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Lu Z, Wang Y, Assumpção ALFV, Liu P, Kopp A, Saka S, Mcilwain SJ, Viny AD, Brand M, Pan X. Yin Yang 1 regulates cohesin complex protein SMC3 in mouse hematopoietic stem cells. Blood Adv 2024; 8:3076-3091. [PMID: 38531064 PMCID: PMC11222949 DOI: 10.1182/bloodadvances.2023011411] [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: 08/09/2023] [Revised: 02/16/2024] [Accepted: 02/26/2024] [Indexed: 03/28/2024] Open
Abstract
ABSTRACT Yin Yang 1 (YY1) and structural maintenance of chromosomes 3 (SMC3) are 2 critical chromatin structural factors that mediate long-distance enhancer-promoter interactions and promote developmentally regulated changes in chromatin architecture in hematopoietic stem/progenitor cells (HSPCs). Although YY1 has critical functions in promoting hematopoietic stem cell (HSC) self-renewal and maintaining HSC quiescence, SMC3 is required for proper myeloid lineage differentiation. However, many questions remain unanswered regarding how YY1 and SMC3 interact with each other and affect hematopoiesis. We found that YY1 physically interacts with SMC3 and cooccupies with SMC3 at a large cohort of promoters genome wide, and YY1 deficiency deregulates the genetic network governing cell metabolism. YY1 occupies the Smc3 promoter and represses SMC3 expression in HSPCs. Although deletion of 1 Smc3 allele partially restores HSC numbers and quiescence in YY1 knockout mice, Yy1-/-Smc3+/- HSCs fail to reconstitute blood after bone marrow transplant. YY1 regulates HSC metabolic pathways and maintains proper intracellular reactive oxygen species levels in HSCs, and this regulation is independent of the YY1-SMC3 axis. Our results establish a distinct YY1-SMC3 axis and its impact on HSC quiescence and metabolism.
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Affiliation(s)
- Zhanping Lu
- Department of Medical Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI
- Carbone Cancer Center, University of Wisconsin, Madison, WI
- Wisconsin Blood Cancer Research Institute, University of Wisconsin, Madison, WI
| | - Yinghua Wang
- Department of Medical Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI
- Carbone Cancer Center, University of Wisconsin, Madison, WI
- Wisconsin Blood Cancer Research Institute, University of Wisconsin, Madison, WI
| | - Anna L. F. V. Assumpção
- Department of Medical Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI
- Carbone Cancer Center, University of Wisconsin, Madison, WI
- Wisconsin Blood Cancer Research Institute, University of Wisconsin, Madison, WI
| | - Peng Liu
- Carbone Cancer Center, University of Wisconsin, Madison, WI
- Department of Biostatistics and Medical Informatics, University of Wisconsin School of Medicine and Public Health, Madison, WI
| | - Audrey Kopp
- Wisconsin Blood Cancer Research Institute, University of Wisconsin, Madison, WI
- Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, WI
| | - Sahitya Saka
- Department of Medical Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI
- Carbone Cancer Center, University of Wisconsin, Madison, WI
- Wisconsin Blood Cancer Research Institute, University of Wisconsin, Madison, WI
| | - Sean J. Mcilwain
- Carbone Cancer Center, University of Wisconsin, Madison, WI
- Department of Biostatistics and Medical Informatics, University of Wisconsin School of Medicine and Public Health, Madison, WI
| | - Aaron D. Viny
- Division of Hematology & Oncology, Department of Medicine, Columbia University Irving Medical Center, New York, NY
- Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY
- Department of Genetics & Development, Columbia University Irving Medical Center, New York, NY
| | - Marjorie Brand
- Wisconsin Blood Cancer Research Institute, University of Wisconsin, Madison, WI
- Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, WI
| | - Xuan Pan
- Department of Medical Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI
- Carbone Cancer Center, University of Wisconsin, Madison, WI
- Wisconsin Blood Cancer Research Institute, University of Wisconsin, Madison, WI
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2
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Gong X, He W, Jin W, Ma H, Wang G, Li J, Xiao Y, Zhao Y, Chen Q, Guo H, Yang J, Qi Y, Dong W, Fu M, Li X, Liu J, Liu X, Yin A, Zhang Y, Wei Y. Disruption of maternal vascular remodeling by a fetal endoretrovirus-derived gene in preeclampsia. Genome Biol 2024; 25:117. [PMID: 38715110 PMCID: PMC11075363 DOI: 10.1186/s13059-024-03265-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 04/30/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND Preeclampsia, one of the most lethal pregnancy-related diseases, is associated with the disruption of uterine spiral artery remodeling during placentation. However, the early molecular events leading to preeclampsia remain unknown. RESULTS By analyzing placentas from preeclampsia, non-preeclampsia, and twin pregnancies with selective intrauterine growth restriction, we show that the pathogenesis of preeclampsia is attributed to immature trophoblast and maldeveloped endothelial cells. Delayed epigenetic reprogramming during early extraembryonic tissue development leads to generation of excessive immature trophoblast cells. We find reduction of de novo DNA methylation in these trophoblast cells results in selective overexpression of maternally imprinted genes, including the endoretrovirus-derived gene PEG10 (paternally expressed gene 10). PEG10 forms virus-like particles, which are transferred from the trophoblast to the closely proximate endothelial cells. In normal pregnancy, only a low amount of PEG10 is transferred to maternal cells; however, in preeclampsia, excessive PEG10 disrupts maternal vascular development by inhibiting TGF-beta signaling. CONCLUSIONS Our study reveals the intricate epigenetic mechanisms that regulate trans-generational genetic conflict and ultimately ensure proper maternal-fetal interface formation.
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Affiliation(s)
- Xiaoli Gong
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
| | - Wei He
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, China
| | - Wan Jin
- Euler Technology, Beijing, China
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Hongwei Ma
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Chengdu, China
- Department Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Gang Wang
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China
- Human Genetic Resources Preservation Center of Hubei Province, Wuhan, China
- Laboratory of Precision Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Jiaxin Li
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
| | - Yu Xiao
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China
- Human Genetic Resources Preservation Center of Hubei Province, Wuhan, China
- Laboratory of Precision Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yangyu Zhao
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
| | | | | | - Jiexia Yang
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, China
| | - Yiming Qi
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, China
| | - Wei Dong
- Maternity Ward, Haidian Maternal and Child Health Hospital, Beijing, China
| | - Meng Fu
- Department of Obstetrics and Gynecology, Haidian Maternal and Child Health Hospital, Beijing, China
| | - Xiaojuan Li
- Euler Technology, Beijing, China
- Present Address: International Max Planck Research School for Genome Science, and University of Göttingen, Göttingen Center for Molecular Biosciences, Göttingen, Germany
| | | | - Xinghui Liu
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Chengdu, China.
- Department Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China.
| | - Aihua Yin
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, China.
| | - Yi Zhang
- Euler Technology, Beijing, China.
| | - Yuan Wei
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China.
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3
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Banerjee S, Sanyal S, Hodawadekar S, Naiyer S, Bano N, Banerjee A, Rhoades J, Dong D, Allman D, Atchison ML. Unusual lineage plasticity revealed by YY1 knockout in pro-B cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.22.586298. [PMID: 38586061 PMCID: PMC10996465 DOI: 10.1101/2024.03.22.586298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
During B cell development, cells progress through multiple developmental stages with the pro-B cell stage defining commitment to the B cell lineage. YY1 is a ubiquitous transcription factor that is capable of both activation and repression functions. We find here that knockout of YY1 at the pro-B cell stage eliminates B lineage commitment. YY1 knockout pro-B cells can generate T lineage cells in vitro using the OP9- DL4 feeder system, as well as in vivo after injection into sub-lethally irradiated Rag1 -/- mice. These T lineage-like cells lose their B lineage transcript profile and gain a T cell lineage profile. Single cell-RNA-seq experiments showed that as YY1 knockout pro-B cells transition into T lineage cells, various cell clusters adopt transcript profiles representing a multiplicity of hematopoietic lineages indicating unusual lineage plasticity. Given the ubiquitous nature of YY1 and its dual activation and repression functions, YY1 likely regulates commitment in multiple cell lineages.
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Li B, Duan Y, Du Z, Wang X, Liu S, Feng Z, Tian L, Song F, Yang H, Cai W, Lin Z, Li H. Natural selection and genetic diversity maintenance in a parasitic wasp during continuous biological control application. Nat Commun 2024; 15:1379. [PMID: 38355730 PMCID: PMC10866907 DOI: 10.1038/s41467-024-45631-2] [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: 05/18/2023] [Accepted: 01/30/2024] [Indexed: 02/16/2024] Open
Abstract
Aphidius gifuensis is a parasitoid wasp and primary endoparasitoid enemy of the peach potato aphid, Myzus persicae. Artificially reared, captive wasps of this species have been extensively and effectively used to control populations of aphids and limit crop loss. However, the consequences of large-scale releasing of captive A. gifuensis, such as genetic erosion and reduced fitness in wild populations of this species, remains unclear. Here, we sequence the genomes of 542 A. gifuensis individuals collected across China, including 265 wild and 277 human-intervened samples. Population genetic analyses on wild individuals recovered Yunnan populations as the ancestral group with the most complex genetic structure. We also find genetic signature of environmental adaptation during the dispersal of wild populations from Yunnan to other regions. While comparative genomic analyses of captive wasps revealed a decrease in genetic diversity during long-term rearing, population genomic analyses revealed signatures of natural selection by several biotic (host plants) or abiotic (climate) factors, which support maintenance of the gene pool of wild populations in spite of the introduction of captive wasps. Therefore, the impact of large-scale release is reduced. Our study suggests that A. gifuensis is a good system for exploring the genetic and evolutionary effects of mass rearing and release on species commonly used as biocontrol agents.
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Affiliation(s)
- Bingyan Li
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Yuange Duan
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Zhenyong Du
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Xuan Wang
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Shanlin Liu
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Zengbei Feng
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Li Tian
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Fan Song
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | | | - Wanzhi Cai
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Zhonglong Lin
- Yunnan Tobacco Company of China National Tobacco Corporation, Kunming, 650011, China.
| | - Hu Li
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China.
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5
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Chen ZS, Ou M, Taylor S, Dafinca R, Peng SI, Talbot K, Chan HYE. Mutant GGGGCC RNA prevents YY1 from binding to Fuzzy promoter which stimulates Wnt/β-catenin pathway in C9ALS/FTD. Nat Commun 2023; 14:8420. [PMID: 38110419 PMCID: PMC10728118 DOI: 10.1038/s41467-023-44215-w] [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: 11/10/2022] [Accepted: 12/05/2023] [Indexed: 12/20/2023] Open
Abstract
The GGGGCC hexanucleotide repeat expansion mutation in the chromosome 9 open reading frame 72 (C9orf72) gene is a major genetic cause of amyotrophic lateral sclerosis and frontotemporal dementia (C9ALS/FTD). In this study, we demonstrate that the zinc finger (ZF) transcriptional regulator Yin Yang 1 (YY1) binds to the promoter region of the planar cell polarity gene Fuzzy to regulate its transcription. We show that YY1 interacts with GGGGCC repeat RNA via its ZF and that this interaction compromises the binding of YY1 to the FuzzyYY1 promoter sites, resulting in the downregulation of Fuzzy transcription. The decrease in Fuzzy protein expression in turn activates the canonical Wnt/β-catenin pathway and induces synaptic deficits in C9ALS/FTD neurons. Our findings demonstrate a C9orf72 GGGGCC RNA-initiated perturbation of YY1-Fuzzy transcriptional control that implicates aberrant Wnt/β-catenin signalling in C9ALS/FTD-associated neurodegeneration. This pathogenic cascade provides a potential new target for disease-modifying therapy.
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Affiliation(s)
- Zhefan Stephen Chen
- School of Life Sciences, Faculty of Science, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
- Oxford Motor Neuron Disease Centre, Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DU, UK
| | - Mingxi Ou
- School of Life Sciences, Faculty of Science, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
| | - Stephanie Taylor
- Oxford Motor Neuron Disease Centre, Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DU, UK
| | - Ruxandra Dafinca
- Oxford Motor Neuron Disease Centre, Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DU, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford, OX1 3QU, UK
| | - Shaohong Isaac Peng
- School of Life Sciences, Faculty of Science, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
| | - Kevin Talbot
- Oxford Motor Neuron Disease Centre, Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DU, UK.
- Kavli Institute for Nanoscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford, OX1 3QU, UK.
| | - Ho Yin Edwin Chan
- School of Life Sciences, Faculty of Science, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China.
- Gerald Choa Neuroscience Institute, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China.
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6
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Abstract
This review article discusses the epigenetic regulation of quiescent stem cells. Quiescent stem cells are a rare population of stem cells that remain in a state of cell cycle arrest until activated to proliferate and differentiate. The molecular signature of quiescent stem cells is characterized by unique epigenetic modifications, including histone modifications and deoxyribonucleic acid (DNA) methylation. These modifications play critical roles in regulating stem cell behavior, including maintenance of quiescence, proliferation, and differentiation. The article specifically focuses on the role of histone modifications and DNA methylation in quiescent stem cells, and how these modifications can be dynamically regulated by environmental cues. The future perspectives of quiescent stem cell research are also discussed, including their potential for tissue repair and regeneration, their role in aging and age-related diseases, and their implications for cancer research. Overall, this review provides a comprehensive overview of the epigenetic regulation of quiescent stem cells and highlights the potential of this research for the development of new therapies in regenerative medicine, aging research, and cancer biology.
