151
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He GH, Liu SD, Shi XQ, Chen Y, Su L, Shi QN, Sun C. rs77283072 influences breast cancer susceptibility by regulating CDKN2A expression. Oncol Lett 2023; 25:76. [PMID: 36742366 PMCID: PMC9853096 DOI: 10.3892/ol.2023.13662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 11/25/2022] [Indexed: 01/06/2023] Open
Abstract
Breast cancer is the cancer type with the highest morbidity rates in women, and previous genome-wide association studies (GWASs) have suggested that the single nucleotide polymorphism (SNP) rs1011970 is significantly associated with this disease. An analysis of data from the 1000 Genomes Project demonstrated that there is an SNP, rs77283072, in almost complete linkage disequilibrium with rs1011970, which should therefore present the same signal in a GWAS. However, the actual causal SNP and its associated underlying mechanism have yet to be elucidated. Therefore, the present study evaluated the role of rs77283072 in terms of its association with breast cancer. A dual-luciferase assay was performed, which demonstrated that the two alleles of rs1011970 did not exhibit significantly different reporter gene activity. However, the A allele of rs77283072 exhibited a significant increase in relative luciferase activity compared with the G allele, which suggested that rs77283072 was the causal SNP for breast cancer. Chromosome conformation capture demonstrated that the enhancer containing rs77283072 interacted with the promoter of cyclin-dependent kinase inhibitor 2A (CDKN2A). Furthermore, expression quantitative trait locus analysis demonstrated that the expression of CDKN2A was dependent on the genotype of rs77283072. Taken together, the findings of the present study provided novel insights into the mechanism underlying how the genetic variation in this locus was able to influence breast cancer susceptibility and further the treatment for this disease.
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Affiliation(s)
- Guang-Huan He
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, P.R. China
| | - Shao-Dong Liu
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, P.R. China
| | - Xiao-Qian Shi
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, P.R. China
| | - Ying Chen
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, P.R. China
| | - Li Su
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, P.R. China
| | - Qiao-Na Shi
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, P.R. China,Correspondence to: Dr Chang Sun or Ms. Qiao-Na Shi, College of Life Sciences, Shaanxi Normal University, 620 West Chang'an Road, Xi'an, Shaanxi 710119, P.R. China, E-mail:
| | - Chang Sun
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, P.R. China,Correspondence to: Dr Chang Sun or Ms. Qiao-Na Shi, College of Life Sciences, Shaanxi Normal University, 620 West Chang'an Road, Xi'an, Shaanxi 710119, P.R. China, E-mail:
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152
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Furlan G, Huyghe A, Combémorel N, Lavial F. Molecular versatility during pluripotency progression. Nat Commun 2023; 14:68. [PMID: 36604434 PMCID: PMC9814743 DOI: 10.1038/s41467-022-35775-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 12/22/2022] [Indexed: 01/07/2023] Open
Abstract
A challenge during development is to ensure lineage segregation while preserving plasticity. Using pluripotency progression as a paradigm, we review how developmental transitions are coordinated by redeployments, rather than global resettings, of cellular components. We highlight how changes in response to extrinsic cues (FGF, WNT, Activin/Nodal, Netrin-1), context- and stoichiometry-dependent action of transcription factors (Oct4, Nanog) and reconfigurations of epigenetic regulators (enhancers, promoters, TrxG, PRC) may confer robustness to naïve to primed pluripotency transition. We propose the notion of Molecular Versatility to regroup mechanisms by which molecules are repurposed to exert different, sometimes opposite, functions in close stem cell configurations.
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Affiliation(s)
- Giacomo Furlan
- Cellular reprogramming, stem cells and oncogenesis laboratory - Equipe labellisée La Ligue Contre le Cancer - LabEx Dev2Can - Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon, Lyon, 69008, France
- Lunenfeld-Tanenbaum Research Institute, University of Toronto, Toronto, ON, Canada
| | - Aurélia Huyghe
- Cellular reprogramming, stem cells and oncogenesis laboratory - Equipe labellisée La Ligue Contre le Cancer - LabEx Dev2Can - Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon, Lyon, 69008, France
| | - Noémie Combémorel
- Cellular reprogramming, stem cells and oncogenesis laboratory - Equipe labellisée La Ligue Contre le Cancer - LabEx Dev2Can - Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon, Lyon, 69008, France
| | - Fabrice Lavial
- Cellular reprogramming, stem cells and oncogenesis laboratory - Equipe labellisée La Ligue Contre le Cancer - LabEx Dev2Can - Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon, Lyon, 69008, France.
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153
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Qin W, Xie Y, Ren Z, Xu C, Sun MA, Yin Z, Bao W. Integrative ATAC-seq and RNA-seq analyses of IPEC-J2 cells reveals porcine transcription and chromatin accessibility changes associated with Escherichia coli F18ac inhibited by Lactobacillus reuteri. Front Microbiol 2023; 14:1101111. [PMID: 36876070 PMCID: PMC9978113 DOI: 10.3389/fmicb.2023.1101111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Accepted: 01/30/2023] [Indexed: 02/18/2023] Open
Abstract
Escherichia coli is the main cause of postweaning diarrhea in pigs, leading to economic loss. As a probiotic, Lactobacillus reuteri has been used to inhibit E. coli in clinical applications; however, its integrative interactions with hosts remain unclear, especially in pigs. Here, we found that L. reuteri effectively inhibited E. coli F18ac adhering to porcine IPEC-J2 cells, and explored the genome-wide transcription and chromatin accessibility landscapes of IPEC-J2 cells by RNA-seq and ATAC-seq. The results showed that some key signal transduction pathways, such as PI3K-AKT and MAPK signaling pathways, were enriched in the differentially expressed genes (DEGs) between E. coli F18ac treatment with and without L. reuteri groups. However, we found less overlap between RNA-seq and ATAC-seq datasets; we speculated that this might be caused by histones modification through ChIP-qPCR detection. Furthermore, we identified the regulation of the actin cytoskeleton pathway and a number of candidate genes (ARHGEF12, EGFR, and DIAPH3) that might be associated with the inhibition of E. coli F18ac adherence to IPEC-J2 cells by L. reuteri. In conclusion, we provide a valuable dataset that can be used to seek potential porcine molecular markers of E. coli F18ac pathogenesis and L. reuteri antibacterial activity, and to guide the antibacterial application of L. reuteri.
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Affiliation(s)
- Weiyun Qin
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China.,College of Veterinary Medicine, Institute of Comparative Medicine, Yangzhou University, Yangzhou, China
| | - Yunxiao Xie
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Zhanshi Ren
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Chao Xu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Ming-An Sun
- College of Veterinary Medicine, Institute of Comparative Medicine, Yangzhou University, Yangzhou, China
| | - Zongjun Yin
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, China
| | - Wenbin Bao
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
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154
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Nguyen HT, Martin LJ. The transcription factors Junb and Fosl2 cooperate to regulate Cdh3 expression in 15P-1 Sertoli cells. Mol Reprod Dev 2023; 90:27-41. [PMID: 36468795 DOI: 10.1002/mrd.23656] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 10/31/2022] [Accepted: 11/18/2022] [Indexed: 12/12/2022]
Abstract
In Sertoli cells of the testis, cadherins (Cdh) are important cell-to-cell interaction proteins and contribute to the formation of the blood-testis barrier being essential for germ cells' protection. P-cadherin or Cdh3 is only expressed in Sertoli cells from embryonic to prepubertal development. Interestingly, the expression profile of Cdh3 correlates with that of activating protein-1 (AP-1) transcription factors during Sertoli cells development. To assess their potential implications in the regulation of Cdh3, different AP-1 transcription factors were overexpressed in 15P-1 Sertoli cells. We found that the overexpressions of Junb and Fosl2 activated Cdh3 promoter. ChIP-qPCR assay and luciferase reporter assay with 5' promoter deletions and site-directed mutagenesis confirmed the recruitment of Junb and Fosl2 to an AP-1 regulatory element at -47 bp in the proximal region of Cdh3 promoter in 15P-1 cells. These findings were further supported by histone modification markers and chromatin accessibility surrounding Cdh3 promoter in mouse testis. Moreover, the knockdowns of Junb and/or Fosl2 by siRNA decreased Cdh3 protein levels. Taken together, these data suggest that in 15P-1 Sertoli cells, the AP-1 family members Junb and Fosl2 are responsible for the regulation of Cdh3 expression, which requires the recruitment of both factors to the proximal region of the Cdh3 promoter.
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Affiliation(s)
- Ha T Nguyen
- Department of Biology, Université de Moncton, Moncton, New Brunswick, Canada
| | - Luc J Martin
- Department of Biology, Université de Moncton, Moncton, New Brunswick, Canada
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155
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Sreekar N, Shrestha S. Bioinformatic Evaluation of Features on Cis-regulatory Elements at 6q25.1. Bioinform Biol Insights 2023; 17:11779322231167971. [PMID: 37124129 PMCID: PMC10134125 DOI: 10.1177/11779322231167971] [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: 12/18/2022] [Accepted: 03/17/2023] [Indexed: 05/02/2023] Open
Abstract
Eukaryotic non-coding regulatory features contribute significantly to cellular plasticity which on aberration leads to cellular malignancy. Enhancers are cis-regulatory elements that contribute to the development of resistance to endocrine therapy in estrogen receptor (ER)-positive breast cancer leading to poor clinical outcome. ER is vital for therapeutic targets in ER-positive breast cancer. Here, we review and report the different regulatory features present on ER with the objective to delineate potential mechanisms which may contribute to development of resistance. The UCSC Genome Browser, data mining, and bioinformatics tools were used to review enhancers, transcription factors (TFs), histone marks, long non-coding RNAs (lncRNAs), and variants residing in the non-coding region of the ER gene. We report 7 enhancers, 3 of which were rich in TF-binding sites and histone marks in a cell line-specific manner. Furthermore, some enhancers contain estrogen resistance variants and sites for lncRNA. Our review speculates putative models suggesting potential aberrations in gene regulation and expression if these regulatory landscapes and assemblies are altered. This review gives an interesting perspective in designing integrated in vitro studies including non-coding elements to study development of endocrine resistance in ER-positive breast cancer.
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Affiliation(s)
| | - Smeeta Shrestha
- Smeeta Shrestha, Lee Kong Chian School of Medicine, Nanyang Technological University (NTU), 636921, Singapore.
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156
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Chen G, Chen P, Zhou J, Luo G. Pan-Cancer Analysis of Histone Methyltransferase KMT2D with Potential Implications for Prognosis and Immunotherapy in Human Cancer. Comb Chem High Throughput Screen 2023; 26:83-92. [PMID: 35189794 DOI: 10.2174/1386207325666220221092318] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 12/13/2021] [Accepted: 12/21/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Pan-cancer analysis is an efficient tool to obtain a panoramic view of cancer- related genes and identify their oncogenic processes, facilitating the development of new therapeutic targets. Lysine methyltransferase 2D (KMT2D), acting as a major enhancer coactivator for mammalian cells, is one of the most frequently mutated genes across various cancer types and is considered an oncogene and a rationale for epigenetic therapeutic targets. OBJECTIVE This study was designed to explore the potential role of KMT2D in human cancer through a pan-cancer analysis. METHODS The expression of KMT2D was assessed in normal tissues and cell lines, and pancancers from The Cancer Genome Atlas (TCGA), Cancer Cell Line Encyclopedia (CCLE), and Genotype-Tissue Expression (GTE) datasets were used to explore its correlation with prognosis, immune cell infiltration, tumor mutation burden, microsatellite instability, and mismatch repair. RESULTS KMT2D expression was heterogeneous across different cancer types. Increased KMT2D indicated a worse prognosis in adrenocortical carcinoma (ACC), brain lower-grade glioma (LGG), and mesothelioma (MESO), while patients with high KMT2D expression showed better outcomes in renal clear cell carcinoma (KIRC). Moreover, KMT2D expression was positively correlated with immune cell infiltration and negative tumor mutation burden in multiple cancers. In addition, a significant correlation between KMT2D and immune checkpoint-related genes or mismatch repair genes was identified. CONCLUSIONS These findings support the hypothesis that KMT2D is not only a potential biomarker for prognosis and immunotherapy response prediction but also an essential immune regulator in human cancer.
