Evidence map›Paper›PMID 42864353›Full record

ArticleNature communications2026

Functional characterization of viral transcriptional regulators reveals extensive rewiring of host pathways.

Jaice T Rottenberg, Xing Liu, Mohamed Y ElSadec, Anna Lagani, Luis F Soto-Ugaldi, James E Corban, Phillip J Dexheimer, Matthew Hass, Clarissa Santoso, Cailing Yin and 21 more

Abstract read
In one paragraph

Article in Nature communications, 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

31 authors.

Jaice T RottenbergDepartment of Biology, Boston University, Boston, MA, USA.
Xing LiuDepartment of Biology, Boston University, Boston, MA, USA.
Mohamed Y ElSadecBioinformatics Program, Boston University, Boston, MA, USA.
Anna LaganiDepartment of Biology, Boston University, Boston, MA, USA.ORCID 0000-0002-3782-6186
Luis F Soto-UgaldiTri-institutional Program, Computational Biology and Medicine, New York, NY, USA.
James E CorbanIntegrated Program in Biochemistry, University of Wisconsin-Madison, Madison, WI, USA.ORCID 0000-0002-0132-4352
Phillip J DexheimerCenter for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.ORCID 0000-0003-3965-6894
Matthew HassCenter for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
Clarissa SantosoDepartment of Biology, Boston University, Boston, MA, USA.
Cailing YinCenter for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
Berkay EnginDepartment of Biology, Boston University, Boston, MA, USA.
Ryan LaneDepartment of Biology, Boston University, Boston, MA, USA.ORCID 0009-0009-0513-9849
Sakshi ShahDepartment of Biology, Boston University, Boston, MA, USA.ORCID 0000-0002-2075-6900
Kerstin Spirohn-FitzgeraldCenter for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA.ORCID 0000-0002-2071-1606
Shubham KhetanDivision of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.ORCID 0000-0001-8347-7493
Cheng-Che LeeDepartment of Biology, Boston University, Boston, MA, USA.
George Muñoz-EsquivelEscuela Profesional de Genetica y Biotecnologia, Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Lima, Peru.ORCID 0009-0007-3765-9967
Zhaorong LiBioinformatics Program, Boston University, Boston, MA, USA.
Lucia Martinez-CuestaDepartment of Biology, Boston University, Boston, MA, USA.
Yunwei LuDepartment of Biology, Boston University, Boston, MA, USA.
Philipp TrollmannBioinformatics Program, Boston University, Boston, MA, USA.ORCID 0009-0008-6421-4215
Tong HaoCenter for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA.ORCID 0000-0001-7908-3256
S Stephen YiDepartment of Neurosurgery, Baylor Research Institute and Baylor College of Medicine, Temple, TX, USA.
Nidhi SahniDepartment of Neurosurgery, Baylor Research Institute and Baylor College of Medicine, Temple, TX, USA.ORCID 0000-0002-9155-5882
Martha L BulykCenter for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA.ORCID 0000-0002-3456-4555
Michael A CalderwoodCenter for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA.ORCID 0000-0001-6475-1418
Leah KottyanCenter for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.ORCID 0000-0003-3979-2220
Matthew T WeirauchCenter for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.ORCID 0000-0001-7977-9122
Marc VidalCenter for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA.
Srivatsan RamanDepartment of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA.ORCID 0000-0003-2461-1589
Juan I Fuxman BassDepartment of Biology, Boston University, Boston, MA, USA. fuxman@bu.edu.ORCID 0000-0001-9457-1207