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Affiliation(s)
- Mehran Radak
- Department of Biology, School of Sciences, Razi University, Baq-e-Abrisham, Kermanshah, Islamic Republic of Iran
| | - Hossein Fallahi
- Department of Biology, School of Sciences, Razi University, Baq-e-Abrisham, Kermanshah, Islamic Republic of Iran
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7
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Noguera NI, Travaglini S, Scalea S, Catalanotto C, Reale A, Zampieri M, Zaza A, Ricciardi MR, Angelini DF, Tafuri A, Ottone T, Voso MT, Zardo G. YY1 Knockdown Relieves the Differentiation Block and Restores Apoptosis in AML Cells. Cancers (Basel) 2023; 15:4010. [PMID: 37568827 PMCID: PMC10417667 DOI: 10.3390/cancers15154010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 08/01/2023] [Accepted: 08/02/2023] [Indexed: 08/13/2023] Open
Abstract
In this study we analyzed the expression of Yin and Yang 1 protein (YY1), a member of the noncanonical PcG complexes, in AML patient samples and AML cell lines and the effect of YY1 downregulation on the AML differentiation block. Our results show that YY1 is significantly overexpressed in AML patient samples and AML cell lines and that YY1 knockdown relieves the differentiation block. YY1 downregulation in two AML cell lines (HL-60 and OCI-AML3) and one AML patient sample restored the expression of members of the CEBP protein family, increased the expression of extrinsic growth factors/receptors and surface antigenic markers, induced morphological cell characteristics typical of myeloid differentiation, and sensitized cells to retinoic acid treatment and to apoptosis. Overall, our data show that YY1 is not a secondary regulator of myeloid differentiation but that, if overexpressed, it can play a predominant role in myeloid differentiation block.
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Affiliation(s)
- Nelida Ines Noguera
- Department of Biomedicine and Prevention, Tor Vergata University, 00133 Rome, Italy; (S.T.); (T.O.); (M.T.V.)
- Unit of Neuro-Oncoematologia, Santa Lucia Foundation IRCCS, 00143 Rome, Italy
| | - Serena Travaglini
- Department of Biomedicine and Prevention, Tor Vergata University, 00133 Rome, Italy; (S.T.); (T.O.); (M.T.V.)
- Unit of Neuro-Oncoematologia, Santa Lucia Foundation IRCCS, 00143 Rome, Italy
| | - Stefania Scalea
- Department of Experimental Medicine, Sapienza University, 00185 Rome, Italy;
| | - Caterina Catalanotto
- Department of Molecular Medicine, Sapienza University, 00185 Rome, Italy; (C.C.); (A.R.); (M.Z.)
| | - Anna Reale
- Department of Molecular Medicine, Sapienza University, 00185 Rome, Italy; (C.C.); (A.R.); (M.Z.)
| | - Michele Zampieri
- Department of Molecular Medicine, Sapienza University, 00185 Rome, Italy; (C.C.); (A.R.); (M.Z.)
| | - Alessandra Zaza
- Unit of Neuro-Oncoematologia, Santa Lucia Foundation IRCCS, 00143 Rome, Italy
- Department of Medical and Surgical Sciences and Biotechnologies, Sapienza University, 00185 Rome, Italy
| | - Maria Rosaria Ricciardi
- Department of Clinical and Molecular Medicine, Sapienza University, 00185 Rome, Italy; (M.R.R.); (A.T.)
| | | | - Agostino Tafuri
- Department of Clinical and Molecular Medicine, Sapienza University, 00185 Rome, Italy; (M.R.R.); (A.T.)
| | - Tiziana Ottone
- Department of Biomedicine and Prevention, Tor Vergata University, 00133 Rome, Italy; (S.T.); (T.O.); (M.T.V.)
- Unit of Neuro-Oncoematologia, Santa Lucia Foundation IRCCS, 00143 Rome, Italy
| | - Maria Teresa Voso
- Department of Biomedicine and Prevention, Tor Vergata University, 00133 Rome, Italy; (S.T.); (T.O.); (M.T.V.)
- Unit of Neuro-Oncoematologia, Santa Lucia Foundation IRCCS, 00143 Rome, Italy
| | - Giuseppe Zardo
- Department of Experimental Medicine, Sapienza University, 00185 Rome, Italy;
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8
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Hosea R, Hillary S, Wu S, Kasim V. Targeting Transcription Factor YY1 for Cancer Treatment: Current Strategies and Future Directions. Cancers (Basel) 2023; 15:3506. [PMID: 37444616 DOI: 10.3390/cancers15133506] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 06/28/2023] [Accepted: 07/03/2023] [Indexed: 07/15/2023] Open
Abstract
Cancer represents a significant and persistent global health burden, with its impact underscored by its prevalence and devastating consequences. Whereas numerous oncogenes could contribute to cancer development, a group of transcription factors (TFs) are overactive in the majority of tumors. Targeting these TFs may also combat the downstream oncogenes activated by the TFs, making them attractive potential targets for effective antitumor therapeutic strategy. One such TF is yin yang 1 (YY1), which plays crucial roles in the development and progression of various tumors. In preclinical studies, YY1 inhibition has shown efficacy in inhibiting tumor growth, promoting apoptosis, and sensitizing tumor cells to chemotherapy. Recent studies have also revealed the potential of combining YY1 inhibition with immunotherapy for enhanced antitumor effects. However, clinical translation of YY1-targeted therapy still faces challenges in drug specificity and delivery. This review provides an overview of YY1 biology, its role in tumor development and progression, as well as the strategies explored for YY1-targeted therapy, with a focus on their clinical implications, including those using small molecule inhibitors, RNA interference, and gene editing techniques. Finally, we discuss the challenges and current limitations of targeting YY1 and the need for further research in this area.
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Affiliation(s)
- Rendy Hosea
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, China
- The 111 Project Laboratory of Biomechanics and Tissue Repair, College of Bioengineering, Chongqing University, Chongqing 400044, China
| | - Sharon Hillary
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, China
- The 111 Project Laboratory of Biomechanics and Tissue Repair, College of Bioengineering, Chongqing University, Chongqing 400044, China
| | - Shourong Wu
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, China
- The 111 Project Laboratory of Biomechanics and Tissue Repair, College of Bioengineering, Chongqing University, Chongqing 400044, China
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing University, Chongqing 400030, China
| | - Vivi Kasim
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, China
- The 111 Project Laboratory of Biomechanics and Tissue Repair, College of Bioengineering, Chongqing University, Chongqing 400044, China
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing University, Chongqing 400030, China
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9
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Abstract
Enhancers confer precise spatiotemporal patterns of gene expression in response to developmental and environmental stimuli. Over the last decade, the transcription of enhancer RNAs (eRNAs) – nascent RNAs transcribed from active enhancers – has emerged as a key factor regulating enhancer activity. eRNAs are relatively short-lived RNA species that are transcribed at very high rates but also quickly degraded. Nevertheless, eRNAs are deeply intertwined within enhancer regulatory networks and are implicated in a number of transcriptional control mechanisms. Enhancers show changes in function and sequence over evolutionary time, raising questions about the relationship between enhancer sequences and eRNA function. Moreover, the vast majority of single nucleotide polymorphisms associated with human complex diseases map to the non-coding genome, with causal disease variants enriched within enhancers. In this Primer, we survey the diverse roles played by eRNAs in enhancer-dependent gene expression, evaluating different models for eRNA function. We also explore questions surrounding the genetic conservation of enhancers and how this relates to eRNA function and dysfunction. Summary: This Primer evaluates the ideas that underpin developing models for eRNA function, exploring cases in which perturbed eRNA function contributes to disease.
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Affiliation(s)
- Laura J. Harrison
- Molecular and Cellular Biology, School of Biosciences, Sheffield Institute For Nucleic Acids, The University of Sheffield, Firth Court, Western Bank , Sheffield S10 2TN , UK
| | - Daniel Bose
- Molecular and Cellular Biology, School of Biosciences, Sheffield Institute For Nucleic Acids, The University of Sheffield, Firth Court, Western Bank , Sheffield S10 2TN , UK
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10
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Yang C, Yao J, Yi H, Huang X, Zhao W, Yang Z. To unwind the biological knots: The DNA/RNA G-quadruplex resolvase RHAU (DHX36) in development and disease. Animal Model Exp Med 2022; 5:542-549. [PMID: 35789129 PMCID: PMC9773310 DOI: 10.1002/ame2.12251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 04/21/2022] [Indexed: 12/30/2022] Open
Abstract
The G-quadruplex (G4) sequences are short fragments of 4-interval triple guanine (G) with frequent and ubiquitous distribution in the genome and RNA transcripts. The G4 sequences are usually folded into secondary "knot" structure via Hoogsteen hydrogen bond to exert negative regulation on a variety of biological processes, including DNA replication and transcription, mRNA translation, and telomere maintenance. Recent structural biological and mouse genetics studies have demonstrated that RHAU (DHX36) can bind and unwind the G4 "knots" to modulate embryonic development and postnatal organ function. Deficiency of RHAU gives rise to embryonic lethality, impaired organogenesis, and organ dysfunction. These studies uncovered the pivotal G4 resolvase function of RHAU to release the G4 barrier, which plays fundamental roles in development and physiological homeostasis. This review discusses the latest advancements and findings in deciphering RHAU functions using animal models.
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Affiliation(s)
- Chensi Yang
- State Key Laboratory of Pharmaceutical Biotechnology and Jiangsu Key Laboratory of Molecular MedicineNanjing University Medical SchoolNanjingChina
| | - Jie Yao
- State Key Laboratory of Pharmaceutical Biotechnology and Jiangsu Key Laboratory of Molecular MedicineNanjing University Medical SchoolNanjingChina
| | - Huijuan Yi
- State Key Laboratory of Pharmaceutical Biotechnology and Jiangsu Key Laboratory of Molecular MedicineNanjing University Medical SchoolNanjingChina
| | - Xinyi Huang
- State Key Laboratory of Pharmaceutical Biotechnology and Jiangsu Key Laboratory of Molecular MedicineNanjing University Medical SchoolNanjingChina
| | - Wukui Zhao
- State Key Laboratory of Pharmaceutical Biotechnology and Jiangsu Key Laboratory of Molecular MedicineNanjing University Medical SchoolNanjingChina
| | - Zhongzhou Yang
- State Key Laboratory of Pharmaceutical Biotechnology and Jiangsu Key Laboratory of Molecular MedicineNanjing University Medical SchoolNanjingChina
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11
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Zhou S, Li P, Qin L, Huang S, Dang N. Transcription factor YY1 contributes to human melanoma cell growth through modulating the p53 signaling pathway. Exp Dermatol 2022; 31:1563-1578. [PMID: 35730240 DOI: 10.1111/exd.14628] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 06/07/2022] [Accepted: 06/19/2022] [Indexed: 11/27/2022]
Abstract
BACKGROUND Melanoma has a higher mortality rate than any other skin cancer, and its cases are increasing. The transcription factor YY1 has been proven to be involved in tumor progression; however, the role of YY1 in melanoma is not well understood. METHODS This study investigates how YY1 functions in melanoma progression, and it also elucidates the underlying mechanisms involved. RESULTS We have found that in clinical human melanoma tissues, YY1 is overexpressed compared to YY1 expression in normal melanocytes and skin tissues. Cellular immunofluorescence shows that YY1 is mainly located in the nucleus. YY1 knockdown reduces proliferation, migration, and invasion of melanoma cell lines. Moreover, the apoptosis rate of cells is significantly increased in low-YY1 environments. The overexpression of YY1 resulted in decreased apoptotic rates in melanoma cells. YY1 also affects the expression of EMT-related proteins. Additional experiments reveal that YY1 knockdown disrupts the interaction of MDM2-p53, and that it both stabilizes and increases p53 activity. The upregulation of p53 expression in turn stimulates p21 expression just as it suppresses CDK4 expression, which then induces cells that were arrested in the G1 phase. The effect then is to constrain cell proliferation in melanoma cells. Upon activation of the p53 pathway, Bax, a pro-apoptotic protein, is upregulated, and Bcl-2, an anti-apoptotic protein, was downregulated in A375 cells. CONCLUSIONS The findings of this study provide novel insights into the pathology of melanoma as well as the role that YY1 plays in tumor progression. The findings also suggest that targeting YY1 has the potential to improve the diagnosis and treatment of melanoma.
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Affiliation(s)
- Shumin Zhou
- School of Clinical Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, China.,Linyi people's Hospital, Linyi, Shandong, China
| | - Pin Li
- Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Shandong, China
| | - Li Qin
- School of Clinical Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Shuhong Huang
- Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Shandong, China.,Institute of Basic Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Ningning Dang
- Department of Dermatology, Shandong Provincial Hospital Affiliated to Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, China
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12
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Cherik F, Reilly J, Kerkhof J, Levy M, McConkey H, Barat-Houari M, Butler KM, Coubes C, Lee JA, Le Guyader G, Louie RJ, Patterson WG, Tedder ML, Bak M, Hammer TB, Craigen W, Démurger F, Dubourg C, Fradin M, Franciskovich R, Frengen E, Friedman J, Palares NR, Iascone M, Misceo D, Monin P, Odent S, Philippe C, Rouxel F, Saletti V, Strømme P, Thulin PC, Sadikovic B, Genevieve D. DNA methylation episignature in Gabriele-de Vries syndrome. Genet Med 2022; 24:905-914. [PMID: 35027293 DOI: 10.1016/j.gim.2021.12.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 12/08/2021] [Indexed: 01/22/2023] Open
Abstract
PURPOSE Gabriele-de Vries syndrome (GADEVS) is a rare genetic disorder characterized by developmental delay and/or intellectual disability, hypotonia, feeding difficulties, and distinct facial features. To refine the phenotype and to better understand the molecular basis of the syndrome, we analyzed clinical data and performed genome-wide DNA methylation analysis of a series of individuals carrying a YY1 variant. METHODS Clinical data were collected for 13 individuals not yet reported through an international call for collaboration. DNA was collected for 11 of these individuals and 2 previously reported individuals in an attempt to delineate a specific DNA methylation signature in GADEVS. RESULTS Phenotype in most individuals overlapped with the previously described features. We described 1 individual with atypical phenotype, heterozygous for a missense variant in a domain usually not involved in individuals with YY1 pathogenic missense variations. We also described a specific peripheral blood DNA methylation profile associated with YY1 variants. CONCLUSION We reported a distinct DNA methylation episignature in GADEVS. We expanded the clinical profile of GADEVS to include thin/sparse hair and cryptorchidism. We also highlighted the utility of DNA methylation episignature analysis for classification of variants of unknown clinical significance.