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Affiliation(s)
- Guoning Chen
- Department of Urology, Zhongshan Hospital, Xiamen University, Xiamen, Fujian, China
| | - Peijie Chen
- Department of Urology, Zhongshan Hospital, Xiamen University, Xiamen, Fujian, China
| | - Jianwen Zhou
- Department of Urology, Zhongshan Hospital, Xiamen University, Xiamen, Fujian, China
| | - Guangcheng Luo
- Department of Urology, Zhongshan Hospital, Xiamen University, Xiamen, Fujian, China
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157
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Preissl S, Gaulton KJ, Ren B. Characterizing cis-regulatory elements using single-cell epigenomics. Nat Rev Genet 2023; 24:21-43. [PMID: 35840754 PMCID: PMC9771884 DOI: 10.1038/s41576-022-00509-1] [Citation(s) in RCA: 65] [Impact Index Per Article: 65.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2022] [Indexed: 12/24/2022]
Abstract
Cell type-specific gene expression patterns and dynamics during development or in disease are controlled by cis-regulatory elements (CREs), such as promoters and enhancers. Distinct classes of CREs can be characterized by their epigenomic features, including DNA methylation, chromatin accessibility, combinations of histone modifications and conformation of local chromatin. Tremendous progress has been made in cataloguing CREs in the human genome using bulk transcriptomic and epigenomic methods. However, single-cell epigenomic and multi-omic technologies have the potential to provide deeper insight into cell type-specific gene regulatory programmes as well as into how they change during development, in response to environmental cues and through disease pathogenesis. Here, we highlight recent advances in single-cell epigenomic methods and analytical tools and discuss their readiness for human tissue profiling.
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Affiliation(s)
- Sebastian Preissl
- Center for Epigenomics, University of California San Diego, La Jolla, CA, USA.
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
| | - Kyle J Gaulton
- Department of Paediatrics, Paediatric Diabetes Research Center, University of California San Diego, La Jolla, CA, USA.
| | - Bing Ren
- Center for Epigenomics, University of California San Diego, La Jolla, CA, USA.
- Department of Cellular and Molecular Medicine, University of California San Diego, School of Medicine, La Jolla, CA, USA.
- Ludwig Institute for Cancer Research, La Jolla, CA, USA.
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158
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Liu YT, Romero C, Xiao X, Guo L, Zhou X, Applebaum MA, Xu L, Skapek SX. Methyltransferase Inhibition Enables Tgf β Driven Induction of CDKN2A and B in Cancer Cells. Mol Cell Biol 2023; 43:115-129. [PMID: 36941772 PMCID: PMC10038032 DOI: 10.1080/10985549.2023.2186074] [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: 08/14/2022] [Revised: 12/21/2022] [Accepted: 02/20/2023] [Indexed: 03/23/2023] Open
Abstract
CDKN2A/B deletion or silencing is common across human cancer, reinforcing the general importance of bypassing its tumor suppression in cancer formation or progression. In rhabdomyosarcoma (RMS) and neuroblastoma, two common childhood cancers, the three CDKN2A/B transcripts are independently expressed to varying degrees, but one, ARF, is uniformly silenced. Although TGFβ induces certain CDKN2A/B transcripts in HeLa cells, it was unable to do so in five tested RMS lines unless the cells were pretreated with a broadly acting methyltransferase inhibitor, DZNep, or one targeting EZH2. CDKN2A/B induction by TGFβ correlated with de novo appearance of three H3K27Ac peaks within a 20 kb cis element ∼150 kb proximal to CDKN2A/B. Deleting that segment prevented their induction by TGFβ but not a basal increase driven by methyltransferase inhibition alone. Expression of two CDKN2A/B transcripts was enhanced by dCas9/CRISPR activation targeting either the relevant promoter or the 20 kb cis elements, and this "precise" manipulation diminished RMS cell propagation in vitro. Our findings show crosstalk between methyltransferase inhibition and TGFβ-dependent activation of a remote enhancer to reverse CDKN2A/B silencing. Though focused on CDKN2A/B here, such crosstalk may apply to other TGFβ-responsive genes and perhaps govern this signaling protein's complex effects promoting or blocking cancer.
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Affiliation(s)
- Yen-Ting Liu
- Division of Hematology/Oncology, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Celeste Romero
- Division of Hematology/Oncology, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Xue Xiao
- Department of Population and Data Sciences, Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Lei Guo
- Department of Population and Data Sciences, Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Xiaoyun Zhou
- Division of Hematology/Oncology, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Mark A. Applebaum
- Section of Hematology/Oncology, Department of Pediatrics, University of Chicago, Chicago, Illinois, USA
| | - Lin Xu
- Division of Hematology/Oncology, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Department of Population and Data Sciences, Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Stephen X. Skapek
- Division of Hematology/Oncology, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas, USA
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159
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Macrae TA, Fothergill-Robinson J, Ramalho-Santos M. Regulation, functions and transmission of bivalent chromatin during mammalian development. Nat Rev Mol Cell Biol 2023; 24:6-26. [PMID: 36028557 DOI: 10.1038/s41580-022-00518-2] [Citation(s) in RCA: 60] [Impact Index Per Article: 60.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/05/2022] [Indexed: 12/25/2022]
Abstract
Cells differentiate and progress through development guided by a dynamic chromatin landscape that mediates gene expression programmes. During development, mammalian cells display a paradoxical chromatin state: histone modifications associated with gene activation (trimethylated histone H3 Lys4 (H3K4me3)) and with gene repression (trimethylated H3 Lys27 (H3K27me3)) co-occur at promoters of developmental genes. This bivalent chromatin modification state is thought to poise important regulatory genes for expression or repression during cell-lineage specification. In this Review, we discuss recent work that has expanded our understanding of the molecular basis of bivalent chromatin and its contributions to mammalian development. We describe the factors that establish bivalency, especially histone-lysine N-methyltransferase 2B (KMT2B) and Polycomb repressive complex 2 (PRC2), and consider evidence indicating that PRC1 shapes bivalency and may contribute to its transmission between generations. We posit that bivalency is a key feature of germline and embryonic stem cells, as well as other types of stem and progenitor cells. Finally, we discuss the relevance of bivalent chromtin to human development and cancer, and outline avenues of future research.
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Affiliation(s)
- Trisha A Macrae
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, USA.
| | - Julie Fothergill-Robinson
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Miguel Ramalho-Santos
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada.
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160
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Aramaki M, Wu X, Liu H, Liu Y, Cho YW, Song M, Fu Y, Ng L, Forrest D. Transcriptional control of cone photoreceptor diversity by a thyroid hormone receptor. Proc Natl Acad Sci U S A 2022; 119:e2209884119. [PMID: 36454759 PMCID: PMC9894165 DOI: 10.1073/pnas.2209884119] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 10/26/2022] [Indexed: 12/05/2022] Open
Abstract
Cone photoreceptor diversity allows detection of wavelength information in light, the first step in color (chromatic) vision. In most mammals, cones express opsin photopigments for sensitivity to medium/long (M, "green") or short (S, "blue") wavelengths and are differentially arrayed over the retina. Cones appear early in retinal neurogenesis but little is understood of the subsequent control of diversity of these postmitotic neurons, because cone populations are sparse and, apart from opsins, poorly defined. It is also a challenge to distinguish potentially subtle differences between cell subtypes within a lineage. Therefore, we derived a Cre driver to isolate individual M and S opsin-enriched cones, which are distributed in counter-gradients over the mouse retina. Fine resolution transcriptome analyses identified expression gradients for groups of genes. The postnatal emergence of gradients indicated divergent differentiation of cone precursors during maturation. Using genetic tagging, we demonstrated a role for thyroid hormone receptor β2 (TRβ2) in control of gradient genes, many of which are enriched for TRβ2 binding sites and TRβ2-regulated open chromatin. Deletion of TRβ2 resulted in poorly distinguished cones regardless of retinal location. We suggest that TRβ2 controls a bipotential transcriptional state to promote cone diversity and the chromatic potential of the species.
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Affiliation(s)
- Michihiko Aramaki
- Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD20892
| | - Xuefeng Wu
- Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD20892
| | - Hong Liu
- Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD20892
| | - Ye Liu
- Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD20892
| | - Young-Wook Cho
- Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD20892
| | - Mina Song
- Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD20892
| | - Yulong Fu
- Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD20892
| | - Lily Ng
- Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD20892
| | - Douglas Forrest
- Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD20892
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161
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Zambanini G, Nordin A, Jonasson M, Pagella P, Cantù C. A new CUT&RUN low volume-urea (LoV-U) protocol optimized for transcriptional co-factors uncovers Wnt/β-catenin tissue-specific genomic targets. Development 2022; 149:dev201124. [PMID: 36355069 PMCID: PMC10112916 DOI: 10.1242/dev.201124] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 10/26/2022] [Indexed: 11/11/2022]
Abstract
Upon WNT/β-catenin pathway activation, stabilized β-catenin travels to the nucleus where it associates with the TCF/LEF transcription factors, constitutively bound to genomic Wnt-responsive elements (WREs), to activate target gene transcription. Discovering the binding profile of β-catenin is therefore required to unambiguously assign direct targets of WNT signaling. Cleavage under targets and release using nuclease (CUT&RUN) has emerged as prime technique for mapping the binding profile of DNA-interacting proteins. Here, we present a modified version of CUT&RUN, named LoV-U (low volume and urea), that enables the robust and reproducible generation of β-catenin binding profiles, uncovering direct WNT/β-catenin target genes in human cells, as well as in cells isolated from developing mouse tissues. CUT&RUN-LoV-U outperforms original CUT&RUN when targeting co-factors that do not bind the DNA, can profile all classes of chromatin regulators and is well suited for simultaneous processing of several samples. We believe that the application of our protocol will allow the detection of the complex system of tissue-specific WNT/β-catenin target genes, together with other non-DNA-binding transcriptional regulators that act downstream of ontogenetically fundamental signaling cascades.
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Affiliation(s)
- Gianluca Zambanini
- Wallenberg Centre for Molecular Medicine, Linköping University, Linköping SE-58183, Sweden
- Department of Biomedical and Clinical Sciences (BKV), Division of Molecular Medicine and Virology (MMV), Faculty of Medicine and Health Sciences, Linköping University, Linköping SE-58183, Sweden
| | - Anna Nordin
- Wallenberg Centre for Molecular Medicine, Linköping University, Linköping SE-58183, Sweden
- Department of Biomedical and Clinical Sciences (BKV), Division of Molecular Medicine and Virology (MMV), Faculty of Medicine and Health Sciences, Linköping University, Linköping SE-58183, Sweden
| | - Mattias Jonasson
- Wallenberg Centre for Molecular Medicine, Linköping University, Linköping SE-58183, Sweden
- Department of Biomedical and Clinical Sciences (BKV), Division of Molecular Medicine and Virology (MMV), Faculty of Medicine and Health Sciences, Linköping University, Linköping SE-58183, Sweden
| | - Pierfrancesco Pagella
- Wallenberg Centre for Molecular Medicine, Linköping University, Linköping SE-58183, Sweden
- Department of Biomedical and Clinical Sciences (BKV), Division of Molecular Medicine and Virology (MMV), Faculty of Medicine and Health Sciences, Linköping University, Linköping SE-58183, Sweden
| | - Claudio Cantù
- Wallenberg Centre for Molecular Medicine, Linköping University, Linköping SE-58183, Sweden
- Department of Biomedical and Clinical Sciences (BKV), Division of Molecular Medicine and Virology (MMV), Faculty of Medicine and Health Sciences, Linköping University, Linköping SE-58183, Sweden
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162
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Gene expression changes during the evolution of the tetrapod limb. Biol Futur 2022; 73:411-426. [PMID: 36355308 DOI: 10.1007/s42977-022-00136-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 10/26/2022] [Indexed: 11/11/2022]
Abstract
Major changes in the vertebrate anatomy have preceded the conquest of land by the members of this taxon, and continuous changes in limb shape and use have occurred during the later radiation of tetrapods. While the main, conserved mechanisms of limb development have been discerned over the past century using a combination of classical embryological and molecular methods, only recent advances made it possible to identify and study the regulatory changes that have contributed to the evolution of the tetrapod appendage. These advances include the expansion of the model repertoire from traditional genetic model species to non-conventional ones, a proliferation of predictive mathematical models that describe gene interactions, an explosion in genomic data and the development of high-throughput methodologies. These revolutionary innovations make it possible to identify specific mutations that are behind specific transitions in limb evolution. Also, as we continue to apply them to more and more extant species, we can expect to gain a fine-grained view of this evolutionary transition that has been so consequential for our species as well.
