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Saito M, Fujimoto S, Kawasaki H. Ecdysone and gene expressions for chromatin remodeling, histone modification, and Broad Complex in relation to pupal commitment in Bombyx mori. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2024; 115:e22076. [PMID: 38288490 DOI: 10.1002/arch.22076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 11/28/2023] [Accepted: 12/08/2023] [Indexed: 02/01/2024]
Abstract
In the present study, we tried to clarify when and how pupal commitment (PT) better to use PC occurs and what is involved in the PT of Bombyx mori. To clarify this, we examined the responsiveness of a wing disc to ecdysone, referring to metamorphosis-related BR-C, development-related Myc and Wnt, and chromatin remodeling-related genes at around the predicted PT stage of the Bombyx wing disc. Wing disc responsiveness to juvenile hormone (JH) and ecdysone was examined using Methoprene and 20-hydroxyecdysone (20E) in vitro. The body weight of B. mori increased after the last larval ecdysis, peaked at Day 5 of the fifth larval instar (D5L5), and then decreased. The responsiveness of the wing disc to JH decreased after the last larval ecdysis up to D3L5. Bmbr-c (the Broad Complex of B. mori) showed enhanced expression in D4L5 wing discs with 20E treatment. Some chromatin remodeler and histone modifier genes (Bmsnr1, Bmutx, and Bmtip60) showed upregulation after being cultured with 20E in D4L5 wing discs. A low concentration of 20E is suggested to induce responsiveness to 20E in D4L5 wing discs. Bmbr-c, Bmsnr1, Bmutx, and Bmtip60 were upregulated after being cultured with a low concentration of 20E in D4L5 wing discs. The expression of Bmmyc and Bmwnt1 did not show a change after being cultured with or without 20E in D4L5 wing discs, while enhanced expression was observed with 20E in D5L5 wing discs. From the present results, we concluded that PT of the wing disc of B. mori occurred beginning on D4L5 with the secretion of low concentrations of ecdysteroids. Bmsnr1, Bmutx, Bmtip60, and BR-C are also involved.
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Affiliation(s)
- Maki Saito
- Department of Bioproductive Science, Faculty of Agriculture, Takasaki University of Health and Welfare, Gunma, Japan
| | - Shota Fujimoto
- Department of Bioproductive Science, Faculty of Agriculture, Takasaki University of Health and Welfare, Gunma, Japan
| | - Hideki Kawasaki
- Department of Bioproductive Science, Faculty of Agriculture, Takasaki University of Health and Welfare, Gunma, Japan
- Faculty of Agriculture, Utsunomiya University, Tochigi, Japan
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2
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Zraly CB, Schultz R, Diaz MO, Dingwall AK. New twists of a TAIL: novel insights into the histone binding properties of a highly conserved PHD finger cluster within the MLR family of H3K4 mono-methyltransferases. Nucleic Acids Res 2023; 51:9672-9689. [PMID: 37638761 PMCID: PMC10570056 DOI: 10.1093/nar/gkad698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 07/19/2023] [Accepted: 08/11/2023] [Indexed: 08/29/2023] Open
Abstract
Enhancer activation by the MLR family of H3K4 mono-methyltransferases requires proper recognition of histones for the deposition of the mono-methyl mark. MLR proteins contain two clusters of PHD zinc finger domains implicated in chromatin regulation. The second cluster is the most highly conserved, preserved as an ancient three finger functional unit throughout evolution. Studies of the isolated 3rd PHD finger within this cluster suggested specificity for the H4 [aa16-20] tail region. We determined the histone binding properties of the full three PHD finger cluster b module (PHDb) from the Drosophila Cmi protein which revealed unexpected recognition of an extended region of H3. Importantly, the zinc finger spacer separating the first two PHDb fingers from the third is critical for proper alignment and coordination among fingers for maximal histone engagement. Human homologs, MLL3 and MLL4, also show conservation of H3 binding, expanding current views of histone recognition for this class of proteins. We further implicate chromatin remodeling by the SWI/SNF complex as a possible mechanism for the accessibility of PHDb to globular regions of histone H3 beyond the tail region. Our results suggest a two-tail histone recognition mechanism by the conserved PHDb domain involving a flexible hinge to promote interdomain coordination.
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Affiliation(s)
- Claudia B Zraly
- Department of Cancer Biology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA
| | - Richard Schultz
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA
| | - Manuel O Diaz
- Department of Cancer Biology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA
| | - Andrew K Dingwall
- Department of Cancer Biology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA
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3
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Stroynowska-Czerwinska AM, Klimczak M, Pastor M, Kazrani AA, Misztal K, Bochtler M. Clustered PHD domains in KMT2/MLL proteins are attracted by H3K4me3 and H3 acetylation-rich active promoters and enhancers. Cell Mol Life Sci 2023; 80:23. [PMID: 36598580 PMCID: PMC9813062 DOI: 10.1007/s00018-022-04651-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 11/18/2022] [Accepted: 11/23/2022] [Indexed: 01/05/2023]
Abstract
Histone lysine-specific methyltransferase 2 (KMT2A-D) proteins, alternatively called mixed lineage leukemia (MLL1-4) proteins, mediate positive transcriptional memory. Acting as the catalytic subunits of human COMPASS-like complexes, KMT2A-D methylate H3K4 at promoters and enhancers. KMT2A-D contain understudied highly conserved triplets and a quartet of plant homeodomains (PHDs). Here, we show that all clustered (multiple) PHDs localize to the well-defined loci of H3K4me3 and H3 acetylation-rich active promoters and enhancers. Surprisingly, we observe little difference in binding pattern between PHDs from promoter-specific KMT2A-B and enhancer-specific KMT2C-D. Fusion of the KMT2A CXXC domain to the PHDs drastically enhances their preference for promoters over enhancers. Hence, the presence of CXXC domains in KMT2A-B, but not KMT2C-D, may explain the promoter/enhancer preferences of the full-length proteins. Importantly, targets of PHDs overlap with KMT2A targets and are enriched in genes involved in the cancer pathways. We also observe that PHDs of KMT2A-D are mutated in cancer, especially within conserved folding motifs (Cys4HisCys2Cys/His). The mutations cause a domain loss-of-function. Taken together, our data suggest that PHDs of KMT2A-D guide the full-length proteins to active promoters and enhancers, and thus play a role in positive transcriptional memory.
