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Wilson PD, Yu X, Buck MJ. Nucleosome-binding by TP53, TP63, and TP73 is determined by the composition, accessibility, and helical orientation of their binding sites. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.03.592419. [PMID: 38746214 PMCID: PMC11092788 DOI: 10.1101/2024.05.03.592419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
The p53 family of transcription factors plays key roles in driving development and combating cancer by regulating gene expression. TP53, TP63, and TP73-the three members of the p53 family-regulate gene expression by binding to their DNA binding sites, many of which are situated within nucleosomes. To thoroughly examine the nucleosome-binding abilities of the p53 family, we used Pioneer-seq, a technique that assesses a transcription factor's binding affinity to its DNA binding sites at all possible positions within the nucleosome core particle. Using Pioneer-seq, we analyzed the binding affinity of TP53, TP63, and TP73 to 10 p53-family binding sites across the nucleosome core particle. We found that the affinity of TP53, TP63, and TP73 for nucleosomes was largely determined by the positioning of p53-family binding sites within nucleosomes; p53-family members bind strongly to the more accessible edges of nucleosomes but weakly to the less accessible centers of nucleosomes. We also found that the DNA-helical orientation of p53-family binding sites within nucleosomal DNA impacted the nucleosome-binding affinity of p53-family members. The composition of their binding sites also impacted each p53-family member's nucleosome-binding affinities only when the binding site was located in an accessible location. Taken together, our results show that the accessibility, composition, and helical orientation of p53-family binding sites collectively determine the nucleosome-binding affinities of TP53, TP63, and TP73. These findings help explain the rules underlying p53-family-nucleosome binding and thus provide requisite insight into how we may better control gene-expression changes involved in development and tumor suppression.
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Yang Q, Saaoud F, Lu Y, Pu Y, Xu K, Shao Y, Jiang X, Wu S, Yang L, Tian Y, Liu X, Gillespie A, Luo JJ, Shi XM, Zhao H, Martinez L, Vazquez-Padron R, Wang H, Yang X. Innate immunity of vascular smooth muscle cells contributes to two-wave inflammation in atherosclerosis, twin-peak inflammation in aortic aneurysms and trans-differentiation potential into 25 cell types. Front Immunol 2024; 14:1348238. [PMID: 38327764 PMCID: PMC10847266 DOI: 10.3389/fimmu.2023.1348238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Accepted: 12/27/2023] [Indexed: 02/09/2024] Open
Abstract
Introduction Vascular smooth muscle cells (VSMCs) are the predominant cell type in the medial layer of the aorta, which plays a critical role in aortic diseases. Innate immunity is the main driving force for cardiovascular diseases. Methods To determine the roles of innate immunity in VSMC and aortic pathologies, we performed transcriptome analyses on aortas from ApoE-/- angiotensin II (Ang II)-induced aortic aneurysm (AAA) time course, and ApoE-/- atherosclerosis time course, as well as VSMCs stimulated with danger-associated molecular patterns (DAMPs). Results We made significant findings: 1) 95% and 45% of the upregulated innate immune pathways (UIIPs, based on data of 1226 innate immune genes) in ApoE-/- Ang II-induced AAA at 7 days were different from that of 14 and 28 days, respectively; and AAA showed twin peaks of UIIPs with a major peak at 7 days and a minor peak at 28 days; 2) all the UIIPs in ApoE-/- atherosclerosis at 6 weeks were different from that of 32 and 78 weeks (two waves); 3) analyses of additional 12 lists of innate immune-related genes with 1325 cytokine and chemokine genes, 2022 plasma membrane protein genes, 373 clusters of differentiation (CD) marker genes, 280 nuclear membrane protein genes, 1425 nucleoli protein genes, 6750 nucleoplasm protein genes, 1496 transcription factors (TFs) including 15 pioneer TFs, 164 histone modification enzymes, 102 oxidative cell death genes, 68 necrotic cell death genes, and 47 efferocytosis genes confirmed two-wave inflammation in atherosclerosis and twin-peak inflammation in AAA; 4) DAMPs-stimulated VSMCs were innate immune cells as judged by the upregulation of innate immune genes and genes from 12 additional lists; 5) DAMPs-stimulated VSMCs increased trans-differentiation potential by upregulating not only some of 82 markers of 7 VSMC-plastic cell types, including fibroblast, osteogenic, myofibroblast, macrophage, adipocyte, foam cell, and mesenchymal cell, but also 18 new cell types (out of 79 human cell types with 8065 cell markers); 6) analysis of gene deficient transcriptomes indicated that the antioxidant transcription factor NRF2 suppresses, however, the other five inflammatory transcription factors and master regulators, including AHR, NF-KB, NOX (ROS enzyme), PERK, and SET7 promote the upregulation of twelve lists of innate immune genes in atherosclerosis, AAA, and DAMP-stimulated VSMCs; and 7) both SET7 and trained tolerance-promoting metabolite itaconate contributed to twin-peak upregulation of cytokines in AAA. Discussion Our findings have provided novel insights on the roles of innate immune responses and nuclear stresses in the development of AAA, atherosclerosis, and VSMC immunology and provided novel therapeutic targets for treating those significant cardiovascular and cerebrovascular diseases.
