1
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Wu X, Wang S, Guo Y, Zeng S. Overexpression of KAT8 induces a failure in early embryonic development in mice. Theriogenology 2024; 221:31-37. [PMID: 38537319 DOI: 10.1016/j.theriogenology.2024.03.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 03/23/2024] [Accepted: 03/23/2024] [Indexed: 04/09/2024]
Abstract
Embryo quality is strongly associated with subsequent embryonic developmental efficiency. However, the detailed function of lysine acetyltransferase 8 (KAT8) during early embryonic development in mice remains elusive. In this study, we reported that KAT8 played a pivotal role in the first cleavage of mouse embryos. Immunostaining results revealed that KAT8 predominantly accumulated in the nucleus throughout the entire embryonic developmental process. Kat8 overexpression (Kat8-OE) was correlated with early developmental potential of embryos to the blastocyst stage. We also found that Kat8-OE embryos showed spindle-assembly defects and chromosomal misalignment, and that Kat8-OE in embryos led to increased levels of reactive oxygen species (ROS), accumulation of phosphorylated γH2AX by affecting the expression of critical genes related to mitochondrial respiratory chain and antioxidation pathways. Subsequently, cellular apoptosis was activated as confirmed by TUNEL (Terminal Deoxynucleotidyl Transferase mediated dUTP Nick-End Labeling) assay. Furthermore, we revealed that KAT8 was related to regulating the acetylation status of H4K16 in mouse embryos, and Kat8-OE induced the hyperacetylation of H4K16, which might be a key factor for the defective spindle/chromosome apparatus. Collectively, our data suggest that KAT8 constitutes an important regulator of spindle assembly and redox homeostasis during early embryonic development in mice.
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Affiliation(s)
- Xuan Wu
- State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Shiwei Wang
- State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yajun Guo
- State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Shenming Zeng
- State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China.
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2
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Zhao H, Lin Y, Lin E, Liu F, Shu L, Jing D, Wang B, Wang M, Shan F, Zhang L, Lam JC, Midla SC, Giardine BM, Keller CA, Hardison RC, Blobel GA, Zhang H. Genome folding principles uncovered in condensin-depleted mitotic chromosomes. Nat Genet 2024; 56:1213-1224. [PMID: 38802567 DOI: 10.1038/s41588-024-01759-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 04/18/2024] [Indexed: 05/29/2024]
Abstract
During mitosis, condensin activity is thought to interfere with interphase chromatin structures. To investigate genome folding principles in the absence of chromatin loop extrusion, we codepleted condensin I and condensin II, which triggered mitotic chromosome compartmentalization in ways similar to that in interphase. However, two distinct euchromatic compartments, indistinguishable in interphase, emerged upon condensin loss with different interaction preferences and dependencies on H3K27ac. Constitutive heterochromatin gradually self-aggregated and cocompartmentalized with facultative heterochromatin, contrasting with their separation during interphase. Notably, some cis-regulatory element contacts became apparent even in the absence of CTCF/cohesin-mediated structures. Heterochromatin protein 1 (HP1) proteins, which are thought to partition constitutive heterochromatin, were absent from mitotic chromosomes, suggesting, surprisingly, that constitutive heterochromatin can self-aggregate without HP1. Indeed, in cells traversing from M to G1 phase in the combined absence of HP1α, HP1β and HP1γ, constitutive heterochromatin compartments are normally re-established. In sum, condensin-deficient mitotic chromosomes illuminate forces of genome compartmentalization not identified in interphase cells.
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Affiliation(s)
- Han Zhao
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, China
| | - Yinzhi Lin
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, China
| | - En Lin
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, China
| | - Fuhai Liu
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, China
| | - Lirong Shu
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, China
| | - Dannan Jing
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, China
- Department of Biology, College of Science, Shantou University, Shantou, China
| | - Baiyue Wang
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, China
| | - Manzhu Wang
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, China
- School of Basic Medicine, Capital Medical University, Beijing, China
| | - Fengnian Shan
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, China
- School of Pharmacology, South China University of Technology, Guangzhou, China
| | - Lin Zhang
- School of Biological Science, Hongkong University, Hongkong, China
| | - Jessica C Lam
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Susannah C Midla
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Belinda M Giardine
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Cheryl A Keller
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Ross C Hardison
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Gerd A Blobel
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Haoyue Zhang
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, China.
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3
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MacDonald KM, Khan S, Lin B, Hurren R, Schimmer AD, Kislinger T, Harding SM. The proteomic landscape of genotoxic stress-induced micronuclei. Mol Cell 2024; 84:1377-1391.e6. [PMID: 38423013 DOI: 10.1016/j.molcel.2024.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 12/20/2023] [Accepted: 02/05/2024] [Indexed: 03/02/2024]
Abstract
Micronuclei (MN) are induced by various genotoxic stressors and amass nuclear- and cytoplasmic-resident proteins, priming the cell for MN-driven signaling cascades. Here, we measured the proteome of micronuclear, cytoplasmic, and nuclear fractions from human cells exposed to a panel of six genotoxins, comprehensively profiling their MN protein landscape. We find that MN assemble a proteome distinct from both surrounding cytoplasm and parental nuclei, depleted of spliceosome and DNA damage repair components while enriched for a subset of the replisome. We show that the depletion of splicing machinery within transcriptionally active MN contributes to intra-MN DNA damage, a known precursor to chromothripsis. The presence of transcription machinery in MN is stress-dependent, causing a contextual induction of MN DNA damage through spliceosome deficiency. This dataset represents a unique resource detailing the global proteome of MN, guiding mechanistic studies of MN generation and MN-associated outcomes of genotoxic stress.
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Affiliation(s)
- Kate M MacDonald
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Shahbaz Khan
- Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 2C4, Canada
| | - Brian Lin
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Rose Hurren
- Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 2C4, Canada
| | - Aaron D Schimmer
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada; Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 2C4, Canada
| | - Thomas Kislinger
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada; Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 2C4, Canada
| | - Shane M Harding
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada; Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 2C4, Canada; Department of Radiation Oncology and Immunology, University of Toronto, Toronto, ON M5T 1P5, Canada.
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4
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Espinosa-Martínez M, Alcázar-Fabra M, Landeira D. The molecular basis of cell memory in mammals: The epigenetic cycle. SCIENCE ADVANCES 2024; 10:eadl3188. [PMID: 38416817 PMCID: PMC10901381 DOI: 10.1126/sciadv.adl3188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 01/26/2024] [Indexed: 03/01/2024]
Abstract
Cell memory refers to the capacity of cells to maintain their gene expression program once the initiating environmental signal has ceased. This exceptional feature is key during the formation of mammalian organisms, and it is believed to be in part mediated by epigenetic factors that can endorse cells with the landmarks required to maintain transcriptional programs upon cell duplication. Here, we review current literature analyzing the molecular basis of epigenetic memory in mammals, with a focus on the mechanisms by which transcriptionally repressive chromatin modifications such as methylation of DNA and histone H3 are propagated through mitotic cell divisions. The emerging picture suggests that cellular memory is supported by an epigenetic cycle in which reversible activities carried out by epigenetic regulators in coordination with cell cycle transition create a multiphasic system that can accommodate both maintenance of cell identity and cell differentiation in proliferating stem cell populations.
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Affiliation(s)
- Mencía Espinosa-Martínez
- Centre for Genomics and Oncological Research (GENYO), Avenue de la Ilustración 114, 18016 Granada, Spain
- Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, Granada, Spain
- Instituto de Investigación Biosanitaria ibs.GRANADA, Granada, Spain
| | - María Alcázar-Fabra
- Centre for Genomics and Oncological Research (GENYO), Avenue de la Ilustración 114, 18016 Granada, Spain
- Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, Granada, Spain
- Instituto de Investigación Biosanitaria ibs.GRANADA, Granada, Spain
| | - David Landeira
- Centre for Genomics and Oncological Research (GENYO), Avenue de la Ilustración 114, 18016 Granada, Spain
- Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, Granada, Spain
- Instituto de Investigación Biosanitaria ibs.GRANADA, Granada, Spain
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5
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Contreras A, Perea-Resa C. Transcriptional repression across mitosis: mechanisms and functions. Biochem Soc Trans 2024; 52:455-464. [PMID: 38372373 PMCID: PMC10903446 DOI: 10.1042/bst20231071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 02/20/2024]
Abstract
Transcription represents a central aspect of gene expression with RNA polymerase machineries (RNA Pol) driving the synthesis of RNA from DNA template molecules. In eukaryotes, a total of three RNA Pol enzymes generate the plethora of RNA species and RNA Pol II is the one transcribing all protein-coding genes. A high number of cis- and trans-acting factors orchestrates RNA Pol II-mediated transcription by influencing the chromatin recruitment, activation, elongation, and/or termination steps. The levels of DNA accessibility, defining open-euchromatin versus close-heterochromatin, delimits RNA Pol II activity as well as the encounter with other factors acting on chromatin such as the DNA replication or DNA repair machineries. The stage of the cell cycle highly influences RNA Pol II activity with mitosis representing the major challenge. In fact, there is a massive inhibition of transcription during the mitotic entry coupled with chromatin dissociation of most of the components of the transcriptional machinery. Mitosis, as a consequence, highly compromises the transcriptional memory and the perpetuation of cellular identity. Once mitosis ends, transcription levels immediately recover to define the cell fate and to safeguard the proper progression of daughter cells through the cell cycle. In this review, we evaluate our current understanding of the transcriptional repression associated with mitosis with a special focus on the molecular mechanisms involved, on the potential function behind the general repression, and on the transmission of the transcriptional machinery into the daughter cells. We finally discuss the contribution that errors in the inheritance of the transcriptional machinery across mitosis might play in stem cell aging.
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Affiliation(s)
- A. Contreras
- Centro de Biología Molecular Severo Ochoa (CBMSO-CSIC), C/Nicolas Cabrera 1, 28049 Madrid, Spain
| | - C. Perea-Resa
- Centro de Biología Molecular Severo Ochoa (CBMSO-CSIC), C/Nicolas Cabrera 1, 28049 Madrid, Spain
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6
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Ramos-Alonso L, Chymkowitch P. Maintaining transcriptional homeostasis during cell cycle. Transcription 2024; 15:1-21. [PMID: 37655806 PMCID: PMC11093055 DOI: 10.1080/21541264.2023.2246868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/31/2023] [Accepted: 08/03/2023] [Indexed: 09/02/2023] Open
Abstract
The preservation of gene expression patterns that define cellular identity throughout the cell division cycle is essential to perpetuate cellular lineages. However, the progression of cells through different phases of the cell cycle severely disrupts chromatin accessibility, epigenetic marks, and the recruitment of transcriptional regulators. Notably, chromatin is transiently disassembled during S-phase and undergoes drastic condensation during mitosis, which is a significant challenge to the preservation of gene expression patterns between cell generations. This article delves into the specific gene expression and chromatin regulatory mechanisms that facilitate the preservation of transcriptional identity during replication and mitosis. Furthermore, we emphasize our recent findings revealing the unconventional role of yeast centromeres and mitotic chromosomes in maintaining transcriptional fidelity beyond mitosis.
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Affiliation(s)
- Lucía Ramos-Alonso
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
| | - Pierre Chymkowitch
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
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7
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Zhao H, Lin Y, Lin E, Liu F, Shu L, Jing D, Wang B, Wang M, Shan F, Zhang L, Lam JC, Midla SC, Giardine BM, Keller CA, Hardison RC, Blobel GA, Zhang H. Genome folding principles revealed in condensin-depleted mitotic chromosomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.09.566494. [PMID: 38014261 PMCID: PMC10680603 DOI: 10.1101/2023.11.09.566494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
During mitosis, condensin activity interferes with interphase chromatin structures. Here, we generated condensin-free mitotic chromosomes to investigate genome folding principles. Co-depletion of condensin I and II, but neither alone, triggered mitotic chromosome compartmentalization in ways that differ from interphase. Two distinct euchromatic compartments, indistinguishable in interphase, rapidly emerged upon condensin loss with different interaction preferences and dependence on H3K27ac. Constitutive heterochromatin gradually self-aggregated and co-compartmentalized with the facultative heterochromatin, contrasting with their separation during interphase. While topologically associating domains (TADs) and CTCF/cohesin mediated structural loops remained undetectable, cis-regulatory element contacts became apparent, providing an explanation for their quick re-establishment during mitotic exit. HP1 proteins, which are thought to partition constitutive heterochromatin, were absent from mitotic chromosomes, suggesting, surprisingly, that constitutive heterochromatin can self-aggregate without HP1. Indeed, in cells traversing from M- to G1-phase in the combined absence of HP1α, HP1β and HP1γ, re-established constitutive heterochromatin compartments normally. In sum, "clean-slate" condensing-deficient mitotic chromosomes illuminate mechanisms of genome compartmentalization not revealed in interphase cells.
