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Review: The superpowers of imprinting control regions
- Bertille Montibus,
- Franck Court,
- and Philippe Arnaud
Genome Res. January 2026 36: 1-19; Published in Advance December 10, 2025, doi:10.1101/gr.281215.125
..., a fraction of the transcripts that shape the oocyte methylome originates from species-specific long terminal repeats (LTRs) of endogenous retroviruses (ERVs) (Veselovska et al. 2015; Brind'Amour et al. 2018). This phenomenon contributes to significant differences in the oocyte methylation pattern between...
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Research: A genome-wide transcriptome and translatome analysis of Arabidopsis transposons identifies a unique and conserved genome expression strategy for Ty1/Copia retroelements
- Stefan Oberlin,
- Alexis Sarazin,
- Clément Chevalier,
- Olivier Voinnet,
- and Arturo Marí-Ordóñez
Genome Res. September 2017 27: 1549-1562; Published in Advance August 7, 2017, doi:10.1101/gr.220723.117
...cryptic poly(A) signal but also, and more importantly, at the cognate, downstream endogenous shGAG poly(A) site, thereby enabling full-length EVD transcription. The proposed repression of premature termination by the U1 snRNP must be efficient because, as shown with endogenous EVD (Fig. 3B), accumulation...
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Research: Somatic retrotransposition in the developing rhesus macaque brain
- Victor Billon,
- Francisco J. Sanchez-Luque,
- Jay Rasmussen,
- Gabriela O. Bodea,
- Daniel J. Gerhardt,
- Patricia Gerdes,
- Seth W. Cheetham,
- Stephanie N. Schauer,
- Prabha Ajjikuttira,
- Thomas J. Meyer,
- Cora E. Layman,
- Kimberly A. Nevonen,
- Natasha Jansz,
- Jose L. Garcia-Perez,
- Sandra R. Richardson,
- Adam D. Ewing,
- Lucia Carbone,
- and Geoffrey J. Faulkner
Genome Res. July 2022 32: 1298-1314; Published in Advance June 21, 2022, doi:10.1101/gr.276451.121
...be endogenous retroviruses (ERVs) (Han et al. 2007; Liu et al. 2009; Tang and Liang 2019; Warren et al. 2020). It is, however, unknown whether TEs retrotranspose in macaque neuronal lineage cells. Here, we exploited an updated macaque reference assembly, which greatly improved TE annotations (Warren et al. 2020...
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Method: RNA sequencing of Sleeping Beauty transposon-induced tumors detects transposon-RNA fusions in forward genetic cancer screens
- Nuri A. Temiz,
- Branden S. Moriarity,
- Natalie K. Wolf,
- Jesse D. Riordan,
- Adam J. Dupuy,
- David A. Largaespada,
- and Aaron L. Sarver
Genome Res. January 2016 26: 119-129; Published in Advance November 9, 2015, doi:10.1101/gr.188649.114
.....org transposon is activating transcription or generating premature truncations. Given these limitations, we set out to determine whether we could use RNA-seq data obtained from SB-mutagenized tumors to identify how transposon insertion in a given tumor was affecting RNA transcripts of nearby loci. We show...
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Research: Transcriptome characterization by RNA sequencing identifies a major molecular and clinical subdivision in chronic lymphocytic leukemia
- Pedro G. Ferreira,
- Pedro Jares,
- Daniel Rico,
- Gonzalo Gómez-López,
- Alejandra Martínez-Trillos,
- Neus Villamor,
- Simone Ecker,
- Abel González-Pérez,
- David G. Knowles,
- Jean Monlong,
- Rory Johnson,
- Victor Quesada,
- Sarah Djebali,
- Panagiotis Papasaikas,
- Mónica López-Guerra,
- Dolors Colomer,
- Cristina Royo,
- Maite Cazorla,
- Magda Pinyol,
- Guillem Clot,
- Marta Aymerich,
- Maria Rozman,
- Marta Kulis,
- David Tamborero,
- Anaïs Gouin,
- Julie Blanc,
- Marta Gut,
- Ivo Gut,
- Xose S. Puente,
- David G. Pisano,
- José Ignacio Martin-Subero,
- Nuria López-Bigas,
- Armando López-Guillermo,
- Alfonso Valencia,
- Carlos López-Otín,
- Elías Campo,
- and Roderic Guigó
Genome Res. February 2014 24: 212-226; Published in Advance November 21, 2013, doi:10.1101/gr.152132.112
...of RNA-seq reads mapping to known transposable elements (TEs) revealed a general trend of derepression of TE transcription in CLL compared with normal cells (P = 0.0084) (Fig. 1B; Supplemental Fig. S19a; Methods, section ‘‘Transposable Elements’’). Among TE classes, Human Endogenous Retroviruses show...
