Widespread variation in molecular interactions and regulatory properties among transcription factor isoforms

Luke Lambourne¹, Kaia Mattioli², Clarissa Santoso³, Gloria Sheynkman¹, Sachi Inukai⁴, Babita Kaundal⁵, Anna Berenson⁶, Kerstin Spirohn-Fitzgerald¹, Anukana Bhattacharjee⁷, Elisabeth Rothman⁴, Shaleen Shrestha⁸, Florent Laval⁹, Brent S Carroll⁴, Stephen P Plassmeyer¹⁰, Ryan J Emenecker¹⁰, Zhipeng Yang¹, Deepa Bisht⁵, Jared A Sewell⁸, Guangyuan Li⁷, Anisa Prasad¹¹, Sabrina Phanor⁴, Ryan Lane⁸, Devlin C Moyer¹², Toby Hunt¹³, Dawit Balcha¹, Marinella Gebbia¹⁴, Jean-Claude Twizere¹⁵, Tong Hao¹, Alex S Holehouse¹⁰, Adam Frankish¹³, Josh A Riback¹⁶, Nathan Salomonis⁷, Michael A Calderwood¹, David E Hill¹, Nidhi Sahni¹⁷, Marc Vidal¹⁸, Martha L Bulyk¹⁹, Juan I Fuxman Bass²⁰

Affiliations

¹ Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
² Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA. Electronic address: kaia.mattioli@gmail.com.
³ Department of Biology, Boston University, Boston, MA 02215, USA; Bioinformatics Program, Boston University, Boston, MA 02215, USA.
⁴ Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.
⁵ Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
⁶ Molecular Biology, Cell Biology & Biochemistry Program, Boston University, Boston, MA 02215, USA.
⁷ Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA; Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.
⁸ Department of Biology, Boston University, Boston, MA 02215, USA.
⁹ Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; TERRA Teaching and Research Centre, University of Liège, Gembloux 5030, Belgium; Laboratory of Viral Interactomes, GIGA Institute, University of Liège, Liège 4000, Belgium.
¹⁰ Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA; Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO 63110, USA.
¹¹ Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Harvard College, Cambridge, MA 02138, USA.
¹² Bioinformatics Program, Boston University, Boston, MA 02215, USA.
¹³ European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CD10 1SD, UK.
¹⁴ Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA 02215, USA; The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada; Lunenfeld-Tanenbaum Research Institute (LTRI), Sinai Health System, Toronto, ON M5G 1X5, Canada.
¹⁵ Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA 02215, USA; TERRA Teaching and Research Centre, University of Liège, Gembloux 5030, Belgium; Laboratory of Viral Interactomes, GIGA Institute, University of Liège, Liège 4000, Belgium.
¹⁶ Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA.
¹⁷ Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA. Electronic address: nidhi.sahni.2025@gmail.com.
¹⁸ Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA. Electronic address: marc_vidal@dfci.harvard.edu.
¹⁹ Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA 02215, USA; Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA. Electronic address: mlbulyk@genetics.med.harvard.edu.
²⁰ Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biology, Boston University, Boston, MA 02215, USA; Bioinformatics Program, Boston University, Boston, MA 02215, USA; Molecular Biology, Cell Biology & Biochemistry Program, Boston University, Boston, MA 02215, USA. Electronic address: fuxman@bu.edu.

PMID: 40147441
PMCID: PMC12121496 (available on 2026-04-03)
DOI: 10.1016/j.molcel.2025.03.004

Widespread variation in molecular interactions and regulatory properties among transcription factor isoforms

Luke Lambourne et al. Mol Cell. 2025.

. 2025 Apr 3;85(7):1445-1466.e13.

doi: 10.1016/j.molcel.2025.03.004. Epub 2025 Mar 26.