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Affiliation(s)
| | - Magdalena Klimczak
- International Institute of Molecular and Cell Biology, 02-109, Warsaw, Poland
| | - Michal Pastor
- International Institute of Molecular and Cell Biology, 02-109, Warsaw, Poland
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106, Warsaw, Poland
| | - Asgar Abbas Kazrani
- International Institute of Molecular and Cell Biology, 02-109, Warsaw, Poland
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch-Graffenstaden, France
| | - Katarzyna Misztal
- International Institute of Molecular and Cell Biology, 02-109, Warsaw, Poland
| | - Matthias Bochtler
- International Institute of Molecular and Cell Biology, 02-109, Warsaw, Poland.
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106, Warsaw, Poland.
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4
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Huang W, Zhu JY, Fu Y, van de Leemput J, Han Z. Lpt, trr, and Hcf regulate histone mono- and dimethylation that are essential for Drosophila heart development. Dev Biol 2022; 490:53-65. [PMID: 35853502 PMCID: PMC10728806 DOI: 10.1016/j.ydbio.2022.07.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 06/30/2022] [Accepted: 07/06/2022] [Indexed: 11/22/2022]
Abstract
Mammalian KMT2C, KMT2D, and HCFC1 are expressed during heart development and have been associated with congenital heart disease, but their roles in heart development remain elusive. We found that the Drosophila Lpt and trr genes encode the N-terminal and C-terminal homologs, respectively, of mammalian KMT2C or KMT2D. Lpt and trr mutant embryos showed reduced cardiac progenitor cells. Silencing of Lpt, trr, or both simultaneously in the heart led to similar abnormal cardiac morphology, tissue fibrosis, and cardiac functional defects. Like KMT2D, Lpt and trr were found to modulate histone H3K4 mono- and dimethylation, but not trimethylation. Investigation of downstream genes regulated by mouse KMT2D in the heart showed that their fly homologs are similarly regulated by Lpt or trr in the fly heart, suggesting that Lpt and trr regulate an evolutionarily conserved transcriptional network for heart development. Moreover, we showed that cardiac silencing of Hcf, the fly homolog of mammalian HCFC1, leads to heart defects similar to those observed in Lpt and trr silencing, as well as reduced H3K4 monomethylation. Our findings suggest that Lpt and trr function together to execute the conserved function of mammalian KMT2C and KMT2D in histone H3 lysine K4 mono- and dimethylation required for heart development. Possibly aided by Hcf, which we show plays a related role in H3K4 methylation during fly heart development.
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Affiliation(s)
- Wen Huang
- Center for Precision Disease Modeling, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA; Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Jun-Yi Zhu
- Center for Precision Disease Modeling, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA; Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Yulong Fu
- Center for Precision Disease Modeling, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA; Genomic Diagnostics and Bioinformatics, Department of Pathology, The University of Alabama at Birmingham, Alabama, USA
| | - Joyce van de Leemput
- Center for Precision Disease Modeling, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA; Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Zhe Han
- Center for Precision Disease Modeling, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA; Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA.
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5
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Rickels R, Wang L, Iwanaszko M, Ozark PA, Morgan MA, Piunti A, Khalatyan N, Soliman SHA, Rendleman EJ, Savas JN, Smith ER, Shilatifard A. A small UTX stabilization domain of Trr is conserved within mammalian MLL3-4/COMPASS and is sufficient to rescue loss of viability in null animals. Genes Dev 2020; 34:1493-1502. [PMID: 33033055 PMCID: PMC7608747 DOI: 10.1101/gad.339762.120] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 09/09/2020] [Indexed: 12/19/2022]
Abstract
Catalytic-inactivating mutations within the Drosophila enhancer H3K4 mono-methyltransferase Trr and its mammalian homologs, MLL3/4, cause only minor changes in gene expression compared with whole-gene deletions for these COMPASS members. To identify essential histone methyltransferase-independent functions of Trr, we screened to identify a minimal Trr domain sufficient to rescue Trr-null lethality and demonstrate that this domain binds and stabilizes Utx in vivo. Using the homologous MLL3/MLL4 human sequences, we mapped a short ∼80-amino-acid UTX stabilization domain (USD) that promotes UTX stability in the absence of the rest of MLL3/4. Nuclear UTX stability is enhanced when the USD is fused with the MLL4 HMG-box. Thus, COMPASS-dependent UTX stabilization is an essential noncatalytic function of Trr/MLL3/MLL4, suggesting that stabilizing UTX could be a therapeutic strategy for cancers with MLL3/4 loss-of-function mutations.
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Affiliation(s)
- Ryan Rickels
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Lu Wang
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Marta Iwanaszko
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Patrick A Ozark
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Marc A Morgan
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Andrea Piunti
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Natalia Khalatyan
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Shimaa H A Soliman
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Emily J Rendleman
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Jeffrey N Savas
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Edwin R Smith
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Ali Shilatifard
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
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Ford DJ, Zraly CB, Perez JH, Dingwall AK. The Drosophila MLR COMPASS-like complex regulates bantam miRNA expression differentially in the context of cell fate. Dev Biol 2020; 468:41-53. [PMID: 32946789 DOI: 10.1016/j.ydbio.2020.09.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 09/10/2020] [Accepted: 09/11/2020] [Indexed: 10/23/2022]
Abstract
The conserved MLR COMPASS-like complexes are histone modifiers that are recruited by a variety of transcription factors to enhancer regions where they act as necessary epigenetic tools for enhancer establishment and function. A critical in vivo target of the Drosophila MLR complex is the bantam miRNA that regulates cell survival and functions in feedback regulation of cellular signaling pathways during development. We determine that loss of Drosophila MLR complex function in developing wing and eye imaginal discs results in growth and patterning defects that are sensitive to bantam levels. Consistent with an essential regulatory role in modulating bantam transcription, the MLR complex binds to tissue-specific bantam enhancers and contributes to fine-tuning expression levels during larval tissue development. In wing imaginal discs, the MLR complex attenuates bantam enhancer activity by negatively regulating expression; whereas, in differentiating eye discs, the complex exerts either positive or negative regulatory activity on bantam transcription depending on cell fate. Furthermore, while the MLR complex is not required to control bantam levels in undifferentiated eye cells anterior to the morphogenetic furrow, it serves to prepare critical enhancer control of bantam transcription for later regulation upon differentiation. Our investigation into the transcriptional regulation of a single target in a developmental context has provided novel insights as to how the MLR complex contributes to the precise timing of gene expression, and how the complex functions to help orchestrate the regulatory output of conserved signaling pathways during animal development.