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Affiliation(s)
- Han Zhao
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, Guangdong, China
| | - Yinzhi Lin
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, Guangdong, China
| | - En Lin
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, Guangdong, China
| | - Fuhai Liu
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, Guangdong, China
| | - Lirong Shu
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, Guangdong, China
| | - Dannan Jing
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, Guangdong, China
- Department of Biology, College of Science, Shantou University, Shantou, China
| | - Baiyue Wang
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, Guangdong, China
| | - Manzhu Wang
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, Guangdong, China
- School of Basic medicine, Capital Medical University, Beijing, China
| | - Fengnian Shan
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, Guangdong, China
- School of Pharmacology, South China University of Technology, Guangzhou, Guangdong, China
| | - Lin Zhang
- School of Biological Science, Hongkong University, Hongkong, China
| | - Jessica C. Lam
- Division of Hematology, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Susannah C. Midla
- Division of Hematology, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Belinda M. Giardine
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Cheryl A. Keller
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Ross C. Hardison
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Gerd A. Blobel
- Division of Hematology, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Haoyue Zhang
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, Guangdong, China
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8
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Harris RJ, Heer M, Levasseur MD, Cartwright TN, Weston B, Mitchell JL, Coxhead JM, Gaughan L, Prendergast L, Rico D, Higgins JMG. Release of Histone H3K4-reading transcription factors from chromosomes in mitosis is independent of adjacent H3 phosphorylation. Nat Commun 2023; 14:7243. [PMID: 37945563 PMCID: PMC10636195 DOI: 10.1038/s41467-023-43115-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 10/31/2023] [Indexed: 11/12/2023] Open
Abstract
Histone modifications influence the recruitment of reader proteins to chromosomes to regulate events including transcription and cell division. The idea of a histone code, where combinations of modifications specify unique downstream functions, is widely accepted and can be demonstrated in vitro. For example, on synthetic peptides, phosphorylation of Histone H3 at threonine-3 (H3T3ph) prevents the binding of reader proteins that recognize trimethylation of the adjacent lysine-4 (H3K4me3), including the TAF3 component of TFIID. To study these combinatorial effects in cells, we analyzed the genome-wide distribution of H3T3ph and H3K4me2/3 during mitosis. We find that H3T3ph anti-correlates with adjacent H3K4me2/3 in cells, and that the PHD domain of TAF3 can bind H3K4me2/3 in isolated mitotic chromatin despite the presence of H3T3ph. Unlike in vitro, H3K4 readers are still displaced from chromosomes in mitosis in Haspin-depleted cells lacking H3T3ph. H3T3ph is therefore unlikely to be responsible for transcriptional downregulation during cell division.
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Affiliation(s)
- Rebecca J Harris
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle Upon Tyne, NE2 1HH, UK
| | - Maninder Heer
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle Upon Tyne, NE2 1HH, UK
| | - Mark D Levasseur
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle Upon Tyne, NE2 1HH, UK
| | - Tyrell N Cartwright
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle Upon Tyne, NE2 1HH, UK
| | - Bethany Weston
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle Upon Tyne, NE2 1HH, UK
| | - Jennifer L Mitchell
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle Upon Tyne, NE2 1HH, UK
| | - Jonathan M Coxhead
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle Upon Tyne, NE2 1HH, UK
| | - Luke Gaughan
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle Upon Tyne, NE2 1HH, UK
- Newcastle University Centre for Cancer, Faculty of Medical Sciences, Framlington Place, Newcastle Upon Tyne, NE2 1HH, UK
| | - Lisa Prendergast
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle Upon Tyne, NE2 1HH, UK
| | - Daniel Rico
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle Upon Tyne, NE2 1HH, UK.
- Newcastle University Centre for Cancer, Faculty of Medical Sciences, Framlington Place, Newcastle Upon Tyne, NE2 1HH, UK.
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), CSIC-Universidad Sevilla-Universidad Pablo de Olavide-Junta de Andalucía, 41092, Seville, Spain.
| | - Jonathan M G Higgins
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle Upon Tyne, NE2 1HH, UK.
- Newcastle University Centre for Cancer, Faculty of Medical Sciences, Framlington Place, Newcastle Upon Tyne, NE2 1HH, UK.
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9
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Gökbuget D, Lenshoek K, Boileau RM, Bayerl J, Huang H, Wiita AP, Laird DJ, Blelloch R. Transcriptional repression upon S phase entry protects genome integrity in pluripotent cells. Nat Struct Mol Biol 2023; 30:1561-1570. [PMID: 37696959 DOI: 10.1038/s41594-023-01092-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 08/07/2023] [Indexed: 09/13/2023]
Abstract
Coincident transcription and DNA replication causes replication stress and genome instability. Rapidly dividing mouse pluripotent stem cells are highly transcriptionally active and experience elevated replication stress, yet paradoxically maintain genome integrity. Here, we study FOXD3, a transcriptional repressor enriched in pluripotent stem cells, and show that its repression of transcription upon S phase entry is critical to minimizing replication stress and preserving genome integrity. Acutely deleting Foxd3 leads to immediate replication stress, G2/M phase arrest, genome instability and p53-dependent apoptosis. FOXD3 binds near highly transcribed genes during S phase entry, and its loss increases the expression of these genes. Transient inhibition of RNA polymerase II in S phase reduces observed replication stress and cell cycle defects. Loss of FOXD3-interacting histone deacetylases induces replication stress, while transient inhibition of histone acetylation opposes it. These results show how a transcriptional repressor can play a central role in maintaining genome integrity through the transient inhibition of transcription during S phase, enabling faithful DNA replication.
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Affiliation(s)
- Deniz Gökbuget
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Kayla Lenshoek
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Ryan M Boileau
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Jonathan Bayerl
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA, USA
- Department of Obstetrics, Gynecology and Reproductive Science, University of California, San Francisco, San Francisco, CA, USA
| | - Hector Huang
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Arun P Wiita
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Diana J Laird
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA, USA
- Department of Obstetrics, Gynecology and Reproductive Science, University of California, San Francisco, San Francisco, CA, USA
| | - Robert Blelloch
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA, USA.
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA.
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.
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10
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Geng Q, Kong Y, Li W, Zhang J, Ma H, Zhang Y, Da L, Zhao Y, Du H. Dynamic Phosphorylation of G9a Regulates its Repressive Activity on Chromatin Accessibility and Mitotic Progression. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2303224. [PMID: 37661576 PMCID: PMC10602519 DOI: 10.1002/advs.202303224] [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: 05/18/2023] [Revised: 07/18/2023] [Indexed: 09/05/2023]
Abstract
Phosphorylation of Ser10 of histone H3 (H3S10p), together with the adjacent methylation of Lys9 (H3K9me), has been proposed to function as a 'phospho-methyl switch' to regulate mitotic chromatin architecture. Despite of immense understanding of the roles of H3S10 phosphorylation, how H3K9me2 are dynamically regulated during mitosis is poorly understood. Here, it is identified that Plk1 kinase phosphorylates the H3K9me1/2 methyltransferase G9a/EHMT2 at Thr1045 (pT1045) during early mitosis, which attenuates its catalytic activity toward H3K9me2. Cells bearing Thr1045 phosphomimic mutant of G9a (T1045E) show decreased H3K9me2 levels, increased chromatin accessibility, and delayed mitotic progression. By contrast, dephosphorylation of pT1045 during late mitosis by the protein phosphatase PPP2CB reactivates G9a activity and upregulates H3K9me2 levels, correlated with decreased levels of H3S10p. Therefore, the results provide a mechanistic explanation of the essential of a 'phospho-methyl switch' and highlight the importance of Plk1 and PPP2CB-mediated dynamic regulation of G9a activity in chromatin organization and mitotic progression.
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Affiliation(s)
- Qizhi Geng
- Hubei Key Laboratory of Cell HomeostasisCollege of Life SciencesHubei Clinical Research Center of Emergency and ResuscitationEmergency Center of Zhongnan Hospital of Wuhan UniversityFrontier Science Center for Immunology and MetabolismRNA InstituteWuhan UniversityWuhan430072China
| | - Yue‐Yu Kong
- Hubei Key Laboratory of Cell HomeostasisCollege of Life SciencesHubei Clinical Research Center of Emergency and ResuscitationEmergency Center of Zhongnan Hospital of Wuhan UniversityFrontier Science Center for Immunology and MetabolismRNA InstituteWuhan UniversityWuhan430072China
| | - Weizhe Li
- Hubei Key Laboratory of Cell HomeostasisCollege of Life SciencesHubei Clinical Research Center of Emergency and ResuscitationEmergency Center of Zhongnan Hospital of Wuhan UniversityFrontier Science Center for Immunology and MetabolismRNA InstituteWuhan UniversityWuhan430072China
| | - Jianhao Zhang
- School of Life Sciences and BiotechnologyShanghai JiaoTong UniversityShanghai200240China
| | - Haoli Ma
- Hubei Clinical Research Center of Emergency and ResuscitationEmergency Center of Zhongnan Hospital of Wuhan UniversityWuhan UniversityWuhan430071China
| | - Yuhang Zhang
- School of Life Sciences and BiotechnologyShanghai JiaoTong UniversityShanghai200240China
| | - Lin‐Tai Da
- Shanghai Center for Systems BiomedicineShanghai JiaoTong UniversityShanghai200240China
| | - Yan Zhao
- Hubei Clinical Research Center of Emergency and ResuscitationEmergency Center of Zhongnan Hospital of Wuhan UniversityWuhan UniversityWuhan430071China
| | - Hai‐Ning Du
- Hubei Key Laboratory of Cell HomeostasisCollege of Life SciencesHubei Clinical Research Center of Emergency and ResuscitationEmergency Center of Zhongnan Hospital of Wuhan UniversityFrontier Science Center for Immunology and MetabolismRNA InstituteWuhan UniversityWuhan430072China
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11
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Spicer MFD, Gerlich DW. The material properties of mitotic chromosomes. Curr Opin Struct Biol 2023; 81:102617. [PMID: 37279615 PMCID: PMC10448380 DOI: 10.1016/j.sbi.2023.102617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 03/28/2023] [Accepted: 05/04/2023] [Indexed: 06/08/2023]
Abstract
Chromosomes transform during the cell cycle, allowing transcription and replication during interphase and chromosome segregation during mitosis. Morphological changes are thought to be driven by the combined effects of DNA loop extrusion and a chromatin solubility phase transition. By extruding the chromatin fibre into loops, condensins enrich at an axial core and provide resistance to spindle pulling forces. Mitotic chromosomes are further compacted by deacetylation of histone tails, rendering chromatin insoluble and resistant to penetration by microtubules. Regulation of surface properties by Ki-67 allows independent chromosome movement in early mitosis and clustering during mitotic exit. Recent progress has provided insight into how the extraordinary material properties of chromatin emerge from these activities, and how these properties facilitate faithful chromosome segregation.
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Affiliation(s)
- Maximilian F D Spicer
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030, Vienna, Austria; Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, A-1030, Vienna, Austria. https://twitter.com/Spicer__Max
| | - Daniel W Gerlich
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030, Vienna, Austria.
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12
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Zhang H, Blobel GA. Genome folding dynamics during the M-to-G1-phase transition. Curr Opin Genet Dev 2023; 80:102036. [PMID: 37099832 PMCID: PMC10280458 DOI: 10.1016/j.gde.2023.102036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 02/24/2023] [Accepted: 02/28/2023] [Indexed: 04/28/2023]
Abstract
All measurable features of higher-order chromosomal architecture undergo drastic reorganization as cells enter and exit mitosis. During mitosis, gene transcription is temporarily halted, the nuclear envelope is dismantled, and chromosomes undergo condensation. At this time, chromatin compartments, topologically associating domains (TADs), and loops that connect enhancers with promoters as well as CTCF/cohesin loops are dissolved. Upon G1 entry, genome organization is rebuilt in the daughter nuclei to resemble that of the mother nucleus. We survey recent studies that traced these features in relation to gene expression during the mitosis-to-G1-phase transition at high temporal resolution. Dissection of fluctuating architectural features informed the hierarchical relationships of chromosomal organization, the mechanisms by which they are formed, and their mutual (in-) dependence. These studies highlight the importance of considering the cell cycle dynamics for studies of chromosomal organization.
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Affiliation(s)
- Haoyue Zhang
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, Guangdong, China.
| | - Gerd A Blobel
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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13
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Zhu Z, Chen X, Guo A, Manzano T, Walsh PJ, Wills KM, Halliburton R, Radko-Juettner S, Carter RD, Partridge JF, Green DR, Zhang J, Roberts CWM. Mitotic bookmarking by SWI/SNF subunits. Nature 2023; 618:180-187. [PMID: 37225980 PMCID: PMC10303083 DOI: 10.1038/s41586-023-06085-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 04/14/2023] [Indexed: 05/26/2023]
Abstract
For cells to initiate and sustain a differentiated state, it is necessary that a 'memory' of this state is transmitted through mitosis to the daughter cells1-3. Mammalian switch/sucrose non-fermentable (SWI/SNF) complexes (also known as Brg1/Brg-associated factors, or BAF) control cell identity by modulating chromatin architecture to regulate gene expression4-7, but whether they participate in cell fate memory is unclear. Here we provide evidence that subunits of SWI/SNF act as mitotic bookmarks to safeguard cell identity during cell division. The SWI/SNF core subunits SMARCE1 and SMARCB1 are displaced from enhancers but are bound to promoters during mitosis, and we show that this binding is required for appropriate reactivation of bound genes after mitotic exit. Ablation of SMARCE1 during a single mitosis in mouse embryonic stem cells is sufficient to disrupt gene expression, impair the occupancy of several established bookmarks at a subset of their targets and cause aberrant neural differentiation. Thus, SWI/SNF subunit SMARCE1 has a mitotic bookmarking role and is essential for heritable epigenetic fidelity during transcriptional reprogramming.