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Affiliation(s)
- Florian Cherik
- Department of Medical Genetics, Reference Centre for Rare Diseases, Developmental Anomalies and Malformation Syndromes Sud-Est, Clermont-Ferrand University Hospital, Clermont-Ferrand, France
| | - Jack Reilly
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
| | - Jennifer Kerkhof
- Molecular Diagnostics Program and Verspeeten Clinical Genome Centre, London Health Sciences and Saint Joseph's Healthcare, London, Ontario, Canada
| | - Michael Levy
- Molecular Diagnostics Program and Verspeeten Clinical Genome Centre, London Health Sciences and Saint Joseph's Healthcare, London, Ontario, Canada
| | - Haley McConkey
- Molecular Diagnostics Program and Verspeeten Clinical Genome Centre, London Health Sciences and Saint Joseph's Healthcare, London, Ontario, Canada
| | - Mouna Barat-Houari
- Autoinflammatory and Rare Diseases Unit, Medical Genetic Department for Rare Diseases and Personalized Medicine, Centre Hospitalier Universitaire de Montpellier, Montpellier, France
| | - Kameryn M Butler
- Greenwood Genetic Center, JC Self Research Institute of Human Genetics, Greenwood, SC
| | - Christine Coubes
- Medical Genetic Department for Rare Diseases and Personalized Medicine, Montpellier University Hospital, Montpellier, France
| | - Jennifer A Lee
- Greenwood Genetic Center, JC Self Research Institute of Human Genetics, Greenwood, SC
| | - Gwenael Le Guyader
- Clinical Genetics Department, Poitiers University Hospital, Poitiers, France
| | - Raymond J Louie
- Greenwood Genetic Center, JC Self Research Institute of Human Genetics, Greenwood, SC
| | - Wesley G Patterson
- Greenwood Genetic Center, JC Self Research Institute of Human Genetics, Greenwood, SC
| | - Matthew L Tedder
- Greenwood Genetic Center, JC Self Research Institute of Human Genetics, Greenwood, SC
| | - Mads Bak
- Clinical genetic department, Righospitalet, Copenhagen, Denmark
| | - Trine Bjørg Hammer
- Clinical genetic department, Righospitalet, Copenhagen, Denmark; Epilepsy Genetics and Personalized Medicine, Danish Epilepsy Centre, Dianalund, Denmark
| | - William Craigen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Florence Démurger
- Medical Genetics Department, Bretagne-Atlantique Hospital, Vannes, France
| | - Christèle Dubourg
- Department of Molecular Genetics and Genomics, Rennes University Hospital, Rennes, France; Univ Rennes, CNRS, IGDR, UMR 6290, Rennes, France
| | - Mélanie Fradin
- Department of Clinical Genetics, Reference Centre for Rare Diseases, CLAD Ouest, Rennes University Hospital, Rennes, France
| | - Rachel Franciskovich
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Texas Children's Hospital, Houston, TX
| | - Eirik Frengen
- Department of Medical Genetics, Oslo University Hospitals and University of Oslo, Oslo, Norway
| | - Jennifer Friedman
- Departments of Neurosciences and Pediatrics, University of California San Diego, San Diego, CA; Division of Neurology, Rady Children's Hospital, San Diego, CA; Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA
| | - Nathalie Ruiz Palares
- Autoinflammatory and Rare Diseases Unit, Medical Genetic Department for Rare Diseases and Personalized Medicine, Centre Hospitalier Universitaire de Montpellier, Montpellier, France
| | - Maria Iascone
- Medical Genetics Laboratory, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Doriana Misceo
- Department of Medical Genetics, Oslo University Hospitals and University of Oslo, Oslo, Norway
| | - Pauline Monin
- Department of Medical Genetics, Women Mother Children Hospital, Hospices Civils de Lyon, Lyon, France
| | - Sylvie Odent
- Department of Medical Genetics, Reference Center for Developmental Anomalies, CLAD Ouest, Rennes University Hospital, ERN ITHACA, CNRS UMR 6290, Genetics and Development Institute, Rennes University, Rennes, France
| | - Christophe Philippe
- Functional Unit of Innovative Diagnosis for Rare Diseases, Dijon Bourgogne University Hospital, Dijon, France
| | - Flavien Rouxel
- Medical Genetic Department for Rare Diseases and Personalized Medicine, Montpellier University Hospital, Montpellier, France
| | - Veronica Saletti
- Developmental Neurology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Petter Strømme
- Division of Pediatric and Adolescent Medicine, Oslo University Hospital, and University of Oslo, Oslo, Norway
| | | | - Bekim Sadikovic
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada; Molecular Diagnostics Program and Verspeeten Clinical Genome Centre, London Health Sciences and Saint Joseph's Healthcare, London, Ontario, Canada.
| | - David Genevieve
- Medical Genetic Department for Rare Diseases and Personalized Medicine, Montpellier University Hospital, Montpellier, France.
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13
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Dual Role of YY1 in HPV Life Cycle and Cervical Cancer Development. Int J Mol Sci 2022; 23:ijms23073453. [PMID: 35408813 PMCID: PMC8998550 DOI: 10.3390/ijms23073453] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/15/2022] [Accepted: 03/16/2022] [Indexed: 01/27/2023] Open
Abstract
Human papillomaviruses (HPVs) are considered to be key etiological agents responsible for the induction and development of cervical cancer. However, it has been suggested that HPV infection alone may not be sufficient to promote cervical carcinogenesis, and other unknown factors might be required to establish the disease. One of the suggested proteins whose deregulation has been linked with oncogenesis is transcription factor Yin Yang 1 (YY1). YY1 is a multifunctional protein that is involved not only in the regulation of gene transcription and protein modification, but can also control important cell signaling pathways, such as cell growth, development, differentiation, and apoptosis. Vital functions of YY1 also indicate that the protein could be involved in tumorigenesis. The overexpression of this protein has been observed in different tumors, and its level has been correlated with poor prognoses of many types of cancers. YY1 can also regulate the transcription of viral genes. It has been documented that YY1 can bind to the HPV long control region and regulate the expression of viral oncogenes E6 and E7; however, its role in the HPV life cycle and cervical cancer development is different. In this review, we explore the role of YY1 in regulating the expression of cellular and viral genes and subsequently investigate how these changes inadvertently contribute toward the development of cervical malignancy.
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14
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Pabian-Jewuła S, Bragiel-Pieczonka A, Rylski M. Ying Yang 1 engagement in brain pathology. J Neurochem 2022; 161:236-253. [PMID: 35199341 DOI: 10.1111/jnc.15594] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 02/10/2022] [Accepted: 02/17/2022] [Indexed: 11/27/2022]
Abstract
Herein, we discuss data concerning the involvement of transcription factor Yin Yang 1 (YY1) in the development of brain diseases, highlighting mechanisms of its pathological actions. YY1 plays an important role in the developmental and adult pathology of the nervous system. YY1 is essential for neurulation as well as maintenance and differentiation of neuronal progenitor cells and oligodendrocytes regulating both neural and glial tissues of the brain. Lack of a YY1 gene causes many developmental abnormalities and anatomical malformations of the central nervous system (CNS). Once dysregulated, YY1 exerts multiple neuropathological actions being involved in the induction of many brain disorders like stroke, epilepsy, Alzheimer's and Parkinson's diseases, autism spectrum disorder, dystonia, and brain tumors. Better understanding of YY1's dysfunction in the nervous system may lead to the development of novel therapeutic strategies related to YY1's actions.
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Affiliation(s)
- Sylwia Pabian-Jewuła
- Department of Clinical Cytology, Centre of Postgraduate Medical Education, 99/103 Marymoncka Street, 01-813, Warsaw, Poland
| | - Aneta Bragiel-Pieczonka
- Department of Clinical Cytology, Centre of Postgraduate Medical Education, 99/103 Marymoncka Street, 01-813, Warsaw, Poland
| | - Marcin Rylski
- Department of Radiology, Institute of Psychiatry and Neurology, 9 Sobieski Street, Warsaw, Poland
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15
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Chen L, Qiao L, Guo Y, Huang Y, Luo W, Feng Y. Localization and regulatory function of Yin Yang 1 (YY1) in chicken testis. Mol Genet Genomics 2021; 297:113-123. [PMID: 34854981 DOI: 10.1007/s00438-021-01840-8] [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: 05/31/2021] [Accepted: 11/17/2021] [Indexed: 11/25/2022]
Abstract
In mammals, Yin Yang 1 (YY1), a pervasively expressed transcription factor related to many biological processes as an activator or inhibitor of the transcription of various genes, plays a critical role in the development of male gonads and spermatogenesis. Although the role of YY1 on the development of male gonads and spermatogenesis in mammals has been reported, its function on chicken testis are yet to be clarified. In this study, we used immunofluorescence analysis to investigate the location of YY1 in chicken testis. In embryo testis, YY1 was detected in spermatogonia and Sertoli cells, while in adult testis, YY1 was shown to be expressed in spermatogenic cells and Sertoli cells, but not in spermatozoa. Furthermore, we investigated the regulatory functions of YY1 in chicken testicular Sertoli cells by combining overexpression with RNA-sequencing. Overexpression of YY1 in Sertoli cells revealed a total of 2955 differentially expressed genes involved in various biological processes, such as male gonad development and seminiferous tubule development. Overexpression of YY1 also caused significant differences in the expression of the androgen receptor gene and the inhibin βA gene, two major genes involved in the regulation of spermatogonia in Sertoli cells. These observations indicate that YY1 may regulate the development and function of the gonads by affecting the secretion of cytokines and hormones in Sertoli cells to mediate the production and differentiation of spermatogonia.
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Affiliation(s)
- Ligen Chen
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology and College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Lingyun Qiao
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology and College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Yan Guo
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology and College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Ying Huang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology and College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Wei Luo
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology and College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Yanping Feng
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology and College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China.
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16
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Park SH, Fong KW, Mong E, Martin MC, Schiltz GE, Yu J. Going beyond Polycomb: EZH2 functions in prostate cancer. Oncogene 2021; 40:5788-5798. [PMID: 34349243 PMCID: PMC8487936 DOI: 10.1038/s41388-021-01982-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 07/20/2021] [Accepted: 07/22/2021] [Indexed: 02/07/2023]
Abstract
The Polycomb group (PcG) protein Enhancer of Zeste Homolog 2 (EZH2) is one of the three core subunits of the Polycomb Repressive Complex 2 (PRC2). It harbors histone methyltransferase activity (MTase) that specifically catalyze histone 3 lysine 27 (H3K27) methylation on target gene promoters. As such, PRC2 are epigenetic silencers that play important roles in cellular identity and embryonic stem cell maintenance. In the past two decades, mounting evidence supports EZH2 mutations and/or over-expression in a wide array of hematological cancers and solid tumors, including prostate cancer. Further, EZH2 is among the most upregulated genes in neuroendocrine prostate cancers, which become abundant due to the clinical use of high-affinity androgen receptor pathway inhibitors. While numerous studies have reported epigenetic functions of EZH2 that inhibit tumor suppressor genes and promote tumorigenesis, discordance between EZH2 and H3K27 methylation has been reported. Further, enzymatic EZH2 inhibitors have shown limited efficacy in prostate cancer, warranting a more comprehensive understanding of EZH2 functions. Here we first review how canonical functions of EZH2 as a histone MTase are regulated and describe the various mechanisms of PRC2 recruitment to the chromatin. We further outline non-histone substrates of EZH2 and discuss post-translational modifications to EZH2 itself that may affect substrate preference. Lastly, we summarize non-canonical functions of EZH2, beyond its MTase activity and/or PRC2, as a transcriptional cofactor and discuss prospects of its therapeutic targeting in prostate cancer.
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Affiliation(s)
- Su H Park
- Division of Hematology/Oncology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Ka-Wing Fong
- Division of Hematology/Oncology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY, USA
| | - Ezinne Mong
- Division of Hematology/Oncology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - M Cynthia Martin
- Department of Chemistry, Northwestern University, Evanston, IL, USA
| | - Gary E Schiltz
- Department of Chemistry, Northwestern University, Evanston, IL, USA
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, USA
| | - Jindan Yu
- Division of Hematology/Oncology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, USA.
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
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17
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Assumpção ALFV, Fu G, Singh DK, Lu Z, Kuehnl AM, Welch R, Ong IM, Wen R, Pan X. A lineage-specific requirement for YY1 Polycomb Group protein function in early T cell development. Development 2021; 148:dev.197319. [PMID: 33766932 DOI: 10.1242/dev.197319] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 03/12/2021] [Indexed: 01/22/2023]
Abstract
Yin Yang 1 (YY1) is a ubiquitous transcription factor and mammalian Polycomb Group protein (PcG) with important functions for regulating lymphocyte development and stem cell self-renewal. YY1 mediates stable PcG-dependent transcriptional repression via recruitment of PcG proteins that result in histone modifications. Many questions remain unanswered regarding how cell- and tissue-specificity is achieved by PcG proteins. Here, we demonstrate that a conditional knockout of Yy1 in the hematopoietic system results in an early T cell developmental blockage at the double negative (DN) 1 stage with reduced Notch1 signaling. There is a lineage-specific requirement for YY1 PcG function. YY1 PcG domain is required for T and B cell development but not necessary for myeloid cells. YY1 functions in early T cell development are multicomponent and involve both PcG-dependent and -independent regulations. Although YY1 promotes early T cell survival through its PcG function, its function to promote the DN1-to-DN2 transition and Notch1 expression and signaling is independent of its PcG function. Our results reveal how a ubiquitously expressed PcG protein mediates lineage-specific and context-specific functions to control early T cell development.
