1
|
Qiu X, Zhang S, Zhang Y, Cai L, Li D, Lu Y. Reduction of ETV1 is Identified as a Prominent Feature of Age-Related Cataract. Curr Eye Res 2024; 49:496-504. [PMID: 38200696 DOI: 10.1080/02713683.2024.2302545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Accepted: 01/01/2024] [Indexed: 01/12/2024]
Abstract
PURPOSE To identify the inactive genes in cataract lenses and explore their function in lens epithelial cells (LECs). METHODS Lens epithelium samples obtained from both age-related cataract (ARC) patients and normal donors were subjected to two forms of histone H3 immunoprecipitation: H3K9ac and H3K27me3 chromatin immunoprecipitation (ChIP), followed by ChIP-seq. The intersection set of "active genes in normal controls" and "repressed genes in cataract lenses" was identified. To validate the role of a specific gene, ETV1, within this set, quantitative polymerase chain reaction (qPCR), western blot, and immunofluorescence were performed using clinical lens epithelium samples. Small interference RNA (siRNA) was utilized to reduce the mRNA level of ETV1 in cultured LECs. Following this, transwell assay and western blot was performed to examine the migration ability of the cells. Furthermore, RNA-seq analysis was conducted on both cell samples with ETV1 knockdown and control cells. Additionally, the expression level of ETV1 in LECs was examined using qPCR under H2O2 treatment. RESULTS Six genes were identified in the intersection set of "active genes in normal controls" and "repressed genes in ARC lenses". Among these genes, ETV1 showed the most significant fold-change decrease in the cataract samples compared to the control samples. After ETV1 knockdown by siRNA in cultured LECs, reduced cell migration was observed, along with a decrease in the expression of β-Catenin and Vimentin, two specific genes associated with cell migration. In addition, under the oxidative stress induced by H2O2 treatment, the expression level of ETV1 in LECs significantly decreased. CONCLUSIONS Based on the findings of this study, it can be concluded that ETV1 is significantly reduced in human ARC lenses. The repression of ETV1 in ARC lenses appears to contribute to the disrupted differentiation of lens epithelium, which is likely caused by the inhibition of both cell differentiation and migration processes.
Collapse
Affiliation(s)
- Xiaodi Qiu
- Eye Institute, Eye & ENT Hospital of Fudan University, Shanghai, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai, China
- NHC Key Laboratory of Myopia, Fudan University, Shanghai, China
- Laboratory of Myopia, Chinese Academy of Medical Sciences, Shanghai, China
| | - Shaohua Zhang
- Eye Institute, Eye & ENT Hospital of Fudan University, Shanghai, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai, China
- NHC Key Laboratory of Myopia, Fudan University, Shanghai, China
- Laboratory of Myopia, Chinese Academy of Medical Sciences, Shanghai, China
| | - Youmeng Zhang
- Department of Stomatology, Eye & ENT Hospital of Fudan University, Shanghai, China
| | - Lei Cai
- Eye Institute, Eye & ENT Hospital of Fudan University, Shanghai, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai, China
- NHC Key Laboratory of Myopia, Fudan University, Shanghai, China
- Laboratory of Myopia, Chinese Academy of Medical Sciences, Shanghai, China
| | - Dan Li
- Eye Institute, Eye & ENT Hospital of Fudan University, Shanghai, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai, China
- NHC Key Laboratory of Myopia, Fudan University, Shanghai, China
- Laboratory of Myopia, Chinese Academy of Medical Sciences, Shanghai, China
| | - Yi Lu
- Eye Institute, Eye & ENT Hospital of Fudan University, Shanghai, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai, China
- NHC Key Laboratory of Myopia, Fudan University, Shanghai, China
- Laboratory of Myopia, Chinese Academy of Medical Sciences, Shanghai, China
| |
Collapse
|
2
|
Harris S, Anwar I, Baksh SS, Pratt RE, Dzau VJ, Hodgkinson CP. Skeletal muscle differentiation induces wide-ranging nucleosome repositioning in muscle gene promoters. Sci Rep 2024; 14:9396. [PMID: 38658615 DOI: 10.1038/s41598-024-60236-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 04/19/2024] [Indexed: 04/26/2024] Open
Abstract
In a previous report, we demonstrated that Cbx1, PurB and Sp3 inhibited cardiac muscle differentiation by increasing nucleosome density around cardiac muscle gene promoters. Since cardiac and skeletal muscle express many of the same proteins, we asked if Cbx1, PurB and Sp3 similarly regulated skeletal muscle differentiation. In a C2C12 model of skeletal muscle differentiation, Cbx1 and PurB knockdown increased myotube formation. In contrast, Sp3 knockdown inhibited myotube formation, suggesting that Sp3 played opposing roles in cardiac muscle and skeletal muscle differentiation. Consistent with this finding, Sp3 knockdown also inhibited various muscle-specific genes. The Cbx1, PurB and Sp3 proteins are believed to influence gene-expression in part by altering nucleosome position. Importantly, we developed a statistical approach to determine if changes in nucleosome positioning were significant and applied it to understanding the architecture of muscle-specific genes. Through this novel statistical approach, we found that during myogenic differentiation, skeletal muscle-specific genes undergo a set of unique nucleosome changes which differ significantly from those shown in commonly expressed muscle genes. While Sp3 binding was associated with nucleosome loss, there appeared no correlation with the aforementioned nucleosome changes. In summary, we have identified a novel role for Sp3 in skeletal muscle differentiation and through the application of quantifiable MNase-seq have discovered unique fingerprints of nucleosome changes for various classes of muscle genes during myogenic differentiation.