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Affiliation(s)
- Zhexin Zhu
- Division of Molecular Oncology, Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA.
| | - Xiaolong Chen
- Department of Computational Biology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Ao Guo
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Trishabelle Manzano
- Division of Molecular Oncology, Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Patrick J Walsh
- Division of Molecular Oncology, Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Kendall M Wills
- Division of Molecular Oncology, Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Rebecca Halliburton
- Division of Molecular Oncology, Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Sandi Radko-Juettner
- Division of Molecular Oncology, Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
- St Jude Graduate School of Biomedical Sciences, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Raymond D Carter
- Division of Molecular Oncology, Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Janet F Partridge
- Division of Molecular Oncology, Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Douglas R Green
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Jinghui Zhang
- Department of Computational Biology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Charles W M Roberts
- Division of Molecular Oncology, Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA.
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14
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Han Y, Haouel A, Georgii E, Priego-Cubero S, Wurm CJ, Hemmler D, Schmitt-Kopplin P, Becker C, Durner J, Lindermayr C. Histone Deacetylases HD2A and HD2B Undergo Feedback Regulation by ABA and Modulate Drought Tolerance via Mediating ABA-Induced Transcriptional Repression. Genes (Basel) 2023; 14:1199. [PMID: 37372378 DOI: 10.3390/genes14061199] [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: 04/24/2023] [Revised: 05/23/2023] [Accepted: 05/24/2023] [Indexed: 06/29/2023] Open
Abstract
Histone deacetylation catalyzed by histone deacetylase plays a critical role in gene silencing and subsequently controls many important biological processes. It was reported that the expression of the plant-specific histone deacetylase subfamily HD2s is repressed by ABA in Arabidopsis. However, little is known about the molecular relationship between HD2A/HD2B and ABA during the vegetative phase. Here, we describe that the hd2ahd2b mutant shows hypersensitivity to exogenous ABA during the germination and post-germination period. Additionally, transcriptome analyses revealed that the transcription of ABA-responsive genes was reprogrammed and the global H4K5ac level is specifically up-regulated in hd2ahd2b plants. ChIP-Seq and ChIP-qPCR results further verified that both HD2A and HD2B could directly and specifically bind to certain ABA-responsive genes. As a consequence, Arabidopsis hd2ahd2b plants displayed enhanced drought resistance in comparison to WT, which is consistent with increased ROS content, reduced stomatal aperture, and up-regulated drought-resistance-related genes. Moreover, HD2A and HD2B repressed ABA biosynthesis via the deacetylation of H4K5ac at NCED9. Taken together, our results indicate that HD2A and HD2B partly function through ABA signaling and act as negative regulators during the drought resistance response via the regulation of ABA biosynthesis and response genes.
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Affiliation(s)
- Yongtao Han
- Institute of Biochemical Plant Pathology, Helmholtz Munich, 85764 Oberschleißheim, Germany
| | - Amira Haouel
- Institute of Biochemical Plant Pathology, Helmholtz Munich, 85764 Oberschleißheim, Germany
| | - Elisabeth Georgii
- Institute of Biochemical Plant Pathology, Helmholtz Munich, 85764 Oberschleißheim, Germany
| | | | - Christoph J Wurm
- Institute of Biochemical Plant Pathology, Helmholtz Munich, 85764 Oberschleißheim, Germany
| | - Daniel Hemmler
- Research Unit Analytical Biogeochemistry, Helmholtz Munich, 85764 Oberschleißheim, Germany
| | | | - Claude Becker
- Genetics, LMU Biocenter, Ludwig-Maximilians-Universität München, 80539 München, Germany
| | - Jörg Durner
- Institute of Biochemical Plant Pathology, Helmholtz Munich, 85764 Oberschleißheim, Germany
- Chair of Biochemical Plant Pathology, Technische Universität München, 85354 Freising, Germany
| | - Christian Lindermayr
- Institute of Biochemical Plant Pathology, Helmholtz Munich, 85764 Oberschleißheim, Germany
- Institute of Lung Health and Immunity, Comprehensive Pneumology Center, Helmholtz Munich, 85764 Oberschleißheim, Germany
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15
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Djeghloul D, Dimond A, Cheriyamkunnel S, Kramer H, Patel B, Brown K, Montoya A, Whilding C, Wang YF, Futschik ME, Veland N, Montavon T, Jenuwein T, Merkenschlager M, Fisher AG. Loss of H3K9 trimethylation alters chromosome compaction and transcription factor retention during mitosis. Nat Struct Mol Biol 2023; 30:489-501. [PMID: 36941433 PMCID: PMC10113154 DOI: 10.1038/s41594-023-00943-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 02/13/2023] [Indexed: 03/23/2023]
Abstract
Recent studies have shown that repressive chromatin machinery, including DNA methyltransferases and polycomb repressor complexes, binds to chromosomes throughout mitosis and their depletion results in increased chromosome size. In the present study, we show that enzymes that catalyze H3K9 methylation, such as Suv39h1, Suv39h2, G9a and Glp, are also retained on mitotic chromosomes. Surprisingly, however, mutants lacking histone 3 lysine 9 trimethylation (H3K9me3) have unusually small and compact mitotic chromosomes associated with increased histone H3 phospho Ser10 (H3S10ph) and H3K27me3 levels. Chromosome size and centromere compaction in these mutants were rescued by providing exogenous first protein lysine methyltransferase Suv39h1 or inhibiting Ezh2 activity. Quantitative proteomic comparisons of native mitotic chromosomes isolated from wild-type versus Suv39h1/Suv39h2 double-null mouse embryonic stem cells revealed that H3K9me3 was essential for the efficient retention of bookmarking factors such as Esrrb. These results highlight an unexpected role for repressive heterochromatin domains in preserving transcription factor binding through mitosis and underscore the importance of H3K9me3 for sustaining chromosome architecture and epigenetic memory during cell division.
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Affiliation(s)
- Dounia Djeghloul
- Epigenetic Memory Group, MRC London Institute of Medical Sciences, Imperial College London, London, UK.
| | - Andrew Dimond
- Epigenetic Memory Group, MRC London Institute of Medical Sciences, Imperial College London, London, UK
| | - Sherry Cheriyamkunnel
- Epigenetic Memory Group, MRC London Institute of Medical Sciences, Imperial College London, London, UK
| | - Holger Kramer
- Biological Mass Spectrometry and Proteomics Facility, MRC London Institute of Medical Sciences, Imperial College London, London, UK
| | - Bhavik Patel
- Flow Cytometry Facility, MRC London Institute of Medical Sciences, Imperial College London, London, UK
| | - Karen Brown
- Epigenetic Memory Group, MRC London Institute of Medical Sciences, Imperial College London, London, UK
| | - Alex Montoya
- Biological Mass Spectrometry and Proteomics Facility, MRC London Institute of Medical Sciences, Imperial College London, London, UK
| | - Chad Whilding
- Microscopy Facility, MRC London Institute of Medical Sciences, Imperial College London, London, UK
| | - Yi-Fang Wang
- Bioinformatics, MRC London Institute of Medical Sciences, Imperial College London, London, UK
| | - Matthias E Futschik
- Bioinformatics, MRC London Institute of Medical Sciences, Imperial College London, London, UK
| | - Nicolas Veland
- Epigenetic Memory Group, MRC London Institute of Medical Sciences, Imperial College London, London, UK
| | - Thomas Montavon
- Max-Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Thomas Jenuwein
- Max-Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Matthias Merkenschlager
- Lymphocyte Development Group, MRC London Institute of Medical Sciences, Imperial College London, London, UK
| | - Amanda G Fisher
- Epigenetic Memory Group, MRC London Institute of Medical Sciences, Imperial College London, London, UK.
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16
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Ye B, Shen W, Li Y, Wang D, Zhang Y, Li P, Yin M, Wang Y, Xie D, Shi S, Yao T, Chen J, Xu P, Zhao Z. FAIRE-MS reveals mitotic retention of transcriptional regulators on a proteome-wide scale. FASEB J 2023; 37:e22724. [PMID: 36583687 DOI: 10.1096/fj.202201038rrr] [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: 06/29/2022] [Revised: 12/01/2022] [Accepted: 12/08/2022] [Indexed: 12/31/2022]
Abstract
Mitosis entails global and dramatic alterations, such as higher-order chromatin organization disruption, concomitant with global transcription downregulation. Cells reliably re-establishing gene expression patterns upon mitotic exit and maintaining cellular identities remain poorly understood. Previous studies indicated that certain transcription factors (TFs) remain associated with individual loci during mitosis and serve as mitotic bookmarkers. However, it is unclear which regulatory factors remain bound to the compacted mitotic chromosomes. We developed formaldehyde-assisted isolation of regulatory elements-coupled mass spectrometry (FAIRE-MS) that combines FAIRE-based open chromatin-associated protein pull-down and mass spectrometry (MS) to quantify the open chromatin-associated proteome during the interphase and mitosis. We identified 189 interphase and mitosis maintained (IM) regulatory factors using FAIRE-MS and found intrinsically disordered proteins and regions (IDP(R)s) are highly enriched, which plays a crucial role in liquid-liquid phase separation (LLPS) and chromatin organization during the cell cycle. Notably, in these IDP(R)s, we identified mitotic bookmarkers, such as CEBPB, HMGB1, and TFAP2A, and several factors, including MAX, HMGB3, hnRNP A2/B1, FUS, hnRNP D, and TIAL1, which are at least partially bound to the mitotic chromosome. Furthermore, it will be essential to study whether these IDP(R)s through LLPS helps cells transit from mitosis to the G1 phase during the cell cycle.
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Affiliation(s)
- Bingyu Ye
- Beijing Institute of Biotechnology, Beijing, China.,State Key Laboratory of Cell Differentiation and Regulation, College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Wenlong Shen
- Beijing Institute of Biotechnology, Beijing, China
| | - Yanchang Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Institute of Lifeomics, Beijing, China
| | - Dong Wang
- Beijing Institute of Biotechnology, Beijing, China
| | - Yan Zhang
- Beijing Institute of Biotechnology, Beijing, China
| | - Ping Li
- Beijing Institute of Biotechnology, Beijing, China
| | - Man Yin
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yahao Wang
- Beijing Institute of Biotechnology, Beijing, China
| | - Dejian Xie
- Beijing Institute of Biotechnology, Beijing, China
| | - Shu Shi
- Beijing Institute of Biotechnology, Beijing, China
| | - Tao Yao
- Beijing Institute of Biotechnology, Beijing, China
| | - Juncai Chen
- Beijing Institute of Biotechnology, Beijing, China
| | - Ping Xu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Institute of Lifeomics, Beijing, China
| | - Zhihu Zhao
- Beijing Institute of Biotechnology, Beijing, China
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17
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Alvarez V, Bandau S, Jiang H, Rios-Szwed D, Hukelmann J, Garcia-Wilson E, Wiechens N, Griesser E, Ten Have S, Owen-Hughes T, Lamond A, Alabert C. Proteomic profiling reveals distinct phases to the restoration of chromatin following DNA replication. Cell Rep 2023; 42:111996. [PMID: 36680776 DOI: 10.1016/j.celrep.2023.111996] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 08/12/2022] [Accepted: 01/03/2023] [Indexed: 01/21/2023] Open
Abstract
Chromatin organization must be maintained during cell proliferation to preserve cellular identity and genome integrity. However, DNA replication results in transient displacement of DNA-bound proteins, and it is unclear how they regain access to newly replicated DNA. Using quantitative proteomics coupled to Nascent Chromatin Capture or isolation of Proteins on Nascent DNA, we provide time-resolved binding kinetics for thousands of proteins behind replisomes within euchromatin and heterochromatin in human cells. This shows that most proteins regain access within minutes to newly replicated DNA. In contrast, 25% of the identified proteins do not, and this delay cannot be inferred from their known function or nuclear abundance. Instead, chromatin organization and G1 phase entry affect their reassociation. Finally, DNA replication not only disrupts but also promotes recruitment of transcription factors and chromatin remodelers, providing a significant advance in understanding how DNA replication could contribute to programmed changes of cell memory.