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Affiliation(s)
- Qiaoxi Yang
- Lemole Center for Integrated Lymphatics and Vascular Research, Department of Cardiovascular Sciences, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, United States
- Beloit College, Beloit, WI, United States
| | - Fatma Saaoud
- Lemole Center for Integrated Lymphatics and Vascular Research, Department of Cardiovascular Sciences, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, United States
| | - Yifan Lu
- Lemole Center for Integrated Lymphatics and Vascular Research, Department of Cardiovascular Sciences, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, United States
| | - Yujiang Pu
- College of Letters & Science, University of Wisconsin-Madison, Madison, WI, United States
| | - Keman Xu
- Lemole Center for Integrated Lymphatics and Vascular Research, Department of Cardiovascular Sciences, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, United States
| | - Ying Shao
- Lemole Center for Integrated Lymphatics and Vascular Research, Department of Cardiovascular Sciences, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, United States
| | - Xiaohua Jiang
- Lemole Center for Integrated Lymphatics and Vascular Research, Department of Cardiovascular Sciences, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, United States
- Center for Metabolic Disease Research and Thrombosis Research, Department of Cardiovascular Sciences, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, United States
| | - Sheng Wu
- Center for Metabolic Disease Research and Thrombosis Research, Department of Cardiovascular Sciences, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, United States
| | - Ling Yang
- Department of Medical Genetics and Molecular Biochemistry, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, United States
| | - Ying Tian
- Lemole Center for Integrated Lymphatics and Vascular Research, Department of Cardiovascular Sciences, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, United States
| | - Xiaolei Liu
- Lemole Center for Integrated Lymphatics and Vascular Research, Department of Cardiovascular Sciences, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, United States
| | - Avrum Gillespie
- Section of Nephrology, Hypertension, and Kidney Transplantation, Department of Medicine, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, United States
| | - Jin Jun Luo
- Department of Neurology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, United States
| | - Xinghua Mindy Shi
- Department of Computer and Information Sciences, College of Science and Technology at Temple University, Philadelphia, PA, United States
| | - Huaqing Zhao
- Center for Biostatistics and Epidemiology, Department of Biomedical Education and Data Science, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, United States
| | - Laisel Martinez
- DeWitt Daughtry Family Department of Surgery, Leonard M. Miller School of Medicine, University of Miami, Miami, FL, United States
| | - Roberto Vazquez-Padron
- DeWitt Daughtry Family Department of Surgery, Leonard M. Miller School of Medicine, University of Miami, Miami, FL, United States
| | - Hong Wang
- Center for Metabolic Disease Research and Thrombosis Research, Department of Cardiovascular Sciences, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, United States
| | - Xiaofeng Yang
- Lemole Center for Integrated Lymphatics and Vascular Research, Department of Cardiovascular Sciences, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, United States
- Center for Metabolic Disease Research and Thrombosis Research, Department of Cardiovascular Sciences, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, United States
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Ahmad K, Brahma S, Henikoff S. Epigenetic pioneering by SWI/SNF family remodelers. Mol Cell 2024; 84:194-201. [PMID: 38016477 PMCID: PMC10842064 DOI: 10.1016/j.molcel.2023.10.045] [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: 07/06/2023] [Revised: 09/20/2023] [Accepted: 10/31/2023] [Indexed: 11/30/2023]
Abstract
In eukaryotic genomes, transcriptional machinery and nucleosomes compete for binding to DNA sequences; thus, a crucial aspect of gene regulatory element function is to modulate chromatin accessibility for transcription factor (TF) and RNA polymerase binding. Recent structural studies have revealed multiple modes of TF engagement with nucleosomes, but how initial "pioneering" results in steady-state DNA accessibility for further TF binding and RNA polymerase II (RNAPII) engagement has been unclear. Even less well understood is how distant sites of open chromatin interact with one another, such as when developmental enhancers activate promoters to release RNAPII for productive elongation. Here, we review evidence for the centrality of the conserved SWI/SNF family of nucleosome remodeling complexes, both in pioneering and in mediating enhancer-promoter contacts. Consideration of the nucleosome unwrapping and ATP hydrolysis activities of SWI/SNF complexes, together with their architectural features, may reconcile steady-state TF occupancy with rapid TF dynamics observed by live imaging.
