The SETD2 L1609P mutation found in leukemia disrupts methyltransferase activity and reduces histone H3K36 trimethylation

Sep 22, 2026

The SET-domain containing protein 2 (SETD2) is a key histone methyltransferase that produces the transcription-regulating mark H3K36me3, with frequent SETD2 mutations reported in cancer yet limited biochemical and structural characterization. This study enzymatically and structurally analyzes the leukemia-associated SETD2 L1609P mutant. L1609 resides in the SET-domain hydrophobic pocket for H3K36 recognition, and mutagenesis indicates L1609-linked cancer alleles may cause loss- or gain-of-function. The L1609P variant shows reduced methyltransferase activity, decreased stability, poor cellular expression, and active-site remodeling in a crystal complex with an H3K36M peptide, supporting disrupted H3K36me3 deposition in oncogenesis, especially hematologic malignancies.

LanguageEnglish

CategoryHealthcare

FormatPDF

Pages15

Reading Time38 min

AccessFree to download

Background

SETD2 and H3K36me3 function

Study focus

Biochemical and structural characterization of L1609P

Key findings

Enzymatic activity, stability, and cellular expression

Crystal structure and active-site remodeling

Conclusion

Implications for oncogenesis in hematologic malignancies

RESEARCH ARTICLE The SETD2 L1609P mutation found in leukemia disrupts methyltransferase activity and reduces histone H3K36 trimethylation Received for publication, July 28, 2025, and in revised form, January 16, 2026 Published, Papers in Press, February 5, 2026 [https://doi.org/10.1016/j.jbc.2026.1](https://doi.org/10.1016/j.jbc.2026.1)11259 Christina Michail 1, Jérémy Berthelet2, Ariel E. Mechaly3, Linh-Chi Bui 1, Haopeng Yang4, Duo Cai 1, Amira Al Mahi 1, Aowei Xie5, Valeria Bisio6, Valentina Sirri 1, Jean-Marie Dupret 1, Fabien Guidez7, Ximing Xu5, Nicolas Joly8, Leslie Regad 1,9, Mireille Viguier 1, Frédérique Deshayes 1, Nicolas Dulphy6, Michael R. Green4, Ahmed Haouz3, and Fernando Rodrigues Lima 1, * From the 1Université Paris Cité, CNRS, Unité de Biologie Fonctionnelle et Adaptative, Paris, France; 2 Université Paris Cité, CNRS, Centre Epigénétique et Destin Cellulaire, Paris, France; 3Institut Pasteur, CNRS, Plate-forme de Cristallographie-C2RT, Paris, France; 4Department of Lymphoma and Myeloma, Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA; 5Marine Biomedical Institute of Qingdao, School of Pharmacy and Medicine, Ocean University of China, Qingdao, Shandong, China; 6Université Paris Cité, INSERM, Institut de Recherche Saint Louis, Paris, France; 7 Université de Bourgogne, INSERM, Dijon, France; 8 Université Paris Cité, CNRS, Institut Jacques Monod, Paris, France; and 9 Université Paris Cité, CNRS, INSERM, Unité de Biologie Fonctionnelle et Adaptative, Paris, France Reviewed by members of the JBC Editorial Board. Edited by Brian D. Strahl SET-domain containing protein 2 (SETD2) is the primary methyltransferase responsible for generating H3K36me3, an epigenetic mark that is essential for transcriptional regulation and chromatin integrity. SETD2 mutations are frequently observed in various cancers and tend to cluster within its catalytic SET domain. Despite the clinical relevance of SETD2 missense mutations in cancer, their biochemical and structural consequences remain insufficiently characterized. Here, we present the enzymatic and structural characterization of the SETD2 L1609P mutant enzyme identified in leukemia. The L1609 residue is located in the SET domain within a conserved hydrophobic pocket that is involved in substrate H3K36 recognition. Interestingly, site-directed mutagenesis of residues within this hydrophobic pocket leads to SETD2 enzyme variants with either decreased or increased H3K36me3 methyltransferase activity, suggesting that cancer mutations affecting the L1609 residue could result in a loss-or gain-offunction enzyme variant. Using molecular and cellular approaches, we show that the SETD2 L1609P mutant exhibits reduced H3K36 methyltransferase activity, decreased protein stability, and poor cellular expression. Consistently, the crystal structure of the SETD2 L1609P in complex with a H3K36M peptide shows remodeling of the active site. These findings support the pivotal role of SETD2 inactivation and subsequent disruption of H3K36me3 deposition in oncogenesis, particularly in hematologic malignancies. Our study provides the first mechanistic and three-dimensional protein structure information on how SETD2-associated cancer mutations can lead to altered H3K36 methyltransferase activity. * For correspondence: Fernando Rodrigues Lima, fernando.rodrigues[lima@u-paris.fr](lima@u-paris.fr). SET-domain containing protein 2 (SETD2) is a critical histone methyltransferase that is responsible for catalyzing the trimethylation of histone H3 at lysine 36, thereby generating the epigenetic mark H3K36me3 in higher eukaryotes (1–4). This pivotal chromatin modification is linked to several key biological processes, including transcriptional activation, DNA damage repair, alternative RNA splicing, and DNA methylation (3, 5–8). Although SETD2 has been shown to catalyze mono-and dimethylation ofH3K36 in vitro, silencing the enzyme results i

FAQs

Why is the SETD2 L1609P mutation important in leukemia?

SETD2 generates the epigenetic mark H3K36me3, and leukemia-associated SETD2 mutations are clinically relevant. The study shows L1609P disrupts methyltransferase activity and reduces H3K36 trimethylation, linking inactivation to oncogenic processes.

What did the authors find about the methyltransferase activity of the L1609P mutant?

The SETD2 L1609P mutant exhibits reduced H3K36 methyltransferase activity compared with the functional expectation for SETD2-mediated H3K36me3 formation.

How does the crystal structure support the functional effects of L1609P?

The crystal structure of SETD2 L1609P in complex with an H3K36M peptide shows remodeling of the active site, consistent with impaired substrate recognition and altered H3K36 methylation outcomes.

Sep 22, 2026

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