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Affiliation(s)
- Vanesa Alvarez
- Division of Molecular, Cell, and Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Susanne Bandau
- Division of Molecular, Cell, and Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Hao Jiang
- Laboratory of Quantitative Proteomics, Division of Molecular, Cell, and Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Diana Rios-Szwed
- Division of Molecular, Cell, and Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Jens Hukelmann
- Laboratory of Quantitative Proteomics, Division of Molecular, Cell, and Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Elisa Garcia-Wilson
- Division of Molecular, Cell, and Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Nicola Wiechens
- Laboratory of Chromatin Remodelling and Cancer Epigenetics, Division of Molecular, Cell & Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Eva Griesser
- Laboratory of Quantitative Proteomics, Division of Molecular, Cell, and Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Sara Ten Have
- Laboratory of Quantitative Proteomics, Division of Molecular, Cell, and Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Tom Owen-Hughes
- Laboratory of Chromatin Remodelling and Cancer Epigenetics, Division of Molecular, Cell & Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Angus Lamond
- Laboratory of Quantitative Proteomics, Division of Molecular, Cell, and Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Constance Alabert
- Division of Molecular, Cell, and Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK.
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18
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19
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Shen W, Zhang Y, Shi M, Ye B, Yin M, Li P, Shi S, Jin Y, Zhang Z, Zhang MQ, Chen Y, Zhao Z. Profiling and characterization of constitutive chromatin-enriched RNAs. iScience 2022; 25:105349. [DOI: 10.1016/j.isci.2022.105349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 08/29/2022] [Accepted: 10/11/2022] [Indexed: 10/31/2022] Open
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20
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Gandhi S, Mitterhoff R, Rapoport R, Farago M, Greenberg A, Hodge L, Eden S, Benner C, Goren A, Simon I. Mitotic H3K9ac is controlled by phase-specific activity of HDAC2, HDAC3, and SIRT1. Life Sci Alliance 2022; 5:5/10/e202201433. [PMID: 35981887 PMCID: PMC9389593 DOI: 10.26508/lsa.202201433] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 07/29/2022] [Accepted: 08/01/2022] [Indexed: 11/24/2022] Open
Abstract
Combination of immunofluorescence, Western blot, and ChIP-seq revealed the interplay between HDAC2, HDAC3, and SIRT1 in H3K9 deacetylation during mitosis of mammalian cells. Histone acetylation levels are reduced during mitosis. To study the mitotic regulation of H3K9ac, we used an array of inhibitors targeting specific histone deacetylases. We evaluated the involvement of the targeted enzymes in regulating H3K9ac during all mitotic stages by immunofluorescence and immunoblots. We identified HDAC2, HDAC3, and SIRT1 as modulators of H3K9ac mitotic levels. HDAC2 inhibition increased H3K9ac levels in prophase, whereas HDAC3 or SIRT1 inhibition increased H3K9ac levels in metaphase. Next, we performed ChIP-seq on mitotic-arrested cells following targeted inhibition of these histone deacetylases. We found that both HDAC2 and HDAC3 have a similar impact on H3K9ac, and inhibiting either of these two HDACs substantially increases the levels of this histone acetylation in promoters, enhancers, and insulators. Altogether, our results support a model in which H3K9 deacetylation is a stepwise process—at prophase, HDAC2 modulates most transcription-associated H3K9ac-marked loci, and at metaphase, HDAC3 maintains the reduced acetylation, whereas SIRT1 potentially regulates H3K9ac by impacting HAT activity.
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Affiliation(s)
- Shashi Gandhi
- Department of Microbiology and Molecular Genetics, Institute of Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University, Jerusalem, Israel
| | - Raizy Mitterhoff
- Department of Microbiology and Molecular Genetics, Institute of Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University, Jerusalem, Israel
| | - Rachel Rapoport
- Department of Microbiology and Molecular Genetics, Institute of Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University, Jerusalem, Israel
| | - Marganit Farago
- Department of Microbiology and Molecular Genetics, Institute of Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University, Jerusalem, Israel
| | - Avraham Greenberg
- Department of Microbiology and Molecular Genetics, Institute of Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University, Jerusalem, Israel
| | - Lauren Hodge
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Sharon Eden
- Department of Microbiology and Molecular Genetics, Institute of Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University, Jerusalem, Israel
| | - Christopher Benner
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Alon Goren
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Itamar Simon
- Department of Microbiology and Molecular Genetics, Institute of Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University, Jerusalem, Israel
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21
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Abstract
Virtually all cell types have the same DNA, yet each type exhibits its own cell-specific pattern of gene expression. During the brief period of mitosis, the chromosomes exhibit changes in protein composition and modifications, a marked condensation, and a consequent reduction in transcription. Yet as cells exit mitosis, they reactivate their cell-specific programs with high fidelity. Initially, the field focused on the subset of transcription factors that are selectively retained in, and hence bookmark, chromatin in mitosis. However, recent studies show that many transcription factors can be retained in mitotic chromatin and that, surprisingly, such retention can be due to nonspecific chromatin binding. Here, we review the latest studies focusing on low-level transcription via promoters, rather than enhancers, as contributing to mitotic memory, as well as new insights into chromosome structure dynamics, histone modifications, cell cycle signaling, and nuclear envelope proteins that together ensure the fidelity of gene expression through a round of mitosis.
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Affiliation(s)
- Kenji Ito
- Institute for Regenerative Medicine and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA;
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22
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A mitotic chromatin phase transition prevents perforation by microtubules. Nature 2022; 609:183-190. [PMID: 35922507 PMCID: PMC9433320 DOI: 10.1038/s41586-022-05027-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 06/27/2022] [Indexed: 12/20/2022]
Abstract
Dividing eukaryotic cells package extremely long chromosomal DNA molecules into discrete bodies to enable microtubule-mediated transport of one genome copy to each of the newly forming daughter cells1–3. Assembly of mitotic chromosomes involves DNA looping by condensin4–8 and chromatin compaction by global histone deacetylation9–13. Although condensin confers mechanical resistance to spindle pulling forces14–16, it is not known how histone deacetylation affects material properties and, as a consequence, segregation mechanics of mitotic chromosomes. Here we show how global histone deacetylation at the onset of mitosis induces a chromatin-intrinsic phase transition that endows chromosomes with the physical characteristics necessary for their precise movement during cell division. Deacetylation-mediated compaction of chromatin forms a structure dense in negative charge and allows mitotic chromosomes to resist perforation by microtubules as they are pushed to the metaphase plate. By contrast, hyperacetylated mitotic chromosomes lack a defined surface boundary, are frequently perforated by microtubules and are prone to missegregation. Our study highlights the different contributions of DNA loop formation and chromatin phase separation to genome segregation in dividing cells. Histone deacetylation at the onset of mitosis induces a chromatin-intrinsic phase transition that endows chromosomes with the physical characteristics necessary for their precise movement during cell division.
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23
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Flashner S, Swift M, Sowash A, Fahmy AN, Azizkhan-Clifford J. Transcription factor Sp1 regulates mitotic chromosome assembly and segregation. Chromosoma 2022; 131:175-191. [PMID: 35916925 PMCID: PMC9470683 DOI: 10.1007/s00412-022-00778-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 06/14/2022] [Accepted: 07/14/2022] [Indexed: 11/30/2022]
Abstract
Aneuploidy is a pervasive feature of cancer cells that results from chromosome missegregation. Several transcription factors have been associated with aneuploidy; however, no studies to date have demonstrated that mammalian transcription factors directly regulate chromosome segregation during mitosis. Here, we demonstrate that the ubiquitously expressed transcription factor specificity protein 1 (Sp1), which we have previously linked to aneuploidy, has a mitosis-specific role regulating chromosome segregation. We find that Sp1 localizes to mitotic centromeres and auxin-induced rapid Sp1 degradation at mitotic onset results in chromosome segregation errors and aberrant mitotic progression. Furthermore, rapid Sp1 degradation results in anomalous mitotic chromosome assembly characterized by loss of condensin complex I localization to mitotic chromosomes and chromosome condensation defects. Consistent with these defects, Sp1 degradation results in reduced chromosome passenger complex activity and histone H3 serine 10 phosphorylation during mitosis, which is essential for condensin complex I recruitment and chromosome condensation. Together, these data provide the first evidence of a mammalian transcription factor acting specifically during mitosis to regulate chromosome segregation.
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Affiliation(s)
- Samuel Flashner
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, 245 N 15th Street, MS 497, Philadelphia, PA, 19102, USA
| | - Michelle Swift
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, 245 N 15th Street, MS 497, Philadelphia, PA, 19102, USA
| | - Aislinn Sowash
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, 245 N 15th Street, MS 497, Philadelphia, PA, 19102, USA
| | - Alexander N Fahmy
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, 245 N 15th Street, MS 497, Philadelphia, PA, 19102, USA
| | - Jane Azizkhan-Clifford
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, 245 N 15th Street, MS 497, Philadelphia, PA, 19102, USA.
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24
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Sigismondo G, Papageorgiou DN, Krijgsveld J. Cracking chromatin with proteomics: From chromatome to histone modifications. Proteomics 2022; 22:e2100206. [PMID: 35633285 DOI: 10.1002/pmic.202100206] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 05/23/2022] [Accepted: 05/24/2022] [Indexed: 11/10/2022]
Abstract
Chromatin is the assembly of genomic DNA and proteins packaged in the nucleus of eukaryotic cells, which together are crucial in regulating a plethora of cellular processes. Histones may be the best known class of protein constituents in chromatin, which are decorated by a range of post-translational modifications to recruit accessory proteins and protein complexes to execute specific functions, ranging from DNA compaction, repair, transcription and duplication, all in a dynamic fashion and depending on the cellular state. The key role of chromatin in cellular fitness is emphasized by the deregulation of chromatin determinants predisposing to different diseases, including cancer. For this reason, deep investigation of chromatin composition is fundamental to better understand cellular physiology. Proteomic approaches have played a crucial role to understand critical aspects of this complex interplay, benefiting from the ability to identify and quantify proteins and their modifications in an unbiased manner. This review gives an overview of the proteomic approaches that have been developed by combining mass spectrometry-based with tailored biochemical and genetic methods to examine overall protein make-up of chromatin, to characterize chromatin domains, to determine protein interactions, and to decipher the broad spectrum of histone modifications that represent the quintessence of chromatin function. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Gianluca Sigismondo
- German Cancer Research Center (DKFZ), Division of Proteomics of Stem Cells and Cancer, Heidelberg, Germany
| | - Dimitris N Papageorgiou
- German Cancer Research Center (DKFZ), Division of Proteomics of Stem Cells and Cancer, Heidelberg, Germany.,Medical Faculty, Heidelberg University, Heidelberg, Germany
| | - Jeroen Krijgsveld
- German Cancer Research Center (DKFZ), Division of Proteomics of Stem Cells and Cancer, Heidelberg, Germany.,Medical Faculty, Heidelberg University, Heidelberg, Germany
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25
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Sister chromatid-sensitive Hi-C to map the conformation of replicated genomes. Nat Protoc 2022; 17:1486-1517. [PMID: 35478248 DOI: 10.1038/s41596-022-00687-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 01/19/2022] [Indexed: 12/23/2022]
Abstract
Chromosome conformation capture (Hi-C) techniques map the 3D organization of entire genomes. How sister chromatids fold in replicated chromosomes, however, cannot be determined with conventional Hi-C because of the identical DNA sequences of sister chromatids. Here, we present a protocol for sister chromatid-sensitive Hi-C (scsHi-C) that enables the distinction of DNA contacts within individual sister chromatids (cis sister contacts) from those between sister chromatids (trans sister contacts), thereby allowing investigation of the organization of replicated genomes. scsHi-C is based on live-cell labeling of nascent DNA by the synthetic nucleoside 4-thio-thymidine (4sT), which incorporates into a distinct DNA strand on each sister chromatid because of semi-conservative DNA replication. After purification of genomic DNA and in situ Hi-C library preparation, 4sT is chemically converted into 5-methyl-cytosine in the presence of OsO4/NH4Cl to introduce T-to-C signature point mutations on 4sT-labeled DNA. The Hi-C library is then sequenced, and ligated fragments are assigned to sister chromatids on the basis of strand orientation and the presence of signature mutations. The ensemble of scsHi-C contacts thereby represents genome-wide contact probabilities within and across sister chromatids. scsHi-C can be completed in 2 weeks, has been successfully applied in HeLa cells and can potentially be established for any cell type that allows proper cell cycle synchronization and incorporation of sufficient amounts of 4sT. The genome-wide maps of replicated chromosomes detected by scsHi-C enable investigation of the molecular mechanisms shaping sister chromatid topologies and the relevance of sister chromatid conformation in crucial processes like DNA repair, mitotic chromosome formation and potentially other biological processes.
