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Research: Multi-species analysis of inflammatory response elements reveals ancient and lineage-specific contributions of transposable elements to NF-kB binding
- Liangxi Wang,
- Tiegh Taylor,
- Kumaragurubaran Rathnakumar,
- Nadiya Khyzha,
- Minggao Liang,
- Azad Alizada,
- Laura F. Campitelli,
- Sara E. Pour,
- Zain M. Patel,
- Lina Antounians,
- Ian C. Tobias,
- Huayun Hou,
- Timothy R. Hughes,
- Sushmita Roy,
- Jennifer A. Mitchell,
- Jason E. Fish,
- and Michael D. Wilson
Genome Res. July 2025 35: 1544-1559; Published in Advance June 6, 2025, doi:10.1101/gr.280357.124
...networks remains to be seen.Previous work cloning and sequencing DNA from RELA ChIP led to the conclusion that ∼11% of NF-kB-bound regions contain an Alu-derived NF-kB motif (Antonaki et al. 2011). However, the extent to which specific subfamilies of repetitive elements contribute to NF-kB binding in human...
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Resource: Charting the regulatory landscape of TP53 on transposable elements in cancer
- Xuan Qu,
- Yonghao Liang,
- Colin McCornack,
- Xiaoyun Xing,
- Heather Schmidt,
- Chad Tomlinson,
- Catrina Fronick,
- Edward A. Belter, Jr.,
- Juan F. Macias-Velasco,
- and Ting Wang
Genome Res. June 2025 35: 1456-1471; Published in Advance May 13, 2025, doi:10.1101/gr.279398.124
...but repressed by the treatment of doxorubicin, making inference of the mechanism of their activity non-trivial (Fig. 4G). The fourth set of TE-derived transcripts is repressed by TP53 regardless of doxorubicin-activation, driven by LTR10F and AluSx copies (Fig. 4H). The last set of transcripts were those...
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Resource: Epigenomic analysis reveals prevalent contribution of transposable elements to cis-regulatory elements, tissue-specific expression, and alternative promoters in zebrafish
- Hyung Joo Lee,
- Yiran Hou,
- Ju Heon Maeng,
- Nakul M. Shah,
- Yujie Chen,
- Heather A. Lawson,
- Hongbo Yang,
- Feng Yue,
- and Ting Wang
Genome Res. July 2022 32: 1424-1436; Published in Advance June 1, 2022, doi:10.1101/gr.276052.121
...diverse cancer types (Jang et al. 2019). The best-characterized example is an intergenic TE AluJB in human lung cancers that has been exapted to be an alternative promoter, up-regulating the oncogene LIN28B. The MIRb element located in the intronic region of the ACE2 gene serves as an alternative promoter...
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Research: Genome-wide analysis of polymerase III–transcribed Alu elements suggests cell-type–specific enhancer function
- Xiao-Ou Zhang,
- Thomas R. Gingeras,
- and Zhiping Weng
Genome Res. September 2019 29: 1402-1414; Published in Advance August 14, 2019, doi:10.1101/gr.249789.119
...that AluY elements, being the youngest and least degenerated in sequences, might represent the most retrotranspositionally active subfamily (Bennett et al. 2008). Indeed, AluY is the only known subfamily currently active in retrotransposition in the human (Konkel et al. 2015).In contrast to expectation...
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Research: Pedigree-based estimation of human mobile element retrotransposition rates
- Julie Feusier,
- W. Scott Watkins,
- Jainy Thomas,
- Andrew Farrell,
- David J. Witherspoon,
- Lisa Baird,
- Hongseok Ha,
- Jinchuan Xing,
- and Lynn B. Jorde
Genome Res. October 2019 29: 1567-1577; doi:10.1101/gr.247965.118
...-platform discovery of haplotype-resolved structural variation in human s. Nat Commun 10: 1784. doi:10.1038/s41467-018-08148-z ↵Comeaux MS, Roy-Engel AM, Hedges DJ, Deininger PL. 2009. Diverse cis factors controlling Alu retrotransposition: What causes Alu elements to die? Genome Res 19: 545–555. doi:10.1101/gr...