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163
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Maneix L, Iakova P, Moree SE, Hsu JI, Mistry RM, Stossi F, Lulla P, Sun Z, Sahin E, Yellapragada SV, Catic A. Proteasome Inhibitors Silence Oncogenes in Multiple Myeloma through Localized Histone Deacetylase 3 (HDAC3) Stabilization and Chromatin Condensation. CANCER RESEARCH COMMUNICATIONS 2022; 2:1693-1710. [PMID: 36846090 PMCID: PMC9949381 DOI: 10.1158/2767-9764.crc-22-0255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 10/04/2022] [Accepted: 12/06/2022] [Indexed: 12/13/2022]
Abstract
Proteasome inhibitors have become the standard of care for multiple myeloma (MM). Blocking protein degradation particularly perturbs the homeostasis of short-lived polypeptides such as transcription factors and epigenetic regulators. To determine how proteasome inhibitors directly impact gene regulation, we performed an integrative genomics study in MM cells. We discovered that proteasome inhibitors reduce the turnover of DNA-associated proteins and repress genes necessary for proliferation through epigenetic silencing. Specifically, proteasome inhibition results in the localized accumulation of histone deacetylase 3 (HDAC3) at defined genomic sites, which reduces H3K27 acetylation and increases chromatin condensation. The loss of active chromatin at super-enhancers critical for MM, including the super-enhancer controlling the proto-oncogene c-MYC, reduces metabolic activity and cancer cell growth. Epigenetic silencing is attenuated by HDAC3 depletion, suggesting a tumor-suppressive element of this deacetylase in the context of proteasome inhibition. In the absence of treatment, HDAC3 is continuously removed from DNA by the ubiquitin ligase SIAH2. Overexpression of SIAH2 increases H3K27 acetylation at c-MYC-controlled genes, increases metabolic output, and accelerates cancer cell proliferation. Our studies indicate a novel therapeutic function of proteasome inhibitors in MM by reshaping the epigenetic landscape in an HDAC3-dependent manner. As a result, blocking the proteasome effectively antagonizes c-MYC and the genes controlled by this proto-oncogene.
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Affiliation(s)
- Laure Maneix
- Huffington Center on Aging, Baylor College of Medicine, Houston, Texas
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, Texas
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
- Cell and Gene Therapy Program at the Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Polina Iakova
- Huffington Center on Aging, Baylor College of Medicine, Houston, Texas
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, Texas
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
- Cell and Gene Therapy Program at the Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Shannon E. Moree
- Huffington Center on Aging, Baylor College of Medicine, Houston, Texas
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, Texas
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
- Cell and Gene Therapy Program at the Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Joanne I. Hsu
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, Texas
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
- Cell and Gene Therapy Program at the Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Ragini M. Mistry
- Integrated Microscopy Core and GCC Center for Advanced Microscopy and Image Informatics, Baylor College of Medicine, Houston, Texas
| | - Fabio Stossi
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
- Integrated Microscopy Core and GCC Center for Advanced Microscopy and Image Informatics, Baylor College of Medicine, Houston, Texas
| | - Premal Lulla
- Cell and Gene Therapy Program at the Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
- Department of Hematology-Oncology, Baylor College of Medicine, Houston, Texas
| | - Zheng Sun
- Huffington Center on Aging, Baylor College of Medicine, Houston, Texas
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
| | - Ergun Sahin
- Huffington Center on Aging, Baylor College of Medicine, Houston, Texas
| | - Sarvari V. Yellapragada
- Department of Hematology-Oncology, Baylor College of Medicine, Houston, Texas
- Michael E. DeBakey Veterans Affairs Medical Center, Houston, Texas
| | - André Catic
- Huffington Center on Aging, Baylor College of Medicine, Houston, Texas
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, Texas
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
- Cell and Gene Therapy Program at the Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
- Michael E. DeBakey Veterans Affairs Medical Center, Houston, Texas
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164
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Kashkin KN, Kotova ES, Alekseenko IV, Bulanenkova SS, Akopov SB, Kopantzev EP, Nikolaev LG, Chernov IP, Didych DA. Efficient Selection of Enhancers and Promoters from MIA PaCa-2 Pancreatic Cancer Cells by ChIP-lentiMPRA. Int J Mol Sci 2022; 23:ijms232315011. [PMID: 36499347 PMCID: PMC9740945 DOI: 10.3390/ijms232315011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 11/17/2022] [Accepted: 11/25/2022] [Indexed: 12/05/2022] Open
Abstract
A library of active genome regulatory elements (putative promoters and enhancers) from MIA PaCa-2 pancreatic adenocarcinoma cells was constructed using a specially designed lentiviral vector and a massive parallel reporter assay (ChIP-lentiMPRA). Chromatin immunoprecipitation of the cell genomic DNA by H3K27ac antibodies was used for primary enrichment of the library for regulatory elements. Totally, 11,264 unique genome regions, many of which are capable of enhancing the expression of the CopGFP reporter gene from the minimal CMV promoter, were identified. The regions tend to be located near promoters. Based on the proximity assay, we found an enrichment of highly expressed genes among those associated with three or more mapped distal regions (2 kb distant from the 5'-ends of genes). It was shown significant enrichment of genes related to carcinogenesis or Mia PaCa-2 cell identity genes in this group. In contrast, genes associated with 1-2 distal regions or only with proximal regions (within 2 kbp of the 5'-ends of genes) are more often related to housekeeping functions. Thus, ChIP-lentiMPRA is a useful strategy for creating libraries of regulatory elements for the study of tumor-specific gene transcription.
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Affiliation(s)
- Kirill Nikitich Kashkin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya, 16/10, 117997 Moscow, Russia
| | - Elena Sergeevna Kotova
- Laboratory of Human Molecular Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya Street, 1a, 119435 Moscow, Russia
| | - Irina Vasilievna Alekseenko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya, 16/10, 117997 Moscow, Russia
| | - Svetlana Sergeevna Bulanenkova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya, 16/10, 117997 Moscow, Russia
| | - Sergey Borisovich Akopov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya, 16/10, 117997 Moscow, Russia
| | - Eugene Pavlovich Kopantzev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya, 16/10, 117997 Moscow, Russia
| | - Lev Grigorievich Nikolaev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya, 16/10, 117997 Moscow, Russia
| | - Igor Pavlovich Chernov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya, 16/10, 117997 Moscow, Russia
| | - Dmitry Alexandrovich Didych
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya, 16/10, 117997 Moscow, Russia
- Correspondence: ; Tel.: +7-919-777-4620
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ARID1A loss induces polymorphonuclear myeloid-derived suppressor cell chemotaxis and promotes prostate cancer progression. Nat Commun 2022; 13:7281. [PMID: 36435834 PMCID: PMC9701216 DOI: 10.1038/s41467-022-34871-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 11/10/2022] [Indexed: 11/28/2022] Open
Abstract
Chronic inflammation and an immunosuppressive microenvironment promote prostate cancer (PCa) progression and diminish the response to immune checkpoint blockade (ICB) therapies. However, it remains unclear how and to what extent these two events are coordinated. Here, we show that ARID1A, a subunit of the SWI/SNF chromatin remodeling complex, functions downstream of inflammation-induced IKKβ activation to shape the immunosuppressive tumor microenvironment (TME). Prostate-specific deletion of Arid1a cooperates with Pten loss to accelerate prostate tumorigenesis. We identify polymorphonuclear myeloid-derived suppressor cells (PMN-MDSCs) as the major infiltrating immune cell type that causes immune evasion and reveal that neutralization of PMN-MDSCs restricts the progression of Arid1a-deficient tumors. Mechanistically, inflammatory cues activate IKKβ to phosphorylate ARID1A, leading to its degradation via β-TRCP. ARID1A downregulation in turn silences the enhancer of A20 deubiquitinase, a critical negative regulator of NF-κB signaling, and thereby unleashes CXCR2 ligand-mediated MDSC chemotaxis. Importantly, our results support the therapeutic strategy of anti-NF-κB antibody or targeting CXCR2 combined with ICB for advanced PCa. Together, our findings highlight that the IKKβ/ARID1A/NF-κB feedback axis integrates inflammation and immunosuppression to promote PCa progression.
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166
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Haque F, Honjo T, Begum NA. XLID syndrome gene Med12 promotes Ig isotype switching through chromatin modification and enhancer RNA regulation. SCIENCE ADVANCES 2022; 8:eadd1466. [PMID: 36427307 PMCID: PMC9699684 DOI: 10.1126/sciadv.add1466] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The transcriptional coactivator Med12 regulates gene expression through its kinase module. Here, we show a kinase module-independent function of Med12 in CSR. Med12 is essential for super-enhancer activation by collaborating with p300-Jmjd6/Carm1 coactivator complexes. Med12 loss decreases H3K27 acetylation and eRNA transcription with concomitant impairment of AID-induced DNA breaks, S-S synapse formation, and 3'RR-Eμ interaction. CRISPR-dCas9-mediated enhancer activation reestablishes the epigenomic and transcriptional hallmarks of the super-enhancer and fully restores the Med12 depletion defects. Moreover, 3'RR-derived eRNAs are critical for promoting S region epigenetic regulation, synapse formation, and recruitment of Med12 and AID to the IgH locus. We find that XLID syndrome-associated Med12 mutations are defective in both 3'RR eRNA transcription and CSR, suggesting that B and neuronal cells may have cell-specific super-enhancer dysfunctions. We conclude that Med12 is essential for IgH 3'RR activation/eRNA transcription and plays a central role in AID-induced antibody gene diversification and genomic instability in B cells.
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Affiliation(s)
- Farazul Haque
- Department of Immunology and Genomic Medicine, Graduate School of Medicine, Kyoto University, Yoshida, Sakyo-Ku, Kyoto 606-8501, Japan
| | - Tasuku Honjo
- Department of Immunology and Genomic Medicine, Graduate School of Medicine, Kyoto University, Yoshida, Sakyo-Ku, Kyoto 606-8501, Japan
| | - Nasim A Begum
- Department of Immunology and Genomic Medicine, Graduate School of Medicine, Kyoto University, Yoshida, Sakyo-Ku, Kyoto 606-8501, Japan
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167
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Wang M, Chen Z, Zhang Y. CBP/p300 and HDAC activities regulate H3K27 acetylation dynamics and zygotic genome activation in mouse preimplantation embryos. EMBO J 2022; 41:e112012. [PMID: 36215692 PMCID: PMC9670200 DOI: 10.15252/embj.2022112012] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 09/20/2022] [Accepted: 09/23/2022] [Indexed: 01/13/2023] Open
Abstract
Epigenome reprogramming after fertilization enables transcriptionally quiescent maternal and paternal chromatin to acquire a permissive state for subsequent zygotic genome activation (ZGA). H3K27 acetylation (H3K27ac) is a well-established chromatin marker of active enhancers and promoters. However, reprogramming dynamics of H3K27ac during maternal-to-zygotic transition (MZT) in mammalian embryos are not well-studied. By profiling the allelic landscape of H3K27ac during mouse MZT, we show that H3K27ac undergoes three waves of rapid global transitions between oocyte stage and 2-cell stage. Notably, germinal vesicle oocyte and zygote chromatin are globally hyperacetylated, with noncanonical, broad H3K27ac domains that correlate with broad H3K4 trimethylation (H3K4me3) and open chromatin. H3K27ac marks genomic regions primed for activation including ZGA genes, retrotransposons, and active alleles of imprinted genes. We show that CBP/p300 and HDAC activities play important roles in regulating H3K27ac dynamics and are essential for preimplantation development. Specifically, CBP/p300 acetyltransferase broadly deposits H3K27ac in zygotes to induce the opening of condensed chromatin at putative enhancers and ensure proper ZGA. On the contrary, HDACs revert broad H3K27ac domains to canonical domains and safeguard ZGA by preventing premature expression of developmental genes. In conclusion, coordinated activities of CBP/p300 and HDACs during mouse MZT are essential for ZGA and preimplantation development.
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Affiliation(s)
- Meng Wang
- Howard Hughes Medical InstituteBoston Children's HospitalBostonMAUSA
- Program in Cellular and Molecular MedicineBoston Children's HospitalBostonMAUSA
- Division of Hematology/Oncology, Department of PediatricsBoston Children's HospitalBostonMAUSA
| | - Zhiyuan Chen
- Howard Hughes Medical InstituteBoston Children's HospitalBostonMAUSA
- Program in Cellular and Molecular MedicineBoston Children's HospitalBostonMAUSA
- Division of Hematology/Oncology, Department of PediatricsBoston Children's HospitalBostonMAUSA
| | - Yi Zhang
- Howard Hughes Medical InstituteBoston Children's HospitalBostonMAUSA
- Program in Cellular and Molecular MedicineBoston Children's HospitalBostonMAUSA
- Division of Hematology/Oncology, Department of PediatricsBoston Children's HospitalBostonMAUSA
- Department of GeneticsHarvard Medical SchoolBostonMAUSA
- Harvard Stem Cell InstituteBostonMAUSA
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168
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Donohue LK, Guo MG, Zhao Y, Jung N, Bussat RT, Kim DS, Neela PH, Kellman LN, Garcia OS, Meyers RM, Altman RB, Khavari PA. A cis-regulatory lexicon of DNA motif combinations mediating cell-type-specific gene regulation. CELL GENOMICS 2022; 2:100191. [PMID: 36742369 PMCID: PMC9894309 DOI: 10.1016/j.xgen.2022.100191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Gene expression is controlled by transcription factors (TFs) that bind cognate DNA motif sequences in cis-regulatory elements (CREs). The combinations of DNA motifs acting within homeostasis and disease, however, are unclear. Gene expression, chromatin accessibility, TF footprinting, and H3K27ac-dependent DNA looping data were generated and a random-forest-based model was applied to identify 7,531 cell-type-specific cis-regulatory modules (CRMs) across 15 diploid human cell types. A co-enrichment framework within CRMs nominated 838 cell-type-specific, recurrent heterotypic DNA motif combinations (DMCs), which were functionally validated using massively parallel reporter assays. Cancer cells engaged DMCs linked to neoplasia-enabling processes operative in normal cells while also activating new DMCs only seen in the neoplastic state. This integrative approach identifies cell-type-specific cis-regulatory combinatorial DNA motifs in diverse normal and diseased human cells and represents a general framework for deciphering cis-regulatory sequence logic in gene regulation.