Collapse
Affiliation(s)
- Sonalí Harris
- Mandel Center for Heart and Vascular Research, The Duke Cardiovascular Research Center, Duke University Medical Center, Duke University, CaRL Building, 213 Research Drive, Durham, NC, 27710, USA
| | - Iqra Anwar
- Mandel Center for Heart and Vascular Research, The Duke Cardiovascular Research Center, Duke University Medical Center, Duke University, CaRL Building, 213 Research Drive, Durham, NC, 27710, USA
| | - Syeda S Baksh
- Mandel Center for Heart and Vascular Research, The Duke Cardiovascular Research Center, Duke University Medical Center, Duke University, CaRL Building, 213 Research Drive, Durham, NC, 27710, USA
| | - Richard E Pratt
- Mandel Center for Heart and Vascular Research, The Duke Cardiovascular Research Center, Duke University Medical Center, Duke University, CaRL Building, 213 Research Drive, Durham, NC, 27710, USA
| | - Victor J Dzau
- Mandel Center for Heart and Vascular Research, The Duke Cardiovascular Research Center, Duke University Medical Center, Duke University, CaRL Building, 213 Research Drive, Durham, NC, 27710, USA
| | - Conrad P Hodgkinson
- Mandel Center for Heart and Vascular Research, The Duke Cardiovascular Research Center, Duke University Medical Center, Duke University, CaRL Building, 213 Research Drive, Durham, NC, 27710, USA.
| |
Collapse
|
3
|
Biot M, Toth A, Brun C, Guichard L, de Massy B, Grey C. Principles of chromosome organization for meiotic recombination. Mol Cell 2024:S1097-2765(24)00279-X. [PMID: 38657614 DOI: 10.1016/j.molcel.2024.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 03/01/2024] [Accepted: 04/02/2024] [Indexed: 04/26/2024]
Abstract
In meiotic cells, chromosomes are organized as chromatin loop arrays anchored to a protein axis. This organization is essential to regulate meiotic recombination, from DNA double-strand break (DSB) formation to their repair. In mammals, it is unknown how chromatin loops are organized along the genome and how proteins participating in DSB formation are tethered to the chromosome axes. Here, we identify three categories of axis-associated genomic sites: PRDM9 binding sites, where DSBs form; binding sites of the insulator protein CTCF; and H3K4me3-enriched sites. We demonstrate that PRDM9 promotes the recruitment of MEI4 and IHO1, two proteins essential for DSB formation. In turn, IHO1 anchors DSB sites to the axis components HORMAD1 and SYCP3. We discovered that IHO1, HORMAD1, and SYCP3 are associated at the DSB ends during DSB repair. Our results highlight how interactions of proteins with specific genomic elements shape the meiotic chromosome organization for recombination.
