Evidence map›Paper›PMID 42282747›Full record

ArticlebioRxiv : the preprint server for biology2026

CTCF regulates wild-type and recombinant AAV gene expression by shaping viral chromatin.

Clairine I S Larsen, Rhiannon R Abrahams, Rea Guertler, Elliott M Wilion, Eda Erata, Zachary H Sykes, Lorelei Stoica, Gopishankar Thirumoorthy, Sinha Divya, Richa Rai and 5 more

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing 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

0 citing papers in PubMed.

No citing paper in PubMed yet.

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

15 authors.

Clairine I S LarsenInstitute for Molecular Virology, University of Wisconsin-Madison, Madison, WI, 53706.
Rhiannon R AbrahamsInstitute for Molecular Virology, University of Wisconsin-Madison, Madison, WI, 53706.
Rea GuertlerUltragenyx Pharmaceuticals, Somerville, MA, 02143.
Elliott M WilionUltragenyx Pharmaceuticals, Somerville, MA, 02143.
Eda ErataUltragenyx Pharmaceuticals, Somerville, MA, 02143.
Zachary H SykesUltragenyx Pharmaceuticals, Somerville, MA, 02143.
Lorelei StoicaUltragenyx Pharmaceuticals, Somerville, MA, 02143.
Gopishankar ThirumoorthyDepartment of Comparative Biosciences, University of Wisconsin School of Veterinary Medicine, Madison, WI, 53706.
Sinha DivyaMcPherson Eye Research Institute, University of Wisconsin-Madison.
Richa RaiMcPherson Eye Research Institute, University of Wisconsin-Madison.
Elizabeth K HoferInstitute for Molecular Virology, University of Wisconsin-Madison, Madison, WI, 53706.
Eleanor HartInstitute for Molecular Virology, University of Wisconsin-Madison, Madison, WI, 53706.
David M GammMcPherson Eye Research Institute, University of Wisconsin-Madison.
Matthew S FullerUltragenyx Pharmaceuticals, Somerville, MA, 02143.ORCID 0000-0002-4704-572X
Kinjal MajumderInstitute for Molecular Virology, University of Wisconsin-Madison, Madison, WI, 53706.ORCID 0000-0002-1898-8251

Funding

UW COMPREHENSIVE CANCER CENTER SUPPORTP30CA014520 · NCI · UNIVERSITY OF WISCONSIN-MADISON · PI Justine Yang Bruce · 1985 to 2026
$142.6M
Waisman Center Intellectual and Developmental Disabilities Research CenterP50HD105353 · NICHD · UNIVERSITY OF WISCONSIN-MADISON · PI Qiang Chang · 2021 to 2026
$8.5M
Defining how cellular DNA replication and repair machinery are hijacked by viral pathogensR35GM154938 · NIGMS · UNIVERSITY OF WISCONSIN-MADISON · PI Kinjal Majumder · 2024 to 2026
$1.1M
How does a viral pathogen manipulate DNA Damage Responses to promote infection?R00AI148511 · NIAID · UNIVERSITY OF WISCONSIN-MADISON · PI MAJUMDER, KINJAL · 2022 to 2023
$498k
How does a viral pathogen manipulate the DNA Damage Response to promote successful viral infection?K99AI148511 · NIAID · UNIVERSITY OF WISCONSIN-MADISON · PI MAJUMDER, KINJAL · 2020 to 2021
$207k
Spatial and Epigenetic Regulation of AAV Localization and PersistenceF31AI191692 · NIAID · UNIVERSITY OF WISCONSIN-MADISON · PI Rhiannon R Abrahams · 2026 to 2026
$37k
NCI NIH HHS P30 CA014520NIAID NIH HHS F31 AI191692NIAID NIH HHS K99 AI148511NIAID NIH HHS R00 AI148511NICHD NIH HHS P50 HD105353NIGMS NIH HHS R35 GM154938
6 · The paper itself

Abstract

Adeno-Associated Viruses (AAVs) are powerful platforms for delivering therapeutic transgenes via recombinant AAV (rAAV) vectors. However, a limited understanding of the regulation of AAV gene expression has narrowed the ability to efficiently express therapeutic transgenes from rAAV vectors. Since rAAVs retain only the wtAAV inverted terminal repeats (ITR), we hypothesized that regulatory elements outside the ITR that govern wild-type AAV (wtAAV) gene expression can be used to modify rAAV genomes to enhance vector performance. Through in silico analysis, biochemical pulldowns, and high-throughput sequencing, we have identified that the host architectural protein CCCTC-binding Factor (CTCF) associates with the wtAAV type 2 (wtAAV2) genome but is absent from rAAV vectors. Global knockdown and site-specific deletion revealed that the CTCF binding element (CBE) on the wtAAV2 genome, located upstream of the viral P5 promoter, regulates expression of the viral

Indexed as

Adeno-Associated Viruseschromatingene therapyParvovirusesrecombinant AAV gene therapy

Identifiers

PMID42282747
PMCPMC13252373

What Socratic 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 Socratic graph.