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Affiliation(s)
- Laura K.H. Donohue
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA,Synthego, Redwood City, CA, USA,These authors contributed equally
| | - Margaret G. Guo
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA,Stanford Program in Biomedical Informatics, Stanford University, Stanford, CA, USA,These authors contributed equally
| | - Yang Zhao
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA,Synthego, Redwood City, CA, USA
| | - Namyoung Jung
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA,Department of Life Science, Pohang University of Science and Technology, Pohang, Korea
| | - Rose T. Bussat
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA,23andMe, Inc., Sunnyvale, CA, USA
| | - Daniel S. Kim
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA,Stanford Program in Biomedical Informatics, Stanford University, Stanford, CA, USA
| | - Poornima H. Neela
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA,Fauna Bio, Emeryville, CA, USA
| | - Laura N. Kellman
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA,Stanford Program in Cancer Biology, Stanford University, Stanford, CA, USA
| | - Omar S. Garcia
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Robin M. Meyers
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Russ B. Altman
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA,Stanford Program in Biomedical Informatics, Stanford University, Stanford, CA, USA,Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Paul A. Khavari
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA,Stanford Program in Cancer Biology, Stanford University, Stanford, CA, USA,Veterans Affairs Palo Alto Healthcare System, Palo Alto, CA, USA,Lead contact,Correspondence:
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169
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Pang B, van Weerd JH, Hamoen FL, Snyder MP. Identification of non-coding silencer elements and their regulation of gene expression. Nat Rev Mol Cell Biol 2022; 24:383-395. [DOI: 10.1038/s41580-022-00549-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/29/2022] [Indexed: 11/09/2022]
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170
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Ito S, Das ND, Umehara T, Koseki H. Factors and Mechanisms That Influence Chromatin-Mediated Enhancer-Promoter Interactions and Transcriptional Regulation. Cancers (Basel) 2022; 14:5404. [PMID: 36358822 PMCID: PMC9659172 DOI: 10.3390/cancers14215404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 10/28/2022] [Accepted: 11/01/2022] [Indexed: 11/06/2022] Open
Abstract
Eukaryotic gene expression is regulated through chromatin conformation, in which enhancers and promoters physically interact (E-P interactions). How such chromatin-mediated E-P interactions affect gene expression is not yet fully understood, but the roles of histone acetylation and methylation, pioneer transcription factors, and architectural proteins such as CCCTC binding factor (CTCF) and cohesin have recently attracted attention. Moreover, accumulated data suggest that E-P interactions are mechanistically involved in biophysical events, including liquid-liquid phase separation, and in biological events, including cancers. In this review, we discuss various mechanisms that regulate eukaryotic gene expression, focusing on emerging views regarding chromatin conformations that are involved in E-P interactions and factors that establish and maintain them.
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Affiliation(s)
- Shinsuke Ito
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Nando Dulal Das
- Laboratory for Epigenetics Drug Discovery, RIKEN Center for Biosystems Dynamics Research, Yokohama 230-0045, Japan
| | - Takashi Umehara
- Laboratory for Epigenetics Drug Discovery, RIKEN Center for Biosystems Dynamics Research, Yokohama 230-0045, Japan
| | - Haruhiko Koseki
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
- Immune Regulation, Advanced Research Departments, Graduate School of Medicine, Chiba University, Chiba 260-8677, Japan
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171
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Bruscadin JJ, Cardoso TF, da Silva Diniz WJ, Afonso J, de Souza MM, Petrini J, Nascimento Andrade BG, da Silva VH, Ferraz JBS, Zerlotini A, Mourão GB, Coutinho LL, de Almeida Regitano LC. Allele-specific expression reveals functional SNPs affecting muscle-related genes in bovine. BIOCHIMICA ET BIOPHYSICA ACTA (BBA) - GENE REGULATORY MECHANISMS 2022; 1865:194886. [DOI: 10.1016/j.bbagrm.2022.194886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 09/27/2022] [Accepted: 10/12/2022] [Indexed: 11/09/2022]
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172
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Diacou R, Nandigrami P, Fiser A, Liu W, Ashery-Padan R, Cvekl A. Cell fate decisions, transcription factors and signaling during early retinal development. Prog Retin Eye Res 2022; 91:101093. [PMID: 35817658 PMCID: PMC9669153 DOI: 10.1016/j.preteyeres.2022.101093] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 06/02/2022] [Accepted: 06/03/2022] [Indexed: 12/30/2022]
Abstract
The development of the vertebrate eyes is a complex process starting from anterior-posterior and dorso-ventral patterning of the anterior neural tube, resulting in the formation of the eye field. Symmetrical separation of the eye field at the anterior neural plate is followed by two symmetrical evaginations to generate a pair of optic vesicles. Next, reciprocal invagination of the optic vesicles with surface ectoderm-derived lens placodes generates double-layered optic cups. The inner and outer layers of the optic cups develop into the neural retina and retinal pigment epithelium (RPE), respectively. In vitro produced retinal tissues, called retinal organoids, are formed from human pluripotent stem cells, mimicking major steps of retinal differentiation in vivo. This review article summarizes recent progress in our understanding of early eye development, focusing on the formation the eye field, optic vesicles, and early optic cups. Recent single-cell transcriptomic studies are integrated with classical in vivo genetic and functional studies to uncover a range of cellular mechanisms underlying early eye development. The functions of signal transduction pathways and lineage-specific DNA-binding transcription factors are dissected to explain cell-specific regulatory mechanisms underlying cell fate determination during early eye development. The functions of homeodomain (HD) transcription factors Otx2, Pax6, Lhx2, Six3 and Six6, which are required for early eye development, are discussed in detail. Comprehensive understanding of the mechanisms of early eye development provides insight into the molecular and cellular basis of developmental ocular anomalies, such as optic cup coloboma. Lastly, modeling human development and inherited retinal diseases using stem cell-derived retinal organoids generates opportunities to discover novel therapies for retinal diseases.
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Affiliation(s)
- Raven Diacou
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Prithviraj Nandigrami
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Andras Fiser
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Wei Liu
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Ruth Ashery-Padan
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Ales Cvekl
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
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173
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Shi Y, Wang M, Liu D, Ullah S, Ma X, Yang H, Liu B. Super-enhancers in esophageal carcinoma: Transcriptional addictions and therapeutic strategies. Front Oncol 2022; 12:1036648. [DOI: 10.3389/fonc.2022.1036648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 10/10/2022] [Indexed: 11/13/2022] Open
Abstract
The tumorigenesis of esophageal carcinoma arises from transcriptional dysregulation would become exceptionally dependent on specific regulators of gene expression, which could be preferentially attributed to the larger non-coding cis-regulatory elements, i.e. super-enhancers (SEs). SEs, large genomic regulatory entity in close genomic proximity, are underpinned by control cancer cell identity. As a consequence, the transcriptional addictions driven by SEs could offer an Achilles’ heel for molecular treatments on patients of esophageal carcinoma and other types of cancer as well. In this review, we summarize the recent findings about the oncogenic SEs upon which esophageal cancer cells depend, and discuss why SEs could be seen as the hallmark of cancer, how transcriptional dependencies driven by SEs, and what opportunities could be supplied based on this cancer-specific SEs.
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174
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Exploration of Tools for the Interpretation of Human Non-Coding Variants. Int J Mol Sci 2022; 23:ijms232112977. [PMID: 36361767 PMCID: PMC9654743 DOI: 10.3390/ijms232112977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 10/17/2022] [Accepted: 10/23/2022] [Indexed: 02/01/2023] Open
Abstract
The advent of Whole Genome Sequencing (WGS) broadened the genetic variation detection range, revealing the presence of variants even in non-coding regions of the genome, which would have been missed using targeted approaches. One of the most challenging issues in WGS analysis regards the interpretation of annotated variants. This review focuses on tools suitable for the functional annotation of variants falling into non-coding regions. It couples the description of non-coding genomic areas with the results and performance of existing tools for a functional interpretation of the effect of variants in these regions. Tools were tested in a controlled genomic scenario, representing the ground-truth and allowing us to determine software performance.
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175
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Xu J, Pratt HE, Moore JE, Gerstein MB, Weng Z. Building integrative functional maps of gene regulation. Hum Mol Genet 2022; 31:R114-R122. [PMID: 36083269 PMCID: PMC9585680 DOI: 10.1093/hmg/ddac195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 08/03/2022] [Accepted: 08/09/2022] [Indexed: 11/13/2022] Open
Abstract
Every cell in the human body inherits a copy of the same genetic information. The three billion base pairs of DNA in the human genome, and the roughly 50 000 coding and non-coding genes they contain, must thus encode all the complexity of human development and cell and tissue type diversity. Differences in gene regulation, or the modulation of gene expression, enable individual cells to interpret the genome differently to carry out their specific functions. Here we discuss recent and ongoing efforts to build gene regulatory maps, which aim to characterize the regulatory roles of all sequences in a genome. Many researchers and consortia have identified such regulatory elements using functional assays and evolutionary analyses; we discuss the results, strengths and shortcomings of their approaches. We also discuss new techniques the field can leverage and emerging challenges it will face while striving to build gene regulatory maps of ever-increasing resolution and comprehensiveness.
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Affiliation(s)
- Jinrui Xu
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Henry E Pratt
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA 01605, USA
| | - Jill E Moore
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA 01605, USA
| | - Mark B Gerstein
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
- Department of Computer Science, Yale University, New Haven, CT 06520, USA
- Department of Statistics and Data Science, Yale University, New Haven, CT 06520, USA
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA 01605, USA
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176
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Loss of CASZ1 tumor suppressor linked to oncogenic subversion of neuroblastoma core regulatory circuitry. Cell Death Dis 2022; 13:871. [PMID: 36243768 PMCID: PMC9569368 DOI: 10.1038/s41419-022-05314-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/27/2022] [Accepted: 09/30/2022] [Indexed: 11/10/2022]
Abstract
The neural crest lineage regulatory transcription factors (TFs) form a core regulatory circuitry (CRC) in neuroblastoma (NB) to specify a noradrenergic tumor phenotype. Oncogenic subversion of CRC TFs is well documented, but the role of loss of tumor suppressors plays remains unclear. Zinc-finger TF CASZ1 is a chromosome 1p36 (chr1p36) tumor suppressor. Single-cell RNA sequencing data analyses indicate that CASZ1 is highly expressed in developing chromaffin cells coincident with an expression of NB CRC TFs. In NB tumor cells, the CASZ1 tumor suppressor is silenced while CRC components are highly expressed. We find the NB CRC component HAND2 directly represses CASZ1 expression. ChIP-seq and transcriptomic analyses reveal that restoration of CASZ1 upregulates noradrenergic neuronal genes and represses expression of CRC components by remodeling enhancer activity. Our study identifies that the restored CASZ1 forms a negative feedback regulatory circuit with the established NB CRC to induce noradrenergic neuronal differentiation of NB.