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Method: Predicting human genes susceptible to genomic instability associated with Alu/Alu-mediated rearrangements
- Xiaofei Song,
- Christine R. Beck,
- Renqian Du,
- Ian M. Campbell,
- Zeynep Coban-Akdemir,
- Shen Gu,
- Amy M. Breman,
- Pawel Stankiewicz,
- Grzegorz Ira,
- Chad A. Shaw,
- and James R. Lupski
Genome Res. August 2018 28: 1228-1242; Published in Advance June 15, 2018, doi:10.1101/gr.229401.117
..., is challenging because the absence of evidence for an Alu to be involved in CNV formation does not mean that the element cannot be used in a heretofore-uncharacterized event. To overcome this issue, we constructed distinct control data sets for analyzing individual features and genomic features (see Methods...
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Resource: Zebrafish transposable elements show extensive diversification in age, genomic distribution, and developmental expression
- Ni-Chen Chang,
- Quirze Rovira,
- Jonathan Wells,
- Cédric Feschotte,
- and Juan M. Vaquerizas
Genome Res. July 2022 32: 1408-1423; Published in Advance January 5, 2022, doi:10.1101/gr.275655.121
...Spm families with lineage-specific expression are nonautonomous elements with no detectable coding sequences. Yet, analysis of individual loci indicates that the expression of each EnSpm family was driven by multiple loci throughout the . Together, these data suggest that diverse TE families encompassing both...
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Research: Transposable elements and their KZFP controllers are drivers of transcriptional innovation in the developing human brain
- Christopher J. Playfoot,
- Julien Duc,
- Shaoline Sheppard,
- Sagane Dind,
- Alexandre Coudray,
- Evarist Planet,
- and Didier Trono
Genome Res. September 2021 31: 1531-1545; Published in Advance August 16, 2021, doi:10.1101/gr.275133.120
...(human endogenous retrovirus K) and SVA (SINE-VNTR-Alu) integrants in human embryonic stem cells (hESC), are expressed in specific regions of the human developing and adult brain (Turelli et al. 2020). Through the control of TEeRS, these KZFPs influence the differentiation and neurotransmission profile...
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Research: A hidden layer of structural variation in transposable elements reveals potential genetic modifiers in human disease-risk loci
- Elisabeth J. van Bree,
- Rita L.F.P. Guimarães,
- Mischa Lundberg,
- Elena R. Blujdea,
- Jimi L. Rosenkrantz,
- Fred T.G. White,
- Josse Poppinga,
- Paula Ferrer-Raventós,
- Anne-Fleur E. Schneider,
- Isabella Clayton,
- David Haussler,
- Marcel J.T. Reinders,
- Henne Holstege,
- Adam D. Ewing,
- Colette Moses,
- and Frank M.J. Jacobs
Genome Res. April 2022 32: 656-670; Published in Advance March 24, 2022, doi:10.1101/gr.275515.121
...-read sequencing data, we discovered widespread structural variation within SINE-VNTR-Alu (SVA) elements, a class of great ape-specific transposable elements with gene-regulatory roles, which represents a major source of structural variability in the human population. We highlight the presence of structurally...
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Research: Retrotransposition creates sloping shores: a graded influence of hypomethylated CpG islands on flanking CpG sites
- Fiorella C. Grandi,
- James M. Rosser,
- Simon J. Newkirk,
- Jun Yin,
- Xiaoling Jiang,
- Zhuo Xing,
- Leanne Whitmore,
- Sanum Bashir,
- Zoltán Ivics,
- Zsuzsanna Izsvák,
- Ping Ye,
- Y. Eugene Yu,
- and Wenfeng An
Genome Res. August 2015 25: 1135-1146; Published in Advance May 20, 2015, doi:10.1101/gr.185132.114
...as epigenetic mediators of phenotypic variation based on early studies of specific LTR-retrotransposons (Whitelaw and Martin 2001). Consistent with this hypothesis, significant interindividual variability in DNA methylation has been observed for discrete Alu and L1 elements (Sandovici et al. 2005; Singer et al...
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