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26
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de Lima MF, Lisboa MDO, Terceiro LEL, Rangel-Pozzo A, Mai S. Chromosome Territories in Hematological Malignancies. Cells 2022; 11:cells11081368. [PMID: 35456046 PMCID: PMC9028803 DOI: 10.3390/cells11081368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/12/2022] [Accepted: 04/15/2022] [Indexed: 11/21/2022] Open
Abstract
Chromosomes are organized in distinct nuclear areas designated as chromosome territories (CT). The structural formation of CT is a consequence of chromatin packaging and organization that ultimately affects cell function. Chromosome positioning can identify structural signatures of genomic organization, especially for diseases where changes in gene expression contribute to a given phenotype. The study of CT in hematological diseases revealed chromosome position as an important factor for specific chromosome translocations. In this review, we highlight the history of CT theory, current knowledge on possible clinical applications of CT analysis, and the impact of CT in the development of hematological neoplasia such as multiple myeloma, leukemia, and lymphomas. Accumulating data on nuclear architecture in cancer allow one to propose the three-dimensional nuclear genomic landscape as a novel cancer biomarker for the future.
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Affiliation(s)
- Matheus Fabiao de Lima
- Department of Physiology and Pathophysiology, CancerCare Manitoba Research Institute, University of Manitoba, Winnipeg, MB R3E 0V9, Canada;
| | - Mateus de Oliveira Lisboa
- Core for Cell Technology, School of Medicine, Pontifícia Universidade Católica do Paraná—PUCPR, Curitiba 80215-901, Brazil;
| | - Lucas E. L. Terceiro
- Department of Pathology, Max Rady College of Medicine, University of Manitoba, Winnipeg, MB R3E 3P5, Canada;
| | - Aline Rangel-Pozzo
- Department of Physiology and Pathophysiology, CancerCare Manitoba Research Institute, University of Manitoba, Winnipeg, MB R3E 0V9, Canada;
- Correspondence: (A.R.-P.); (S.M.); Tel.: +1-204-787-2135 (S.M.)
| | - Sabine Mai
- Department of Physiology and Pathophysiology, CancerCare Manitoba Research Institute, University of Manitoba, Winnipeg, MB R3E 0V9, Canada;
- Correspondence: (A.R.-P.); (S.M.); Tel.: +1-204-787-2135 (S.M.)
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27
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SETDB1-like MET-2 promotes transcriptional silencing and development independently of its H3K9me-associated catalytic activity. Nat Struct Mol Biol 2022; 29:85-96. [PMID: 35102319 PMCID: PMC8850192 DOI: 10.1038/s41594-021-00712-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 12/02/2021] [Indexed: 12/30/2022]
Abstract
Transcriptionally silenced heterochromatin bearing methylation of histone H3 on lysine 9 (H3K9me) is critical for maintaining organismal viability and tissue integrity. Here we show that in addition to ensuring H3K9me, MET-2, the Caenorhabditis elegans homolog of the SETDB1 histone methyltransferase, has a noncatalytic function that contributes to gene repression. Subnuclear foci of MET-2 coincide with H3K9me deposition, yet these foci also form when MET-2 is catalytically deficient and H3K9me is compromised. Whereas met-2 deletion triggers a loss of silencing and increased histone acetylation, foci of catalytically deficient MET-2 maintain silencing of a subset of genes, blocking acetylation on H3K9 and H3K27. In normal development, this noncatalytic MET-2 activity helps to maintain fertility. Under heat stress MET-2 foci disperse, coinciding with increased acetylation and transcriptional derepression. Our study suggests that the noncatalytic, focus-forming function of this SETDB1-like protein and its intrinsically disordered cofactor LIN-65 is physiologically relevant. Genetic and genome-wide analysis of a catalytically deficient SETDB1-like enzyme, MET-2, in Caenorhabditiselegans reveals that MET-2 promotes transcriptional silencing and fertility through both H3K9 methylation and focus formation, which blocks histone acetylation.
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28
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Shvedunova M, Akhtar A. Modulation of cellular processes by histone and non-histone protein acetylation. Nat Rev Mol Cell Biol 2022; 23:329-349. [PMID: 35042977 DOI: 10.1038/s41580-021-00441-y] [Citation(s) in RCA: 267] [Impact Index Per Article: 133.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/25/2021] [Indexed: 12/12/2022]
Abstract
Lysine acetylation is a widespread and versatile protein post-translational modification. Lysine acetyltransferases and lysine deacetylases catalyse the addition or removal, respectively, of acetyl groups at both histone and non-histone targets. In this Review, we discuss several features of acetylation and deacetylation, including their diversity of targets, rapid turnover, exquisite sensitivity to the concentrations of the cofactors acetyl-CoA, acyl-CoA and NAD+, and tight interplay with metabolism. Histone acetylation and non-histone protein acetylation influence a myriad of cellular and physiological processes, including transcription, phase separation, autophagy, mitosis, differentiation and neural function. The activity of lysine acetyltransferases and lysine deacetylases can, in turn, be regulated by metabolic states, diet and specific small molecules. Histone acetylation has also recently been shown to mediate cellular memory. These features enable acetylation to integrate the cellular state with transcriptional output and cell-fate decisions.
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Affiliation(s)
- Maria Shvedunova
- Department of Chromatin Regulation, Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
| | - Asifa Akhtar
- Department of Chromatin Regulation, Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany.
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29
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Rafiee MR, Zagalak JA, Sidorov S, Steinhauser S, Davey K, Ule J, Luscombe NM. Chromatin-contact atlas reveals disorder-mediated protein interactions and moonlighting chromatin-associated RBPs. Nucleic Acids Res 2021; 49:13092-13107. [PMID: 34871434 PMCID: PMC8682780 DOI: 10.1093/nar/gkab1180] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 11/05/2021] [Accepted: 11/12/2021] [Indexed: 11/13/2022] Open
Abstract
RNA-binding proteins (RBPs) play diverse roles in regulating co-transcriptional RNA-processing and chromatin functions, but our knowledge of the repertoire of chromatin-associated RBPs (caRBPs) and their interactions with chromatin remains limited. Here, we developed SPACE (Silica Particle Assisted Chromatin Enrichment) to isolate global and regional chromatin components with high specificity and sensitivity, and SPACEmap to identify the chromatin-contact regions in proteins. Applied to mouse embryonic stem cells, SPACE identified 1459 chromatin-associated proteins, ∼48% of which are annotated as RBPs, indicating their dual roles in chromatin and RNA-binding. Additionally, SPACEmap stringently verified chromatin-binding of 403 RBPs and identified their chromatin-contact regions. Notably, SPACEmap showed that about 40% of the caRBPs bind chromatin by intrinsically disordered regions (IDRs). Studying SPACE and total proteome dynamics from mES cells grown in 2iL and serum medium indicates significant correlation (R = 0.62). One of the most dynamic caRBPs is Dazl, which we find co-localized with PRC2 at transcription start sites of genes that are distinct from Dazl mRNA binding. Dazl and other PRC2-colocalised caRBPs are rich in intrinsically disordered regions (IDRs), which could contribute to the formation and regulation of phase-separated PRC condensates. Together, our approach provides an unprecedented insight into IDR-mediated interactions and caRBPs with moonlighting functions in native chromatin.
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Affiliation(s)
| | - Julian A Zagalak
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.,Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | | | | | - Karen Davey
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Jernej Ule
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.,Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, UK.,National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia
| | - Nicholas M Luscombe
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.,Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, UK.,UCL Genetics Institute, University College London, Gower Street, London WC1E 6BT, UK.,Okinawa Institute of Science & Technology Graduate University, Okinawa 904-0495, Japan
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30
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Gupta R, Jha A, Ambasta RK, Kumar P. Regulatory mechanism of cyclins and cyclin-dependent kinases in post-mitotic neuronal cell division. Life Sci 2021; 285:120006. [PMID: 34606852 DOI: 10.1016/j.lfs.2021.120006] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 09/24/2021] [Accepted: 09/25/2021] [Indexed: 12/18/2022]
Abstract
Neurodegenerative diseases (NDDs) are the most common life-threatening disease of the central nervous system and it cause the progressive loss of neuronal cells. The exact mechanism of the disease's progression is not clear and thus line of treatment for NDDs is a baffling issue. During the progression of NDDs, oxidative stress and DNA damage play an important regulatory function, and ultimately induces neurodegeneration. Recently, aberrant cell cycle events have been demonstrated in the progression of different NDDs. However, the pertinent role of signaling mechanism, for instance, post-translational modifications, oxidative stress, DNA damage response pathway, JNK/p38 MAPK, MEK/ERK cascade, actively participated in the aberrant cell cycle reentry induced neuronal cell death. Mounting evidence has demonstrated that aberrant cell cycle re-entry is a major contributing factor in the pathogenesis of NDDs rather than a secondary phenomenon. In the brain of AD patients with mild cognitive impairment, post miotic cell division can be seen in the early stage of the disease. However, in the brain of PD patients, response to various neurotoxic signals, the cell cycle re-entry has been observed that causes neuronal apoptosis. On contrary, the contributing factors that leads to the induction of cell cycle events in mature neurons in HD and ALS brain pathology is remain unclear. Various pharmacological drugs have been developed to reduce the pathogenesis of NDDs, but they are still not helpful in eliminating the cause of these NDDs.
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Affiliation(s)
- Rohan Gupta
- Molecular Neuroscience and Functional Genomics Laboratory, Delhi Technological University (Formerly Delhi College of Engineering), India
| | - Ankita Jha
- Molecular Neuroscience and Functional Genomics Laboratory, Delhi Technological University (Formerly Delhi College of Engineering), India
| | - Rashmi K Ambasta
- Molecular Neuroscience and Functional Genomics Laboratory, Delhi Technological University (Formerly Delhi College of Engineering), India
| | - Pravir Kumar
- Molecular Neuroscience and Functional Genomics Laboratory, Delhi Technological University (Formerly Delhi College of Engineering), India.
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31
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Hurst V, Challa K, Jonas F, Forey R, Sack R, Seebacher J, Schmid CD, Barkai N, Shimada K, Gasser SM, Poli J. A regulatory phosphorylation site on Mec1 controls chromatin occupancy of RNA polymerases during replication stress. EMBO J 2021; 40:e108439. [PMID: 34569643 PMCID: PMC8561635 DOI: 10.15252/embj.2021108439] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 09/08/2021] [Accepted: 09/10/2021] [Indexed: 01/16/2023] Open
Abstract
Upon replication stress, budding yeast checkpoint kinase Mec1ATR triggers the downregulation of transcription, thereby reducing the level of RNA polymerase (RNAP) on chromatin to facilitate replication fork progression. Here, we identify a hydroxyurea-induced phosphorylation site on Mec1, Mec1-S1991, that contributes to the eviction of RNAPII and RNAPIII during replication stress. The expression of the non-phosphorylatable mec1-S1991A mutant reduces replication fork progression genome-wide and compromises survival on hydroxyurea. This defect can be suppressed by destabilizing chromatin-bound RNAPII through a TAP fusion to its Rpb3 subunit, suggesting that lethality in mec1-S1991A mutants arises from replication-transcription conflicts. Coincident with a failure to repress gene expression on hydroxyurea in mec1-S1991A cells, highly transcribed genes such as GAL1 remain bound at nuclear pores. Consistently, we find that nuclear pore proteins and factors controlling RNAPII and RNAPIII are phosphorylated in a Mec1-dependent manner on hydroxyurea. Moreover, we show that Mec1 kinase also contributes to reduced RNAPII occupancy on chromatin during an unperturbed S phase by promoting degradation of the Rpb1 subunit.
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Affiliation(s)
- Verena Hurst
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,Faculty of Natural Sciences, University of Basel, Basel, Switzerland
| | - Kiran Challa
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Felix Jonas
- Departments of Molecular Genetics and Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel
| | - Romain Forey
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Equipe labélisée Ligue contre le Cancer, Montpellier, France
| | - Ragna Sack
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Jan Seebacher
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Christoph D Schmid
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Naama Barkai
- Departments of Molecular Genetics and Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel
| | - Kenji Shimada
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Susan M Gasser
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,Faculty of Natural Sciences, University of Basel, Basel, Switzerland
| | - Jérôme Poli
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,Institut de Génétique Humaine, CNRS, Université de Montpellier, Equipe labélisée Ligue contre le Cancer, Montpellier, France
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32
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Sarnataro S, Riba A, Molina N. Regulation of transcription reactivation dynamics exiting mitosis. PLoS Comput Biol 2021; 17:e1009354. [PMID: 34606497 PMCID: PMC8516288 DOI: 10.1371/journal.pcbi.1009354] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 10/14/2021] [Accepted: 08/17/2021] [Indexed: 11/23/2022] Open
Abstract
Proliferating cells experience a global reduction of transcription during mitosis, yet their cell identity is maintained and regulatory information is propagated from mother to daughter cells. Mitotic bookmarking by transcription factors has been proposed as a potential mechanism to ensure the reactivation of transcription at the proper set of genes exiting mitosis. Recently, mitotic transcription and waves of transcription reactivation have been observed in synchronized populations of human hepatoma cells. However, the study did not consider that mitotic-arrested cell populations progressively desynchronize leading to measurements of gene expression on a mixture of cells at different internal cell-cycle times. Moreover, it is not well understood yet what is the precise role of mitotic bookmarking on mitotic transcription as well as on the transcription reactivation waves. Ultimately, the core gene regulatory network driving the precise transcription reactivation dynamics remains to be identified. To address these questions, we developed a mathematical model to correct for the progressive desynchronization of cells and estimate gene expression dynamics with respect to a cell-cycle pseudotime. Furthermore, we used a multiple linear regression model to infer transcription factor activity dynamics. Our analysis allows us to characterize waves of transcription factor activities exiting mitosis and predict a core gene regulatory network responsible of the transcription reactivation dynamics. Moreover, we identified more than 60 transcription factors that are highly active during mitosis and represent new candidates of mitotic bookmarking factors which could be relevant therapeutic targets to control cell proliferation. Specific gene expression patterns confer particular identities to cells. During proliferation, cells undergo mitosis when chromosomes are formed and segregated into two new cells leading to a global downregulation of gene expression. Yet, cell identity is propagated from mother to daughter cells by the reactivation of gene expression at the appropriate set of genes once mitosis is completed. Mitotic bookmarking has been proposed as a mechanism to regulate this process. Indeed certain regulatory factors tag genes during mitosis to promote gene reactivation in the next cycle. Here we analyze gene expression over time measured on synchronized cell populations by using a new generation sequencing technique. To do so, we proposed a mathematical model to obtain the exact gene expression dynamics with respect to the cell-cycle progression and identified waves of genes reactivation during mitosis and the transition to the next cycle. Also, we developed a computational method that allowed us to predict key regulatory factors that drive this process and predict new candidates that could be involved in mitotic bookmarking. These regulatory factors could be relevant therapeutic targets to control cell proliferation.