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177
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Simper MS, Coletta LD, Gaddis S, Lin K, Mikulec CD, Takata T, Tomida MW, Zhang D, Tang DG, Estecio MR, Shen J, Lu Y. Commercial ChIP-Seq Library Preparation Kits Performed Differently for Different Classes of Protein Targets. J Biomol Tech 2022; 33:3fc1f5fe.7910785e. [PMID: 36910579 PMCID: PMC10001930 DOI: 10.7171/3fc1f5fe.7910785e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Background Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-Seq) is a powerful method commonly used to study global protein-DNA interactions including both transcription factors and histone modifications. We have found that the choice of ChIP-Seq library preparation protocol plays an important role in overall ChIP-Seq data quality. However, very few studies have compared ChIP-Seq libraries prepared by different protocols using multiple targets and a broad range of input DNA levels. Results In this study, we evaluated the performance of 4 ChIP-Seq library preparation protocols (New England Biolabs [NEB] NEBNext Ultra II, Roche KAPA HyperPrep, Diagenode MicroPlex, and Bioo [now PerkinElmer] NEXTflex) on 3 target proteins, chosen to represent the 3 typical signal enrichment patterns in ChIP-Seq experiments: sharp peaks (H3K4me3), broad domains (H3K27me3), and punctate peaks with a protein binding motif (CTCF). We also tested a broad range of different input DNA levels from 0.10 to 10 ng for H3K4me3 and H3K27me3 experiments. Conclusions Our results suggest that the NEB protocol may be better for preparing H3K4me3 (and potentially other histone modifications with sharp peak enrichment) libraries; the Bioo protocol may be better for preparing H3K27me3 (and potentially other histone modifications with broad domain enrichment) libraries, and the Diagenode protocol may be better for preparing CTCF (and potentially other transcription factors with well-defined binding motifs) libraries. For ChIP-Seq experiments using novel targets without a known signal enrichment pattern, the NEB protocol might be the best choice, as it performed well for each of the 3 targets we tested across a wide array of input DNA levels.
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Affiliation(s)
- M S Simper
- Department of Epigenetics and Molecular Carcinogenesis The University of Texas MD Anderson Cancer Center Science ParkSmithvilleTexas78957 USA
| | - L Della Coletta
- Department of Epigenetics and Molecular Carcinogenesis The University of Texas MD Anderson Cancer Center Science ParkSmithvilleTexas78957 USA
| | - S Gaddis
- Department of Epigenetics and Molecular Carcinogenesis The University of Texas MD Anderson Cancer Center Science ParkSmithvilleTexas78957 USA
| | - K Lin
- Department of Epigenetics and Molecular Carcinogenesis The University of Texas MD Anderson Cancer Center Science ParkSmithvilleTexas78957 USA
| | - C D Mikulec
- Department of Epigenetics and Molecular Carcinogenesis The University of Texas MD Anderson Cancer Center Science ParkSmithvilleTexas78957 USA
| | - True Takata
- Department of Epigenetics and Molecular Carcinogenesis The University of Texas MD Anderson Cancer Center Science ParkSmithvilleTexas78957 USA
| | - M W Tomida
- Department of Epigenetics and Molecular Carcinogenesis The University of Texas MD Anderson Cancer Center Science ParkSmithvilleTexas78957 USA
| | - D Zhang
- Department of Epigenetics and Molecular Carcinogenesis The University of Texas MD Anderson Cancer Center Science ParkSmithvilleTexas78957 USA.,Present Address: College of Biology Hunan University Changsha410082 China
| | - D G Tang
- Department of Epigenetics and Molecular Carcinogenesis The University of Texas MD Anderson Cancer Center Science ParkSmithvilleTexas78957 USA.,Present Address: Department of Pharmacology and Therapeutics Roswell Park Cancer Institute BuffaloNew York14263 USA
| | - M R Estecio
- Department of Epigenetics and Molecular Carcinogenesis The University of Texas MD Anderson Cancer Center Science ParkSmithvilleTexas78957 USA
| | - J Shen
- Department of Epigenetics and Molecular Carcinogenesis.,Department of Epigenetics and Molecular Carcinogenesis The University of Texas MD Anderson Cancer Center Science ParkSmithvilleTexas78957 USA.,Program in Genetics and Epigenetics MD Anderson Cancer Center UT Health Graduate School of Biomedical Sciences The University of Texas MD Anderson Cancer Center SmithvilleTexas78957 USA
| | - Yue Lu
- Department of Epigenetics and Molecular Carcinogenesis The University of Texas MD Anderson Cancer Center Science ParkSmithvilleTexas78957 USA
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178
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Giacoman-Lozano M, Meléndez-Ramírez C, Martinez-Ledesma E, Cuevas-Diaz Duran R, Velasco I. Epigenetics of neural differentiation: Spotlight on enhancers. Front Cell Dev Biol 2022; 10:1001701. [PMID: 36313573 PMCID: PMC9606577 DOI: 10.3389/fcell.2022.1001701] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 10/03/2022] [Indexed: 11/28/2022] Open
Abstract
Neural induction, both in vivo and in vitro, includes cellular and molecular changes that result in phenotypic specialization related to specific transcriptional patterns. These changes are achieved through the implementation of complex gene regulatory networks. Furthermore, these regulatory networks are influenced by epigenetic mechanisms that drive cell heterogeneity and cell-type specificity, in a controlled and complex manner. Epigenetic marks, such as DNA methylation and histone residue modifications, are highly dynamic and stage-specific during neurogenesis. Genome-wide assessment of these modifications has allowed the identification of distinct non-coding regulatory regions involved in neural cell differentiation, maturation, and plasticity. Enhancers are short DNA regulatory regions that bind transcription factors (TFs) and interact with gene promoters to increase transcriptional activity. They are of special interest in neuroscience because they are enriched in neurons and underlie the cell-type-specificity and dynamic gene expression profiles. Classification of the full epigenomic landscape of neural subtypes is important to better understand gene regulation in brain health and during diseases. Advances in novel next-generation high-throughput sequencing technologies, genome editing, Genome-wide association studies (GWAS), stem cell differentiation, and brain organoids are allowing researchers to study brain development and neurodegenerative diseases with an unprecedented resolution. Herein, we describe important epigenetic mechanisms related to neurogenesis in mammals. We focus on the potential roles of neural enhancers in neurogenesis, cell-fate commitment, and neuronal plasticity. We review recent findings on epigenetic regulatory mechanisms involved in neurogenesis and discuss how sequence variations within enhancers may be associated with genetic risk for neurological and psychiatric disorders.
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Affiliation(s)
- Mayela Giacoman-Lozano
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey, NL, Mexico
| | - César Meléndez-Ramírez
- Instituto de Fisiología Celular—Neurociencias, Universidad Nacional Autónoma de Mexico, Mexico City, Mexico
- Laboratorio de Reprogramación Celular, Instituto Nacional de Neurología y Neurocirugía “Manuel Velasco Suárez”, Mexico City, Mexico
| | - Emmanuel Martinez-Ledesma
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey, NL, Mexico
- Tecnologico de Monterrey, The Institute for Obesity Research, Monterrey, NL, Mexico
| | - Raquel Cuevas-Diaz Duran
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey, NL, Mexico
- *Correspondence: Raquel Cuevas-Diaz Duran, ; Iván Velasco,
| | - Iván Velasco
- Instituto de Fisiología Celular—Neurociencias, Universidad Nacional Autónoma de Mexico, Mexico City, Mexico
- Laboratorio de Reprogramación Celular, Instituto Nacional de Neurología y Neurocirugía “Manuel Velasco Suárez”, Mexico City, Mexico
- *Correspondence: Raquel Cuevas-Diaz Duran, ; Iván Velasco,
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179
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Shi Q, Yao XY, Wang HY, Li YJ, Zhang XX, Sun C. Breast cancer-associated SNP rs72755295 is a cis-regulatory variation for human EXO1. Genet Mol Biol 2022; 45:e20210420. [PMID: 36255267 PMCID: PMC9631386 DOI: 10.1590/1678-4685-gmb-2021-0420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 08/07/2022] [Indexed: 11/04/2022] Open
Abstract
Breast cancer is the most common malignant tumor in women. A previous genome-wide association study reports that rs72755295, a SNP locating at intron of EXO1 (exonuclease 1), is associated with breast cancer. Due to the complete linkage disequilibrium between rs72755295 and rs4149909, a nonsynonymous mutation for EXO1, rs4149909 is supposed to be the causal SNP. Since EXO1 is overexpressed in breast carcinoma samples, we hypothesized that the genetic variations in this locus might confer breast cancer risk by regulating EXO1 expression. To substantiate this, a functional genomics study was performed. The dual luciferase assay indicated that G of rs72755295 presents significantly higher relative enhancer activity than A, thus verifying that this SNP can influence gene expression in breast cell. Through chromosome conformation capture it was disclosed that the enhancer containing rs72755295 can interact with the EXO1 promoter. RNA-seq analysis indicated that EXO1 expression is dependent on the rs72755295 genotype. By chromatin immunoprecipitation, the transcription factor PAX6 (paired box 6) was recognized to bind the region spanning rs72755295. In electrophoretic mobility shift assay, G of rs72755295 displays obviously higher binding affinity with nuclear protein than A. Our results indicated that rs72755295 is a cis-regulatory variation for EXO1 and might confer breast cancer risk besides rs4149909.
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Affiliation(s)
- Qiang Shi
- Shaanxi Normal University, College of Life Sciences, Xi'an, Shaanxi, P.R. China
| | - Xing-Yuan Yao
- Shaanxi Normal University, College of Life Sciences, Xi'an, Shaanxi, P.R. China
| | - Hong-Yan Wang
- Shaanxi Normal University, College of Life Sciences, Xi'an, Shaanxi, P.R. China
| | - Ya-Jie Li
- Shaanxi Normal University, College of Life Sciences, Xi'an, Shaanxi, P.R. China
| | - Xin-Xin Zhang
- Shaanxi Normal University, College of Life Sciences, Xi'an, Shaanxi, P.R. China
| | - Chang Sun
- Shaanxi Normal University, College of Life Sciences, Xi'an, Shaanxi, P.R. China
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180
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Lin D, Xu W, Hong P, Wu C, Zhang Z, Zhang S, Xing L, Yang B, Zhou W, Xiao Q, Wang J, Wang C, He Y, Chen X, Cao X, Man J, Reheman A, Wu X, Hao X, Hu Z, Chen C, Cao Z, Yin R, Fu ZF, Zhou R, Teng Z, Li G, Cao G. Decoding the spatial chromatin organization and dynamic epigenetic landscapes of macrophage cells during differentiation and immune activation. Nat Commun 2022; 13:5857. [PMID: 36195603 PMCID: PMC9532393 DOI: 10.1038/s41467-022-33558-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 09/22/2022] [Indexed: 11/09/2022] Open
Abstract
Immunocytes dynamically reprogram their gene expression profiles during differentiation and immunoresponse. However, the underlying mechanism remains elusive. Here, we develop a single-cell Hi-C method and systematically delineate the 3D genome and dynamic epigenetic atlas of macrophages during these processes. We propose "degree of disorder" to measure genome organizational patterns inside topologically-associated domains, which is correlated with the chromatin epigenetic states, gene expression, and chromatin structure variability in individual cells. Furthermore, we identify that NF-κB initiates systematic chromatin conformation reorganization upon Mycobacterium tuberculosis infection. The integrated Hi-C, eQTL, and GWAS analysis depicts the atlas of the long-range target genes of mycobacterial disease susceptible loci. Among these, the SNP rs1873613 is located in the anchor of a dynamic chromatin loop with LRRK2, whose inhibitor AdoCbl could be an anti-tuberculosis drug candidate. Our study provides comprehensive resources for the 3D genome structure of immunocytes and sheds insights into the order of genome organization and the coordinated gene transcription during immunoresponse.
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Affiliation(s)
- Da Lin
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- College of Bio-Medicine and Health, Huazhong Agricultural University, Wuhan, China
| | - Weize Xu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Ping Hong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, Huazhong Agricultural University, Wuhan, China
- College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Chengchao Wu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Zhihui Zhang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Siheng Zhang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Lingyu Xing
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Bing Yang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Wei Zhou
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Qin Xiao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Bio-Medicine and Health, Huazhong Agricultural University, Wuhan, China
| | - Jinyue Wang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Bio-Medicine and Health, Huazhong Agricultural University, Wuhan, China
| | - Cong Wang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Yu He
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Xi Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Xiaojian Cao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Jiangwei Man
- College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Aikebaier Reheman
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- College of Animal Science and Technology, Tarim University, Alar, China
| | - Xiaofeng Wu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Xingjie Hao
- School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhe Hu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Chunli Chen
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region, Guizhou University, Guiyang, China
| | - Zimeng Cao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- College of Bio-Medicine and Health, Huazhong Agricultural University, Wuhan, China
- College of Animal Sciences, Yangtze River University, Jingzhou, China
| | - Rong Yin
- Department of Hematology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Zhen F Fu
- Department of Pathology, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Rong Zhou
- Dapartment of Reproductive Medicine Center, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Zhaowei Teng
- The First People's Hospital of Yunnan Province, Affiliated Hospital of Kunming University of Science and Technology, Kunming, China
| | - Guoliang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.
- Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, Huazhong Agricultural University, Wuhan, China.