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Affiliation(s)
- David J Ford
- Department of Cancer Biology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Claudia B Zraly
- Department of Cancer Biology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
| | - John Hertenstein Perez
- Department of Cancer Biology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Andrew K Dingwall
- Department of Cancer Biology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA; Department of Pathology & Laboratory Medicine, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA.
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7
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Sugeedha J, Gautam J, Tyagi S. SET1/MLL family of proteins: functions beyond histone methylation. Epigenetics 2020; 16:469-487. [PMID: 32795105 PMCID: PMC8078731 DOI: 10.1080/15592294.2020.1809873] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The SET1 family of enzymes are well known for their involvement in the histone 3 lysine 4 (H3K4) methylation, a conserved trait of euchromatin associated with transcriptional activation. These methyltransferases are distinct, and involved in various biological functions in the cell. Impairment in the function of SET1 family members leads to a number of abnormalities such as skeletal and neurological defects, leukaemogenesis and even lethality. Tremendous progress has been made in understanding the unique biological roles and the mechanism of SET1 enzymes in context with H3K4 methylation/canonical functions. However, in recent years, several studies have indicated the novel role of SET1 family proteins, other than H3K4 methylation, which are equally important for cellular functions. In this review, we focus on these non-canonical function of SET1 family members.
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Affiliation(s)
- Jeyapal Sugeedha
- Laboratory of Cell Cycle Regulation, Centre for DNA Fingerprinting and Diagnostics (CDFD), Uppal, Hyderabad, India
| | - Jyoti Gautam
- Laboratory of Cell Cycle Regulation, Centre for DNA Fingerprinting and Diagnostics (CDFD), Uppal, Hyderabad, India
| | - Shweta Tyagi
- Laboratory of Cell Cycle Regulation, Centre for DNA Fingerprinting and Diagnostics (CDFD), Uppal, Hyderabad, India
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8
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Zraly CB, Zakkar A, Perez JH, Ng J, White KP, Slattery M, Dingwall AK. The Drosophila MLR COMPASS complex is essential for programming cis-regulatory information and maintaining epigenetic memory during development. Nucleic Acids Res 2020; 48:3476-3495. [PMID: 32052053 PMCID: PMC7144903 DOI: 10.1093/nar/gkaa082] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 01/17/2020] [Accepted: 01/30/2020] [Indexed: 12/29/2022] Open
Abstract
The MLR COMPASS complex monomethylates H3K4 that serves to epigenetically mark transcriptional enhancers to drive proper gene expression during animal development. Chromatin enrichment analyses of the Drosophila MLR complex reveals dynamic association with promoters and enhancers in embryos with late stage enrichments biased toward both active and poised enhancers. RNAi depletion of the Cmi (also known as Lpt) subunit that contains the chromatin binding PHD finger domains attenuates enhancer functions, but unexpectedly results in inappropriate enhancer activation during stages when hormone responsive enhancers are poised, revealing critical epigenetic roles involved in both the activation and repression of enhancers depending on developmental context. Cmi is necessary for robust H3K4 monomethylation and H3K27 acetylation that mark active enhancers, but not for the chromatin binding of Trr, the MLR methyltransferase. Our data reveal two likely major regulatory modes of MLR function, contributions to enhancer commissioning in early embryogenesis and bookmarking enhancers to enable rapid transcriptional re-activation at subsequent developmental stages.
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Affiliation(s)
- Claudia B Zraly
- Department of Cancer Biology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA
| | - Abdul Zakkar
- Department of Biology, Program in Bioinformatics, Loyola University Chicago, Chicago, IL 60660, USA
| | - John Hertenstein Perez
- Department of Cancer Biology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA
| | - Jeffrey Ng
- Department of Cancer Biology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA.,Department of Biology, Program in Bioinformatics, Loyola University Chicago, Chicago, IL 60660, USA
| | - Kevin P White
- Institute for Genomics and Systems Biology and Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Matthew Slattery
- Institute for Genomics and Systems Biology and Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA.,Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, MN 55812, USA
| | - Andrew K Dingwall
- Department of Cancer Biology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA.,Department of Pathology & Laboratory Medicine, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA
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9
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Ashokkumar D, Zhang Q, Much C, Bledau AS, Naumann R, Alexopoulou D, Dahl A, Goveas N, Fu J, Anastassiadis K, Stewart AF, Kranz A. MLL4 is required after implantation, whereas MLL3 becomes essential during late gestation. Development 2020; 147:dev186999. [PMID: 32439762 DOI: 10.1242/dev.186999] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 04/24/2020] [Indexed: 12/26/2022]
Abstract
Methylation of histone 3 lysine 4 (H3K4) is a major epigenetic system associated with gene expression. In mammals there are six H3K4 methyltransferases related to yeast Set1 and fly Trithorax, including two orthologs of fly Trithorax-related: MLL3 and MLL4. Exome sequencing has documented high frequencies of MLL3 and MLL4 mutations in many types of human cancer. Despite this emerging importance, the requirements of these paralogs in mammalian development have only been incompletely reported. Here, we examined the null phenotypes to establish that MLL3 is first required for lung maturation, whereas MLL4 is first required for migration of the anterior visceral endoderm that initiates gastrulation in the mouse. This collective cell migration is preceded by a columnar-to-squamous transition in visceral endoderm cells that depends on MLL4. Furthermore, Mll4 mutants display incompletely penetrant, sex-distorted, embryonic haploinsufficiency and adult heterozygous mutants show aspects of Kabuki syndrome, indicating that MLL4 action, unlike MLL3, is dosage dependent. The highly specific and discordant functions of these paralogs in mouse development argues against their action as general enhancer factors.