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Affiliation(s)
- Kami Ahmad
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Sandipan Brahma
- University of Nebraska Medical Center, Department of Genetics, Cell Biology & Anatomy, Omaha, NE, USA
| | - Steven Henikoff
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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Herbert A. Flipons and small RNAs accentuate the asymmetries of pervasive transcription by the reset and sequence-specific microcoding of promoter conformation. J Biol Chem 2023; 299:105140. [PMID: 37544644 PMCID: PMC10474125 DOI: 10.1016/j.jbc.2023.105140] [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: 05/11/2023] [Revised: 07/25/2023] [Accepted: 07/31/2023] [Indexed: 08/08/2023] Open
Abstract
The role of alternate DNA conformations such as Z-DNA in the regulation of transcription is currently underappreciated. These structures are encoded by sequences called flipons, many of which are enriched in promoter and enhancer regions. Through a change in their conformation, flipons provide a tunable mechanism to mechanically reset promoters for the next round of transcription. They act as actuators that capture and release energy to ensure that the turnover of the proteins at promoters is optimized to cell state. Likewise, the single-stranded DNA formed as flipons cycle facilitates the docking of RNAs that are able to microcode promoter conformations and canalize the pervasive transcription commonly observed in metazoan genomes. The strand-specific nature of the interaction between RNA and DNA likely accounts for the known asymmetry of epigenetic marks present on the histone tetramers that pair to form nucleosomes. The role of these supercoil-dependent processes in promoter choice and transcriptional interference is reviewed. The evolutionary implications are examined: the resilience and canalization of flipon-dependent gene regulation is contrasted with the rapid adaptation enabled by the spread of flipon repeats throughout the genome. Overall, the current findings underscore the important role of flipons in modulating the readout of genetic information and how little we know about their biology.
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Affiliation(s)
- Alan Herbert
- Discovery Division, InsideOutBio, Charlestown, Massachusetts, USA.
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Ankill J, Aure MR, Bjørklund S, Langberg S, Kristensen VN, Vitelli V, Tekpli X, Fleischer T. Epigenetic alterations at distal enhancers are linked to proliferation in human breast cancer. NAR Cancer 2022; 4:zcac008. [PMID: 35350772 PMCID: PMC8947789 DOI: 10.1093/narcan/zcac008] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 02/23/2022] [Accepted: 03/14/2022] [Indexed: 11/26/2022] Open
Abstract
Aberrant DNA methylation is an early event in breast carcinogenesis and plays a critical role in regulating gene expression. Here, we perform genome-wide expression-methylation Quantitative Trait Loci (emQTL) analysis through the integration of DNA methylation and gene expression to identify disease-driving pathways under epigenetic control. By grouping the emQTLs using biclustering we identify associations representing important biological processes associated with breast cancer pathogenesis including regulation of proliferation and tumor-infiltrating fibroblasts. We report genome-wide loss of enhancer methylation at binding sites of proliferation-driving transcription factors including CEBP-β, FOSL1, and FOSL2 with concomitant high expression of proliferation-related genes in aggressive breast tumors as we confirm with scRNA-seq. The identified emQTL-CpGs and genes were found connected through chromatin loops, indicating that proliferation in breast tumors is under epigenetic regulation by DNA methylation. Interestingly, the associations between enhancer methylation and proliferation-related gene expression were also observed within known subtypes of breast cancer, suggesting a common role of epigenetic regulation of proliferation. Taken together, we show that proliferation in breast cancer is linked to loss of methylation at specific enhancers and transcription factor binding and gene activation through chromatin looping.
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Affiliation(s)
- Jørgen Ankill
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Miriam Ragle Aure
- Department of Medical Genetics, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Sunniva Bjørklund
- Department of Medical Genetics, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | | | | | - Vessela N Kristensen
- Department of Medical Genetics, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Valeria Vitelli
- Oslo Centre for Biostatistics and Epidemiology, Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Xavier Tekpli
- Department of Medical Genetics, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Thomas Fleischer
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
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