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Affiliation(s)
- Sergio Sarnataro
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC) Université de Strasbourg – CNRS – INSERM, Illkirch, France
| | - Andrea Riba
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC) Université de Strasbourg – CNRS – INSERM, Illkirch, France
| | - Nacho Molina
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC) Université de Strasbourg – CNRS – INSERM, Illkirch, France
- * E-mail:
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33
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Lan HC, Du TH, Yao YL, Yang WM. Ocular disease-associated mutations diminish the mitotic chromosome retention ability of PAX6. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2021; 1864:194751. [PMID: 34500082 DOI: 10.1016/j.bbagrm.2021.194751] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 08/25/2021] [Accepted: 08/25/2021] [Indexed: 10/20/2022]
Abstract
Transcription factors play a key role in maintaining cell identity. One mechanism of such cell memory after multiple rounds of cell division cycles is through persistent mitotic chromosome binding, although how individual transcription factors achieve mitotic chromosome retention is not completely understood. Here we show that PAX6, a lineage-determining transcription factor, coats mitotic chromosomes. Using deletion and point mutants associated with human ocular diseases in live-cell imaging analysis, we identified two regions, MCR-D1 and MCR-D2, that were responsible for mitotic chromosome retention of PAX6. We also identified three nuclear localization signals (NLSs) that contributed to mitotic chromosome retention independent of their nuclear import functions. Full mitotic chromosome retention required the presence of DNA-binding domains as well as NLSs within MCR-Ds. Furthermore, disease-associated mutations and NLS mutations changed the distribution of intrinsically disordered regions (IDRs) in PAX6. Our findings not only identify PAX6 as a novel mitotic chromosome retention factor but also demonstrate that the mechanism of mitotic chromosome retention involves sequence-specific DNA binding, NLSs, and molecular conformation determined by IDRs. These findings link mitotic chromosome retention with PAX6-related pathogenesis and imply similar mechanisms for other lineage-determining factors in the PAX family.
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Affiliation(s)
- Hsin-Chi Lan
- Institute of Molecular Biology, National Chung Hsing University, Taichung 40227, Taiwan
| | - Ting-Huei Du
- Institute of Molecular Biology, National Chung Hsing University, Taichung 40227, Taiwan
| | - Ya-Li Yao
- Department of Medical Laboratory Science and Biotechnology, Asia University, Taichung 41354, Taiwan.
| | - Wen-Ming Yang
- Institute of Molecular Biology, National Chung Hsing University, Taichung 40227, Taiwan; Ph.D. Program in Translational Medicine, National Chung Hsing University, Taichung 40227, Taiwan.
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34
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CTCF and transcription influence chromatin structure re-configuration after mitosis. Nat Commun 2021; 12:5157. [PMID: 34453048 PMCID: PMC8397779 DOI: 10.1038/s41467-021-25418-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 08/06/2021] [Indexed: 02/02/2023] Open
Abstract
During mitosis, transcription is globally attenuated and chromatin architecture is dramatically reconfigured. We exploited the M- to G1-phase progression to interrogate the contributions of the architectural factor CTCF and the process of transcription to genome re-sculpting in newborn nuclei. Depletion of CTCF during the M- to G1-phase transition alters short-range compartmentalization after mitosis. Chromatin domain boundary re-formation is impaired upon CTCF loss, but a subset of boundaries, characterized by transitions in chromatin states, is established normally. Without CTCF, structural loops fail to form, leading to illegitimate contacts between cis-regulatory elements (CREs). Transient CRE contacts that are normally resolved after telophase persist deeply into G1-phase in CTCF-depleted cells. CTCF loss-associated gains in transcription are often linked to increased, normally illegitimate enhancer-promoter contacts. In contrast, at genes whose expression declines upon CTCF loss, CTCF seems to function as a conventional transcription activator, independent of its architectural role. CTCF-anchored structural loops facilitate formation of CRE loops nested within them, especially those involving weak CREs. Transcription inhibition does not significantly affect global architecture or transcription start site-associated boundaries. However, ongoing transcription contributes considerably to the formation of gene domains, regions of enriched contacts along gene bodies. Notably, gene domains emerge in ana/telophase prior to completion of the first round of transcription, suggesting that epigenetic features in gene bodies contribute to genome reconfiguration prior to transcription. The focus on the de novo formation of nuclear architecture during G1 entry yields insights into the contributions of CTCF and transcription to chromatin architecture dynamics during the mitosis to G1-phase progression.
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35
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Perutka Z, Kaduchová K, Chamrád I, Beinhauer J, Lenobel R, Petrovská B, Bergougnoux V, Vrána J, Pecinka A, Doležel J, Šebela M. Proteome Analysis of Condensed Barley Mitotic Chromosomes. FRONTIERS IN PLANT SCIENCE 2021; 12:723674. [PMID: 34497629 PMCID: PMC8419432 DOI: 10.3389/fpls.2021.723674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 07/21/2021] [Indexed: 06/13/2023]
Abstract
Proteins play a major role in the three-dimensional organization of nuclear genome and its function. While histones arrange DNA into a nucleosome fiber, other proteins contribute to higher-order chromatin structures in interphase nuclei, and mitotic/meiotic chromosomes. Despite the key role of proteins in maintaining genome integrity and transferring hereditary information to daughter cells and progenies, the knowledge about their function remains fragmentary. This is particularly true for the proteins of condensed chromosomes and, in particular, chromosomes of plants. Here, we purified barley mitotic metaphase chromosomes by a flow cytometric sorting and characterized their proteins. Peptides from tryptic protein digests were fractionated either on a cation exchanger or reversed-phase microgradient system before liquid chromatography coupled to tandem mass spectrometry. Chromosomal proteins comprising almost 900 identifications were classified based on a combination of software prediction, available database localization information, sequence homology, and domain representation. A biological context evaluation indicated the presence of several groups of abundant proteins including histones, topoisomerase 2, POLYMERASE 2, condensin subunits, and many proteins with chromatin-related functions. Proteins involved in processes related to DNA replication, transcription, and repair as well as nucleolar proteins were found. We have experimentally validated the presence of FIBRILLARIN 1, one of the nucleolar proteins, on metaphase chromosomes, suggesting that plant chromosomes are coated with proteins during mitosis, similar to those of human and animals. These results improve significantly the knowledge of plant chromosomal proteins and provide a basis for their functional characterization and comparative phylogenetic analyses.
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Affiliation(s)
- Zdeněk Perutka
- Department of Protein Biochemistry and Proteomics, Faculty of Science, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University Olomouc, Olomouc, Czechia
| | - Kateřina Kaduchová
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
| | - Ivo Chamrád
- Department of Protein Biochemistry and Proteomics, Faculty of Science, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University Olomouc, Olomouc, Czechia
| | - Jana Beinhauer
- Department of Protein Biochemistry and Proteomics, Faculty of Science, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University Olomouc, Olomouc, Czechia
| | - René Lenobel
- Department of Protein Biochemistry and Proteomics, Faculty of Science, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University Olomouc, Olomouc, Czechia
| | - Beáta Petrovská
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
| | - Véronique Bergougnoux
- Department of Molecular Biology, Faculty of Science, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University Olomouc, Olomouc, Czechia
| | - Jan Vrána
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
| | - Ales Pecinka
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
| | - Jaroslav Doležel
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
| | - Marek Šebela
- Department of Protein Biochemistry and Proteomics, Faculty of Science, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University Olomouc, Olomouc, Czechia
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36
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Shi M, You K, Chen T, Hou C, Liang Z, Liu M, Wang J, Wei T, Qin J, Chen Y, Zhang MQ, Li T. Quantifying the phase separation property of chromatin-associated proteins under physiological conditions using an anti-1,6-hexanediol index. Genome Biol 2021; 22:229. [PMID: 34404448 PMCID: PMC8369651 DOI: 10.1186/s13059-021-02456-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 07/30/2021] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Liquid-liquid phase separation (LLPS) is an important organizing principle for biomolecular condensation and chromosome compartmentalization. However, while many proteins have been reported to undergo LLPS, quantitative and global analysis of chromatin LLPS property remains absent. RESULTS Here, by combining chromatin-associated protein pull-down, quantitative proteomics and 1,6-hexanediol (1,6-HD) treatment, we develop Hi-MS and define an anti-1,6-HD index of chromatin-associated proteins (AICAP) to quantify 1,6-HD sensitivity of chromatin-associated proteins under physiological conditions. Compared with known physicochemical properties involved in phase separation, we find that proteins with lower AICAP are associated with higher content of disordered regions, higher hydrophobic residue preference, higher mobility and higher predicted LLPS potential. We also construct BL-Hi-C libraries following 1,6-HD treatment to study the sensitivity of chromatin conformation to 1,6-HD treatment. We find that the active chromatin and high-order structures, as well as the proteins enriched in corresponding regions, are more sensitive to 1,6-HD treatment. CONCLUSIONS Our work provides a global quantitative measurement of LLPS properties of chromatin-associated proteins and higher-order chromatin structure. Hi-MS and AICAP data provide an experimental tool and quantitative resources valuable for future studies of biomolecular condensates.
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Affiliation(s)
- Minglei Shi
- MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic & Systems Biology, BNRist, School of Medicine, Tsinghua University, Beijing, 100084, China.
| | - Kaiqiang You
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Taoyu Chen
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Chao Hou
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Zhengyu Liang
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California, La Jolla, San Diego, CA, 92093, USA
| | - Mingwei Liu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Jifeng Wang
- Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Taotao Wei
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jun Qin
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Yang Chen
- MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic & Systems Biology, BNRist, School of Medicine, Tsinghua University, Beijing, 100084, China.
- The State Key Laboratory of Medical Molecular Biology, Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China.
| | - Michael Q Zhang
- MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic & Systems Biology, BNRist, School of Medicine, Tsinghua University, Beijing, 100084, China.
- Department of Biological Sciences, Center for Systems Biology, The University of Texas, Richardson, TX, 75080-3021, USA.
| | - Tingting Li
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China.
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37
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van Mierlo G, Vermeulen M. Chromatin Proteomics to Study Epigenetics - Challenges and Opportunities. Mol Cell Proteomics 2021; 20:100056. [PMID: 33556626 PMCID: PMC7973309 DOI: 10.1074/mcp.r120.002208] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Regulation of gene expression is essential for the functioning of all eukaryotic organisms. Understanding gene expression regulation requires determining which proteins interact with regulatory elements in chromatin. MS-based analysis of chromatin has emerged as a powerful tool to identify proteins associated with gene regulation, as it allows studying protein function and protein complex formation in their in vivo chromatin-bound context. Total chromatin isolated from cells can be directly analyzed using MS or further fractionated into transcriptionally active and inactive chromatin prior to MS-based analysis. Newly formed chromatin that is assembled during DNA replication can also be specifically isolated and analyzed. Furthermore, capturing specific chromatin domains facilitates the identification of previously unknown transcription factors interacting with these domains. Finally, in recent years, advances have been made toward identifying proteins that interact with a single genomic locus of interest. In this review, we highlight the power of chromatin proteomics approaches and how these provide complementary alternatives compared with conventional affinity purification methods. Furthermore, we discuss the biochemical challenges that should be addressed to consolidate and expand the role of chromatin proteomics as a key technology in the context of gene expression regulation and epigenetics research in health and disease. An overview of proteomics methods to study chromatin and gene regulation. Strength and limitations of the different approaches are highlighted. An outlook on the outstanding challenges for chromatin proteomics. Future directions for chromatin proteomics are discussed.