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Affiliation(s)
- Deepthi Ashokkumar
- Genomics, Center for Molecular and Cellular Bioengineering, Biotechnology Center, Technische Universität Dresden, Tatzberg 47, 01307 Dresden, Germany
| | - Qinyu Zhang
- Genomics, Center for Molecular and Cellular Bioengineering, Biotechnology Center, Technische Universität Dresden, Tatzberg 47, 01307 Dresden, Germany
| | - Christian Much
- Genomics, Center for Molecular and Cellular Bioengineering, Biotechnology Center, Technische Universität Dresden, Tatzberg 47, 01307 Dresden, Germany
| | - Anita S Bledau
- Stem Cell Engineering, Center for Molecular and Cellular Bioengineering, Biotechnology Center, Technische Universität Dresden, Tatzberg 47, 01307 Dresden, Germany
| | - Ronald Naumann
- Transgenic Core Facility, Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany
| | - Dimitra Alexopoulou
- DRESDEN-concept Genome Center, Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Fetscherstr. 105, 01307 Dresden, Germany
| | - Andreas Dahl
- DRESDEN-concept Genome Center, Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Fetscherstr. 105, 01307 Dresden, Germany
| | - Neha Goveas
- Genomics, Center for Molecular and Cellular Bioengineering, Biotechnology Center, Technische Universität Dresden, Tatzberg 47, 01307 Dresden, Germany
| | - Jun Fu
- Genomics, Center for Molecular and Cellular Bioengineering, Biotechnology Center, Technische Universität Dresden, Tatzberg 47, 01307 Dresden, Germany
| | - Konstantinos Anastassiadis
- Stem Cell Engineering, Center for Molecular and Cellular Bioengineering, Biotechnology Center, Technische Universität Dresden, Tatzberg 47, 01307 Dresden, Germany
| | - A Francis Stewart
- Genomics, Center for Molecular and Cellular Bioengineering, Biotechnology Center, Technische Universität Dresden, Tatzberg 47, 01307 Dresden, Germany
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany
| | - Andrea Kranz
- Genomics, Center for Molecular and Cellular Bioengineering, Biotechnology Center, Technische Universität Dresden, Tatzberg 47, 01307 Dresden, Germany
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10
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Kranz A, Anastassiadis K. The role of SETD1A and SETD1B in development and disease. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194578. [PMID: 32389824 DOI: 10.1016/j.bbagrm.2020.194578] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 04/16/2020] [Accepted: 05/03/2020] [Indexed: 12/13/2022]
Abstract
The Trithorax-related Set1 H3K4 methyltransferases are conserved from yeast to human. In yeast loss of Set1 causes pleiotropic effects but is compatible with life. In contrast, both mammalian Set1 orthologs: SETD1A and SETD1B are essential for embryonic development, however they have distinct functions. SETD1A is required shortly after epiblast formation whereas SETD1B becomes indispensible during early organogenesis. In adult mice both SETD1A and SETD1B regulate hematopoiesis differently: SETD1A is required for the establishment of definitive hematopoiesis whereas SETD1B is important for the maintenance of long-term hematopoietic stem cells. Both are implicated in different diseases with accumulating evidence for the association of SETD1A variants in neurological disorders and SETD1B variants with cancer. Why the two paralogs cannot or only partially compensate for the loss of each other is part of the puzzle that we try to sort out in this review.
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Affiliation(s)
- Andrea Kranz
- Genomics, Center for Molecular and Cellular Bioengineering, Biotechnology Center, Technische Universität Dresden, Tatzberg 47, 01307 Dresden, Germany
| | - Konstantinos Anastassiadis
- Stem Cell Engineering, Center for Molecular and Cellular Bioengineering, Biotechnology Center, Technische Universität Dresden, Tatzberg 47, 01307 Dresden, Germany.
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11
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MLL2 regulates glucocorticoid receptor-mediated transcription of ENACα in human retinal pigment epithelial cells. Biochem Biophys Res Commun 2020; 525:675-680. [PMID: 32139118 DOI: 10.1016/j.bbrc.2020.02.046] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Accepted: 02/07/2020] [Indexed: 11/24/2022]
Abstract
Glucocorticoids require the glucocorticoid receptor (GR), a type of ligand-dependent nuclear receptor to transmit their downstream effects. Upon glucocorticoid binding, GR associates with glucocorticoid response elements (GREs) and recruits other transcriptional coregulators to activate or repress target gene transcription. Many SET-domain family proteins have been demonstrated to contribute to GR-mediated transcriptional activity. However, whether histone H3K4-specific methyltransferase plays a cell-type-specific role in GR transcriptional regulation remains poorly understood. In this report, we examined MLL2 (KMT2D), a histone-lysine methyltransferase that catalyzes histone H3 lysine 4 methylation (H3K4me). Furthermore, we demonstrated that MLL2 specifically regulates the transcription of some GR target genes (e.g., ENACα and FLJ20371) in ARPE-19 cells, but has no effect in A549 cells. Mechanistically, co-immunoprecipitation assays revealed that MLL2 is associated with GR in a ligand-independent manner in APRE-19 cells. Moreover, chromatin immunoprecipitation analyses demonstrated that MLL2 could co-occupy glucocorticoid response elements (GREs) of GR target genes along with GR following Dex stimulation. Finally, the FAIRE-qPCR results illustrated that MLL2 is pivotal in establishing chromatin structure accessibility at the GREs of ARPE-19 specific genes in the presence of Dex. Taken together, our study determined that MLL2 regulates GR-mediated transcription in a cell-type-specific manner, and we provide a molecular mechanism to explain the specific role of MLL2 in regulating GR target gene expression in ARPE-19 cells.
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12
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Structural insights into trans-histone regulation of H3K4 methylation by unique histone H4 binding of MLL3/4. Nat Commun 2019; 10:36. [PMID: 30604749 PMCID: PMC6318328 DOI: 10.1038/s41467-018-07906-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 12/04/2018] [Indexed: 12/29/2022] Open
Abstract
MLL3 and MLL4 are two closely related members of the SET1/MLL family of histone H3K4 methyltransferases and are responsible for monomethylating histone H3K4 on enhancers, which are essential in regulating cell-type-specific gene expression. Mutations of MLL3 or MLL4 have been reported in different types of cancer. Recently, the PHD domains of MLL3/4 have been reported to recruit the MLL3/4 complexes to their target genes by binding to histone H4 during the NT2/D1 stem cell differentiation. Here we show that an extended PHD domain (ePHD6) involving the sixth PHD domain and its preceding zinc finger in MLL3 and MLL4 specifically recognizes an H4H18-containing histone H4 fragment and that modifications of residues surrounding H4H18 modulate H4 binding to MLL3/4. Our in vitro methyltransferase assays and cellular experiments further reveal that the interaction between ePHD6 of MLL3/4 and histone H4 is required for their nucleosomal methylation activity and MLL4-mediated neuronal differentiation of NT2/D1 cells. MLL3 and MLL4 are members of the SET1/MLL family of histone H3K4 methyltransferases, which are responsible for monomethylating histone H3K4 on enhancers. Here the authors show that an extended PHD domain (ePHD6) in MLL3 and MLL4 specifically recognizes an H4H18-containing fragment of histone H4, and that modifications of residues surrounding H4H18 modulate H4 binding to MLL3/4.