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LETTER: An active murine transposon family pair: Retrotransposition of “master” MusD copies and ETn trans-mobilization
- David Ribet,
- Marie Dewannieux,
- and Thierry Heidmann
Genome Res. November 2004 14: 2261-2267; Published in Advance October 12, 2004, doi:10.1101/gr.2924904
...; Waterston et al. 2002 ). The complete sequencing of the human has left only a remote possibility that some LTR-retrotransposons might still be active, with the exception of a few still fully coding elements from the HERV-K(HML2) family of endogenous retroviruses ( Löwer et al. 1996 ; Mayer et al. 1999...
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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
...the gene regulatory network of the cancer .One of the most important and well-studied guardians of genomic integrity, TP53 (protein product of TP53, also known as p53), leverages regulatory opportunities provided by TEs for its function. One group of TE families, human endogenous retroviruses (ERVs...
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Research: Immune signatures correlate with L1 retrotransposition in gastrointestinal cancers
- Hyunchul Jung,
- Jung Kyoon Choi,
- and Eunjung Alice Lee
Genome Res. August 2018 28: 1136-1146; Published in Advance July 3, 2018, doi:10.1101/gr.231837.117
...32 esophageal cancer samples. We found that the exon skipping induced a frameshift and a premature termination codon in exon 21, which likely triggered nonsense-mediated decay (NMD). Indeed, we found that only the transcripts from the allele linked with exon skipping showed decreased expression (Fig...
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Research: Heritable L1 retrotransposition in the mouse primordial germline and early embryo
- Sandra R. Richardson,
- Patricia Gerdes,
- Daniel J. Gerhardt,
- Francisco J. Sanchez-Luque,
- Gabriela-Oana Bodea,
- Martin Muñoz-Lopez,
- J. Samuel Jesuadian,
- Marie-Jeanne H.C. Kempen,
- Patricia E. Carreira,
- Jeffrey A. Jeddeloh,
- Jose L. Garcia-Perez,
- Haig H. Kazazian, Jr.,
- Adam D. Ewing,
- and Geoffrey J. Faulkner
Genome Res. August 2017 27: 1395-1405; Published in Advance May 8, 2017, doi:10.1101/gr.219022.116
...presently active mouse endogenous retrotransposons: TF, GF, and A subfamily L1 elements, B1 and B2 SINEs, and IAP and ETn long terminal repeat (LTR) elements (mRC-seq) (Supplemental Fig. S1A; Mager and Stoye 2015; Richardson et al. 2015). We apply this technology to pedigrees of wild-type C57BL/6J mice...
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Research: Unmasking alternative splicing inside protein-coding exons defines exitrons and their role in proteome plasticity
- Yamile Marquez,
- Markus Höpfler,
- Zahra Ayatollahi,
- Andrea Barta,
- and Maria Kalyna
Genome Res. July 2015 25: 995-1007; Published in Advance May 1, 2015, doi:10.1101/gr.186585.114
...protein C-termini (orange) or can produce NMD-sensitive transcripts (red No sign indicates premature termination codon [PTC]). t (% Exitrons p-value ≤ 3.3e-16 p-value ≤ 2.2e-16 p-value ≤ 2.2e-16 p-value ≤ 2.2e-16 t (% Exitrons B D p-value ≤ 1.458e-05 p-value ≤ 0.000263 p-value ≤ 2.2e-16 p-value ≤ 2.2e-16...
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