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Affiliation(s)
- Anna L F V Assumpção
- Department of Medical Sciences, School of Veterinary Medicine, University of Wisconsin, 2015 Linden Dr., Madison, WI 57306, USA.,Carbone Cancer Center, UW-Madison Blood Research Program, Madison, WI 53705, USA
| | - Guoping Fu
- Versiti, Blood Research Institute, 8701 Watertown Plank Road, Milwaukee, WI 53223, USA
| | - Deependra K Singh
- Department of Medical Sciences, School of Veterinary Medicine, University of Wisconsin, 2015 Linden Dr., Madison, WI 57306, USA.,Carbone Cancer Center, UW-Madison Blood Research Program, Madison, WI 53705, USA
| | - Zhanping Lu
- Department of Medical Sciences, School of Veterinary Medicine, University of Wisconsin, 2015 Linden Dr., Madison, WI 57306, USA.,Carbone Cancer Center, UW-Madison Blood Research Program, Madison, WI 53705, USA
| | - Ashley M Kuehnl
- Department of Medical Sciences, School of Veterinary Medicine, University of Wisconsin, 2015 Linden Dr., Madison, WI 57306, USA.,Carbone Cancer Center, UW-Madison Blood Research Program, Madison, WI 53705, USA
| | - Rene Welch
- Department of Obstetrics and Gynecology, University of Wisconsin School of Medicine and Public Health, 750 Highland Ave, Madison, WI 53705, USA.,Department of Biostatistics and Medical Informatics, University of Wisconsin School of Medicine and Public Health, 610 Walnut St, Madison, WI 53726, USA
| | - Irene M Ong
- Carbone Cancer Center, UW-Madison Blood Research Program, Madison, WI 53705, USA.,Department of Obstetrics and Gynecology, University of Wisconsin School of Medicine and Public Health, 750 Highland Ave, Madison, WI 53705, USA.,Department of Biostatistics and Medical Informatics, University of Wisconsin School of Medicine and Public Health, 610 Walnut St, Madison, WI 53726, USA
| | - Renren Wen
- Versiti, Blood Research Institute, 8701 Watertown Plank Road, Milwaukee, WI 53223, USA
| | - Xuan Pan
- Department of Medical Sciences, School of Veterinary Medicine, University of Wisconsin, 2015 Linden Dr., Madison, WI 57306, USA.,Carbone Cancer Center, UW-Madison Blood Research Program, Madison, WI 53705, USA
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18
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Katoch A, Tripathi SK, Pal A, Das S. Regulation of miR-186-YY1 axis by the p53 translational isoform ∆40p53: implications in cell proliferation. Cell Cycle 2021; 20:561-574. [PMID: 33629930 DOI: 10.1080/15384101.2021.1875670] [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] [Indexed: 02/01/2023] Open
Abstract
We have earlier shown that p53-FL and its translational isoform ∆40p53 are differentially regulated. In this study, we have investigated the cellular effect of ∆40p53 regulation on downstream gene expression, specifically miRNAs. Interestingly, ∆40p53 showed antagonistic regulation of miR-186-5p as compared to either p53 alone or a combination of both the isoforms. We have elucidated the miR-186-5p mediated effect of ∆40p53 in cell proliferation. Upon expression of ∆40p53, we observed a significant decrease in YY1 levels, an established target of miR-186-5p, which is involved in cell proliferation. Further assays with anti-miR-186 established the interdependence of ∆40p53- miR-186-5p-YY1- cell proliferation. The results unravel a new dimension toward the understanding of ∆40p53 functions, which seems to regulate cellular fate independent of p53FL.
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Affiliation(s)
- Aanchal Katoch
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Sachin Kumar Tripathi
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Apala Pal
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Saumitra Das
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India.,National Institute of Biomedical Genomics, Kalyani, India
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19
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Lee Yu K, Jung YM, Park SH, Lee SD, You JC. Human transcription factor YY1 could upregulate the HIV-1 gene expression. BMB Rep 2021. [PMID: 31818358 PMCID: PMC7262509 DOI: 10.5483/bmbrep.2020.53.5.222] [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] [Indexed: 11/25/2022] Open
Abstract
Gene expression in HIV-1 is regulated by the promoters in 5’ long-terminal repeat (LTR) element, which contain multiple DNA regulatory elements that serve as binding sites for cellular transcription factors. YY1 could repress HIV-1 gene expression and latent infection. Here, however, we observed that virus production can be increased by YY1 over-expression and decreased under YY1 depleted condition by siRNA treatment. To identify functional domain(s) of YY1 activation, we constructed a number of YY1 truncated mutants. Our data show that full-length YY1 enhances the viral transcription both through U3 and U3RU5 promoters. Moreover, the C-terminal region (296-414 residues) of YY1 is responsible for the transcriptional upregulation, which could be enhanced further in the presence of the viral Tat protein. The central domain of YY1 (155-295 residues) does not affect LTR activity but has a negative effect on HIV-1 gene expression. Taken together, our study shows that YY1 could act as a transcriptional activator in HIV-1 replication, at least in the early stages of infection.
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Affiliation(s)
- Kyung Lee Yu
- National Research Laboratory of Molecular Virology, Department of Pathology, The Catholic University of Korea, Seoul 63071, Korea
| | - Yu Mi Jung
- National Research Laboratory of Molecular Virology, Department of Pathology, The Catholic University of Korea, Seoul 63071, Korea
| | - Seong Hyun Park
- National Research Laboratory of Molecular Virology, Department of Pathology, The Catholic University of Korea, Seoul 63071, Korea
| | - Seong Deok Lee
- National Research Laboratory of Molecular Virology, Department of Pathology, The Catholic University of Korea, Seoul 63071, Korea
| | - Ji Chang You
- National Research Laboratory of Molecular Virology, Department of Pathology, The Catholic University of Korea, Seoul 63071, Korea
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20
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Obesity-linked circular RNA circTshz2-2 regulates the neuronal cell cycle and spatial memory in the brain. Mol Psychiatry 2021; 26:6350-6364. [PMID: 34561612 PMCID: PMC8760052 DOI: 10.1038/s41380-021-01303-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 09/06/2021] [Accepted: 09/09/2021] [Indexed: 12/26/2022]
Abstract
Metabolic syndromes, including obesity, cause neuropathophysiological changes in the brain, resulting in cognitive deficits. Only a few studies explored the contribution of non-coding genes in these pathophysiologies. Recently, we identified obesity-linked circular RNAs (circRNA) by analyzing the brain cortices of high-fat-fed obese mice. In this study, we scrutinized a conserved and neuron-specific circRNA, circTshz2-2, which affects neuronal cell cycle and spatial memory in the brain. Transcriptomic and cellular analysis indicated that circTshz2-2 dysregulation altered the expression of cell division-related genes and induced cell cycle arrest at the G2/M phase of the neuron. We found that circTshz2-2 bound to the YY1 transcriptional complex and suppressed Bdnf transcription. Suppression of circTshz2-2 increased BDNF expression and reduced G2/M checkpoint proteins such as Cyclin B2 and CDK1 through BDNF/TrkB signaling pathway, resulting in cell cycle arrest and neurite elongation. Inversely, overexpression of circTshz2-2 decreased BDNF expression, induced cell cycle proteins, and shortened the neurite length, indicating that circTshz2-2 regulates neuronal cell cycle and structure. Finally, we showed that circTshz2-2 affects spatial memory in wild-type and obese mice. Our data have revealed potential regulatory roles of obesity-related circTshz2-2 on the neuronal cell cycle and memory function providing a novel link between metabolic syndromes and cognitive deficits.
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21
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Verheul TCJ, van Hijfte L, Perenthaler E, Barakat TS. The Why of YY1: Mechanisms of Transcriptional Regulation by Yin Yang 1. Front Cell Dev Biol 2020; 8:592164. [PMID: 33102493 PMCID: PMC7554316 DOI: 10.3389/fcell.2020.592164] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 09/09/2020] [Indexed: 12/11/2022] Open
Abstract
First described in 1991, Yin Yang 1 (YY1) is a transcription factor that is ubiquitously expressed throughout mammalian cells. It regulates both transcriptional activation and repression, in a seemingly context-dependent manner. YY1 has a well-established role in the development of the central nervous system, where it is involved in neurogenesis and maintenance of homeostasis in the developing brain. In neurodevelopmental and neurodegenerative disease, the crucial role of YY1 in cellular processes in the central nervous system is further underscored. In this mini-review, we discuss the various mechanisms leading to the transcriptional activating and repressing roles of YY1, including its role as a traditional transcription factor, its interactions with cofactors and chromatin modifiers, the role of YY1 in the non-coding genome and 3D chromatin organization and the possible implications of the phase-separation mechanism on YY1 function. We provide examples on how these processes can be involved in normal development and how alterations can lead to various diseases.
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Affiliation(s)
- Thijs C J Verheul
- Department of Cell Biology, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - Levi van Hijfte
- Department of Neurology, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - Elena Perenthaler
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - Tahsin Stefan Barakat
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, Netherlands
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22
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Kang SJ, Chun T. Structural heterogeneity of the mammalian polycomb repressor complex in immune regulation. Exp Mol Med 2020; 52:1004-1015. [PMID: 32636442 PMCID: PMC8080698 DOI: 10.1038/s12276-020-0462-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 04/21/2020] [Accepted: 05/25/2020] [Indexed: 12/16/2022] Open
Abstract
Epigenetic regulation is mainly mediated by enzymes that can modify the structure of chromatin by altering the structure of DNA or histones. Proteins involved in epigenetic processes have been identified to study the detailed molecular mechanisms involved in the regulation of specific mRNA expression. Evolutionarily well-conserved polycomb group (PcG) proteins can function as transcriptional repressors by the trimethylation of histone H3 at the lysine 27 residue (H3K27me3) and the monoubiquitination of histone H2A at the lysine 119 residue (H2AK119ub). PcG proteins form two functionally distinct protein complexes: polycomb repressor complex 1 (PRC1) and PRC2. In mammals, the structural heterogeneity of each PRC complex is dramatically increased by several paralogs of its subunit proteins. Genetic studies with transgenic mice along with RNA-seq and chromatin immunoprecipitation (ChIP)-seq analyses might be helpful for defining the cell-specific functions of paralogs of PcG proteins. Here, we summarize current knowledge about the immune regulatory role of PcG proteins related to the compositional diversity of each PRC complex and introduce therapeutic drugs that target PcG proteins in hematopoietic malignancy. Protein complexes that suppress gene activity by remodeling chromatin, the substance that contains most of a cell’s DNA, play a critical role in regulating the immune system and provide a therapeutic target for treating blood cancers. Seok-Jin Kang and Taehoon Chun from Korea University in Seoul, South Korea, review how polycomb group proteins, best known for their function in embryonic development, also contribute to the formation of immune cells from blood stem cell precursors. Studies with stem cells and cancer cells have begun to reveal many targets of these proteins, and drug companies are evaluating candidate agents directed against some polycomb group proteins in patients with lymphoma and other cancers. More comprehensive profiling of protein function across a broad range of immune cell types could reveal new targets for additional diseases associated with immune dysfunction.
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Affiliation(s)
- Seok-Jin Kang
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Republic of Korea
| | - Taehoon Chun
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Republic of Korea.
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23
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Nandi S, Liang G, Sindhava V, Angireddy R, Basu A, Banerjee S, Hodawadekar S, Zhang Y, Avadhani NG, Sen R, Atchison ML. YY1 control of mitochondrial-related genes does not account for regulation of immunoglobulin class switch recombination in mice. Eur J Immunol 2020; 50:822-838. [PMID: 32092784 PMCID: PMC8287517 DOI: 10.1002/eji.201948385] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 12/30/2019] [Accepted: 02/18/2020] [Indexed: 12/18/2022]
Abstract
Immunoglobulin class switch recombination (CSR) occurs in activated B cells with increased mitochondrial mass and membrane potential. Transcription factor Yin Yang 1 (YY1) is critical for CSR and for formation of the DNA loops involved in this process. We therefore sought to determine if YY1 knockout impacts mitochondrial gene expression and mitochondrial function in murine splenic B cells, providing a potential mechanism for regulating CSR. We identified numerous genes in splenic B cells differentially regulated when cells are induced to undergo CSR. YY1 conditional knockout caused differential expression of 1129 genes, with 59 being mitochondrial-related genes. ChIP-seq analyses showed YY1 was directly bound to nearly half of these mitochondrial-related genes. Surprisingly, at the time when YY1 knockout dramatically reduces DNA loop formation and CSR, mitochondrial mass and membrane potential were not significantly impacted, nor was there a significant change in mitochondrial oxygen consumption, extracellular acidification rate, or mitochondrial complex I or IV activities. Our results indicate that YY1 regulates numerous mitochondrial-related genes in splenic B cells, but this does not account for the impact of YY1 on CSR or long-distance DNA loop formation.
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Affiliation(s)
- Satabdi Nandi
- School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Guanxiang Liang
- School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Vishal Sindhava
- School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Rajesh Angireddy
- School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Arindam Basu
- School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Sarmistha Banerjee
- School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Suchita Hodawadekar
- School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yue Zhang
- School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Narayan G. Avadhani
- School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ranjan Sen
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD, USA
| | - Michael L. Atchison
- School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
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24
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Abstract
At the nuclear periphery, associations of chromatin with the nuclear lamina through lamina-associated domains (LADs) aid functional organization of the genome. We review the organization of LADs and provide evidence of LAD heterogeneity from cell ensemble and single-cell data. LADs are typically repressive environments in the genome; nonetheless, we discuss findings of lamin interactions with regulatory elements of active genes, and the role lamins may play in genome regulation. We address the relationship between LADs and other genome organizers, and the involvement of LADs in laminopathies. The current data lay the basis for future studies on the significance of lamin-chromatin interactions in health and disease.