- College of Informatics, Huazhong Agricultural University, Wuhan, China.
| | - Gang Cao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.
- College of Bio-Medicine and Health, Huazhong Agricultural University, Wuhan, China.
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181
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Gao L, Rong H. Potential mechanisms and prognostic model of eRNAs-regulated genes in stomach adenocarcinoma. Sci Rep 2022; 12:16545. [PMID: 36192427 PMCID: PMC9529949 DOI: 10.1038/s41598-022-20824-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 09/19/2022] [Indexed: 11/09/2022] Open
Abstract
Gastric Carcinoma is the fourth leading cause of cancer deaths worldwide, in which stomach adenocarcinoma (STAD) is the most common histological type. A growing amount of evidence has suggested the importance of enhancer RNAs (eRNAs) in the cancer. However, the potential mechanism of eRNAs in STAD remains unclear. The eRNAs-regulated genes (eRRGs) were identified through four different enhancer resources. The differentially expressed eRRGs were obtained by ‘DESeq2’ R package. The prognosis prediction model was constructed by Cox and Lasso regression analysis. The ‘ChAMP’ R package and ‘maftools’ R package were used to investigate the multi-omics characters. In this study, combining the concept of contact domain, a total of 9014 eRRGs including 4926 PCGs and 4088 lncRNAs were identified and these eRRGs showed higher and more stable expression. Besides, the functions of these genes were mainly associated with tumor-related biological processes. Then, a prognostic prediction model was constructed and the AUC values of the 1-, 3- and 5-year survival prediction reached 0.76, 0.84 and 0.84, respectively, indicating that this model has a high accuracy. Finally, the difference between high-risk group and low-risk group were investigated using multi-omics data including gene expression, DNA methylation and somatic mutations. Our study provides significant clues for the elucidation of eRNAs in STAD and may help improve the overall survival for STAD patients.
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Affiliation(s)
- Liuying Gao
- The Affiliated People's Hospital of Ningbo University, Ningbo, 315040, China. .,Department of Preventive Medicine, Zhejiang Provincial Key Laboratory of Pathological and Physiological Technology, School of Medicine, Ningbo, 315211, China.
| | - Hao Rong
- The Affiliated People's Hospital of Ningbo University, Ningbo, 315040, China.,Department of Preventive Medicine, Zhejiang Provincial Key Laboratory of Pathological and Physiological Technology, School of Medicine, Ningbo, 315211, China
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182
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Regulation of KDM5C stability and enhancer reprogramming in breast cancer. Cell Death Dis 2022; 13:843. [PMID: 36192394 PMCID: PMC9530161 DOI: 10.1038/s41419-022-05296-5] [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: 04/15/2022] [Revised: 09/10/2022] [Accepted: 09/23/2022] [Indexed: 01/23/2023]
Abstract
Abnormality of enhancer regulation has emerged as one of the critical features for cancer cells. KDM5C is a histone H3K4 demethylase and frequently mutated in several types of cancer. It is critical for H3K4me3 and activity of enhancers, but its regulatory mechanisms remain elusive. Here, we identify TRIM11 as one ubiquitin E3 ligase for KDM5C. TRIM11 interacts with KDM5C, catalyzes K48-linked ubiquitin chain on KDM5C, and promotes KDM5C degradation through proteasome. TRIM11 deficiency in an animal model represses the growth of breast tumor and stabilizes KDM5C. In breast cancer patient tissues, TRIM11 is highly expressed and KDM5C is lower expressed, and their expression is negatively correlated. Mechanistically, TRIM11 regulates the enhancer activity of genes involved in cell migration and immune response by targeting KDM5C. TRIM11 and KDM5C regulate MCAM expression and cell migration through targeting H3K4me3 on MCAM enhancer. Taken together, our study reveals novel mechanisms for enhancer regulation during breast cancer tumorigenesis and development.
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183
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Li Z, Liang N, Wang N, Jia Y, Tian C. WDR5 is a prognostic biomarker of brain metastasis from non-small cell lung cancer. Front Oncol 2022; 12:1023776. [PMID: 36249032 PMCID: PMC9557102 DOI: 10.3389/fonc.2022.1023776] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 09/13/2022] [Indexed: 12/09/2022] Open
Abstract
Background Lung cancer (LC) is the most frequent caner type and causes the most cancer-related death. Brain metastases (BM) are the deadliest complications of lung cancer, and the prognostic biomarkers of BM are urgently needed. Materials and methods In our study, we established an inception cohort including 122 patients with asynchronous BM from NSCLC, and further selected 70 patients who received surgical resection, which compromised the validation cohort. With immunohistochemistry, we investigated the expression of WDR5 in the cohort. By chi-square method, the correlations between WDR5 and clinicopathological factors were analyzed. The prognostic indicators were analyzed with the univariate analysis, and independent prognostic factors were identified by multivariate analysis with Cox-regression model. Results WDR5 is frequently expressed in the cytoplasm of BM from NSCLC. Patients with low or high expression of WDR5 account for 60% and 40% respectively. High expression of WDR5 indicates poor prognosis of BM from NSCLC (P=0.001). In addition to WDR5, KPS is also a prognostic factor of BM, and high KPS predicts favorable prognosis (P=0.006). WDR5 is an independent prognostic biomarker for poor prognosis of BM from NSCLC, with the cancer-related odds as 2.48. Conclusions High expression of WDR5 can predict the poor prognosis of BM, and WDR5 is an independent prognostic biomarker of BM from NSCLC. Patients with WDR5 overexpression are more high-risk to suffer BM-related death and should receive more intense post-operational supervision.
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Affiliation(s)
- Zheng Li
- Department of Neurosurgery, The Second Affiliated Hospital of Shandong First Medical University, Tai’an, China
| | - Nan Liang
- Department of Neurosurgery, The Second Affiliated Hospital of Shandong First Medical University, Tai’an, China
| | - Na Wang
- Department of Anesthesiology, The First People’s Hospital of Tai’an, Tai’an, China
| | - Yan Jia
- Department of Intensive Care Unit, Shandong Provincial Tai’shan Hospital, Tai’an, China
| | - Cui Tian
- Department of Intensive Care Unit, The Second Affiliated Hospital of Shandong First Medical University, Tai’an, China
- *Correspondence: Cui Tian,
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184
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Pudjihartono M, Perry JK, Print C, O'Sullivan JM, Schierding W. Interpretation of the role of germline and somatic non-coding mutations in cancer: expression and chromatin conformation informed analysis. Clin Epigenetics 2022; 14:120. [PMID: 36171609 PMCID: PMC9520844 DOI: 10.1186/s13148-022-01342-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 09/21/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND There has been extensive scrutiny of cancer driving mutations within the exome (especially amino acid altering mutations) as these are more likely to have a clear impact on protein functions, and thus on cell biology. However, this has come at the neglect of systematic identification of regulatory (non-coding) variants, which have recently been identified as putative somatic drivers and key germline risk factors for cancer development. Comprehensive understanding of non-coding mutations requires understanding their role in the disruption of regulatory elements, which then disrupt key biological functions such as gene expression. MAIN BODY We describe how advancements in sequencing technologies have led to the identification of a large number of non-coding mutations with uncharacterized biological significance. We summarize the strategies that have been developed to interpret and prioritize the biological mechanisms impacted by non-coding mutations, focusing on recent annotation of cancer non-coding variants utilizing chromatin states, eQTLs, and chromatin conformation data. CONCLUSION We believe that a better understanding of how to apply different regulatory data types into the study of non-coding mutations will enhance the discovery of novel mechanisms driving cancer.
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Affiliation(s)
| | - Jo K Perry
- Liggins Institute, The University of Auckland, Auckland, New Zealand
- The Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand
| | - Cris Print
- The Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand
- Department of Molecular Medicine and Pathology, School of Medical Sciences, University of Auckland, Auckland, 1142, New Zealand
| | - Justin M O'Sullivan
- Liggins Institute, The University of Auckland, Auckland, New Zealand
- The Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand
- Australian Parkinson's Mission, Garvan Institute of Medical Research, Sydney, NSW, Australia
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK
| | - William Schierding
- Liggins Institute, The University of Auckland, Auckland, New Zealand.
- The Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand.
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185
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Fischer DK, Krick KS, Han C, Woolf MT, Heller EA. Cocaine regulation of Nr4a1 chromatin bivalency and mRNA in male and female mice. Sci Rep 2022; 12:15735. [PMID: 36130958 PMCID: PMC9492678 DOI: 10.1038/s41598-022-19908-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 09/06/2022] [Indexed: 11/08/2022] Open
Abstract
Cocaine epigenetically regulates gene expression via changes in histone post-translational modifications (HPTMs). We previously found that the immediate early gene Nr4a1 is epigenetically activated by cocaine in mouse brain reward regions. However, few studies have examined multiple HPTMs at a single gene. Bivalent gene promoters are simultaneously enriched in both activating (H3K4me3 (K4)) and repressive (H3K27me3 (K27)) HPTMs. As such, bivalent genes are lowly expressed but poised for activity-dependent gene regulation. In this study, we identified K4&K27 bivalency at Nr4a1 following investigator-administered cocaine in male and female mice. We applied sequential chromatin immunoprecipitation and qPCR to define Nr4a1 bivalency and expression in striatum (STR), prefrontal cortex (PFC), and hippocampus (HPC). We used Pearson's correlation to quantify relationships within each brain region across treatment conditions for each sex. In female STR, cocaine increased Nr4a1 mRNA while maintaining Nr4a1 K4&K27 bivalency. In male STR, cocaine enriched repressive H3K27me3 and K4&K27 bivalency at Nr4a1 and maintained Nr4a1 mRNA. Furthermore, cocaine epigenetically regulated a putative NR4A1 target, Cartpt, in male PFC. This study defined the epigenetic regulation of Nr4a1 in reward brain regions in male and female mice following cocaine, and, thus, shed light on the biological relevance of sex to cocaine use disorder.
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Affiliation(s)
- Delaney K Fischer
- Neuroscience Graduate Group, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Keegan S Krick
- Cell and Molecular Biology Graduate Group, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Chloe Han
- College of Arts & Sciences, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Morgan T Woolf
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
| | - Elizabeth A Heller
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA.
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186
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Shi Q, Zhang XX, Shi XQ, Chen Y, Sun C. Identification of rs2736099 as a novel cis-regulatory variation for TERT and implications for tumorigenesis and cell proliferation. J Cancer Res Clin Oncol 2022:10.1007/s00432-022-04372-9. [PMID: 36131156 DOI: 10.1007/s00432-022-04372-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 09/19/2022] [Indexed: 11/29/2022]
Abstract
PURPOSE Lung cancer is a malignant tumor with obvious genetic predisposition. Association studies have proposed that rs2853677, a SNP localizing at intron region of TERT (telomerase reverse transcriptase), is significantly associated with TERT expression, telomere length and eventually lung cancer risk. However, functional genomics work indicates that rs2853677 is not with the ability to alter gene expression. All these facts make us hypothesize that some other genetic variation(s) are in linkage disequilibrium (LD) with rs2853677 and influence TERT expression. METHODS LD pattern in rs2853677 nearby region was analyzed based on 1000 genomes data for three representative populations in the world and functional genomics research was performed for this locus. RESULTS Only one SNP, rs2736099, is in strong LD with rs2853677 in East Asian. Dual-luciferase reporter assay verifies that rs2736099 can regulate gene expression and should be the causal SNP for this disease. Through chromosome conformation capture assay, it is disclosed that the enhancer surrounding rs2736099 can interact with TERT promoter. Through chromatin immunoprecipitation, the transcription factor SP1 (Sp1 transcription factor) is recognized for the chromatin segment spanning rs2736099. CONCLUSIONS Our results provide the missing piece between genetic variation at this locus and lung cancer risk, which is also applied to tumorigenesis in other tissues and cell proliferation.
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Affiliation(s)
- Qiang Shi
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, Shaanxi, People's Republic of China.
| | - Xin-Xin Zhang
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, Shaanxi, People's Republic of China
| | - Xiao-Qian Shi
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, Shaanxi, People's Republic of China
| | - Ying Chen
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, Shaanxi, People's Republic of China
| | - Chang Sun
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, Shaanxi, People's Republic of China.
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187
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Abstract
Chromatin architecture, a key regulator of gene expression, can be inferred using chromatin contact data from chromosome conformation capture, or Hi-C. However, classical Hi-C does not preserve multi-way contacts. Here we use long sequencing reads to map genome-wide multi-way contacts and investigate higher order chromatin organization in the human genome. We use hypergraph theory for data representation and analysis, and quantify higher order structures in neonatal fibroblasts, biopsied adult fibroblasts, and B lymphocytes. By integrating multi-way contacts with chromatin accessibility, gene expression, and transcription factor binding, we introduce a data-driven method to identify cell type-specific transcription clusters. We provide transcription factor-mediated functional building blocks for cell identity that serve as a global signature for cell types. Mapping higher order chromatin architecture is important. Here the authors use long sequencing reads to map genome-wide multi-way contacts and investigate higher order chromatin organisation; they use hypergraph theory for data representation and analysis, and apply this to different cell types.