Funding

HLA GENE COMPLEMENTATION IN PRIMARY SJOGREN'S AND LUPUSR01AI024717 · NIAID · OKLAHOMA MEDICAL RESEARCH FOUNDATION · PI KOTTYAN, LEAH CLAIRE, WEIRAUCH, MATTHEW TYSON · 1987 to 2025
$7.8M
Binding of Epstein Barr Virus EBNA2 Unifies Multiple Sclerosis Genetic MechanismsR01NS099068 · NINDS · CINCINNATI CHILDRENS HOSP MED CTR · PI Leah Claire Kottyan, Matthew Tyson Weirauch · 2017 to 2026
$4.2M
Rewiring of regulatory networks in breast cancer by transcription factor isoformsU01CA232161 · NCI · DANA-FARBER CANCER INST · PI BULYK, MARTHA L, FUXMAN BASS, JUAN IGNACIO · 2018 to 2022
$4.1M
Structure and Function of Immune Gene Regulatory NetworksR35GM128625 · NIGMS · BOSTON UNIVERSITY (CHARLES RIVER CAMPUS) · PI Juan Ignacio Fuxman Bass · 2018 to 2026
$4.0M
Virus-driven human gene misregulation in diseaseR01HG010730 · NHGRI · CINCINNATI CHILDRENS HOSP MED CTR · PI WEIRAUCH, MATTHEW TYSON · 2020 to 2023
$2.7M
Network-based Framework to Decode Novel Gain-of-Function Mutations and their Mechanistic Roles in General Human DiseasesR35GM133658 · NIGMS · UNIVERSITY OF TEXAS AT AUSTIN · PI S. Stephen Yi · 2019 to 2026
$2.6M
Deciphering Functional Consequences of Specific and Combinatorial Mutations in Protein Interaction NetworksR35GM137836 · NIGMS · UNIVERSITY OF TX MD ANDERSON CAN CTR · PI SAHNI, NIDHI · 2020 to 2023
$1.8M
CINCINNATI TRAINING PROGRAM IN PEDIATRIC RHEUMATOLOGYRESEARCHT32AR069512 · NIAMS · CINCINNATI CHILDRENS HOSP MED CTR · PI ALEXEI A GROM, Grant Sanford Schulert · 2016 to 2026
$1.6M
CisBP and CisBP-RNA: web resources for protein-DNA and protein-RNA binding modelsU24HG013078 · NHGRI · CINCINNATI CHILDRENS HOSP MED CTR · PI Matthew Tyson Weirauch · 2024 to 2026
$1.6M
Predoctoral Training in Bioinformatics and Computational BiologyT32GM150533 · NIGMS · BOSTON UNIVERSITY (CHARLES RIVER CAMPUS) · PI GARY E. BENSON, Daniel Segre · 2023 to 2026
$1.3M
Synthetic Biology and Biotechnology (SB2) Predoctoral Training ProgramT32GM154655 · NIGMS · BOSTON UNIVERSITY (CHARLES RIVER CAMPUS) · PI CHRISTOPHER S CHEN, Ahmad Samir Khalil · 2025 to 2026
$858k
Studying Protein Affinity to DNA by in vitro Transcription and Sequencing (PADIT-seq)K99HG013675 · NHGRI · BRIGHAM AND WOMEN'S HOSPITAL · PI KHETAN, SHUBHAM · 2024 to 2025
$273k
Alfred P. Sloan Foundation FG-2018-10723Division of Cancer Prevention, National Cancer Institute (NCI Division of Cancer Prevention) U01CA232161Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID) R01AI024717NCI NIH HHS U01 CA232161NHGRI NIH HHS K99 HG013675NHGRI NIH HHS R01 HG010730NHGRI NIH HHS U24 HG013078NIAID NIH HHS R01 AI024717NIAMS NIH HHS T32 AR069512NIGMS NIH HHS R35 GM128625NIGMS NIH HHS R35 GM133658NIGMS NIH HHS R35 GM137836NIGMS NIH HHS T32 GM150533NIGMS NIH HHS T32 GM154655NINDS NIH HHS R01 NS099068U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (NHGRI) K99HG013675U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (NHGRI) R01HG010730U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (NHGRI) U24HG013078U.S. Department of Health & Human Services | NIH | National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS) T32AR069512U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS) R35GM128625U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS) R35GM133658U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS) R35GM137836U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS) T32GM150533U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS) T32GM154655U.S. Department of Health & Human Services | NIH | National Institute of Neurological Disorders and Stroke (NINDS) R01NS099068
6 · The paper itself

Abstract

Viral transcriptional regulators (vTRs) reprogram host gene regulatory networks to promote replication, persistence, and immune evasion. Despite the identification of hundreds of vTRs in human viruses, how they rewire host pathways remains unclear. Here, we systematically profiled 95 vTRs from diverse human viruses across multiple functional assays. vTRs perturb immune, cell proliferation/death, and signaling pathways through various mechanisms; some bind DNA directly, others cooperate or antagonize human transcription factors (hTFs), and some remodel chromatin. vTRs can act as activators or repressors and recruit similar but not identical repertoires of proteins as hTFs. These findings reveal vTRs as versatile transcriptional modulators that converge on conserved host "pressure points" while diversifying across pathways to promote viral replication and persistence. Notably, many vTR dysregulate genes within autoimmune, neurological, and cardiovascular risk loci, revealing potential mechanistic links to disease. Together, we provide a large-scale resource for understanding and targeting viral control of human transcription.

Indexed as

Host-Pathogen InteractionsViral ProteinsVirusesGene Expression RegulationGene Expression Regulation, ViralGene Regulatory NetworksHumansSignal TransductionTranscription FactorsTranscription, GeneticVirus ReplicationTranscription FactorsViral Proteins

Identifiers

PMID42864353
PMCPMC13658809

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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.