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Affiliation(s)
- Guido van Mierlo
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, the Netherlands.
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, the Netherlands.
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38
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Halsall JA, Andrews S, Krueger F, Rutledge CE, Ficz G, Reik W, Turner BM. Histone modifications form a cell-type-specific chromosomal bar code that persists through the cell cycle. Sci Rep 2021; 11:3009. [PMID: 33542322 PMCID: PMC7862352 DOI: 10.1038/s41598-021-82539-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 01/18/2021] [Indexed: 01/30/2023] Open
Abstract
Chromatin configuration influences gene expression in eukaryotes at multiple levels, from individual nucleosomes to chromatin domains several Mb long. Post-translational modifications (PTM) of core histones seem to be involved in chromatin structural transitions, but how remains unclear. To explore this, we used ChIP-seq and two cell types, HeLa and lymphoblastoid (LCL), to define how changes in chromatin packaging through the cell cycle influence the distributions of three transcription-associated histone modifications, H3K9ac, H3K4me3 and H3K27me3. We show that chromosome regions (bands) of 10-50 Mb, detectable by immunofluorescence microscopy of metaphase (M) chromosomes, are also present in G1 and G2. They comprise 1-5 Mb sub-bands that differ between HeLa and LCL but remain consistent through the cell cycle. The same sub-bands are defined by H3K9ac and H3K4me3, while H3K27me3 spreads more widely. We found little change between cell cycle phases, whether compared by 5 Kb rolling windows or when analysis was restricted to functional elements such as transcription start sites and topologically associating domains. Only a small number of genes showed cell-cycle related changes: at genes encoding proteins involved in mitosis, H3K9 became highly acetylated in G2M, possibly because of ongoing transcription. In conclusion, modified histone isoforms H3K9ac, H3K4me3 and H3K27me3 exhibit a characteristic genomic distribution at resolutions of 1 Mb and below that differs between HeLa and lymphoblastoid cells but remains remarkably consistent through the cell cycle. We suggest that this cell-type-specific chromosomal bar-code is part of a homeostatic mechanism by which cells retain their characteristic gene expression patterns, and hence their identity, through multiple mitoses.
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Affiliation(s)
- John A Halsall
- Chromatin and Gene Regulation Group, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, B15 2TT, UK.
| | - Simon Andrews
- Bioinformatics, The Babraham Institute, Cambridge, UK
| | - Felix Krueger
- Bioinformatics, The Babraham Institute, Cambridge, UK
| | - Charlotte E Rutledge
- Chromatin and Gene Regulation Group, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Gabriella Ficz
- Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Wolf Reik
- Epigenetics Programme, The Babraham Institute, Cambridge, UK
| | - Bryan M Turner
- Chromatin and Gene Regulation Group, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, B15 2TT, UK.
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39
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Challa K, Schmid CD, Kitagawa S, Cheblal A, Iesmantavicius V, Seeber A, Amitai A, Seebacher J, Hauer MH, Shimada K, Gasser SM. Damage-induced chromatome dynamics link Ubiquitin ligase and proteasome recruitment to histone loss and efficient DNA repair. Mol Cell 2021; 81:811-829.e6. [PMID: 33529595 DOI: 10.1016/j.molcel.2020.12.021] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 11/13/2020] [Accepted: 12/09/2020] [Indexed: 10/22/2022]
Abstract
Eukaryotic cells package their genomes around histone octamers. In response to DNA damage, checkpoint activation in yeast induces core histone degradation resulting in 20%-40% reduction in nucleosome occupancy. To gain insight into this process, we developed a new approach to analyze the chromatin-associated proteome comprehensively before and after damage. This revealed extensive changes in protein composition after Zeocin-induced damage. First, core histones and the H1 homolog Hho1 were partially lost from chromatin along with replication, transcription, and chromatin remodeling machineries, while ubiquitin ligases and the proteasome were recruited. We found that the checkpoint- and INO80C-dependent recruitment of five ubiquitin-conjugating factors (Rad6, Bre1, Pep5, Ufd4, and Rsp5) contributes to core and linker histone depletion, reducing chromatin compaction and enhancing DNA locus mobility. Importantly, loss of Rad6/Bre1, Ufd4/TRIP12, and Pep5/VPS11 compromise DNA strand invasion kinetics during homology-driven repair. Thus we provide a comprehensive overview of a functionally relevant genome-wide chromatin response to DNA damage.
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Affiliation(s)
- Kiran Challa
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland
| | - Christoph D Schmid
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland
| | - Saho Kitagawa
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland; Laboratory of Molecular Biology, Graduate School of Agricultural Science, Tohoku University, Aramaki Aza Aoba 468-1, Aoba-ku, Sendai, 981-8545, Japan
| | - Anaïs Cheblal
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland; Faculty of Natural Sciences, University of Basel, Klingelbergstrasse 70, CH-4056 Basel, Switzerland
| | - Vytautas Iesmantavicius
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland
| | - Andrew Seeber
- Center for Advanced Imaging, Northwest Building, 52 Oxford St., Harvard University, Cambridge, MA 02138, USA
| | - Assaf Amitai
- Department of Chemical Engineering, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA; The Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Jan Seebacher
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland
| | - Michael H Hauer
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland
| | - Kenji Shimada
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland
| | - Susan M Gasser
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland; Faculty of Natural Sciences, University of Basel, Klingelbergstrasse 70, CH-4056 Basel, Switzerland.
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40
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Elsherbiny A, Dobreva G. Epigenetic memory of cell fate commitment. Curr Opin Cell Biol 2021; 69:80-87. [PMID: 33535129 DOI: 10.1016/j.ceb.2020.12.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 12/15/2020] [Accepted: 12/22/2020] [Indexed: 12/23/2022]
Abstract
During development, discrete cell fates are established in precise spatiotemporal order guided by morphogen signals. These signals converge in the nucleus to induce transcriptional and epigenetic programming that determines cell fate. Once cell identity is established, cell programs have to be accurately sustained through multiple rounds of cell division, during which DNA replication serves as a window of opportunity for altering cell fate. In this review, we summarize recent advances in understanding the molecular players that underlie epigenetic memory of cell fate decisions, with a particular focus on histone modifications and mitotic bookmarking factors. We also discuss the different mechanisms of inheritance of repressed and active chromatin states.
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Affiliation(s)
- Adel Elsherbiny
- Department of Anatomy and Developmental Biology, European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany; German Centre for Cardiovascular Research (DZHK), Germany
| | - Gergana Dobreva
- Department of Anatomy and Developmental Biology, European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany; German Centre for Cardiovascular Research (DZHK), Germany.
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41
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Gonzalez I, Molliex A, Navarro P. Mitotic memories of gene activity. Curr Opin Cell Biol 2021; 69:41-47. [PMID: 33454629 DOI: 10.1016/j.ceb.2020.12.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 12/08/2020] [Accepted: 12/13/2020] [Indexed: 11/28/2022]
Abstract
When cells enter mitosis, they undergo series of dramatic changes in their structure and function that severely hamper gene regulatory processes and gene transcription. This raises the question of how daughter cells efficiently recapitulate the gene expression profile of their mother such that cell identity can be preserved. Here, we review recent evidence supporting the view that distinct chromatin-associated mechanisms of gene-regulatory inheritance assist daughter cells in the postmitotic reestablishment of gene activity with increased fidelity.
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Affiliation(s)
- Inma Gonzalez
- Epigenomics, Proliferation and the Identity of Cells, Department of Developmental and Stem Cell Biology, Institut Pasteur, CNRS, UMR3738, Paris, France
| | - Amandine Molliex
- Epigenomics, Proliferation and the Identity of Cells, Department of Developmental and Stem Cell Biology, Institut Pasteur, CNRS, UMR3738, Paris, France
| | - Pablo Navarro
- Epigenomics, Proliferation and the Identity of Cells, Department of Developmental and Stem Cell Biology, Institut Pasteur, CNRS, UMR3738, Paris, France.
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42
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Brunet M, Vargas C, Larrieu D, Torrisani J, Dufresne M. E3 Ubiquitin Ligase TRIP12: Regulation, Structure, and Physiopathological Functions. Int J Mol Sci 2020; 21:ijms21228515. [PMID: 33198194 PMCID: PMC7697007 DOI: 10.3390/ijms21228515] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 11/04/2020] [Accepted: 11/05/2020] [Indexed: 02/06/2023] Open
Abstract
The Thyroid hormone Receptor Interacting Protein 12 (TRIP12) protein belongs to the 28-member Homologous to the E6-AP C-Terminus (HECT) E3 ubiquitin ligase family. First described as an interactor of the thyroid hormone receptor, TRIP12’s biological importance was revealed by the embryonic lethality of a murine model bearing an inactivating mutation in the TRIP12 gene. Further studies showed the participation of TRIP12 in the regulation of major biological processes such as cell cycle progression, DNA damage repair, chromatin remodeling, and cell differentiation by an ubiquitination-mediated degradation of key protein substrates. Moreover, alterations of TRIP12 expression have been reported in cancers that can serve as predictive markers of therapeutic response. The TRIP12 gene is also referenced as a causative gene associated to intellectual disorders such as Clark–Baraitser syndrome and is clearly implicated in Autism Spectrum Disorder. The aim of the review is to provide an exhaustive and integrated overview of the different aspects of TRIP12 ranging from its regulation, molecular functions and physio-pathological implications.
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Affiliation(s)
- Manon Brunet
- Institut National de la Santé et de la Recherche Médicale, INSERM Unit 1037, Centre de Recherches en Cancérologie de Toulouse, CEDEX 1, 31 037 Toulouse, France; (M.B.); (C.V.); (D.L.)
- Université Toulouse III-Paul Sabatier, CEDEX 9, 31 062 Toulouse, France
| | - Claire Vargas
- Institut National de la Santé et de la Recherche Médicale, INSERM Unit 1037, Centre de Recherches en Cancérologie de Toulouse, CEDEX 1, 31 037 Toulouse, France; (M.B.); (C.V.); (D.L.)
- Université Toulouse III-Paul Sabatier, CEDEX 9, 31 062 Toulouse, France
| | - Dorian Larrieu
- Institut National de la Santé et de la Recherche Médicale, INSERM Unit 1037, Centre de Recherches en Cancérologie de Toulouse, CEDEX 1, 31 037 Toulouse, France; (M.B.); (C.V.); (D.L.)
- Université Toulouse III-Paul Sabatier, CEDEX 9, 31 062 Toulouse, France
| | - Jérôme Torrisani
- Institut National de la Santé et de la Recherche Médicale, INSERM Unit 1037, Centre de Recherches en Cancérologie de Toulouse, CEDEX 1, 31 037 Toulouse, France; (M.B.); (C.V.); (D.L.)
- Université Toulouse III-Paul Sabatier, CEDEX 9, 31 062 Toulouse, France
- Correspondence: (J.T.); (M.D.); Tel.: +33-582-741-644 (J.T.); +33-582-741-643 (M.D.)
| | - Marlène Dufresne
- Institut National de la Santé et de la Recherche Médicale, INSERM Unit 1037, Centre de Recherches en Cancérologie de Toulouse, CEDEX 1, 31 037 Toulouse, France; (M.B.); (C.V.); (D.L.)
- Université Toulouse III-Paul Sabatier, CEDEX 9, 31 062 Toulouse, France
- Correspondence: (J.T.); (M.D.); Tel.: +33-582-741-644 (J.T.); +33-582-741-643 (M.D.)
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43
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Espejo I, Di Croce L, Aranda S. The changing chromatome as a driver of disease: A panoramic view from different methodologies. Bioessays 2020; 42:e2000203. [PMID: 33169398 DOI: 10.1002/bies.202000203] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 08/27/2020] [Indexed: 12/16/2022]
Abstract
Chromatin-bound proteins underlie several fundamental cellular functions, such as control of gene expression and the faithful transmission of genetic and epigenetic information. Components of the chromatin proteome (the "chromatome") are essential in human life, and mutations in chromatin-bound proteins are frequently drivers of human diseases, such as cancer. Proteomic characterization of chromatin and de novo identification of chromatin interactors could, thus, reveal important and perhaps unexpected players implicated in human physiology and disease. Recently, intensive research efforts have focused on developing strategies to characterize the chromatome composition. In this review, we provide an overview of the dynamic composition of the chromatome, highlight the importance of its alterations as a driving force in human disease (and particularly in cancer), and discuss the different approaches to systematically characterize the chromatin-bound proteome in a global manner.