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13
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Mihaylova Y, Abnave P, Kao D, Hughes S, Lai A, Jaber-Hijazi F, Kosaka N, Aboobaker AA. Conservation of epigenetic regulation by the MLL3/4 tumour suppressor in planarian pluripotent stem cells. Nat Commun 2018; 9:3633. [PMID: 30194301 PMCID: PMC6128892 DOI: 10.1038/s41467-018-06092-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 08/13/2018] [Indexed: 12/18/2022] Open
Abstract
Currently, little is known about the evolution of epigenetic regulation in animal stem cells. Here we demonstrate, using the planarian stem cell system to investigate the role of the COMPASS family of MLL3/4 histone methyltransferases that their function as tumor suppressors in mammalian stem cells is conserved over a long evolutionary distance. To investigate the potential conservation of a genome-wide epigenetic regulatory program in animal stem cells, we assess the effects of Mll3/4 loss of function by performing RNA-seq and ChIP-seq on the G2/M planarian stem cell population, part of which contributes to the formation of outgrowths. We find many oncogenes and tumor suppressors among the affected genes that are likely candidates for mediating MLL3/4 tumor suppression function. Our work demonstrates conservation of an important epigenetic regulatory program in animals and highlights the utility of the planarian model system for studying epigenetic regulation.
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Affiliation(s)
- Yuliana Mihaylova
- Department of Zoology, Tinbergen Building, South Parks Road, Oxford, OX1 3PS, UK
| | - Prasad Abnave
- Department of Zoology, Tinbergen Building, South Parks Road, Oxford, OX1 3PS, UK
| | - Damian Kao
- Department of Zoology, Tinbergen Building, South Parks Road, Oxford, OX1 3PS, UK
| | - Samantha Hughes
- HAN University of Applied Sciences, Institute of Applied Sciences, Laan van Scheut 2, 6525EM, Nijmegen, The Netherlands
| | - Alvina Lai
- Department of Zoology, Tinbergen Building, South Parks Road, Oxford, OX1 3PS, UK
| | - Farah Jaber-Hijazi
- Beatson Institute for Cancer Research, Switchback Road, Bearsden, Glasgow, G61 1BD, UK
| | - Nobuyoshi Kosaka
- Department of Zoology, Tinbergen Building, South Parks Road, Oxford, OX1 3PS, UK
| | - A Aziz Aboobaker
- Department of Zoology, Tinbergen Building, South Parks Road, Oxford, OX1 3PS, UK.
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14
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Schmidt K, Zhang Q, Tasdogan A, Petzold A, Dahl A, Arneth BM, Slany R, Fehling HJ, Kranz A, Stewart AF, Anastassiadis K. The H3K4 methyltransferase Setd1b is essential for hematopoietic stem and progenitor cell homeostasis in mice. eLife 2018; 7:27157. [PMID: 29916805 PMCID: PMC6025962 DOI: 10.7554/elife.27157] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 06/08/2018] [Indexed: 12/11/2022] Open
Abstract
Hematopoietic stem cells require MLL1, which is one of six Set1/Trithorax-type histone 3 lysine 4 (H3K4) methyltransferases in mammals and clinically the most important leukemia gene. Here, we add to emerging evidence that all six H3K4 methyltransferases play essential roles in the hematopoietic system by showing that conditional mutagenesis of Setd1b in adult mice provoked aberrant homeostasis of hematopoietic stem and progenitor cells (HSPCs). Using both ubiquitous and hematopoietic-specific deletion strategies, the loss of Setd1b resulted in peripheral thrombo- and lymphocytopenia, multilineage dysplasia, myeloid-biased extramedullary hematopoiesis in the spleen, and lethality. By transplantation experiments and expression profiling, we determined that Setd1b is autonomously required in the hematopoietic lineages where it regulates key lineage specification components, including Cebpa, Gata1, and Klf1. Altogether, these data imply that the Set1/Trithorax-type epigenetic machinery sustains different aspects of hematopoiesis and constitutes a second framework additional to the transcription factor hierarchy of hematopoietic homeostasis.
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Affiliation(s)
- Kerstin Schmidt
- Stem Cell Engineering, Biotechnology Center, Technische Universität Dresden, Dresden, Germany
| | - Qinyu Zhang
- Genomics, Biotechnology Center, Technische Universität Dresden, Dresden, Germany
| | - Alpaslan Tasdogan
- Institute of Immunology, University Hospital Ulm, Ulm, Germany.,Department of Dermatology, University Hospital Ulm, Ulm, Germany
| | - Andreas Petzold
- Deep Sequencing Group, DFG - Center for Regenerative Therapies Dresden, Dresden, Germany
| | - Andreas Dahl
- Deep Sequencing Group, DFG - Center for Regenerative Therapies Dresden, Dresden, Germany
| | - Borros M Arneth
- Institute of Laboratory Medicine and Pathobiochemistry, Molecular Diagnostics, Hospital of the Universities Giessen and Marburg, Giessen, Germany
| | - Robert Slany
- Department of Genetics, Friedrich Alexander Universität Erlangen, Erlangen, Germany
| | | | - Andrea Kranz
- Genomics, Biotechnology Center, Technische Universität Dresden, Dresden, Germany
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15
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Association between expression of nuclear receptor co-activator 5 protein and prognosis in postoperative patients with osteosarcoma. Oncol Lett 2017; 15:1888-1892. [PMID: 29434886 DOI: 10.3892/ol.2017.7513] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 08/01/2017] [Indexed: 02/07/2023] Open
Abstract
The aim of the present study was to investigate the association between the expression of nuclear receptor co-activator 5 protein (NCOA5) and the prognosis of postoperative patients with osteosarcoma. Human osteosarcoma samples were collected from 145 patients and normal bone tissues were collected from 100 individuals as controls. Immunohistochemistry (IHC) and reverse transcription-polymerase chain reaction (RT-PCR) were employed to measure the levels of NCOA5 protein in cases of human osteosarcoma. The results from the RT-PCR analysis demonstrated that the positive rate of NCOA5 mRNA expression in human osteosarcoma was 17.24% (25/145). The positive rate in normal bone tissues was 84.00% (84/100), which was significantly higher compared with that of human osteosarcoma tissues (χ2=33.166; P<0.001). IHC staining indicated that the positive rate of NCOA5 protein in the osteosarcoma samples was 26.21% (38/145). The positive rate in normal bone tissues was 82.00% (82/100), which was significantly increased compared with that of human osteosarcoma tissues (χ2=28.166; P<0.001). NCOA5 mRNA and protein expression levels were consistent in human osteosarcoma tissues, and were lower than in control tissues. The expression of NCOA5 was low in human osteosarcoma tissues, while it was high in normal bone tissues. These low NCOA5 expression levels were associated with postoperative survival of human osteosarcoma.