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188
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Trinh LT, Osipovich AB, Sampson L, Wong J, Wright CV, Magnuson MA. Differential regulation of alternate promoter regions in Sox17 during endodermal and vascular endothelial development. iScience 2022; 25:104905. [PMID: 36046192 PMCID: PMC9421400 DOI: 10.1016/j.isci.2022.104905] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 04/06/2022] [Accepted: 08/05/2022] [Indexed: 11/20/2022] Open
Abstract
Sox17 gene expression is essential for both endothelial and endodermal cell differentiation. To better understand the genetic basis for the expression of multiple Sox17 mRNA forms, we identified and performed CRISPR/Cas9 mutagenesis of two evolutionarily conserved promoter regions (CRs). The deletion of the upstream and endothelial cell-specific CR1 caused only a modest increase in lympho-vasculogenesis likely via reduced Notch signaling downstream of SOX17. In contrast, the deletion of the downstream CR2 region, which functions in both endothelial and endodermal cells, impairs both vascular and endodermal development causing death by embryonic day 12.5. Analyses of 3D chromatin looping, transcription factor binding, histone modification, and chromatin accessibility data at the Sox17 locus and surrounding region further support differential regulation of the two promoters during the development.
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Affiliation(s)
- Linh T. Trinh
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA
- Center for Stem Cell Biology, Vanderbilt University, Nashville, TN 37232, USA
- Program in Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Anna B. Osipovich
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA
- Center for Stem Cell Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Leesa Sampson
- Center for Stem Cell Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Jonathan Wong
- College of Arts and Science, Vanderbilt University, Nashville, TN 37232, USA
| | - Chris V.E. Wright
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA
- Center for Stem Cell Biology, Vanderbilt University, Nashville, TN 37232, USA
- Program in Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Mark A. Magnuson
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA
- Center for Stem Cell Biology, Vanderbilt University, Nashville, TN 37232, USA
- Program in Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA
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189
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Transcriptional Activation of Ecdysone-Responsive Genes Requires H3K27 Acetylation at Enhancers. Int J Mol Sci 2022; 23:ijms231810791. [PMID: 36142704 PMCID: PMC9502983 DOI: 10.3390/ijms231810791] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 09/05/2022] [Accepted: 09/09/2022] [Indexed: 11/23/2022] Open
Abstract
The steroid hormone ecdysone regulates insect development via its nuclear receptor (the EcR protein), which functions as a ligand-dependent transcription factor. The EcR regulates target gene expression by binding to ecdysone response elements (EcREs) in their promoter or enhancer regions. Its role in epigenetic regulation and, particularly, in histone acetylation remains to be clarified. Here, we analyzed the dynamics of histone acetylation and demonstrated that the acetylation of histone H3 on lysine 27 (H3K27) at enhancers was required for the transcriptional activation of ecdysone-responsive genes. Western blotting and ChIP-qPCR revealed that ecdysone altered the acetylation of H3K27. For E75B and Hr4, ecdysone-responsive genes, enhancer activity, and transcription required the histone acetyltransferase activity of the CBP. EcR binding was critical in inducing enhancer activity and H3K27 acetylation. The CREB-binding protein (CBP) HAT domain catalyzed H3K27 acetylation and CBP coactivation with EcR, independent of the presence of ecdysone. Increased H3K27 acetylation promoted chromatin accessibility, with the EcR and CBP mediating a local chromatin opening in response to ecdysone. Hence, epigenetic mechanisms, including the modification of acetylation and chromatin accessibility, controlled ecdysone-dependent gene transcription.
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190
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Li Z, Qiao J, Ma W, Zhou J, Gu L, Deng D, Zhang B. P14AS upregulates gene expression in the CDKN2A/2B locus through competitive binding to PcG protein CBX7. Front Cell Dev Biol 2022; 10:993525. [PMID: 36176277 PMCID: PMC9513069 DOI: 10.3389/fcell.2022.993525] [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: 07/13/2022] [Accepted: 08/24/2022] [Indexed: 12/27/2022] Open
Abstract
Background: It is well known that P16 INK4A , P14 ARF , P15 INK4B mRNAs, and ANRIL lncRNA are transcribed from the CDKN2A/2B locus. LncRNA P14AS is a lncRNA transcribed from antisense strand of P14 ARF promoter to intron-1. Our previous study showed that P14AS could upregulate the expression level of ANRIL and P16 INK4A and promote the proliferation of cancer cells. Because polycomb group protein CBX7 could repress P16 INK4A expression and bind ANRIL, we wonder whether the P14AS-upregulated ANRIL and P16 INK4A expression is mediated with CBX7. Results: In this study, we found that the upregulation of P16 INK4A , P14 ARF , P15 INK4B and ANRIL expression was induced by P14AS overexpression only in HEK293T and HCT116 cells with active endogenous CBX7 expression, but not in MGC803 and HepG2 cells with weak CBX7 expression. Further studies showed that the stable shRNA-knockdown of CBX7 expression abolished the P14AS-induced upregulation of these P14AS target genes in HEK293T and HCT116 cells whereas enforced CBX7 overexpression enabled P14AS to upregulate expression of these target genes in MGC803 and HepG2 cells. Moreover, a significant association between the expression levels of P14AS and its target genes were observed only in human colon cancer tissue samples with high level of CBX7 expression (n = 38, p < 0.05), but not in samples (n = 37) with low level of CBX7 expression, nor in paired surgical margin tissues. In addition, the results of RNA immunoprecipitation (RIP)- and chromatin immunoprecipitation (ChIP)-PCR analyses revealed that lncRNA P14AS could competitively bind to CBX7 protein which prevented the bindings of CBX7 to both lncRNA ANRIL and the promoters of P16 INK4A , P14 ARF and P15 INK4B genes. The amounts of repressive histone modification H3K9m3 was also significantly decreased at the promoters of these genes by P14AS in CBX7 actively expressing cells. Conclusions: CBX7 expression is essential for P14AS to upregulate the expression of P16 INK4A , P14 ARF , P15 INK4B and ANRIL genes in the CDKN2A/2Blocus. P14AS may upregulate these genes' expression through competitively blocking CBX7-binding to ANRIL lncRNA and target gene promoters.
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Affiliation(s)
| | | | | | | | | | - Dajun Deng
- *Correspondence: Dajun Deng, ; Baozhen Zhang,
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191
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Hino Y, Nagaoka K, Oki S, Etoh K, Hino S, Nakao M. Mitochondrial stress induces AREG expression and epigenomic remodeling through c-JUN and YAP-mediated enhancer activation. Nucleic Acids Res 2022; 50:9765-9779. [PMID: 36095121 PMCID: PMC9508833 DOI: 10.1093/nar/gkac735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 08/08/2022] [Accepted: 08/19/2022] [Indexed: 11/24/2022] Open
Abstract
Nucleus–mitochondria crosstalk is essential for cellular and organismal homeostasis. Although anterograde (nucleus-to-mitochondria) pathways have been well characterized, retrograde (mitochondria-to-nucleus) pathways remain to be clarified. Here, we found that mitochondrial dysfunction triggered a retrograde signaling via unique transcriptional and chromatin factors in hepatic cells. Our transcriptomic analysis revealed that the loss of mitochondrial transcription factor A led to mitochondrial dysfunction and dramatically induced expression of amphiregulin (AREG) and other secretory protein genes. AREG expression was also induced by various mitochondria stressors and was upregulated in murine liver injury models, suggesting that AREG expression is a hallmark of mitochondrial damage. Using epigenomic and informatic approaches, we identified that mitochondrial dysfunction-responsive enhancers of AREG gene were activated by c-JUN/YAP1/TEAD axis and were repressed by chromatin remodeler BRG1. Furthermore, while mitochondrial dysfunction-activated enhancers were enriched with JUN and TEAD binding motifs, the repressed enhancers possessed the binding motifs for hepatocyte nuclear factor 4α, suggesting that both stress responsible and cell type-specific enhancers were reprogrammed. Our study revealed that c-JUN and YAP1-mediated enhancer activation shapes the mitochondrial stress-responsive phenotype, which may shift from metabolism to stress adaptation including protein secretion under such stressed conditions.
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Affiliation(s)
- Yuko Hino
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-0811, Japan
| | - Katsuya Nagaoka
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-0811, Japan
| | - Shinya Oki
- Department of Drug Discovery Medicine, Kyoto University Graduate School of Medicine, Kyoto 606-8507, Japan
| | - Kan Etoh
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-0811, Japan
| | - Shinjiro Hino
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-0811, Japan
| | - Mitsuyoshi Nakao
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-0811, Japan
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192
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Typical Enhancers, Super-Enhancers, and Cancers. Cancers (Basel) 2022; 14:cancers14184375. [PMID: 36139535 PMCID: PMC9496678 DOI: 10.3390/cancers14184375] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 08/29/2022] [Accepted: 09/05/2022] [Indexed: 11/21/2022] Open
Abstract
Simple Summary The cancer genome has been exhaustively studied upon the advent of Next-Generation Sequencing technologies. Coding and non-coding sequences have been defined as hotspots of genomic variations that affect the naïve gene expression programs established in normal cells, thus working as endogenous drivers of carcinogenesis. In this review, we comprehensively summarize fundamental aspects of gene expression regulation, with emphasis on the impact of sequence and structural variations mapped across non-coding cis-acting elements of genes encoding for tumor-related transcription factors. Chromatin architecture, epigenome reprogramming, transcriptional enhancers and Super-enhancers, oncogene regulation, cutting-edge technologies, and pharmacological treatment are substantially highlighted. Abstract Non-coding segments of the human genome are enriched in cis-regulatory modules that constitute functional elements, such as transcriptional enhancers and Super-enhancers. A hallmark of cancer pathogenesis is the dramatic dysregulation of the “archetype” gene expression profiles of normal human cells. Genomic variations can promote such deficiencies when occurring across enhancers and Super-enhancers, since they affect their mechanistic principles, their functional capacity and specificity, and the epigenomic features of the chromatin microenvironment across which these regulatory elements reside. Here, we comprehensively describe: fundamental mechanisms of gene expression dysregulation in cancers that involve genomic abnormalities within enhancers’ and Super-enhancers’ (SEs) sequences, which alter the expression of oncogenic transcription factors (TFs); cutting-edge technologies applied for the analysis of variation-enriched hotspots of the cancer genome; and pharmacological approaches for the treatment of Super-enhancers’ aberrant function. Finally, we provide an intratumor meta-analysis, which highlights that genomic variations in transcription-factor-driven tumors are accompanied overexpression of genes, a portion of which encodes for additional cancer-related transcription factors.
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193
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van der Noord VE, van de Water B, Le Dévédec SE. Targeting the Heterogeneous Genomic Landscape in Triple-Negative Breast Cancer through Inhibitors of the Transcriptional Machinery. Cancers (Basel) 2022; 14:4353. [PMID: 36139513 PMCID: PMC9496798 DOI: 10.3390/cancers14184353] [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: 08/10/2022] [Revised: 08/28/2022] [Accepted: 08/30/2022] [Indexed: 11/16/2022] Open
Abstract
Triple-negative breast cancer (TNBC) is an aggressive subtype of breast cancer defined by lack of the estrogen, progesterone and human epidermal growth factor receptor 2. Although TNBC tumors contain a wide variety of oncogenic mutations and copy number alterations, the direct targeting of these alterations has failed to substantially improve therapeutic efficacy. This efficacy is strongly limited by interpatient and intratumor heterogeneity, and thereby a lack in uniformity of targetable drivers. Most of these genetic abnormalities eventually drive specific transcriptional programs, which may be a general underlying vulnerability. Currently, there are multiple selective inhibitors, which target the transcriptional machinery through transcriptional cyclin-dependent kinases (CDKs) 7, 8, 9, 12 and 13 and bromodomain extra-terminal motif (BET) proteins, including BRD4. In this review, we discuss how inhibitors of the transcriptional machinery can effectively target genetic abnormalities in TNBC, and how these abnormalities can influence sensitivity to these inhibitors. These inhibitors target the genomic landscape in TNBC by specifically suppressing MYC-driven transcription, inducing further DNA damage, improving anti-cancer immunity, and preventing drug resistance against MAPK and PI3K-targeted therapies. Because the transcriptional machinery enables transcription and propagation of multiple cancer drivers, it may be a promising target for (combination) treatment, especially of heterogeneous malignancies, including TNBC.