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Affiliation(s)
- Nolwenn Briand
- Department of Molecular Medicine, Faculty of Medicine, University of Oslo, PO Box 1112 Blindern, 0317, Oslo, Norway
- Department of Immunology and Transfusion Medicine, Oslo University Hospital, 0424, Oslo, Norway
| | - Philippe Collas
- Department of Molecular Medicine, Faculty of Medicine, University of Oslo, PO Box 1112 Blindern, 0317, Oslo, Norway.
- Department of Immunology and Transfusion Medicine, Oslo University Hospital, 0424, Oslo, Norway.
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25
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Qian S, Wang W, Li M. Transcriptional factor Yin Yang 1 facilitates the stemness of ovarian cancer via suppressing miR-99a activity through enhancing its deacetylation level. Biomed Pharmacother 2020; 126:110085. [PMID: 32199224 DOI: 10.1016/j.biopha.2020.110085] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 03/04/2020] [Accepted: 03/05/2020] [Indexed: 02/08/2023] Open
Abstract
The promoting effects of transcriptional factor Yin Yang 1 (YY1) have been confirmed in various tumors, however, its roles in ovarian cancer (OC) progression are still unclear. Here, Kaplan-Meier Plotter analysis was used to determine the correlation between YY1 expression and the survival of OC patients. It was found that YY1 expression was negatively correlated with the overall survival, progression-free survival and post-progression survival of OC patients. Functional experiments indicated that overexpression of YY1 facilitated the stemness of OC cells, while YY1 knockdown reduced it. MiRNAs-based RNA-sequencing analysis showed that miR-99a was the mostly upregulated miRNA in RNA extracted from OC cells with YY1 knockdown. Mechanistic studies revealed that YY1 recruited (Histone deacetylase) HDAC5 to the promoter of miR-99a, and subsequently enhanced miR-99a deacetylation level and decreased miR-99a level. Additionally, overexpression of miR-99a or knockdown of HDAC5 attenuated the promoting effects of YY1 on the stemness of OC cells. This work firstly indicated a novel YY1/miR-99a axis, which promotes the stemness of OC cells.
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Affiliation(s)
- Sumin Qian
- The Second Department of Gynecology, Cangzhou Central Hospital, 16 Xinhua West Road, Cangzhou, 061000, China.
| | - Wei Wang
- The Second Department of Gynecology, Cangzhou Central Hospital, 16 Xinhua West Road, Cangzhou, 061000, China
| | - Meng Li
- The Fifth Department of Neurology, The Brain Hospital of Cangzhou Central Hospital, 16 Xinhua West Road, Cangzhou, 061000, China
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26
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Meliala ITS, Hosea R, Kasim V, Wu S. The biological implications of Yin Yang 1 in the hallmarks of cancer. Theranostics 2020; 10:4183-4200. [PMID: 32226547 PMCID: PMC7086370 DOI: 10.7150/thno.43481] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Accepted: 02/09/2020] [Indexed: 12/24/2022] Open
Abstract
Tumorigenesis is a multistep process characterized by the acquisition of genetic and epigenetic alterations. During the course of malignancy development, tumor cells acquire several features that allow them to survive and adapt to the stress-related conditions of the tumor microenvironment. These properties, which are known as hallmarks of cancer, include uncontrolled cell proliferation, metabolic reprogramming, tumor angiogenesis, metastasis, and immune system evasion. Zinc-finger protein Yin Yang 1 (YY1) regulates numerous genes involved in cell death, cell cycle, cellular metabolism, and inflammatory response. YY1 is highly expressed in many cancers, whereby it is associated with cell proliferation, survival, and metabolic reprogramming. Furthermore, recent studies also have demonstrated the important role of YY1-related non-coding RNAs in acquiring cancer-specific characteristics. Therefore, these YY1-related non-coding RNAs are also crucial for YY1-mediated tumorigenesis. Herein, we summarize recent progress with respect to YY1 and its biological implications in the context of hallmarks of cancer.
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27
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Evolving Role of RING1 and YY1 Binding Protein in the Regulation of Germ-Cell-Specific Transcription. Genes (Basel) 2019; 10:genes10110941. [PMID: 31752312 PMCID: PMC6895862 DOI: 10.3390/genes10110941] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 11/07/2019] [Accepted: 11/14/2019] [Indexed: 12/11/2022] Open
Abstract
Separation of germline cells from somatic lineages is one of the earliest decisions of embryogenesis. Genes expressed in germline cells include apoptotic and meiotic factors, which are not transcribed in the soma normally, but a number of testis-specific genes are active in numerous cancer types. During germ cell development, germ-cell-specific genes can be regulated by specific transcription factors, retinoic acid signaling and multimeric protein complexes. Non-canonical polycomb repressive complexes, like ncPRC1.6, play a critical role in the regulation of the activity of germ-cell-specific genes. RING1 and YY1 binding protein (RYBP) is one of the core members of the ncPRC1.6. Surprisingly, the role of Rybp in germ cell differentiation has not been defined yet. This review is focusing on the possible role of Rybp in this process. By analyzing whole-genome transcriptome alterations of the Rybp-/- embryonic stem (ES) cells and correlating this data with experimentally identified binding sites of ncPRC1.6 subunits and retinoic acid receptors in ES cells, we propose a model how germ-cell-specific transcription can be governed by an RYBP centered regulatory network, underlining the possible role of RYBP in germ cell differentiation and tumorigenesis.
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28
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Wang AW, Wang YJ, Zahm AM, Morgan AR, Wangensteen KJ, Kaestner KH. The Dynamic Chromatin Architecture of the Regenerating Liver. Cell Mol Gastroenterol Hepatol 2019; 9:121-143. [PMID: 31629814 PMCID: PMC6909351 DOI: 10.1016/j.jcmgh.2019.09.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 09/19/2019] [Accepted: 09/23/2019] [Indexed: 12/12/2022]
Abstract
BACKGROUND & AIMS The adult liver is the main detoxification organ and routinely is exposed to environmental insults but retains the ability to restore its mass and function upon tissue damage. However, extensive injury can lead to liver failure, and chronic injury causes fibrosis, cirrhosis, and hepatocellular carcinoma. Currently, the transcriptional regulation of organ repair in the adult liver is incompletely understood. METHODS We isolated nuclei from quiescent as well as repopulating hepatocytes in a mouse model of hereditary tyrosinemia, which recapitulates the injury and repopulation seen in toxic liver injury in human beings. We then performed the assay for transposase accessible chromatin with high-throughput sequencing specifically in repopulating hepatocytes to identify differentially accessible chromatin regions and nucleosome positioning. In addition, we used motif analysis to predict differential transcription factor occupancy and validated the in silico results with chromatin immunoprecipitation followed by sequencing for hepatocyte nuclear factor 4α (HNF4α) and CCCTC-binding factor (CTCF). RESULTS Chromatin accessibility in repopulating hepatocytes was increased in the regulatory regions of genes promoting proliferation and decreased in the regulatory regions of genes involved in metabolism. The epigenetic changes at promoters and liver enhancers correspond with the regulation of gene expression, with enhancers of many liver function genes showing a less accessible state during the regenerative process. Moreover, increased CTCF occupancy at promoters and decreased HNF4α binding at enhancers implicate these factors as key drivers of the transcriptomic changes in replicating hepatocytes that enable liver repopulation. CONCLUSIONS Our analysis of hepatocyte-specific epigenomic changes during liver repopulation identified CTCF and HNF4α as key regulators of hepatocyte proliferation and regulation of metabolic programs. Thus, liver repopulation in the setting of toxic injury makes use of both general transcription factors (CTCF) for promoter activation, and reduced binding by a hepatocyte-enriched factor (HNF4α) to temporarily limit enhancer activity. All sequencing data in this study were deposited to the Gene Expression Omnibus database and can be downloaded with accession number GSE109466.
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Affiliation(s)
- Amber W Wang
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Yue J Wang
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Biomedical Sciences, Florida State University College of Medicine, Tallahassee, Florida
| | - Adam M Zahm
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Ashleigh R Morgan
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Kirk J Wangensteen
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Klaus H Kaestner
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania.
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29
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Lu Z, Hong CC, Kong G, Assumpção ALFV, Ong IM, Bresnick EH, Zhang J, Pan X. Polycomb Group Protein YY1 Is an Essential Regulator of Hematopoietic Stem Cell Quiescence. Cell Rep 2019; 22:1545-1559. [PMID: 29425509 PMCID: PMC6140794 DOI: 10.1016/j.celrep.2018.01.026] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 10/25/2017] [Accepted: 01/08/2018] [Indexed: 01/04/2023] Open
Abstract
Yin yang 1 (YY1) is a ubiquitous transcription factor and mammalian polycomb group protein (PcG) with important functions to regulate embryonic development, lineage differentiation, and cell proliferation. YY1 mediates stable PcG-dependent transcriptional repression via recruitment of PcG proteins that catalyze histone modifications. Many questions remain unanswered regarding how cell- and tissue-specificity is achieved by PcG proteins. Here, we demonstrate that a conditional knockout of Yy1 in hematopoietic stem cells (HSCs) decreases long-term repopulating activity and ectopic YY1 expression expands HSCs. Although the YY1 PcG domain is required for Igk chain rearrangement in B cells, the YY1 mutant lacking the PcG domain retained the capacity to stimulate HSC self-renewal. YY1 deficiency deregulated the genetic network governing HSC cell proliferation and impaired stem cell factor/c-Kit signaling, disrupting mechanisms conferring HSC quiescence. These results reveal a mechanism for how a ubiquitously expressed transcriptional repressor mediates lineage-specific functions to control adult hematopoiesis. Lu et al. investigate the function of the polycomb group (PcG) protein YY1 in hematopoietic stem cells. Independent of its REPO domain/PcG function, YY1 promotes hematopoietic stem cell selfrenewal and quiescence, suggesting that REPO domain/PcG function is not utilized in all contexts within the hematopoietic hierarchy.
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Affiliation(s)
- Zhanping Lu
- Department of Medical Sciences, School of Veterinary Medicine, University of Wisconsin, 2015 Linden Dr., Madison, WI 57306, USA; Carbone Cancer Center, UW-Madison Blood Research Program, Madison, WI 53706, USA
| | - Courtney C Hong
- Department of Medical Sciences, School of Veterinary Medicine, University of Wisconsin, 2015 Linden Dr., Madison, WI 57306, USA; Carbone Cancer Center, UW-Madison Blood Research Program, Madison, WI 53706, USA
| | - Guangyao Kong
- McArdle Laboratory for Cancer Research, University of Wisconsin School of Medicine and Public Health, 1111 Highland Ave., Madison, WI 53705, USA; National Local Joint Engineering Research Center of Biodiagnostics and Biotherapy, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, PRC; Carbone Cancer Center, UW-Madison Blood Research Program, Madison, WI 53706, USA
| | - Anna L F V Assumpção
- Department of Medical Sciences, School of Veterinary Medicine, University of Wisconsin, 2015 Linden Dr., Madison, WI 57306, USA; Carbone Cancer Center, UW-Madison Blood Research Program, Madison, WI 53706, USA
| | - Irene M Ong
- Department of Biostatistics and Medical Informatics, University of Wisconsin School of Medicine and Public Health, 1111 Highland Ave., Madison, WI 53705, USA; Carbone Cancer Center, UW-Madison Blood Research Program, Madison, WI 53706, USA
| | - Emery H Bresnick
- Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, 1111 Highland Ave., Madison, WI 53705, USA; Carbone Cancer Center, UW-Madison Blood Research Program, Madison, WI 53706, USA
| | - Jing Zhang
- McArdle Laboratory for Cancer Research, University of Wisconsin School of Medicine and Public Health, 1111 Highland Ave., Madison, WI 53705, USA; Carbone Cancer Center, UW-Madison Blood Research Program, Madison, WI 53706, USA
| | - Xuan Pan
- Department of Medical Sciences, School of Veterinary Medicine, University of Wisconsin, 2015 Linden Dr., Madison, WI 57306, USA; Carbone Cancer Center, UW-Madison Blood Research Program, Madison, WI 53706, USA.
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30
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Mikulski P, Hohenstatt ML, Farrona S, Smaczniak C, Stahl Y, Kaufmann K, Angenent G, Schubert D. The Chromatin-Associated Protein PWO1 Interacts with Plant Nuclear Lamin-like Components to Regulate Nuclear Size. THE PLANT CELL 2019; 31:1141-1154. [PMID: 30914470 PMCID: PMC6533023 DOI: 10.1105/tpc.18.00663] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 02/27/2019] [Accepted: 03/22/2019] [Indexed: 05/23/2023]
Abstract
Spatial organization of chromatin contributes to gene regulation of many cellular processes and includes a connection of chromatin with the nuclear lamina (NL). The NL is a protein mesh that resides underneath the inner nuclear membrane and consists of lamins and lamina-associated proteins. Chromatin regions associated with lamins in animals are characterized mostly by constitutive heterochromatin, but association with facultative heterochromatin mediated by Polycomb-group (PcG) proteins has been reported as well. In contrast with animals, plant NL components are largely not conserved and NL association with chromatin is poorly explored. Here, we present the connection between the lamin-like protein, CROWDED NUCLEI1 (CRWN1), and the chromatin- and PcG-associated component, PROLINE-TRYPTOPHANE-TRYPTOPHANE-PROLINE INTERACTOR OF POLYCOMBS1, in Arabidopsis (Arabidopsis thaliana). We show that PWO1 and CRWN1 proteins associate physically with each other, act in the same pathway to maintain nuclear morphology, and control expression of a similar set of target genes. Moreover, we demonstrate that transiently expressed PWO1 proteins form foci located partially at the subnuclear periphery. Ultimately, as CRWN1 and PWO1 are plant-specific, our results argue that plants might have developed an equivalent, rather than homologous, mechanism of linking chromatin repression and NL.