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Brici D, Zhang Q, Reinhardt S, Dahl A, Hartmann H, Schmidt K, Goveas N, Huang J, Gahurova L, Kelsey G, Anastassiadis K, Stewart AF, Kranz A. Setd1b, encoding a histone 3 lysine 4 methyltransferase, is a maternal effect gene required for the oogenic gene expression program. Development 2017; 144:2606-2617. [PMID: 28619824 DOI: 10.1242/dev.143347] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 06/02/2017] [Indexed: 12/16/2022]
Abstract
Germ cell development involves major reprogramming of the epigenome to prime the zygote for totipotency. Histone 3 lysine 4 (H3K4) methylations are universal epigenetic marks mediated in mammals by six H3K4 methyltransferases related to fly Trithorax, including two yeast Set1 orthologs: Setd1a and Setd1b. Whereas Setd1a plays no role in oogenesis, we report that Setd1b deficiency causes female sterility in mice. Oocyte-specific Gdf9-iCre conditional knockout (Setd1bGdf9 cKO) ovaries develop through all stages; however, follicular loss accumulated with age and unfertilized metaphase II (MII) oocytes exhibited irregularities of the zona pellucida and meiotic spindle. Most Setd1bGdf9 cKO zygotes remained in the pronuclear stage and displayed polyspermy in the perivitelline space. Expression profiling of Setd1bGdf9 cKO MII oocytes revealed (1) that Setd1b promotes the expression of the major oocyte transcription factors including Obox1, 2, 5, 7, Meis2 and Sall4; and (2) twice as many mRNAs were upregulated than downregulated, suggesting that Setd1b also promotes the expression of negative regulators of oocyte development with multiple Zfp-KRAB factors implicated. Together, these findings indicate that Setd1b serves as maternal effect gene through regulation of the oocyte gene expression program.
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Affiliation(s)
- David Brici
- Genomics, Biotechnology Center, Technische Universität Dresden, BioInnovationsZentrum, Tatzberg 47, Dresden 01307, Germany
| | - Qinyu Zhang
- Genomics, Biotechnology Center, Technische Universität Dresden, BioInnovationsZentrum, Tatzberg 47, Dresden 01307, Germany
| | - Susanne Reinhardt
- Deep Sequencing Group SFB 655, Biotechnology Center, Technische Universität Dresden, 01307 Dresden, Germany
| | - Andreas Dahl
- Deep Sequencing Group SFB 655, Biotechnology Center, Technische Universität Dresden, 01307 Dresden, Germany
| | - Hella Hartmann
- Light Microscopy Core Facility of the Biotechnology Center/Center for Regenerative Therapies Dresden, Technische Universität Dresden, 01307 Dresden, Germany
| | - Kerstin Schmidt
- Stem Cell Engineering, Biotechnology Center, Technische Universität Dresden, BioInnovationsZentrum, Tatzberg 47, Dresden 01307, Germany
| | - Neha Goveas
- Genomics, Biotechnology Center, Technische Universität Dresden, BioInnovationsZentrum, Tatzberg 47, Dresden 01307, Germany
| | - Jiahao Huang
- Epigenetics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK
| | - Lenka Gahurova
- Epigenetics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK
| | - Gavin Kelsey
- Epigenetics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK
| | - Konstantinos Anastassiadis
- Stem Cell Engineering, Biotechnology Center, Technische Universität Dresden, BioInnovationsZentrum, Tatzberg 47, Dresden 01307, Germany
| | - A Francis Stewart
- Genomics, Biotechnology Center, Technische Universität Dresden, BioInnovationsZentrum, Tatzberg 47, Dresden 01307, Germany
| | - Andrea Kranz
- Genomics, Biotechnology Center, Technische Universität Dresden, BioInnovationsZentrum, Tatzberg 47, Dresden 01307, Germany
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Kimura S, Loppin B. Two bromodomain proteins functionally interact to recapitulate an essential BRDT-like function in Drosophila spermatocytes. Open Biol 2015; 5:140145. [PMID: 25652540 PMCID: PMC4345279 DOI: 10.1098/rsob.140145] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
In mammals, the testis-specific bromodomain and extra terminal (BET) protein BRDT is essential for spermatogenesis. In Drosophila, it was recently reported that the tBRD-1 protein is similarly required for male fertility. Interestingly, however, tBRD-1 has two conserved bromodomains in its N-terminus but it lacks an extra terminal (ET) domain characteristic of BET proteins. Here, using proteomics approaches to search for tBRD-1 interactors, we identified tBRD-2 as a novel testis-specific bromodomain protein. In contrast to tBRD-1, tBRD-2 contains a single bromodomain, but which is associated with an ET domain in its C-terminus. Strikingly, we show that tbrd-2 knock-out males are sterile and display aberrant meiosis in a way highly similar to tbrd-1 mutants. Furthermore, these two factors co-localize and are interdependent in spermatocytes. We propose that Drosophila tBRD-1 and tBRD-2 associate into a functional BET complex in spermatocytes, which recapitulates the activity of the single mammalian BRDT-like protein.
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Affiliation(s)
- Shuhei Kimura
- Centre de Génétique et de Physiologie Moléculaire et Cellulaire, CNRS UMR5534, Université Claude Bernard Lyon 1, 69622 Villeurbanne cedex, France
| | - Benjamin Loppin
- Centre de Génétique et de Physiologie Moléculaire et Cellulaire, CNRS UMR5534, Université Claude Bernard Lyon 1, 69622 Villeurbanne cedex, France
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18
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The cancer COMPASS: navigating the functions of MLL complexes in cancer. Cancer Genet 2015; 208:178-91. [PMID: 25794446 DOI: 10.1016/j.cancergen.2015.01.005] [Citation(s) in RCA: 98] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 01/20/2015] [Accepted: 01/21/2015] [Indexed: 12/13/2022]
Abstract
The mixed-lineage leukemia family of histone methyltransferases (MLL1-4, or KMT2A-D) were previously linked to cancer through the founding member, MLL1/KMT2A, which is often involved in translocation-associated gene fusion events in childhood leukemias. However, in recent years, a multitude of tumor exome sequencing studies have revealed that orthologues MLL3/KMT2C and MLL2/KMT2D are mutated in a significant percentage of a large variety of malignancies, particularly solid tumors. These unexpected findings necessitate a deeper inspection into the activities and functional differences between the MLL/KMT2 family members. This review provides an overview of this protein family and its relation to cancers, focusing on the recent links between MLL3/KMT2C and MLL2/4/KMT2D and their potential roles as tumor suppressors in an assortment of cell types.
