Evidence map›Paper›PMID 40341501›Full record

ArticleNature communications2025

Massively parallel jumping assay decodes Alu retrotransposition activity.

Navneet Matharu, Jingjing Zhao, Ajuni Sohota, Linbei Deng, Yan Hung, Zizheng Li, Kelly An, Jasmine Sims, Sawitree Rattanasopha, Thomas J Meyer and 3 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature communications, 2025. 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

5 · Who and what money

Authors and funding

13 authors.

Navneet Matharu *Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA. nkmatharu@gmail.com.
Jingjing Zhao *Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.ORCID http://orcid.org/0000-0002-4298-8817
Ajuni SohotaDepartment of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.
Linbei DengDepartment of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.
Yan HungDepartment of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.
Zizheng LiDepartment of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.ORCID http://orcid.org/0000-0002-6953-7733
Kelly AnDepartment of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.
Jasmine SimsDepartment of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.
Sawitree RattanasophaDepartment of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.
Thomas J MeyerDivision of Genetics, Oregon National Primate Research Center, Beaverton, OR, USA.ORCID http://orcid.org/0000-0002-7185-5597
Lucia CarboneDivision of Genetics, Oregon National Primate Research Center, Beaverton, OR, USA.ORCID http://orcid.org/0000-0002-2118-107X
Martin KircherBerlin Institute of Health of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany. martin.kircher@uni-luebeck.de.ORCID http://orcid.org/0000-0001-9278-5471
Nadav AhituvDepartment of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA. nadav.ahituv@ucsf.edu.ORCID http://orcid.org/0000-0002-7434-8144

Funding

Massively parallel characterization of variants and elements impacting transcriptional regulation in dynamic cellular systemsUM1HG011966 · NHGRI · UNIVERSITY OF WASHINGTON · PI Nadav Ahituv, Jay Ashok Shendure · 2021 to 2026
$9.7M
Massively parallel reporter assays and genome editing of ENCODE predicted regulatory elementsUM1HG009408 · NHGRI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI AHITUV, NADAV, SHENDURE, JAY ASHOK · 2017 to 2021
$7.6M
Rarely Common: Uncovering the dominant role of rare variants in the genetic architecture of complex human traits.R01GM142112 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI HERNANDEZ, RYAN D. · 2021 to 2024
$2.2M
NHGRI NIH HHS UM1 HG009408NHGRI NIH HHS UM1 HG011966NIGMS NIH HHS R01 GM142112U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (NHGRI) UM1HG009408U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (NHGRI) UM1HG011966U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS) R01GM142112
6 · The paper itself

Abstract

The human genome contains millions of copies of retrotransposons that are silenced but many of these copies have potential to become active if mutated, having phenotypic consequences, including disease. However, it is not thoroughly understood how nucleotide changes in retrotransposons affect their jumping activity. Here, we develop a massively parallel jumping assay (MPJA) that tests the jumping potential of thousands of transposons en masse. We generate a nucleotide variant library of four Alu retrotransposons containing 165,087 different haplotypes and test them for their jumping ability using MPJA. We found 66,821 unique jumping haplotypes, allowing us to pinpoint domains and variants vital for transposition. Mapping these variants to the Alu-RNA secondary structure revealed stem-loop features that contribute to jumping potential. Combined, our work provides a high-throughput assay that assesses the ability of retrotransposons to jump and identifies nucleotide changes that have the potential to reactivate them in the human genome.

Indexed as

Alu ElementsRetroelementsGene LibraryGenome, HumanHaplotypesHigh-Throughput Nucleotide SequencingHumansNucleic Acid ConformationRetroelements

Identifiers

PMID40341501
PMCPMC12062377

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.