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Affiliation(s)
- Pawel Mikulski
- Institute for Biology, Freie Universität Berlin, Berlin 14195, Germany
- Institute for Biology, Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
| | - Mareike L Hohenstatt
- Institute for Biology, Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
| | - Sara Farrona
- Institute for Biology, Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
| | - Cezary Smaczniak
- Institute for Biology, Humboldt-University Berlin, Berlin 10115, Germany
- Laboratory of Molecular Biology, Wageningen University, Wageningen 6700 AP, The Netherlands
| | - Yvonne Stahl
- Institute for Biology, Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
| | - Kerstin Kaufmann
- Institute for Biology, Humboldt-University Berlin, Berlin 10115, Germany
- Laboratory of Molecular Biology, Wageningen University, Wageningen 6700 AP, The Netherlands
| | - Gerco Angenent
- Laboratory of Molecular Biology, Wageningen University, Wageningen 6700 AP, The Netherlands
| | - Daniel Schubert
- Institute for Biology, Freie Universität Berlin, Berlin 14195, Germany
- Institute for Biology, Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
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31
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Zhou X, Xian W, Zhang J, Zhu Y, Shao X, Han Y, Qi Y, Ding X, Wang X. YY1 binds to the E3' enhancer and inhibits the expression of the immunoglobulin κ gene via epigenetic modifications. Immunology 2018; 155:491-498. [PMID: 30098214 DOI: 10.1111/imm.12990] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Revised: 06/08/2018] [Accepted: 06/22/2018] [Indexed: 01/11/2023] Open
Abstract
The rearrangement and expression of immunoglobulin genes are regulated by enhancers and their binding transcriptional factors that activate or suppress the activities of the enhancers. The immunoglobulin κ (Igκ) gene locus has three important enhancers: the intrinsic enhancer (Ei), 3' enhancer (E3'), and distal enhancer (Ed). Ei and E3' are both required for Igκ gene rearrangement during early stages of B-cell development, whereas optimal expression of the rearranged Igκ gene relies on both E3' and Ed. The transcription factor YY1 affects the expression of many genes involved in B-cell development, probably by mediating interactions between their enhancers and promoters. Herein, we found that YY1 binds to the E3' enhancer and suppresses Igκ expression in B lymphoma cells by epigenetically modifying the enhancer. Knocking down YY1 enhanced Igκ expression, which was associated with increased levels of E2A (encoded by the TCF3 gene) and its binding to the E3' enhancer. Moreover, in germinal centre B cells and plasma cells, YY1 expression was reversely associated with Igκ levels, implying that YY1 might facilitate antibody affinity maturation in germinal centre B cells through the transient attenuation of Igκ expression.
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Affiliation(s)
- Xiaorong Zhou
- Department of Immunology, School of Medicine, Nantong University, Nantong, Jiangsu, China
| | - Weiwei Xian
- Department of Immunology, School of Medicine, Nantong University, Nantong, Jiangsu, China
| | - Jie Zhang
- Department of Immunology, School of Medicine, Nantong University, Nantong, Jiangsu, China
| | - Yiqing Zhu
- Department of Immunology, School of Medicine, Nantong University, Nantong, Jiangsu, China
| | - Xiaoyi Shao
- Department of Immunology, School of Medicine, Nantong University, Nantong, Jiangsu, China
| | - Yu Han
- Department of Occupational Medicine and Environmental Hygiene, School of Public Health, Nantong University, Nantong, Jiangsu, China
| | - Yue Qi
- Department of Immunology, School of Medicine, Nantong University, Nantong, Jiangsu, China
| | - Xiaoling Ding
- Department of Gastroenterology, The Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Xiaoying Wang
- Department of Immunology, School of Medicine, Nantong University, Nantong, Jiangsu, China
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32
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Chen ZS, Li L, Peng S, Chen FM, Zhang Q, An Y, Lin X, Li W, Koon AC, Chan TF, Lau KF, Ngo JCK, Wong WT, Kwan KM, Chan HYE. Planar cell polarity gene Fuz triggers apoptosis in neurodegenerative disease models. EMBO Rep 2018; 19:embr.201745409. [PMID: 30026307 DOI: 10.15252/embr.201745409] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 06/15/2018] [Accepted: 06/22/2018] [Indexed: 01/04/2023] Open
Abstract
Planar cell polarity (PCP) describes a cell-cell communication process through which individual cells coordinate and align within the plane of a tissue. In this study, we show that overexpression of Fuz, a PCP gene, triggers neuronal apoptosis via the dishevelled/Rac1 GTPase/MEKK1/JNK/caspase signalling axis. Consistent with this finding, endogenous Fuz expression is upregulated in models of polyglutamine (polyQ) diseases and in fibroblasts from spinocerebellar ataxia type 3 (SCA3) patients. The disruption of this upregulation mitigates polyQ-induced neurodegeneration in Drosophila We show that the transcriptional regulator Yin Yang 1 (YY1) associates with the Fuz promoter. Overexpression of YY1 promotes the hypermethylation of Fuz promoter, causing transcriptional repression of Fuz Remarkably, YY1 protein is recruited to ATXN3-Q84 aggregates, which reduces the level of functional, soluble YY1, resulting in Fuz transcriptional derepression and induction of neuronal apoptosis. Furthermore, Fuz transcript level is elevated in amyloid beta-peptide, Tau and α-synuclein models, implicating its potential involvement in other neurodegenerative diseases, such as Alzheimer's and Parkinson's diseases. Taken together, this study unveils a generic Fuz-mediated apoptotic cell death pathway in neurodegenerative disorders.
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Affiliation(s)
- Zhefan Stephen Chen
- Laboratory of Drosophila Research, School of Life Sciences Faculty of Science The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China.,Biochemistry Program, School of Life Sciences Faculty of Science The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
| | - Li Li
- Laboratory of Drosophila Research, School of Life Sciences Faculty of Science The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China.,Biochemistry Program, School of Life Sciences Faculty of Science The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
| | - Shaohong Peng
- Laboratory of Drosophila Research, School of Life Sciences Faculty of Science The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China.,Biochemistry Program, School of Life Sciences Faculty of Science The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
| | - Francis M Chen
- Cell and Molecular Biology Program, School of Life Sciences Faculty of Science The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
| | - Qian Zhang
- Laboratory of Drosophila Research, School of Life Sciences Faculty of Science The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China.,Biochemistry Program, School of Life Sciences Faculty of Science The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
| | - Ying An
- Laboratory of Drosophila Research, School of Life Sciences Faculty of Science The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China.,Biochemistry Program, School of Life Sciences Faculty of Science The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
| | - Xiao Lin
- Biochemistry Program, School of Life Sciences Faculty of Science The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
| | - Wen Li
- Biochemistry Program, School of Life Sciences Faculty of Science The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
| | - Alex Chun Koon
- Laboratory of Drosophila Research, School of Life Sciences Faculty of Science The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China.,Biochemistry Program, School of Life Sciences Faculty of Science The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
| | - Ting-Fung Chan
- Biochemistry Program, School of Life Sciences Faculty of Science The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China.,Cell and Molecular Biology Program, School of Life Sciences Faculty of Science The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China.,Molecular Biotechnology Program, School of Life Sciences, Faculty of Science, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China.,Gerald Choa Neuroscience Centre, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
| | - Kwok-Fai Lau
- Biochemistry Program, School of Life Sciences Faculty of Science The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China.,Cell and Molecular Biology Program, School of Life Sciences Faculty of Science The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China.,Molecular Biotechnology Program, School of Life Sciences, Faculty of Science, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
| | - Jacky Chi Ki Ngo
- Biochemistry Program, School of Life Sciences Faculty of Science The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China.,Cell and Molecular Biology Program, School of Life Sciences Faculty of Science The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
| | - Wing Tak Wong
- Cell and Molecular Biology Program, School of Life Sciences Faculty of Science The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
| | - Kin Ming Kwan
- Cell and Molecular Biology Program, School of Life Sciences Faculty of Science The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China.,Partner State Key Laboratory of Agrobiotechnology (CUHK), The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China.,Centre for Cell and Developmental Biology, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
| | - Ho Yin Edwin Chan
- Laboratory of Drosophila Research, School of Life Sciences Faculty of Science The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China .,Biochemistry Program, School of Life Sciences Faculty of Science The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China.,Cell and Molecular Biology Program, School of Life Sciences Faculty of Science The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China.,Molecular Biotechnology Program, School of Life Sciences, Faculty of Science, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China.,Gerald Choa Neuroscience Centre, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
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Zhao W, Liu M, Ji H, Zhu Y, Wang C, Huang Y, Ma X, Xing G, Xia Y, Jiang Q, Qin J. The polycomb group protein Yaf2 regulates the pluripotency of embryonic stem cells in a phosphorylation-dependent manner. J Biol Chem 2018; 293:12793-12804. [PMID: 29959227 DOI: 10.1074/jbc.ra118.003299] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 06/25/2018] [Indexed: 01/04/2023] Open
Abstract
The polycomb group (PcG) proteins are key epigenetic regulators in stem cell maintenance. PcG proteins have been thought to act through one of two polycomb repressive complexes (PRCs), but more recent biochemical analyses have challenged this model in the identification of noncanonical PRC1 (nc-PRC1) complexes characterized by the presence of Rybp or Yaf2 in place of the canonical Chromobox proteins. However, the biological significance of these nc-PRC1s and the potential mechanisms by which they mediate gene repression are largely unknown. Here, we explore the functional consequences of Yaf2 disruption on stem cell regulation. We show that deletion of Yaf2 results in compromised proliferation and abnormal differentiation of mouse embryonic stem cells (mESCs). Genome-wide profiling indicates Yaf2 functions primarily as a transcriptional repressor, particularly impacting genes associated with ectoderm cell fate in a manner distinct from Rybp. We confirm that Yaf2 assembles into a noncanonical PRC complex, with deletion analysis identifying the region encompassing amino acid residues 102-150 as required for this assembly. Furthermore, we identified serine 166 as a Yaf2 phosphorylation site, and we demonstrate that mutation of this site to alanine (S166A) compromises Ring1B-mediated H2A monoubiquitination and in turn its ability to repress target gene expression. We therefore propose that Yaf2 and its phosphorylation status serve as dual regulators to maintain the pluripotent state in mESCs.
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Affiliation(s)
- Wukui Zhao
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Nanjing University, Nanjing 210032
| | - Mengjie Liu
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Nanjing University, Nanjing 210032
| | - Haijing Ji
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095
| | - Yaru Zhu
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Nanjing University, Nanjing 210032
| | - Congcong Wang
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Nanjing University, Nanjing 210032
| | - Yikai Huang
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Nanjing University, Nanjing 210032
| | - Xiaoqi Ma
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Nanjing University, Nanjing 210032
| | - Guangdong Xing
- Institute of Animal Science, Jiangsu Academy of Agricultural Sciences, Nanjing 210014
| | - Yin Xia
- School of Biomedical Sciences, Chinese University of Hong Kong, Hong Kong
| | - Qing Jiang
- Department of Sports Medicine and Adult Reconstructive Surgery, Nanjing Drum Tower Hospital Affiliated to Medical School of Nanjing University, Nanjing 210008, China
| | - Jinzhong Qin
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Nanjing University, Nanjing 210032.
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34
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From Flies to Mice: The Emerging Role of Non-Canonical PRC1 Members in Mammalian Development. EPIGENOMES 2018. [DOI: 10.3390/epigenomes2010004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
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35
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Syrett CM, Sindhava V, Hodawadekar S, Myles A, Liang G, Zhang Y, Nandi S, Cancro M, Atchison M, Anguera MC. Loss of Xist RNA from the inactive X during B cell development is restored in a dynamic YY1-dependent two-step process in activated B cells. PLoS Genet 2017; 13:e1007050. [PMID: 28991910 PMCID: PMC5648283 DOI: 10.1371/journal.pgen.1007050] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Revised: 10/19/2017] [Accepted: 09/28/2017] [Indexed: 12/05/2022] Open
Abstract
X-chromosome inactivation (XCI) in female lymphocytes is uniquely regulated, as the inactive X (Xi) chromosome lacks localized Xist RNA and heterochromatin modifications. Epigenetic profiling reveals that Xist RNA is lost from the Xi at the pro-B cell stage and that additional heterochromatic modifications are gradually lost during B cell development. Activation of mature B cells restores Xist RNA and heterochromatin to the Xi in a dynamic two-step process that differs in timing and pattern, depending on the method of B cell stimulation. Finally, we find that DNA binding domain of YY1 is necessary for XCI in activated B cells, as ex-vivo YY1 deletion results in loss of Xi heterochromatin marks and up-regulation of X-linked genes. Ectopic expression of the YY1 zinc finger domain is sufficient to restore Xist RNA localization during B cell activation. Together, our results indicate that Xist RNA localization is critical for maintaining XCI in female lymphocytes, and that chromatin changes on the Xi during B cell development and the dynamic nature of YY1-dependent XCI maintenance in mature B cells predisposes X-linked immunity genes to reactivation. Females are predisposed to develop various autoimmune disorders, and the genetic basis for this susceptibility is the X-chromosome. X-linked genes are dosage compensated between sexes by X-chromosome Inactivation (XCI) during embryogenesis and maintained into adulthood. Here we show that the chromatin of the inactive X loses epigenetic modifications during B cell lineage development. We found that female mature B cells, which are the pathogenic cells in autoimmunity, have a dynamic two-step mechanism of maintaining XCI during stimulation. The transcription factor YY1, which regulates DNA looping during V(D)J recombination in B cells, is necessary for relocalizing Xist RNA back to the inactive X in activated B cells. YY1 deletion ex vivo in mature B cells impairs heterochromatin mark enrichment on the inactive X, and results in increased X-linked gene expression. We demonstrate that the DNA binding domain of YY1 is sufficient for localizing Xist RNA to the inactive X during B cell stimulation. Our study indicates that Xist RNA localization is critical for maintaining XCI in female lymphocytes. We propose that chromatin changes on the Xi during B cell development and the dynamic nature of YY1-dependent XCI maintenance in mature B cells predisposes X-linked immunity genes to reactivation.