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19
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López-Falcón B, Meyer-Nava S, Hernández-Rodríguez B, Campos A, Montero D, Rudiño E, Vázquez M, Zurita M, Valadez-Graham V. Characterization of the Drosophila group ortholog to the amino-terminus of the alpha-thalassemia and mental retardation X-Linked (ATRX) vertebrate protein. PLoS One 2014; 9:e113182. [PMID: 25437195 PMCID: PMC4249797 DOI: 10.1371/journal.pone.0113182] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 10/21/2014] [Indexed: 12/11/2022] Open
Abstract
The human ATRX gene encodes hATRX, a chromatin-remodeling protein harboring an helicase/ATPase and ADD domains. The ADD domain has two zinc fingers that bind to histone tails and mediate hATRX binding to chromatin. dAtrx, the putative ATRX homolog in Drosophila melanogaster, has a conserved helicase/ATPase domain but lacks the ADD domain. A bioinformatic search of the Drosophila genome using the human ADD sequence allowed us to identify the CG8290 annotated gene, which encodes three ADD harboring- isoforms generated by alternative splicing. This Drosophila ADD domain is highly similar in structure and in the amino acids which mediate the histone tail contacts to the ADD domain of hATRX as shown by 3D modeling. Very recently the CG8290 annotated gene has been named dadd1. We show through pull-down and CoIP assays that the products of the dadd1 gene interact physically with dAtrxL and HP1a and all of them mainly co-localize in the chromocenter, although euchromatic localization can also be observed through the chromosome arms. We confirm through ChIP analyses that these proteins are present in vivo in the same heterochromatic regions. The three isoforms are expressed throughout development. Flies carrying transheterozygous combinations of the dadd1 and atrx alleles are semi-viable and have different phenotypes including the appearance of melanotic masses. Interestingly, the dAdd1-b and c isoforms have extra domains, such as MADF, which suggest newly acquired functions of these proteins. These results strongly support that, in Drosophila, the atrx gene diverged and that the dadd1-encoded proteins participate with dAtrx in some cellular functions such as heterochromatin maintenance.
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Affiliation(s)
- Brenda López-Falcón
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Silvia Meyer-Nava
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Benjamín Hernández-Rodríguez
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Adam Campos
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Daniel Montero
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Enrique Rudiño
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Martha Vázquez
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Mario Zurita
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
- * E-mail: (VVG); (MZ)
| | - Viviana Valadez-Graham
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
- * E-mail: (VVG); (MZ)
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20
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Tie F, Banerjee R, Saiakhova AR, Howard B, Monteith KE, Scacheri PC, Cosgrove MS, Harte PJ. Trithorax monomethylates histone H3K4 and interacts directly with CBP to promote H3K27 acetylation and antagonize Polycomb silencing. Development 2014; 141:1129-39. [PMID: 24550119 DOI: 10.1242/dev.102392] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Trithorax (TRX) antagonizes epigenetic silencing by Polycomb group (PcG) proteins, stimulates enhancer-dependent transcription, and establishes a 'cellular memory' of active transcription of PcG-regulated genes. The mechanisms underlying these TRX functions remain largely unknown, but are presumed to involve its histone H3K4 methyltransferase activity. We report that the SET domains of TRX and TRX-related (TRR) have robust histone H3K4 monomethyltransferase activity in vitro and that Tyr3701 of TRX and Tyr2404 of TRR prevent them from being trimethyltransferases. The trx(Z11) missense mutation (G3601S), which abolishes H3K4 methyltransferase activity in vitro, reduces the H3K4me1 but not the H3K4me3 level in vivo. trx(Z11) also suppresses the impaired silencing phenotypes of the Pc(3) mutant, suggesting that H3K4me1 is involved in antagonizing Polycomb silencing. Polycomb silencing is also antagonized by TRX-dependent H3K27 acetylation by CREB-binding protein (CBP). We show that perturbation of Polycomb silencing by TRX overexpression requires CBP. We also show that TRX and TRR are each physically associated with CBP in vivo, that TRX binds directly to the CBP KIX domain, and that the chromatin binding patterns of TRX and TRR are highly correlated with CBP and H3K4me1 genome-wide. In vitro acetylation of H3K27 by CBP is enhanced on K4me1-containing H3 substrates, and independently altering the H3K4me1 level in vivo, via the H3K4 demethylase LSD1, produces concordant changes in H3K27ac. These data indicate that the catalytic activities of TRX and CBP are physically coupled and suggest that both activities play roles in antagonizing Polycomb silencing, stimulating enhancer activity and cellular memory.
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Affiliation(s)
- Feng Tie
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
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21
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Herz HM, Garruss A, Shilatifard A. SET for life: biochemical activities and biological functions of SET domain-containing proteins. Trends Biochem Sci 2013; 38:621-39. [PMID: 24148750 DOI: 10.1016/j.tibs.2013.09.004] [Citation(s) in RCA: 219] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2013] [Revised: 09/06/2013] [Accepted: 09/12/2013] [Indexed: 01/23/2023]
Affiliation(s)
- Hans-Martin Herz
- Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA
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22
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The MLL3/MLL4 branches of the COMPASS family function as major histone H3K4 monomethylases at enhancers. Mol Cell Biol 2013; 33:4745-54. [PMID: 24081332 DOI: 10.1128/mcb.01181-13] [Citation(s) in RCA: 293] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Histone H3 lysine 4 (H3K4) can be mono-, di-, and trimethylated by members of the COMPASS (complex of proteins associated with Set1) family from Saccharomyces cerevisiae to humans, and these modifications can be found at distinct regions of the genome. Monomethylation of histone H3K4 (H3K4me1) is relatively more enriched at metazoan enhancer regions compared to trimethylated histone H3K4 (H3K4me3), which is enriched at transcription start sites in all eukaryotes. Our recent studies of Drosophila melanogaster demonstrated that the Trithorax-related (Trr) branch of the COMPASS family regulates enhancer activity and is responsible for the implementation of H3K4me1 at these regions. There are six COMPASS family members in mammals, two of which, MLL3 (GeneID 58508) and MLL4 (GeneID 8085), are most closely related to Drosophila Trr. Here, we use chromatin immunoprecipitation-sequencing (ChIP-seq) of this class of COMPASS family members in both human HCT116 cells and mouse embryonic stem cells and find that MLL4 is preferentially found at enhancer regions. MLL3 and MLL4 are frequently mutated in cancer, and indeed, the widely used HCT116 cancer cell line contains inactivating mutations in the MLL3 gene. Using HCT116 cells in which MLL4 has also been knocked out, we demonstrate that MLL3 and MLL4 are major regulators of H3K4me1 in these cells, with the greatest loss of monomethylation at enhancer regions. Moreover, we find a redundant role between Mll3 (GeneID 231051) and Mll4 (GeneID 381022) in enhancer H3K4 monomethylation in mouse embryonic fibroblast (MEF) cells. These findings suggest that mammalian MLL3 and MLL4 function in the regulation of enhancer activity and that mutations of MLL3 and MLL4 that are found in cancers could exert their properties through malfunction of these Trr/MLL3/MLL4-specific (Trrific) enhancers.
