Alternative mRNA Splicing Controls the Functions of the Histone H3K27 Demethylase UTX/KDM6A
The UTX/KDM6A histone H3K27 demethylase plays an important role in development and is frequently mutated in cancers such as urothelial cancer. Despite many studies on UTX proteins, variations in mRNA splicing have been overlooked. Using Nanopore sequencing, we present a comprehensive analysis of UTX...
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MDPI AG
2023-06-01
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| Series: | Cancers |
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| Online Access: | https://www.mdpi.com/2072-6694/15/12/3117 |
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| author | Omid Fotouhi Sheikh Nizamuddin Stephanie Falk Oliver Schilling Ruth Knüchel-Clarke Martin L. Biniossek H. T. Marc Timmers |
| author_facet | Omid Fotouhi Sheikh Nizamuddin Stephanie Falk Oliver Schilling Ruth Knüchel-Clarke Martin L. Biniossek H. T. Marc Timmers |
| author_sort | Omid Fotouhi |
| collection | DOAJ |
| description | The UTX/KDM6A histone H3K27 demethylase plays an important role in development and is frequently mutated in cancers such as urothelial cancer. Despite many studies on UTX proteins, variations in mRNA splicing have been overlooked. Using Nanopore sequencing, we present a comprehensive analysis of UTX/KDM6A splicing events in human cell lines and in tissue samples from bladder cancer cases and normal epithelia. We found that the central region of UTX mRNAs encoded by exons 12 to 17 undergoes extensive alternative splicing. Up to half of all stable mRNAs (8–48% in bladder tissues and 18–58% in cell lines) are represented by the UTX canonical isoform lacking exon 14 encoding a nuclear localization sequence, and hence exon 14-containing UTX isoforms exclusively localize to the nucleus, unlike the cytonuclear localization of the canonical isoform. Chromatin association was also higher for exon-14-containing isoforms compared to the canonical UTX. Using quantitative mass spectrometry, we found that all UTX isoforms integrated into the MLL3 and MLL4, PR-DUB and MiDAC complexes. Interestingly, one of the novel UTX isoforms, which lacks exons 14 and 16, fails to interact with PR-DUB and MiDAC complex members. In conclusion, UTX mRNAs undergo extensive alternative splicing, which controls the subcellular localization of UTX and its interactions with other chromatin regulatory complexes. |
| first_indexed | 2024-03-09T10:58:01Z |
| format | Article |
| id | doaj.art-3ae14620188d4a848f6b6c4deb308765 |
| institution | Directory Open Access Journal |
| issn | 2072-6694 |
| language | English |
| last_indexed | 2024-03-09T10:58:01Z |
| publishDate | 2023-06-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Cancers |
| spelling | doaj.art-3ae14620188d4a848f6b6c4deb3087652023-12-01T01:30:16ZengMDPI AGCancers2072-66942023-06-011512311710.3390/cancers15123117Alternative mRNA Splicing Controls the Functions of the Histone H3K27 Demethylase UTX/KDM6AOmid Fotouhi0Sheikh Nizamuddin1Stephanie Falk2Oliver Schilling3Ruth Knüchel-Clarke4Martin L. Biniossek5H. T. Marc Timmers6Department of Urology, Medical Center-University of Freiburg, 79106 Freiburg, GermanyDepartment of Urology, Medical Center-University of Freiburg, 79106 Freiburg, GermanyMax Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, GermanyGerman Cancer Consortium (DKTK) Partner Site Freiburg, German Cancer Research Center (DKFZ), 69120 Heidelberg, GermanyInstitute of Pathology, University Hospital RWTH Aachen, 52074 Aachen, GermanyInstitute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, 79106 Freiburg, GermanyDepartment of Urology, Medical Center-University of Freiburg, 79106 Freiburg, GermanyThe UTX/KDM6A histone H3K27 demethylase plays an important role in development and is frequently mutated in cancers such as urothelial cancer. Despite many studies on UTX proteins, variations in mRNA splicing have been overlooked. Using Nanopore sequencing, we present a comprehensive analysis of UTX/KDM6A splicing events in human cell lines and in tissue samples from bladder cancer cases and normal epithelia. We found that the central region of UTX mRNAs encoded by exons 12 to 17 undergoes extensive alternative splicing. Up to half of all stable mRNAs (8–48% in bladder tissues and 18–58% in cell lines) are represented by the UTX canonical isoform lacking exon 14 encoding a nuclear localization sequence, and hence exon 14-containing UTX isoforms exclusively localize to the nucleus, unlike the cytonuclear localization of the canonical isoform. Chromatin association was also higher for exon-14-containing isoforms compared to the canonical UTX. Using quantitative mass spectrometry, we found that all UTX isoforms integrated into the MLL3 and MLL4, PR-DUB and MiDAC complexes. Interestingly, one of the novel UTX isoforms, which lacks exons 14 and 16, fails to interact with PR-DUB and MiDAC complex members. In conclusion, UTX mRNAs undergo extensive alternative splicing, which controls the subcellular localization of UTX and its interactions with other chromatin regulatory complexes.https://www.mdpi.com/2072-6694/15/12/3117alternative splicinghistone demethylasehistone methylationcancer biologychromatinproteomics |
| spellingShingle | Omid Fotouhi Sheikh Nizamuddin Stephanie Falk Oliver Schilling Ruth Knüchel-Clarke Martin L. Biniossek H. T. Marc Timmers Alternative mRNA Splicing Controls the Functions of the Histone H3K27 Demethylase UTX/KDM6A Cancers alternative splicing histone demethylase histone methylation cancer biology chromatin proteomics |
| title | Alternative mRNA Splicing Controls the Functions of the Histone H3K27 Demethylase UTX/KDM6A |
| title_full | Alternative mRNA Splicing Controls the Functions of the Histone H3K27 Demethylase UTX/KDM6A |
| title_fullStr | Alternative mRNA Splicing Controls the Functions of the Histone H3K27 Demethylase UTX/KDM6A |
| title_full_unstemmed | Alternative mRNA Splicing Controls the Functions of the Histone H3K27 Demethylase UTX/KDM6A |
| title_short | Alternative mRNA Splicing Controls the Functions of the Histone H3K27 Demethylase UTX/KDM6A |
| title_sort | alternative mrna splicing controls the functions of the histone h3k27 demethylase utx kdm6a |
| topic | alternative splicing histone demethylase histone methylation cancer biology chromatin proteomics |
| url | https://www.mdpi.com/2072-6694/15/12/3117 |
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