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Affiliation(s)
- Camille M. Syrett
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia PA, United States of America
| | - Vishal Sindhava
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia PA, United States of America
- Department of Pathology, School of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America
| | - Suchita Hodawadekar
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia PA, United States of America
| | - Arpita Myles
- Department of Pathology, School of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America
| | - Guanxiang Liang
- Department of Pathology, School of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America
| | - Yue Zhang
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia PA, United States of America
| | - Satabdi Nandi
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia PA, United States of America
| | - Michael Cancro
- Department of Pathology, School of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America
| | - Michael Atchison
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia PA, United States of America
| | - Montserrat C. Anguera
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia PA, United States of America
- * E-mail:
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36
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Toda T, Hsu JY, Linker SB, Hu L, Schafer ST, Mertens J, Jacinto FV, Hetzer MW, Gage FH. Nup153 Interacts with Sox2 to Enable Bimodal Gene Regulation and Maintenance of Neural Progenitor Cells. Cell Stem Cell 2017; 21:618-634.e7. [PMID: 28919367 DOI: 10.1016/j.stem.2017.08.012] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 06/17/2017] [Accepted: 08/16/2017] [Indexed: 12/14/2022]
Abstract
Neural progenitor cells (NeuPCs) possess a unique nuclear architecture that changes during differentiation. Nucleoporins are linked with cell-type-specific gene regulation, coupling physical changes in nuclear structure to transcriptional output; but, whether and how they coordinate with key fate-determining transcription factors is unclear. Here we show that the nucleoporin Nup153 interacts with Sox2 in adult NeuPCs, where it is indispensable for their maintenance and controls neuronal differentiation. Genome-wide analyses show that Nup153 and Sox2 bind and co-regulate hundreds of genes. Binding of Nup153 to gene promoters or transcriptional end sites correlates with increased or decreased gene expression, respectively, and inhibiting Nup153 expression alters open chromatin configurations at its target genes, disrupts genomic localization of Sox2, and promotes differentiation in vitro and a gliogenic fate switch in vivo. Together, these findings reveal that nuclear structural proteins may exert bimodal transcriptional effects to control cell fate.
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Affiliation(s)
- Tomohisa Toda
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Jonathan Y Hsu
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Sara B Linker
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Lauren Hu
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Simon T Schafer
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Jerome Mertens
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Filipe V Jacinto
- Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Martin W Hetzer
- Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Fred H Gage
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA.
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Gregoire S, Li G, Sturzu AC, Schwartz RJ, Wu SM. YY1 Expression Is Sufficient for the Maintenance of Cardiac Progenitor Cell State. Stem Cells 2017; 35:1913-1923. [PMID: 28580685 DOI: 10.1002/stem.2646] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 03/22/2017] [Accepted: 04/17/2017] [Indexed: 01/19/2023]
Abstract
During cardiac development, DNA binding transcription factors and epigenetic modifiers regulate gene expression in cardiac progenitor cells (CPCs). We have previously shown that Yin Yang 1 (YY1) is essential for the commitment of mesodermal precursors into CPCs. However, the role of YY1 in the maintenance of CPC phenotype and their differentiation into cardiomyocytes is unknown. In this study, we found, by genome-wide transcriptional profiling and phenotypic assays, that YY1 overexpression prevents cardiomyogenic differentiation and maintains the proliferative capacity of CPCs. We show further that the ability of YY1 to regulate CPC phenotype is associated with its ability to modulate histone modifications specifically at a developmentally critical enhancer of Nkx2-5 and other key cardiac transcription factor such as Tbx5. Specifically, YY1 overexpression helps to maintain markers of gene activation such as the acetylation of histone H3 at lysine 9 (H3K9Ac) and lysine 27 (H3K27Ac) as well as trimethylation at lysine 4 (H3K4Me3) at the Nkx2-5 cardiac enhancer. Furthermore, transcription factors associated proteins such as PoIII, p300, and Brg1 are also enriched at the Nkx2-5 enhancer with YY1 overexpression. The biological activities of YY1 in CPCs appear to be cell autonomous, based coculture assays in differentiating embryonic stem cells. Altogether, these results demonstrate that YY1 overexpression is sufficient to maintain a CPC phenotype through its ability to sustain the presence of activating epigenetic/chromatin marks at key cardiac enhancers. Stem Cells 2017;35:1913-1923.
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Affiliation(s)
- Serge Gregoire
- Cardiovascular Research Center, Division of Cardiology, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Guang Li
- Cardiovascular Institute, Institute of Stem Cell and Regenerative Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Anthony C Sturzu
- Cardiovascular Research Center, Division of Cardiology, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Robert J Schwartz
- Texas Heart Institute and Center for Molecular Medicine and Experimental Therapeutics, University of Houston, Houston, Texas, USA
| | - Sean M Wu
- Cardiovascular Institute, Institute of Stem Cell and Regenerative Biology, Stanford University School of Medicine, Stanford, California, USA.,Division of Cardiovascular Medicine, Department of Medicine, Institute of Stem Cell and Regenerative Biology, Stanford University School of Medicine, Stanford, California, USA
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Kim JS, Chae JH, Cheon YP, Kim CG. Reciprocal localization of transcription factors YY1 and CP2c in spermatogonial stem cells and their putative roles during spermatogenesis. Acta Histochem 2016; 118:685-692. [PMID: 27612612 DOI: 10.1016/j.acthis.2016.08.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2016] [Revised: 08/24/2016] [Accepted: 08/24/2016] [Indexed: 01/12/2023]
Abstract
Maintaining stemness and permitting differentiation mediated by combinations of transcription factors (TFs) are key aspects of mammalian spermatogenesis. It has been established that yin yang 1 (YY1), a target factor of mammalian polycomb repressive complex 2 (PRC2) and a regulator of stemness, is involved in the stable maintenance of prophase stage spermatocytes. Recently, we have demonstrated that the TF CP2c partners with YY1 in some cells to antagonistically regulate the other protein's function. To date, the functional roles of YY1 and CP2c in spermatogonial stem cells and their derived germ cells remain unclear. Here, we investigated the expression of YY1 and CP2c in mouse gonocytes and germ cells using tissue immunohistochemical and immunofluorescence analyses. At E14.5, both YY1 and CP2c were stained in gonocytes and Sertoli cells in testicular cords, showing different proportion and density of immunoreactivity. However, in adult testes, YY1 was localized in the nuclei of spermatogonial stem cells and spermatocytes, but not in spermatozoa. It was also detected in spermatogonia and spermatids in a stage-specific manner during spermatogenic cycle. CP2c could be detected mostly in the cytoplasm of spermatocytes but not at all in spermatogonial stem cells, indicating mutually exclusive expression of CP2c and YY1. Interestingly, however, CP2c was stained in the cytoplasm and nucleus of spermatogonia at elongation and release stages, and co-localized with YY1 in the nucleus at grouping, maturation, and releasing stages. Neither YY1 nor CP2c was expressed in spermatozoa. Our data indicate that YY1 strongly localizes in the spermatogonial stem cells and co-localizes heterogeneously with CP2c to permit spermatogenesis, and also suggest that YY1 is essential for stemness of spermatogonial stem cells (SCs) whereas CP2c is critical for the commitment of spermatogonia and during the progression of spermatogonia to spermatids. This evaluation expands our understanding of the molecular mechanism of spermatogonia formation as well as spermatogenesis in general.
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Abstract
Ying Yang 1 (YY1) is a ubiquitously expressed transcription factor shown to be essential for pro-B-cell development. However, the role of YY1 in other B-cell populations has never been investigated. Recent bioinformatics analysis data have implicated YY1 in the germinal center (GC) B-cell transcriptional program. In accord with this prediction, we demonstrated that deletion of YY1 by Cγ1-Cre completely prevented differentiation of GC B cells and plasma cells. To determine if YY1 was also required for the differentiation of other B-cell populations, we deleted YY1 with CD19-Cre and found that all peripheral B-cell subsets, including B1 B cells, require YY1 for their differentiation. Transitional 1 (T1) B cells were the most dependent upon YY1, being sensitive to even a half-dosage of YY1 and also to short-term YY1 deletion by tamoxifen-induced Cre. We show that YY1 exerts its effects, in part, by promoting B-cell survival and proliferation. ChIP-sequencing shows that YY1 predominantly binds to promoters, and pathway analysis of the genes that bind YY1 show enrichment in ribosomal functions, mitochondrial functions such as bioenergetics, and functions related to transcription such as mRNA splicing. By RNA-sequencing analysis of differentially expressed genes, we demonstrated that YY1 normally activates genes involved in mitochondrial bioenergetics, whereas it normally down-regulates genes involved in transcription, mRNA splicing, NF-κB signaling pathways, the AP-1 transcription factor network, chromatin remodeling, cytokine signaling pathways, cell adhesion, and cell proliferation. Our results show the crucial role that YY1 plays in regulating broad general processes throughout all stages of B-cell differentiation.
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Abstract
YY1 has been implicated as a master regulator of germinal center B cell development as YY1 binding sites are frequently present in promoters of germinal center-expressed genes. YY1 is known to be important for other stages of B cell development including the pro-B and pre-B cells stages. To determine if YY1 plays a critical role in germinal center development, we evaluated YY1 expression during B cell development, and used a YY1 conditional knock-out approach for deletion of YY1 in germinal center B cells (CRE driven by the immunoglobulin heavy chain γ1 switch region promoter; γ1-CRE). We found that YY1 is most highly expressed in germinal center B cells and is increased 3 fold in splenic B cells activated by treatment with anti-IgM and anti-CD40. In addition, deletion of the yy1 gene by action of γ1-CRE recombinase resulted in significant loss of GC cells in both un-immunized and immunized contexts with corresponding loss of serum IgG1. Our results show a crucial role for YY1 in the germinal center reaction.
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Unusual maintenance of X chromosome inactivation predisposes female lymphocytes for increased expression from the inactive X. Proc Natl Acad Sci U S A 2016; 113:E2029-38. [PMID: 27001848 DOI: 10.1073/pnas.1520113113] [Citation(s) in RCA: 186] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Females have a greater immunological advantage than men, yet they are more prone to autoimmune disorders. The basis for this sex bias lies in the X chromosome, which contains many immunity-related genes. Female mammals use X chromosome inactivation (XCI) to generate a transcriptionally silent inactive X chromosome (Xi) enriched with heterochromatic modifications and XIST/Xist RNA, which equalizes gene expression between the sexes. Here, we examine the maintenance of XCI in lymphocytes from females in mice and humans. Strikingly, we find that mature naïve T and B cells have dispersed patterns of XIST/Xist RNA, and they lack the typical heterochromatic modifications of the Xi. In vitro activation of lymphocytes triggers the return of XIST/Xist RNA transcripts and some chromatin marks (H3K27me3, ubiquitin-H2A) to the Xi. Single-cell RNA FISH analysis of female T cells revealed that the X-linked immunity genes CD40LG and CXCR3 are biallelically expressed in some cells. Using knockout and knockdown approaches, we find that Xist RNA-binding proteins, YY1 and hnRNPU, are critical for recruitment of XIST/Xist RNA back to the Xi. Furthermore, we examined B cells from patients with systemic lupus erythematosus, an autoimmune disorder with a strong female bias, and observed different XIST RNA localization patterns, evidence of biallelic expression of immunity-related genes, and increased transcription of these genes. We propose that the Xi in female lymphocytes is predisposed to become partially reactivated and to overexpress immunity-related genes, providing the first mechanistic evidence to our knowledge for the enhanced immunity of females and their increased susceptibility for autoimmunity.
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Shiu WL, Huang KR, Hung JC, Wu JL, Hong JR. Knockdown of zebrafish YY1a can downregulate the phosphatidylserine (PS) receptor expression, leading to induce the abnormal brain and heart development. J Biomed Sci 2016; 23:31. [PMID: 26924789 PMCID: PMC4770675 DOI: 10.1186/s12929-016-0248-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 02/16/2016] [Indexed: 01/08/2023] Open
Abstract
Background Yin Yang 1 (YY1) is a ubiquitously expressed GLI-Kruppel zinc finger-containing transcriptional regulator. YY1 plays a fundamental role in normal biologic processes such as embryogenesis, differentiation, and cellular proliferation. YY1 effects on the genes involved in these processes are mediated via initiation, activation, or repression of transcription depending upon the context in which it binds. The role of the multifunctional transcription factor Yin Yang 1 (YY1) in tissue development is poorly understood. In the present, we investigated YY1a role in developing zebrafish on PSR-mediated apoptotic cell engulfment during organic morphogenesis. Results YY1a is first expressed 0.5 h post-fertilization (hpf), in the whole embryo 12 hpf, and in brain, eyes, and heart 72 hpf by in situ hybridization assay. The nucleotide sequence of zebrafish YY1a transcription factor (clone zfYY1a; HQ 166834) was found to be similar to that of zebrafish YY1a (99 % sequence identity; NM 212617). With the loss-of-function assay, YY1a knockdown by a morpholino oligonucleotide led to downregulation of the phosphatidylserine engulfing receptor zfPSR during embryonic segmentation and to the accumulation of a large number of dead apoptotic cells throughout the entire early embryo, especially in the posterior area. Up to 24 hpf, these cells interfered with embryonic cell migration and cell-cell interactions that normally occur in the brain, heart, eye, and notochord. Finally, with gain-of-function assay, defective morphants could be rescued by injecting both YY1a mRNA and PSR mRNA and trigger resumption of normal development. Conclusions Taken together, our results suggest that YY1a regulates PS receptor expression that linked to function of PSR-phagocyte mediated apoptotic cell engulfment during development, especially the development of organs such as the brain and heart. YY1a/PSR-mediated engulfing system may involve in diseases.
