Evidence map›Paper›PMID 41741738›Full record

ArticleNature structural & molecular biology2026

Transposable element-gene chimera cartography, origination and role in enhancing transcriptome plasticity.

Youngseo Cheon, Erik Glen Alvstad, Denis Torre, Daniel Tu Quach, Jennifer Nguyen, Kwangbeom Hyun, Mingqi Zhou, Tianxiong Yu, Liang Liu, Yoseop Yoon and 15 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature structural & molecular biology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

25 authors.

Youngseo Cheon *Center for Epigenetics and Metabolism, Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA, USA.ORCID http://orcid.org/0000-0003-0715-3053
Erik Glen Alvstad *Center for Epigenetics and Metabolism, Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA, USA.ORCID http://orcid.org/0000-0003-1081-8706
Denis TorreDevelopmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York City, NY, USA.ORCID http://orcid.org/0000-0003-4615-223X
Daniel Tu QuachCenter for Epigenetics and Metabolism, Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA, USA.ORCID http://orcid.org/0009-0002-8854-5947
Jennifer NguyenCenter for Epigenetics and Metabolism, Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA, USA.ORCID http://orcid.org/0000-0001-7019-0311
Kwangbeom HyunCenter for Epigenetics and Metabolism, Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA, USA.ORCID http://orcid.org/0000-0002-2377-3642
Mingqi ZhouCenter for Epigenetics and Metabolism, Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA, USA.ORCID http://orcid.org/0009-0007-7643-7873
Tianxiong YuDepartment of Genomics and Computational Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA.ORCID http://orcid.org/0000-0003-1151-4624
Liang LiuDepartment of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, CA, USA.ORCID http://orcid.org/0000-0002-9655-204X
Yoseop YoonDepartment of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, CA, USA.ORCID http://orcid.org/0000-0002-6062-0979
Fairlie ReeseDepartment of Life Sciences, Barcelona Supercomputing Center (BCN-CNS), Barcelona, Spain.ORCID http://orcid.org/0000-0002-9240-0102
Lauren FaraoneCenter for Epigenetics and Metabolism, Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA, USA.ORCID http://orcid.org/0009-0002-4317-0774
Yingcong LiCenter for Epigenetics and Metabolism, Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA, USA.ORCID http://orcid.org/0000-0002-0746-0531
Frederick J ArnoldDepartment of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO, USA.ORCID http://orcid.org/0000-0003-1927-264X
Yesai S FstkchyanDepartment of Urology, Cedars-Sinai Medical Center, Los Angeles, CA, USA.ORCID http://orcid.org/0000-0001-9950-2841
Uttiya BasuDepartment of Microbiology & Immunology, Columbia University Medical Center, New York, NY, USA.ORCID http://orcid.org/0000-0002-0185-7052
Evgeny KvonDepartment of Developmental and Cell Biology, Charlie Dunlop School of Biological Sciences, University of California, Irvine, CA, USA.ORCID http://orcid.org/0000-0002-1562-0945
Enza Maria ValenteDepartment of Molecular Medicine, University of Pavia, Pavia, Italy.ORCID http://orcid.org/0000-0002-0600-6820
Jessica Sook Yuin HoProgramme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore.ORCID http://orcid.org/0000-0003-2234-2602
Minji ByunDepartment of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, CA, USA.ORCID http://orcid.org/0000-0002-2830-4079
Ernesto GuccioneDepartment of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.ORCID http://orcid.org/0000-0001-7764-5307
Yongsheng ShiCenter for Epigenetics and Metabolism, Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA, USA.ORCID http://orcid.org/0000-0003-2967-1230
Zhiping WengDepartment of Genomics and Computational Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA.ORCID http://orcid.org/0000-0002-3032-7966
Marcus SeldinCenter for Epigenetics and Metabolism, Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA, USA. mseldin@uci.edu.ORCID http://orcid.org/0000-0001-8026-4759
Ivan MarazziCenter for Epigenetics and Metabolism, Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA, USA. imarazzi@uci.edu.ORCID http://orcid.org/0000-0003-3376-0922

Funding

X-RAY CRYSTALLOGRAPHYP30CA008748 · NCI · SLOAN-KETTERING INSTITUTE FOR CANCER RES · PI SELWYN M VICKERS · 1985 to 2026
$347.4M
Univ.of Calif., Irvine Cancer Center Support GrantP30CA062203 · NCI · UNIVERSITY OF CALIFORNIA-IRVINE · PI Melanie Funes · 1994 to 2026
$57.9M
NCI NIH HHS P30 CA008748NCI NIH HHS P30 CA062203
6 · The paper itself

Abstract

Transposable elements (TEs) in the human genome are the heritage of ancient parasitic infections. While most of human DNA comprises TEs and TE-derived elements, their repetitive nature poses technical challenges; thus, little is known about their positional identity and regulatory roles. Here, by integrating long-read and multidimensional transcriptional analyses, we investigate when, where and how TEs become part of a gene. We characterize how TE-derived isoforms change across mouse-human variation and how they are linked to gene regulatory networks controlling cell states during differentiation, organogenesis and health (aging and pathological states). Mechanistically, we identify an RNA degradation-dependent and splicing-dependent quality control mechanism that operates independently of conventional mechanisms of TE suppression, such as DNA methylation and heterochromatinization, and prevents TE-chimera expression and TE-induced cell differentiation. Overall, our findings unveil mechanisms by which viral-derived elements enhance transcriptome plasticity.

Indexed as

DNA Transposable ElementsTranscriptomeAnimalsCell DifferentiationDNA MethylationGene Regulatory NetworksHumansMiceRNA SplicingRNA StabilityDNA Transposable Elements

Identifiers

PMID41741738
PMCPMC12999487

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.