173.120 · Cited by 64
Endogenous retroviruses drive KRAB zinc-finger protein family expression for tumor suppression
Ito, J., Kimura, I., Soper, A., Coudray, A., Koyanagi, Y., Nakaoka, H., Inoue, I., Turelli, P., Trono, D., & Sato, K. (2020) · Science Advances · doi:10.1126/sciadv.abc3020 · Cited by 63
CpG Deamination Creates Transcription Factor–Binding Sites with High Efficiency
Żemojtel, T., Kiełbasa, S. M., Arndt, P. F., Behrens, S., Bourque, G., & Vingron, M. (2011) · Genome Biology and Evolution · doi:10.1093/gbe/evr107 · Cited by 61
Wilson, K. D., Ameen, M., Guo, H., Abilez, O. J., Tian, L., Mumbach, M. R., Diecke, S., Qin, X., Liu, Y., Yang, H., et al. (2020) · Developmental Cell · doi:10.1016/j.devcel.2020.07.006 · Cited by 61
Nishihara, H., Kobayashi, N., Kimura-Yoshida, C., Yan, K., Bormuth, O., Ding, Q. J., Nakanishi, A., Sasaki, T., Hirakawa, M., Sumiyama, K., et al. (2016) · PLoS Genetics · doi:10.1371/journal.pgen.1006380 · Cited by 59
Reactivation of Endogenous Retroelements in Cancer Development and Therapy
Ishak, C. A., & Carvalho, D. D. D. (2019) · Annual Review of Cancer Biology · doi:10.1146/annurev-cancerbio-030419-033525 · Cited by 59
TFIIIC bound DNA elements in nuclear organization and insulation
Kirkland, J. G., Raab, J. R., & Kamakaka, R. T. (2012) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2012.09.006 · Cited by 58
Wang, L., Norris, E. T., & Jordan, I. K. (2017) · Frontiers in Microbiology · doi:10.3389/fmicb.2017.01418 · Cited by 54
Detecting Endogenous Retrovirus-Driven Tissue-Specific Gene Transcription
Pavličev, M., Hiratsuka, K., Swaggart, K. A., Dunn, C., & Muglia, L. J. (2015) · Genome Biology and Evolution · doi:10.1093/gbe/evv049 · Cited by 52
Sun, M., Wolf, G., Wang, Y., Senft, A. D., Ralls, S., Jin, J., Dunn-Fletcher, C., Muglia, L. J., & Macfarlan, T. S. (2021) · Molecular Biology and Evolution · doi:10.1093/molbev/msab223 · Cited by 52
Sundaram, V., & Wang, T. (2017) · BioEssays · doi:10.1002/bies.201700155 · Cited by 50
Research works printed but not linked: 2
- Hoyt, S. J. et al. From telomere to telomere: the transcriptional and epigenetic state of human repeat elements. bioRxiv https://doi.org/10.1101/2021.07.12.451456v1 (2021). · DOI
- Carter, T. A. et al. Mosaic cis-regulatory evolution drives transcriptional partitioning of HERVH endogenous retrovirus in the human embryo. bioRxiv https://doi.org/10.1101/2021.07.08.451617v1 (2021). · DOI
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Mattick, J. S., Amaral, P., Carninci, P., Carpenter, S. B., Chang, H. Y., Chen, L., Chen, R., Dean, C., Dinger, M. E., Fitzgerald, K. A., et al. (2023) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-022-00566-8 · Cited by 2,509
Repetitive DNA sequence detection and its role in the human genome
Liao, X., Zhu, W., Zhou, J., Li, H., Xu, X., Zhang, B., & Gao, X. (2023) · Communications Biology · doi:10.1038/s42003-023-05322-y · Cited by 192
Emerging evidence that the mammalian sperm epigenome serves as a template for embryo development
Lismer, A., & Kimmins, S. (2023) · Nature Communications · doi:10.1038/s41467-023-37820-2 · Cited by 183
Transposable elements as essential elements in the control of gene expression
Gebrie, A. (2023) · Mobile DNA · doi:10.1186/s13100-023-00297-3 · Cited by 157
A spatially resolved multi-omic single-cell atlas of soybean development
Zhang, X., Luo, Z., Marand, A. P., Yan, H., Jang, H., Bang, S., Mendieta, J. P., Minow, M. A. A., & Schmitz, R. J. (2024) · Cell · doi:10.1016/j.cell.2024.10.050 · Cited by 152
Metadata
- Authors
- Fueyo, R., Judd, J., Feschotte, C., & Wysocka, J.
- Affiliations
- Stanford Medicine (US)
- Cornell University (US)
- Howard Hughes Medical Institute (US)
- Corresponding author
- Wysocka, Joanna
- Venue
- Nature Reviews Molecular Cell Biology
- Published
- 2022-02-28
- Volume
- 23
- Issue
- 7
- Pages
- 481-497
- ISSN
- 1471-0072 (ISSN-L)
- 1471-0080
- PMC
- PMC10470143
- OpenAlex
- W4214672693
- Cited by
- 451
- References
- 226
- Citations by year
- 2026: 80 · 2025: 139 · 2024: 119 · 2023: 89 · 2022: 24
- FWCI
- 9.07
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Nature Reviews Molecular Cell Biology (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- Howard Hughes Medical Institute
- Cancer Research Institute
- Bristol-Myers Squibb
- National Institutes of Health
- National Human Genome Research Institute (U01HG009391, F31HG010820)
- National Cancer Institute (R01CA260691)
- National Institute of General Medical Sciences (R35GM122550, R35GM131757)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Chromosomal and Genetic Variations
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Keywords
- transposable elements, transcriptional regulation, mammalian genomes, cis-regulatory elements, enhancers, promoter, 3D genome organization, non-coding RNA, transcription factors, regulatory evolution, genetic novelty, genomic context, repetitive DNA
- MeSH terms
- Animals, DNA Transposable Elements, Gene Expression Regulation, Mammals, Promoter Regions, Genetic, Regulatory Sequences, Nucleic Acid, Transcription Factors, Evolution, Molecular
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