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Affiliation(s)
- Wei-Lun Shiu
- Laboratory of Molecular Virology and Biotechnology, Institute of Biotechnology, National Cheng Kung University, Tainan, 701, Taiwan, ROC
| | - Kuan-Rong Huang
- Laboratory of Molecular Virology and Biotechnology, Institute of Biotechnology, National Cheng Kung University, Tainan, 701, Taiwan, ROC
| | - Jo-Chi Hung
- Laboratory of Molecular Virology and Biotechnology, Institute of Biotechnology, National Cheng Kung University, Tainan, 701, Taiwan, ROC
| | - Jen-Leih Wu
- Laboratory of Marine Molecular Biology and Biotechnology, Institute of Cellular and Organismic Biology, Academia Sinica, Nankang, Taipei, 115, Taiwan, ROC
| | - Jiann-Ruey Hong
- Laboratory of Molecular Virology and Biotechnology, Institute of Biotechnology, National Cheng Kung University, Tainan, 701, Taiwan, ROC.
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43
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Abstract
The role of genome architecture in transcription regulation has become the focus of an increasing number of studies over the past decade. Chromatin organization can have a significant impact on gene expression by promoting or restricting the physical proximity between regulatory DNA elements. Given that any change in chromatin state has the potential to alter DNA folding and the proximity between control elements, the spatial organization of chromatin is inherently linked to its molecular composition. In this review, we explore how modulators of chromatin state and organization might keep gene expression in check. We discuss recent findings and present some of the less well-studied aspects of spatial genome organization such as chromatin dynamics and regulation by non-coding RNAs.
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44
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Harr JC, Gonzalez-Sandoval A, Gasser SM. Histones and histone modifications in perinuclear chromatin anchoring: from yeast to man. EMBO Rep 2016; 17:139-55. [PMID: 26792937 PMCID: PMC4783997 DOI: 10.15252/embr.201541809] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 12/21/2015] [Indexed: 01/01/2023] Open
Abstract
It is striking that within a eukaryotic nucleus, the genome can assume specific spatiotemporal distributions that correlate with the cell's functional states. Cell identity itself is determined by distinct sets of genes that are expressed at a given time. On the level of the individual gene, there is a strong correlation between transcriptional activity and associated histone modifications. Histone modifications act by influencing the recruitment of non-histone proteins and by determining the level of chromatin compaction, transcription factor binding, and transcription elongation. Accumulating evidence also shows that the subnuclear position of a gene or domain correlates with its expression status. Thus, the question arises whether this spatial organization results from or determines a gene's chromatin status. Although the association of a promoter with the inner nuclear membrane (INM) is neither necessary nor sufficient for repression, the perinuclear sequestration of heterochromatin is nonetheless conserved from yeast to man. How does subnuclear localization influence gene expression? Recent work argues that the common denominator between genome organization and gene expression is the modification of histones and in some cases of histone variants. This provides an important link between local chromatin structure and long-range genome organization in interphase cells. In this review, we will evaluate how histones contribute to the latter, and discuss how this might help to regulate genes crucial for cell differentiation.
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Affiliation(s)
- Jennifer C Harr
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Adriana Gonzalez-Sandoval
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland Faculty of Natural Sciences, University of Basel, Basel, Switzerland
| | - Susan M Gasser
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland Faculty of Natural Sciences, University of Basel, Basel, Switzerland
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Brown Adipose YY1 Deficiency Activates Expression of Secreted Proteins Linked to Energy Expenditure and Prevents Diet-Induced Obesity. Mol Cell Biol 2015; 36:184-96. [PMID: 26503783 DOI: 10.1128/mcb.00722-15] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 10/12/2015] [Indexed: 01/26/2023] Open
Abstract
Mitochondrial oxidative and thermogenic functions in brown and beige adipose tissues modulate rates of energy expenditure. It is unclear, however, how beige or white adipose tissue contributes to brown fat thermogenic function or compensates for partial deficiencies in this tissue and protects against obesity. Here, we show that the transcription factor Yin Yang 1 (YY1) in brown adipose tissue activates the canonical thermogenic and uncoupling gene expression program. In contrast, YY1 represses a series of secreted proteins, including fibroblast growth factor 21 (FGF21), bone morphogenetic protein 8b (BMP8b), growth differentiation factor 15 (GDF15), angiopoietin-like 6 (Angptl6), neuromedin B, and nesfatin, linked to energy expenditure. Despite substantial decreases in mitochondrial thermogenic proteins in brown fat, mice lacking YY1 in this tissue are strongly protected against diet-induced obesity and exhibit increased energy expenditure and oxygen consumption in beige and white fat depots. The increased expression of secreted proteins correlates with elevation of energy expenditure and promotion of beige and white fat activation. These results indicate that YY1 in brown adipose tissue controls antagonistic gene expression programs associated with energy balance and maintenance of body weight.
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The quest for mammalian Polycomb response elements: are we there yet? Chromosoma 2015; 125:471-96. [PMID: 26453572 PMCID: PMC4901126 DOI: 10.1007/s00412-015-0539-4] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Revised: 08/31/2015] [Accepted: 09/02/2015] [Indexed: 12/12/2022]
Abstract
A long-standing mystery in the field of Polycomb and Trithorax regulation is how these proteins, which are highly conserved between flies and mammals, can regulate several hundred equally highly conserved target genes, but recognise these targets via cis-regulatory elements that appear to show no conservation in their DNA sequence. These elements, termed Polycomb/Trithorax response elements (PRE/TREs or PREs), are relatively well characterised in flies, but their mammalian counterparts have proved to be extremely difficult to identify. Recent progress in this endeavour has generated a wealth of data and raised several intriguing questions. Here, we ask why and to what extent mammalian PREs are so different to those of the fly. We review recent advances, evaluate current models and identify open questions in the quest for mammalian PREs.
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Yin-Yang 1 and Yin-Yang 2 exert opposing effects on the promoter activity of interleukin 4. Arch Pharm Res 2015; 39:547-554. [PMID: 26345265 DOI: 10.1007/s12272-015-0622-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 06/01/2015] [Indexed: 10/23/2022]
Abstract
Interleukin (IL)-4 acts on T cells as a growth and activation factor, and promotes the differentiation of type 2 T helper cells. In T cells, expression of the gene encoding IL-4 is regulated by inducible or constitutive factors. Yin-Yang (YY)-1 is one of constitutive transcription factors binding to the IL-4 promoter. The recently identified YY2 protein is similar to YY1, with both sharing high levels of homology in their zinc finger motifs. However, the role of YY2 in T cells is unclear. YY1 and YY2 were constitutively expressed in EL4 T cells, and their expression was not dependent on stimulation. IL-4 promoter (-741/+56 fragment) activity was enhanced by YY1, but inhibited by YY2. The enhanced IL-4 promoter activity by YY1 was reduced by simultaneous expression of YY2. In addition, the DNA binding affinity of YY1 to the IL-4 promoter was adversely affected by YY2. Our results suggest that YY1 and YY2 exert opposing effects on the IL-4 promoter as they compete for the same DNA binding sites.
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Kang H, McElroy KA, Jung YL, Alekseyenko AA, Zee BM, Park PJ, Kuroda MI. Sex comb on midleg (Scm) is a functional link between PcG-repressive complexes in Drosophila. Genes Dev 2015; 29:1136-50. [PMID: 26063573 PMCID: PMC4470282 DOI: 10.1101/gad.260562.115] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
In this study, Kang et al. investigate how PcG complexes form repressive chromatin domains. The findings show that Scm, a transcriptional repressor, is an important regulator of PRC1, PRC2, and transcriptional silencing and suggest that Scm coordinates PcG complexes and polymerizes, resulting in PcG silencing. The Polycomb group (PcG) proteins are key regulators of development in Drosophila and are strongly implicated in human health and disease. How PcG complexes form repressive chromatin domains remains unclear. Using cross-linked affinity purifications of BioTAP-Polycomb (Pc) or BioTAP-Enhancer of zeste [E(z)], we captured all PcG-repressive complex 1 (PRC1) or PRC2 core components and Sex comb on midleg (Scm) as the only protein strongly enriched with both complexes. Although previously not linked to PRC2, we confirmed direct binding of Scm and PRC2 using recombinant protein expression and colocalization of Scm with PRC1, PRC2, and H3K27me3 in embryos and cultured cells using ChIP-seq (chromatin immunoprecipitation [ChIP] combined with deep sequencing). Furthermore, we found that RNAi knockdown of Scm and overexpression of the dominant-negative Scm-SAM (sterile α motif) domain both affected the binding pattern of E(z) on polytene chromosomes. Aberrant localization of the Scm-SAM domain in long contiguous regions on polytene chromosomes revealed its independent ability to spread on chromatin, consistent with its previously described ability to oligomerize in vitro. Pull-downs of BioTAP-Scm captured PRC1 and PRC2 and additional repressive complexes, including PhoRC, LINT, and CtBP. We propose that Scm is a key mediator connecting PRC1, PRC2, and transcriptional silencing. Combined with previous structural and genetic analyses, our results strongly suggest that Scm coordinates PcG complexes and polymerizes to produce broad domains of PcG silencing.
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Affiliation(s)
- Hyuckjoon Kang
- Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Kyle A McElroy
- Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA; Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Youngsook Lucy Jung
- Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA; Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Artyom A Alekseyenko
- Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Barry M Zee
- Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Peter J Park
- Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA; Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Mitzi I Kuroda
- Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA;
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Wang W, Qin JJ, Voruganti S, Nag S, Zhou J, Zhang R. Polycomb Group (PcG) Proteins and Human Cancers: Multifaceted Functions and Therapeutic Implications. Med Res Rev 2015; 35:1220-67. [PMID: 26227500 DOI: 10.1002/med.21358] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Polycomb group (PcG) proteins are transcriptional repressors that regulate several crucial developmental and physiological processes in the cell. More recently, they have been found to play important roles in human carcinogenesis and cancer development and progression. The deregulation and dysfunction of PcG proteins often lead to blocking or inappropriate activation of developmental pathways, enhancing cellular proliferation, inhibiting apoptosis, and increasing the cancer stem cell population. Genetic and molecular investigations of PcG proteins have long been focused on their PcG functions. However, PcG proteins have recently been shown to exert non-classical-Pc-functions, contributing to the regulation of diverse cellular functions. We and others have demonstrated that PcG proteins regulate the expression and function of several oncogenes and tumor suppressor genes in a PcG-independent manner, and PcG proteins are associated with the survival of patients with cancer. In this review, we summarize the recent advances in the research on PcG proteins, including both the Pc-repressive and non-classical-Pc-functions. We specifically focus on the mechanisms by which PcG proteins play roles in cancer initiation, development, and progression. Finally, we discuss the potential value of PcG proteins as molecular biomarkers for the diagnosis and prognosis of cancer, and as molecular targets for cancer therapy.
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Affiliation(s)
- Wei Wang
- Department of Pharmaceutical Sciences, School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, TX, 79106.,Center for Cancer Biology and Therapy, School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, TX, 79106
| | - Jiang-Jiang Qin
- Department of Pharmaceutical Sciences, School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, TX, 79106
| | - Sukesh Voruganti
- Department of Pharmaceutical Sciences, School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, TX, 79106
| | - Subhasree Nag
- Department of Pharmaceutical Sciences, School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, TX, 79106
| | - Jianwei Zhou
- Department of Molecular Cell Biology and Toxicology, Cancer Center, School of Public Health, Nanjing Medical University, Nanjing, 210029, P. R. China
| | - Ruiwen Zhang
- Department of Pharmaceutical Sciences, School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, TX, 79106.,Center for Cancer Biology and Therapy, School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, TX, 79106
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Inoue K, Fry EA, Frazier DP. Transcription factors that interact with p53 and Mdm2. Int J Cancer 2015; 138:1577-85. [PMID: 26132471 DOI: 10.1002/ijc.29663] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 06/22/2015] [Indexed: 01/21/2023]
Abstract
The tumor suppressor p53 is activated upon cellular stresses such as DNA damage, oncogene activation, hypoxia, which transactivates sets of genes that induce DNA repair, cell cycle arrest, apoptosis, or autophagy, playing crucial roles in the prevention of tumor formation. The central regulator of the p53 pathway is Mdm2 which inhibits transcriptional activity, nuclear localization and protein stability. More than 30 cellular p53-binding proteins have been isolated and characterized including Mdm2, Mdm4, p300, BRCA1/2, ATM, ABL and 53BP-1/2. Most of them are nuclear proteins; however, not much is known about p53-binding transcription factors. In this review, we focus on transcription factors that directly interact with p53/Mdm2 through direct binding including Dmp1, E2F1, YB-1 and YY1. Dmp1 and YB-1 bind only to p53 while E2F1 and YY1 bind to both p53 and Mdm2. Dmp1 has been shown to bind to p53 and block all the known functions for Mdm2 on p53 inhibition, providing a secondary mechanism for tumor suppression in Arf-null cells. Although E2F1-p53 binding provides a checkpoint mechanism to silence hyperactive E2F1, YB-1 or YY1 interaction with p53 subverts the activity of p53, contributing to cell cycle progression and tumorigenesis. Thus, the modes and consequences for each protein-protein interaction vary from the viewpoint of tumor development and suppression.
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Affiliation(s)
- Kazushi Inoue
- Department of Pathology, Wake Forest University School of Medicine, Medical Center Boulevard, Winston-Salem, NC, 27157
| | - Elizabeth A Fry
- Department of Pathology, Wake Forest University School of Medicine, Medical Center Boulevard, Winston-Salem, NC, 27157
| | - Donna P Frazier
- Department of Pathology, Wake Forest University School of Medicine, Medical Center Boulevard, Winston-Salem, NC, 27157
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