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The Drosophila COMPASS-like Cmi-Trr coactivator complex regulates dpp/BMP signaling in pattern formation. Dev Biol 2013; 380:185-98. [DOI: 10.1016/j.ydbio.2013.05.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Revised: 05/01/2013] [Accepted: 05/13/2013] [Indexed: 01/01/2023]
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24
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A remarkable career in science-Joseph G. Gall. Chromosome Res 2013; 21:339-43. [PMID: 23828690 DOI: 10.1007/s10577-013-9369-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Accepted: 06/10/2013] [Indexed: 10/26/2022]
Abstract
A festive group of ∼150 current and former students, postdoctoral and other associates, and colleagues gathered during the weekend of April 12-14, 2013 to celebrate Joe Gall's 85th birthday. The gathering, hosted by the Carnegie Institution for Science, Department of Embryology (Allan Spradling, Director) and organized by a group of Joe's current and former students (Zehra Nizami, Alison Singer, Ji-Long Liu, Virginia Zakian, Susan Gerbi), was held in Baltimore, MD. Dinners and symposia extending over 3 days celebrated Joe's scientific findings over the years, together with those of his former students, postdoctoral fellows, and other associates (see program at https://sites.google.com/site/gallsymposium2013/ ).
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The Drosophila ortholog of MLL3 and MLL4, trithorax related, functions as a negative regulator of tissue growth. Mol Cell Biol 2013; 33:1702-10. [PMID: 23459941 DOI: 10.1128/mcb.01585-12] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The human MLL genes (MLL1 to MLL4) and their Drosophila orthologs, trithorax (trx) and trithorax related (trr), encode proteins capable of methylating histone H3 on lysine 4. MLL1 and MLL2 are most similar to trx, while MLL3 and MLL4 are more closely related to trr. Several MLL genes are mutated in human cancers, but how these proteins regulate cell proliferation is not known. Here we show that trr mutant cells have a growth advantage over their wild-type neighbors and display changes in the levels of multiple proteins that regulate growth and cell division, including Notch, Capicua, and cyclin B. trr mutant clones display markedly reduced levels of H3K4 monomethylation without obvious changes in the levels of H3K4 di- and trimethylation. The trr mutant phenotype resembles that of Utx, which encodes a H3K27 demethylase, consistent with the observation that Trr and Utx are found in the same protein complex. In contrast to the overgrowth displayed by trr mutant tissue, trx clones are underrepresented, express low levels of the antiapoptotic protein Diap1, and exhibit only modest changes in global levels of H3K4 methylation. Thus, in Drosophila eye imaginal discs, Trr, likely functioning together with Utx, restricts tissue growth. In contrast, Trx appears to promote cell survival.
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Carbonell A, Mazo A, Serras F, Corominas M. Ash2 acts as an ecdysone receptor coactivator by stabilizing the histone methyltransferase Trr. Mol Biol Cell 2012. [PMID: 23197473 PMCID: PMC3565548 DOI: 10.1091/mbc.e12-04-0267] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The molting hormone ecdysone triggers chromatin changes via histone modifications that are important for gene regulation. On hormone activation, the ecdysone receptor (EcR) binds to the SET domain-containing histone H3 methyltransferase trithorax-related protein (Trr). Methylation of histone H3 at lysine 4 (H3K4me), which is associated with transcriptional activation, requires several cofactors, including Ash2. We find that ash2 mutants have severe defects in pupariation and metamorphosis due to a lack of activation of ecdysone-responsive genes. This transcriptional defect is caused by the absence of the H3K4me3 marks set by Trr in these genes. We present evidence that Ash2 interacts with Trr and is required for its stabilization. Thus we propose that Ash2 functions together with Trr as an ecdysone receptor coactivator.
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Affiliation(s)
- Albert Carbonell
- Departament de Genètica and Institut de Biomedicina, Universitat de Barcelona, 08028 Barcelona, Spain
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Herz HM, Mohan M, Garruss AS, Liang K, Takahashi YH, Mickey K, Voets O, Verrijzer CP, Shilatifard A. Enhancer-associated H3K4 monomethylation by Trithorax-related, the Drosophila homolog of mammalian Mll3/Mll4. Genes Dev 2012; 26:2604-20. [PMID: 23166019 DOI: 10.1101/gad.201327.112] [Citation(s) in RCA: 285] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Monomethylation of histone H3 on Lys 4 (H3K4me1) and acetylation of histone H3 on Lys 27 (H3K27ac) are histone modifications that are highly enriched over the body of actively transcribed genes and on enhancers. Although in yeast all H3K4 methylation patterns, including H3K4me1, are implemented by Set1/COMPASS (complex of proteins associated with Set1), there are three classes of COMPASS-like complexes in Drosophila that could carry out H3K4me1 on enhancers: dSet1, Trithorax, and Trithorax-related (Trr). Here, we report that Trr, the Drosophila homolog of the mammalian Mll3/4 COMPASS-like complexes, can function as a major H3K4 monomethyltransferase on enhancers in vivo. Loss of Trr results in a global decrease of H3K4me1 and H3K27ac levels in various tissues. Assays with the cut wing margin enhancer implied a functional role for Trr in enhancer-mediated processes. A genome-wide analysis demonstrated that Trr is required to maintain the H3K4me1 and H3K27ac chromatin signature that resembles the histone modification patterns described for enhancers. Furthermore, studies in the mammalian system suggested a role for the Trr homolog Mll3 in similar processes. Since Trr and mammalian Mll3/4 complexes are distinguished by bearing a unique subunit, the H3K27 demethylase UTX, we propose a model in which the H3K4 monomethyltransferases Trr/Mll3/Mll4 and the H3K27 demethylase UTX cooperate to regulate the transition from inactive/poised to active enhancers.
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Affiliation(s)
- Hans-Martin Herz
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
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