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Affiliation(s)
| | | | - Sylvia E. Le Dévédec
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, 2333 CC Leiden, The Netherlands
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194
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Xiao Y, Jiao S, He M, Lin D, Zuo H, Han J, Sun Y, Cao G, Chen Z, Liu H. Chromatin conformation of human oral epithelium can identify orofacial cleft missing functional variants. Int J Oral Sci 2022; 14:43. [PMID: 36008388 PMCID: PMC9411193 DOI: 10.1038/s41368-022-00194-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 07/19/2022] [Accepted: 07/29/2022] [Indexed: 11/09/2022] Open
Abstract
Genome-wide association studies (GWASs) are the most widely used method to identify genetic risk loci associated with orofacial clefts (OFC). However, despite the increasing size of cohort, GWASs are still insufficient to detect all the heritability, suggesting there are more associations under the current stringent statistical threshold. In this study, we obtained an integrated epigenomic dataset based on the chromatin conformation of a human oral epithelial cell line (HIOEC) using RNA-seq, ATAC-seq, H3K27ac ChIP-seq, and DLO Hi-C. Presumably, this epigenomic dataset could reveal the missing functional variants located in the oral epithelial cell active enhancers/promoters along with their risk target genes, despite relatively less-stringent statistical association with OFC. Taken a non-syndromic cleft palate only (NSCPO) GWAS data of the Chinese Han population as an example, 3664 SNPs that cannot reach the strict significance threshold were subjected to this functional identification pipeline. In total, 254 potential risk SNPs residing in active cis-regulatory elements interacting with 1 718 promoters of oral epithelium-expressed genes were screened. Gapped k-mer machine learning based on enhancers interacting with epithelium-expressed genes along with in vivo and in vitro reporter assays were employed as functional validation. Among all the potential SNPs, we chose and confirmed that the risk alleles of rs560789 and rs174570 reduced the epithelial-specific enhancer activity by preventing the binding of transcription factors related to epithelial development. In summary, we established chromatin conformation datasets of human oral epithelial cells and provided a framework for testing and understanding how regulatory variants impart risk for clefts.
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Affiliation(s)
- Yao Xiao
- The State Key Laboratory Breeding Base of Basic Science of Stomatology & Key Laboratory for Oral Biomedicine of Ministry of Education, School and Hospital of Stomatology, Wuhan University, 237 Luoyu Road, Wuhan, China.,Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Shengbo Jiao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, Institute of Hydrobiology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Wuhan, China.,College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Miao He
- The State Key Laboratory Breeding Base of Basic Science of Stomatology & Key Laboratory for Oral Biomedicine of Ministry of Education, School and Hospital of Stomatology, Wuhan University, 237 Luoyu Road, Wuhan, China
| | - Da Lin
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Huanyan Zuo
- The State Key Laboratory Breeding Base of Basic Science of Stomatology & Key Laboratory for Oral Biomedicine of Ministry of Education, School and Hospital of Stomatology, Wuhan University, 237 Luoyu Road, Wuhan, China
| | - Jiahao Han
- The State Key Laboratory Breeding Base of Basic Science of Stomatology & Key Laboratory for Oral Biomedicine of Ministry of Education, School and Hospital of Stomatology, Wuhan University, 237 Luoyu Road, Wuhan, China
| | - Yonghua Sun
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, Institute of Hydrobiology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Wuhan, China.,College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Gang Cao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Zhi Chen
- The State Key Laboratory Breeding Base of Basic Science of Stomatology & Key Laboratory for Oral Biomedicine of Ministry of Education, School and Hospital of Stomatology, Wuhan University, 237 Luoyu Road, Wuhan, China.
| | - Huan Liu
- The State Key Laboratory Breeding Base of Basic Science of Stomatology & Key Laboratory for Oral Biomedicine of Ministry of Education, School and Hospital of Stomatology, Wuhan University, 237 Luoyu Road, Wuhan, China. .,Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, China.
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195
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Neiro J, Sridhar D, Dattani A, Aboobaker A. Identification of putative enhancer-like elements predicts regulatory networks active in planarian adult stem cells. eLife 2022; 11:79675. [PMID: 35997250 PMCID: PMC9522251 DOI: 10.7554/elife.79675] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 08/23/2022] [Indexed: 11/13/2022] Open
Abstract
Planarians have become an established model system to study regeneration and stem cells, but the regulatory elements in the genome remain almost entirely undescribed. Here, by integrating epigenetic and expression data we use multiple sources of evidence to predict enhancer elements active in the adult stem cell populations that drive regeneration. We have used ChIP-seq data to identify genomic regions with histone modifications consistent with enhancer activity, and ATAC-seq data to identify accessible chromatin. Overlapping these signals allowed for the identification of a set of high-confidence candidate enhancers predicted to be active in planarian adult stem cells. These enhancers are enriched for predicted transcription factor (TF) binding sites for TFs and TF families expressed in planarian adult stem cells. Footprinting analyses provided further evidence that these potential TF binding sites are likely to be occupied in adult stem cells. We integrated these analyses to build testable hypotheses for the regulatory function of TFs in stem cells, both with respect to how pluripotency might be regulated, and to how lineage differentiation programs are controlled. We found that our predicted GRNs were independently supported by existing TF RNAi/RNA-seq datasets, providing further evidence that our work predicts active enhancers that regulate adult stem cells and regenerative mechanisms.
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Affiliation(s)
- Jakke Neiro
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Divya Sridhar
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Anish Dattani
- Living Systems Institute, University of Exeter, Exeter, United Kingdom
| | - Aziz Aboobaker
- Department of Zoology, University of Oxford, Oxford, United Kingdom
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196
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Turpin M, Salbert G. 5-methylcytosine turnover: Mechanisms and therapeutic implications in cancer. Front Mol Biosci 2022; 9:976862. [PMID: 36060265 PMCID: PMC9428128 DOI: 10.3389/fmolb.2022.976862] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 07/26/2022] [Indexed: 12/04/2022] Open
Abstract
DNA methylation at the fifth position of cytosine (5mC) is one of the most studied epigenetic mechanisms essential for the control of gene expression and for many other biological processes including genomic imprinting, X chromosome inactivation and genome stability. Over the last years, accumulating evidence suggest that DNA methylation is a highly dynamic mechanism driven by a balance between methylation by DNMTs and TET-mediated demethylation processes. However, one of the main challenges is to understand the dynamics underlying steady state DNA methylation levels. In this review article, we give an overview of the latest advances highlighting DNA methylation as a dynamic cycling process with a continuous turnover of cytosine modifications. We describe the cooperative actions of DNMT and TET enzymes which combine with many additional parameters including chromatin environment and protein partners to govern 5mC turnover. We also discuss how mathematical models can be used to address variable methylation levels during development and explain cell-type epigenetic heterogeneity locally but also at the genome scale. Finally, we review the therapeutic implications of these discoveries with the use of both epigenetic clocks as predictors and the development of epidrugs that target the DNA methylation/demethylation machinery. Together, these discoveries unveil with unprecedented detail how dynamic is DNA methylation during development, underlying the establishment of heterogeneous DNA methylation landscapes which could be altered in aging, diseases and cancer.
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Affiliation(s)
- Marion Turpin
- Sp@rte Team, UMR6290 CNRS, Institute of Genetics and Development of Rennes, Rennes, France
- University of Rennes 1, Rennes, France
| | - Gilles Salbert
- Sp@rte Team, UMR6290 CNRS, Institute of Genetics and Development of Rennes, Rennes, France
- University of Rennes 1, Rennes, France
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197
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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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198
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Abstract
Cochlear hair cells (HCs) in the inner ear are responsible for sound detection. For HC fate specification, the master transcription factor Atoh1 is both necessary and sufficient. Atoh1 expression is dynamic and tightly regulated during development, but the cis-regulatory elements mediating this regulation remain unresolved. Unexpectedly, we found that deleting the only recognized Atoh1 enhancer, defined here as Eh1, failed to impair HC development. By using the assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq), we discovered two additional Atoh1 enhancers: Eh2 and Eh3. Notably, Eh2 deletion was sufficient for impairing HC development, and concurrent deletion of Eh1 and Eh2 or all three enhancers resulted in nearly complete absence of HCs. Lastly, we showed that Atoh1 binds to all three enhancers, consistent with its autoregulatory function. Our findings reveal that the cooperative action of three distinct enhancers underpins effective Atoh1 regulation during HC development, indicating potential therapeutic approaches for HC regeneration.
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199
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Ramirez M, Badayeva Y, Yeung J, Wu J, Abdalla-Wyse A, Yang E, Trost B, Scherer SW, Goldowitz D. Temporal analysis of enhancers during mouse cerebellar development reveals dynamic and novel regulatory functions. eLife 2022; 11:74207. [PMID: 35942939 PMCID: PMC9398453 DOI: 10.7554/elife.74207] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Accepted: 08/05/2022] [Indexed: 11/13/2022] Open
Abstract
We have identified active enhancers in the mouse cerebellum at embryonic and postnatal stages which provides a view of novel enhancers active during cerebellar development. The majority of cerebellar enhancers have dynamic activity between embryonic and postnatal development. Cerebellar enhancers were enriched for neural transcription factor binding sites with temporally specific expression. Putative gene targets displayed spatially restricted expression patterns, indicating cell-type specific expression regulation. Functional analysis of target genes indicated that enhancers regulate processes spanning several developmental epochs such as specification, differentiation and maturation. We use these analyses to discover one novel regulator and one novel marker of cerebellar development: Bhlhe22 and Pax3, respectively. We identified an enrichment of de novo mutations and variants associated with autism spectrum disorder in cerebellar enhancers. Furthermore, by comparing our data with relevant brain development ENCODE histone profiles and cerebellar single-cell datasets we have been able to generalize and expand on the presented analyses, respectively. We have made the results of our analyses available online in the Developing Mouse Cerebellum Enhancer Atlas (https://goldowitzlab.shinyapps.io/developing_mouse_cerebellum_enhancer_atlas/), where our dataset can be efficiently queried, curated and exported by the scientific community to facilitate future research efforts. Our study provides a valuable resource for studying the dynamics of gene expression regulation by enhancers in the developing cerebellum and delivers a rich dataset of novel gene-enhancer associations providing a basis for future in-depth studies in the cerebellum.
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Affiliation(s)
- Miguel Ramirez
- Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital, Vancouver, Canada
| | - Yuliya Badayeva
- Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital, Vancouver, Canada
| | - Joanna Yeung
- Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital, Vancouver, Canada
| | - Joshua Wu
- Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital, Vancouver, Canada
| | - Ayasha Abdalla-Wyse
- Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital, Vancouver, Canada
| | - Erin Yang
- Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital, Vancouver, Canada
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- Department of Molecular Genetics, Hospital for Sick Children, Toronto, Canada
| | - Brett Trost
- The Centre for Applied Genomics, Hospital for Sick Children, Toronto, Canada
| | - Stephen W Scherer
- Department of Molecular Genetics, Hospital for Sick Children, Toronto, Canada
| | - Daniel Goldowitz
- Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital, Vancouver, Canada
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200
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Xiao Q, Xiao Y, Li LY, Chen MK, Wu M. Multifaceted regulation of enhancers in cancer. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2022; 1865:194839. [PMID: 35750313 DOI: 10.1016/j.bbagrm.2022.194839] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 05/24/2022] [Accepted: 06/14/2022] [Indexed: 12/12/2022]
Abstract
Enhancer is one kind of cis-elements regulating gene transcription, whose activity is tightly controlled by epigenetic enzymes and histone modifications. Active enhancers are classified into typical enhancers, super-enhancers and over-active enhancers, according to the enrichment and location of histone modifications. Epigenetic factors control the level of histone modifications on enhancers to determine their activity, such as histone methyltransferases and acetylases. Transcription factors, cofactors and mediators co-operate together and are required for enhancer functions. In turn, abnormalities in these trans-acting factors affect enhancer activity. Recent studies have revealed enhancer dysregulation as one of the important features for cancer. Variations in enhancer regions and mutations of enhancer regulatory genes are frequently observed in cancer cells, and altering the activity of onco-enhancers is able to repress oncogene expression, and suppress tumorigenesis and metastasis. Here we summarize the recent discoveries about enhancer regulation in cancer and discuss their potential application in diagnosis and treatment.
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Affiliation(s)
- Qiong Xiao
- Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, Hubei 430072, China
| | - Yong Xiao
- Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, Hubei 430072, China
| | - Lian-Yun Li
- Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, Hubei 430072, China
| | - Ming-Kai Chen
- Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, Hubei 430072, China.
| | - Min Wu
- Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, Hubei 430072, China.
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