Authors

Affiliations

¹ Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
² Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA. Electronic address: kaia.mattioli@gmail.com.
³ Department of Biology, Boston University, Boston, MA 02215, USA; Bioinformatics Program, Boston University, Boston, MA 02215, USA.
⁴ Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.
⁵ Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
⁶ Molecular Biology, Cell Biology & Biochemistry Program, Boston University, Boston, MA 02215, USA.
⁷ Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA; Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.
⁸ Department of Biology, Boston University, Boston, MA 02215, USA.
⁹ Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; TERRA Teaching and Research Centre, University of Liège, Gembloux 5030, Belgium; Laboratory of Viral Interactomes, GIGA Institute, University of Liège, Liège 4000, Belgium.
¹⁰ Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA; Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO 63110, USA.
¹¹ Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Harvard College, Cambridge, MA 02138, USA.
¹² Bioinformatics Program, Boston University, Boston, MA 02215, USA.
¹³ European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CD10 1SD, UK.
¹⁴ Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA 02215, USA; The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada; Lunenfeld-Tanenbaum Research Institute (LTRI), Sinai Health System, Toronto, ON M5G 1X5, Canada.
¹⁵ Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA 02215, USA; TERRA Teaching and Research Centre, University of Liège, Gembloux 5030, Belgium; Laboratory of Viral Interactomes, GIGA Institute, University of Liège, Liège 4000, Belgium.
¹⁶ Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA.
¹⁷ Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA. Electronic address: nidhi.sahni.2025@gmail.com.
¹⁸ Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA. Electronic address: marc_vidal@dfci.harvard.edu.
¹⁹ Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA 02215, USA; Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA. Electronic address: mlbulyk@genetics.med.harvard.edu.
²⁰ Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biology, Boston University, Boston, MA 02215, USA; Bioinformatics Program, Boston University, Boston, MA 02215, USA; Molecular Biology, Cell Biology & Biochemistry Program, Boston University, Boston, MA 02215, USA. Electronic address: fuxman@bu.edu.

PMID: 40147441
PMCID: PMC12121496 (available on 2026-04-03)
DOI: 10.1016/j.molcel.2025.03.004

Abstract

Most human transcription factor (TF) genes encode multiple protein isoforms differing in DNA-binding domains, effector domains, or other protein regions. The global extent to which this results in functional differences between isoforms remains unknown. Here, we systematically compared 693 isoforms of 246 TF genes, assessing DNA binding, protein binding, transcriptional activation, subcellular localization, and condensate formation. Relative to reference isoforms, two-thirds of alternative TF isoforms exhibit differences in one or more molecular activities, which often could not be predicted from sequence. We observed two primary categories of alternative TF isoforms: "rewirers" and "negative regulators," both of which were associated with differentiation and cancer. Our results support a model wherein the relative expression levels of, and interactions involving, TF isoforms add an understudied layer of complexity to gene regulatory networks, demonstrating the importance of isoform-aware characterization of TF functions and providing a rich resource for further studies.

Keywords: alternative splicing; gene regulation; isoforms; transcription factors; transcriptional regulation.

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Conflict of interest statement

Declaration of interests M.L.B. is a co-inventor on US patents #6,548,021 and #8,530,638 on PBM technology and corresponding universal sequence designs, respectively. Universal PBM array designs used in this study are available via a materials transfer agreement with The Brigham & Women’s Hospital, Inc. M.L.B. is a member of the Molecular Cell advisory board.

Update of

Widespread variation in molecular interactions and regulatory properties among transcription factor isoforms.
Lambourne L, Mattioli K, Santoso C, Sheynkman G, Inukai S, Kaundal B, Berenson A, Spirohn-Fitzgerald K, Bhattacharjee A, Rothman E, Shrestha S, Laval F, Yang Z, Bisht D, Sewell JA, Li G, Prasad A, Phanor S, Lane R, Campbell DM, Hunt T, Balcha D, Gebbia M, Twizere JC, Hao T, Frankish A, Riback JA, Salomonis N, Calderwood MA, Hill DE, Sahni N, Vidal M, Bulyk ML, Fuxman Bass JI. Lambourne L, et al. bioRxiv [Preprint]. 2024 Apr 10:2024.03.12.584681. doi: 10.1101/2024.03.12.584681. bioRxiv. 2024. Update in: Mol Cell. 2025 Apr 03;85(7):1445-1466.e13. doi: 10.1016/j.molcel.2025.03.004. PMID: 38617209 Free PMC article. Updated. Preprint.

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Widespread variation in molecular interactions and regulatory properties among transcription factor isoforms

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Widespread variation in molecular interactions and regulatory properties among transcription factor isoforms

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