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Affiliation(s)
- Isabel Espejo
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Luciano Di Croce
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain.,UniversitatPompeuFabra (UPF), Barcelona, Spain.,ICREA, Barcelona, Spain
| | - Sergi Aranda
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
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44
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Stützer A, Welp LM, Raabe M, Sachsenberg T, Kappert C, Wulf A, Lau AM, David SS, Chernev A, Kramer K, Politis A, Kohlbacher O, Fischle W, Urlaub H. Analysis of protein-DNA interactions in chromatin by UV induced cross-linking and mass spectrometry. Nat Commun 2020; 11:5250. [PMID: 33067435 PMCID: PMC7567871 DOI: 10.1038/s41467-020-19047-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 09/24/2020] [Indexed: 02/08/2023] Open
Abstract
Protein–DNA interactions are key to the functionality and stability of the genome. Identification and mapping of protein–DNA interaction interfaces and sites is crucial for understanding DNA-dependent processes. Here, we present a workflow that allows mass spectrometric (MS) identification of proteins in direct contact with DNA in reconstituted and native chromatin after cross-linking by ultraviolet (UV) light. Our approach enables the determination of contact interfaces at amino-acid level. With the example of chromatin-associated protein SCML2 we show that our technique allows differentiation of nucleosome-binding interfaces in distinct states. By UV cross-linking of isolated nuclei we determined the cross-linking sites of several factors including chromatin-modifying enzymes, demonstrating that our workflow is not restricted to reconstituted materials. As our approach can distinguish between protein–RNA and DNA interactions in one single experiment, we project that it will be possible to obtain insights into chromatin and its regulation in the future. Cross-linking mass spectrometry (XLMS) allows mapping of protein-protein and protein-RNA interactions, but the analysis of protein-DNA complexes remains challenging. Here, the authors develop a UV light-based XLMS workflow to determine protein-DNA interfaces in reconstituted chromatin and isolated nuclei.
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Affiliation(s)
- Alexandra Stützer
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany
| | - Luisa M Welp
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany
| | - Monika Raabe
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany
| | - Timo Sachsenberg
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, 72076, Tübingen, Germany.,Applied Bioinformatics, Department for Computer Science, University of Tübingen, 72076, Tübingen, Germany
| | - Christin Kappert
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany.,Somatosensory Signaling and Systems Biology Group, Max Planck Institute of Experimental Medicine, 37075, Göttingen, Germany
| | - Alexander Wulf
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany
| | - Andy M Lau
- Department of Chemistry, King's College London, London, SE1 1DB, UK
| | - Stefan-Sebastian David
- Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany.,King Abdullah University of Science and Technology (KAUST), Biological and Environmental Science and Engineering Division, Laboratory of Chromatin Biochemistry, 23955, Thuwal, Saudi Arabia
| | - Aleksandar Chernev
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany
| | | | - Argyris Politis
- Department of Chemistry, King's College London, London, SE1 1DB, UK
| | - Oliver Kohlbacher
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, 72076, Tübingen, Germany.,Applied Bioinformatics, Department for Computer Science, University of Tübingen, 72076, Tübingen, Germany.,Institute for Translational Bioinformatics, University Hospital Tübingen, 72076, Tübingen, Germany.,Biomolecular Interactions, Max Planck Institute for Developmental Biology, 72076, Tübingen, Germany
| | - Wolfgang Fischle
- Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany.,King Abdullah University of Science and Technology (KAUST), Biological and Environmental Science and Engineering Division, Laboratory of Chromatin Biochemistry, 23955, Thuwal, Saudi Arabia
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany. .,Bioanalytics Group, Institute for Clinical Chemistry, University Medical Center Göttingen, 37075, Göttingen, Germany.
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45
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Fan X, Kraynak J, Knisely JPS, Formenti SC, Shen WH. PTEN as a Guardian of the Genome: Pathways and Targets. Cold Spring Harb Perspect Med 2020; 10:cshperspect.a036194. [PMID: 31932469 DOI: 10.1101/cshperspect.a036194] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Faithful transmission of genetic information is only possible with the structural and functional integrity of the genome. PTEN has been recognized as a guardian of the genome since the identification of its noncanonical localization and function in the nucleus. Yet, the role of PTEN in guarding the genome relies on integration of diverse mechanisms elicited by its canonical activity in antagonizing PI3K as well as emerging noncanonical functions. In the nucleus, PTEN maintains the structural integrity of chromosomes and the architecture of heterochromatin by physically interacting with chromosomal and nucleosomal components. PTEN also controls the functional integrity of key genetic transmission machineries by promoting proper assembly of the replisome and mitotic spindles. Deregulation of PTEN signaling impairs genome integrity, leading to spontaneous replication/mitotic stress and subsequent stress tolerance. Identification of novel targets of PTEN signaling and illumination of the interplay of diverse PTEN pathways in genome maintenance will help us better understand mechanisms underlying tumor evolution and therapeutic resistance.
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Affiliation(s)
- Xinyi Fan
- Department of Radiation Oncology, Weill Cornell Medicine, Cornell University, New York, New York 10065, USA
| | - Jeffrey Kraynak
- Department of Radiation Oncology, Weill Cornell Medicine, Cornell University, New York, New York 10065, USA
| | - Jonathan P S Knisely
- Department of Radiation Oncology, Weill Cornell Medicine, Cornell University, New York, New York 10065, USA
| | - Silvia C Formenti
- Department of Radiation Oncology, Weill Cornell Medicine, Cornell University, New York, New York 10065, USA.,Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, Cornell University, New York, New York 10065, USA
| | - Wen H Shen
- Department of Radiation Oncology, Weill Cornell Medicine, Cornell University, New York, New York 10065, USA.,Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, Cornell University, New York, New York 10065, USA
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46
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Djeghloul D, Patel B, Kramer H, Dimond A, Whilding C, Brown K, Kohler AC, Feytout A, Veland N, Elliott J, Bharat TAM, Tarafder AK, Löwe J, Ng BL, Guo Y, Guy J, Huseyin MK, Klose RJ, Merkenschlager M, Fisher AG. Identifying proteins bound to native mitotic ESC chromosomes reveals chromatin repressors are important for compaction. Nat Commun 2020; 11:4118. [PMID: 32807789 PMCID: PMC7431861 DOI: 10.1038/s41467-020-17823-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 07/15/2020] [Indexed: 12/14/2022] Open
Abstract
Epigenetic information is transmitted from mother to daughter cells through mitosis. Here, to identify factors that might play a role in conveying epigenetic memory through cell division, we report on the isolation of unfixed, native chromosomes from metaphase-arrested cells using flow cytometry and perform LC-MS/MS to identify chromosome-bound proteins. A quantitative proteomic comparison between metaphase-arrested cell lysates and chromosome-sorted samples reveals a cohort of proteins that were significantly enriched on mitotic ESC chromosomes. These include pluripotency-associated transcription factors, repressive chromatin-modifiers such as PRC2 and DNA methyl-transferases, and proteins governing chromosome architecture. Deletion of PRC2, Dnmt1/3a/3b or Mecp2 in ESCs leads to an increase in the size of individual mitotic chromosomes, consistent with de-condensation. Similar results were obtained by the experimental cleavage of cohesin. Thus, we identify chromosome-bound factors in pluripotent stem cells during mitosis and reveal that PRC2, DNA methylation and Mecp2 are required to maintain chromosome compaction.
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Affiliation(s)
- Dounia Djeghloul
- Lymphocyte Development Group, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Bhavik Patel
- Flow Cytometry Facility, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Holger Kramer
- Biological Mass Spectrometry and Proteomics Facility, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Andrew Dimond
- Lymphocyte Development Group, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Chad Whilding
- Microscopy Facility, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Karen Brown
- Lymphocyte Development Group, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Anne-Céline Kohler
- Lymphocyte Development Group, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Amelie Feytout
- Lymphocyte Development Group, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Nicolas Veland
- Lymphocyte Development Group, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - James Elliott
- Flow Cytometry Facility, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Tanmay A M Bharat
- Sir William Dunn School of Pathology, University of Oxford, OX1 3RE, Oxford, UK
| | - Abul K Tarafder
- Sir William Dunn School of Pathology, University of Oxford, OX1 3RE, Oxford, UK
| | - Jan Löwe
- MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Bee L Ng
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Ya Guo
- Lymphocyte Development Group, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Jacky Guy
- The Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, EH9 3BH, UK
| | - Miles K Huseyin
- Department of Biochemistry, University of Oxford, OX1 3QU, Oxford, UK
| | - Robert J Klose
- Department of Biochemistry, University of Oxford, OX1 3QU, Oxford, UK
| | - Matthias Merkenschlager
- Lymphocyte Development Group, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Amanda G Fisher
- Lymphocyte Development Group, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK.
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47
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Samata M, Alexiadis A, Richard G, Georgiev P, Nuebler J, Kulkarni T, Renschler G, Basilicata MF, Zenk FL, Shvedunova M, Semplicio G, Mirny L, Iovino N, Akhtar A. Intergenerationally Maintained Histone H4 Lysine 16 Acetylation Is Instructive for Future Gene Activation. Cell 2020; 182:127-144.e23. [DOI: 10.1016/j.cell.2020.05.026] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Revised: 02/22/2020] [Accepted: 05/14/2020] [Indexed: 10/24/2022]
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48
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Kang H, Shokhirev MN, Xu Z, Chandran S, Dixon JR, Hetzer MW. Dynamic regulation of histone modifications and long-range chromosomal interactions during postmitotic transcriptional reactivation. Genes Dev 2020; 34:913-930. [PMID: 32499403 PMCID: PMC7328517 DOI: 10.1101/gad.335794.119] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 04/28/2020] [Indexed: 12/18/2022]
Abstract
During mitosis, transcription of genomic DNA is dramatically reduced, before it is reactivated during nuclear reformation in anaphase/telophase. Many aspects of the underlying principles that mediate transcriptional memory and reactivation in the daughter cells remain unclear. Here, we used ChIP-seq on synchronized cells at different stages after mitosis to generate genome-wide maps of histone modifications. Combined with EU-RNA-seq and Hi-C analyses, we found that during prometaphase, promoters, enhancers, and insulators retain H3K4me3 and H3K4me1, while losing H3K27ac. Enhancers globally retaining mitotic H3K4me1 or locally retaining mitotic H3K27ac are associated with cell type-specific genes and their transcription factors for rapid transcriptional activation. As cells exit mitosis, promoters regain H3K27ac, which correlates with transcriptional reactivation. Insulators also gain H3K27ac and CCCTC-binding factor (CTCF) in anaphase/telophase. This increase of H3K27ac in anaphase/telophase is required for posttranscriptional activation and may play a role in the establishment of topologically associating domains (TADs). Together, our results suggest that the genome is reorganized in a sequential order, in which histone methylations occur first in prometaphase, histone acetylation, and CTCF in anaphase/telophase, transcription in cytokinesis, and long-range chromatin interactions in early G1. We thus provide insights into the histone modification landscape that allows faithful reestablishment of the transcriptional program and TADs during cell division.
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Affiliation(s)
- Hyeseon Kang
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Maxim N Shokhirev
- The Razavi Newman Integrative Genomics and Bioinformatics Core (IGC), Salk Institute for Biological Studies, 92037 La Jolla, California, USA
| | - Zhichao Xu
- Peptide Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Sahaana Chandran
- Peptide Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Jesse R Dixon
- Peptide Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Martin W Hetzer
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037, USA
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49
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Hildebrand EM, Dekker J. Mechanisms and Functions of Chromosome Compartmentalization. Trends Biochem Sci 2020; 45:385-396. [PMID: 32311333 PMCID: PMC7275117 DOI: 10.1016/j.tibs.2020.01.002] [Citation(s) in RCA: 131] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 01/13/2020] [Accepted: 01/17/2020] [Indexed: 01/23/2023]
Abstract
Active and inactive chromatin are spatially separated in the nucleus. In Hi-C data, this is reflected by the formation of compartments, whose interactions form a characteristic checkerboard pattern in chromatin interaction maps. Only recently have the mechanisms that drive this separation come into view. Here, we discuss new insights into these mechanisms and possible functions in genome regulation. Compartmentalization can be understood as a microphase-segregated block co-polymer. Microphase separation can be facilitated by chromatin factors that associate with compartment domains, and that can engage in liquid-liquid phase separation to form subnuclear bodies, as well as by acting as bridging factors between polymer sections. We then discuss how a spatially segregated state of the genome can contribute to gene regulation, and highlight experimental challenges for testing these structure-function relationships.
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Affiliation(s)
- Erica M Hildebrand
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Job Dekker
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
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50
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Suter DM. Transcription Factors and DNA Play Hide and Seek. Trends Cell Biol 2020; 30:491-500. [PMID: 32413318 DOI: 10.1016/j.tcb.2020.03.003] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 03/12/2020] [Accepted: 03/16/2020] [Indexed: 01/12/2023]
Abstract
Transcription factors (TFs) bind to specific DNA motifs to regulate the expression of target genes. To reach their binding sites, TFs diffuse in 3D and perform local motions such as 1D sliding, hopping, or intersegmental transfer. TF-DNA interactions depend on multiple parameters, such as the chromatin environment, TF partitioning into distinct subcellular regions, and cooperativity with other DNA-binding proteins. In this review, how current understanding of the search process has initially been shaped by prokaryotic studies is discussed, as well as what is known about the parameters regulating TF search efficiency in the context of the complex eukaryotic chromatin landscape.
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Affiliation(s)
- David M Suter
- Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
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