Collapse
Affiliation(s)
- Mathilde Biot
- Institute of Human Genetics, University of Montpellier, CNRS, Montpellier, France
| | - Attila Toth
- Institute of Physiological Chemistry, Faculty of Medicine at the TU Dresden, Dresden, Germany
| | - Christine Brun
- Institute of Human Genetics, University of Montpellier, CNRS, Montpellier, France
| | - Leon Guichard
- Institute of Human Genetics, University of Montpellier, CNRS, Montpellier, France
| | - Bernard de Massy
- Institute of Human Genetics, University of Montpellier, CNRS, Montpellier, France.
| | - Corinne Grey
- Institute of Human Genetics, University of Montpellier, CNRS, Montpellier, France.
| |
Collapse
|
4
|
Cui Y, Ru M, Wang Y, Weng L, Haji RA, Liang H, Zeng Q, Wei Q, Xie X, Yin C, Huang J. Epigenetic regulation of H3K27me3 in laying hens with fatty liver hemorrhagic syndrome induced by high-energy and low-protein diets. BMC Genomics 2024; 25:374. [PMID: 38627644 PMCID: PMC11022457 DOI: 10.1186/s12864-024-10270-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 03/29/2024] [Indexed: 04/19/2024] Open
Abstract
BACKGROUND Fatty liver hemorrhagic syndrome (FLHS) in the modern poultry industry is primarily caused by nutrition. Despite encouraging progress on FLHS, the mechanism through which nutrition influences susceptibility to FLHS is still lacking in terms of epigenetics. RESULTS In this study, we analyzed the genome-wide patterns of trimethylated lysine residue 27 of histone H3 (H3K27me3) enrichment by chromatin immunoprecipitation-sequencing (ChIP-seq), and examined its association with transcriptomes in healthy and FLHS hens. The study results indicated that H3K27me3 levels were increased in the FLHS hens on a genome-wide scale. Additionally, H3K27me3 was found to occupy the entire gene and the distant intergenic region, which may function as silencer-like regulatory elements. The analysis of transcription factor (TF) motifs in hypermethylated peaks has demonstrated that 23 TFs are involved in the regulation of liver metabolism and development. Transcriptomic analysis indicated that differentially expressed genes (DEGs) were enriched in fatty acid metabolism, amino acid, and carbohydrate metabolism. The hub gene identified from PPI network is fatty acid synthase (FASN). Combined ChIP-seq and transcriptome analysis revealed that the increased H3K27me3 and down-regulated genes have significant enrichment in the ECM-receptor interaction, tight junction, cell adhesion molecules, adherens junction, and TGF-beta signaling pathways. CONCLUSIONS Overall, the trimethylation modification of H3K27 has been shown to have significant regulatory function in FLHS, mediating the expression of crucial genes associated with the ECM-receptor interaction pathway. This highlights the epigenetic mechanisms of H3K27me3 and provides insights into exploring core regulatory targets and nutritional regulation strategies in FLHS.
Collapse
Affiliation(s)
- Yong Cui
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Meng Ru
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Yujie Wang
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Linjian Weng
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Ramlat Ali Haji
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Haiping Liang
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Qingjie Zeng
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Qing Wei
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Xianhua Xie
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Chao Yin
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Jianzhen Huang
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
| |
Collapse
|
5
|
Schroeder JW, Freddolino PL. Enricherator: A Bayesian Method for Inferring Regularized Genome-wide Enrichments from Sequencing Count Data. J Mol Biol 2024:168567. [PMID: 38583516 DOI: 10.1016/j.jmb.2024.168567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/31/2024] [Accepted: 04/02/2024] [Indexed: 04/09/2024]
Abstract
A pervasive question in biological research studying gene regulation, chromatin structure, or genomics is where, and to what extent, does a signal of interest arise genome-wide? This question is addressed using a variety of methods relying on high-throughput sequencing data as their final output, including ChIP-seq for protein-DNA interactions,1 GapR-seq for measuring supercoiling,2 and HBD-seq or DRIP-seq for R-loop positioning.3,4 Current computational methods to calculate genome-wide enrichment of the signal of interest usually do not properly handle the count-based nature of sequencing data, they often do not make use of the local correlation structure of sequencing data, and they do not apply any regularization of enrichment estimates. This can result in unrealistic estimates of the true underlying biological enrichment of interest, unrealistically low estimates of confidence in point estimates of enrichment (or no estimates of confidence at all), unrealistic gyrations in enrichment estimates at very close (<10 bp) genomic loci due to noise inherent in sequencing data, and in a multiple-hypothesis testing problem during interpretation of genome-wide enrichment estimates. We developed a tool called Enricherator to infer genome-wide enrichments from sequencing count data. Enricherator uses the variational Bayes algorithm to fit a generalized linear model to sequencing count data and to sample from the approximate posterior distribution of enrichment estimates (https://github.com/jwschroeder3/enricherator). Enrichments inferred by Enricherator more precisely identify known binding sites in cases where low coverage between binding sites leads to false-positive peak calls in these noisy regions of the genome; these benefits extend to published datasets.
Collapse
Affiliation(s)
- Jeremy W Schroeder
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - P Lydia Freddolino
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA.
| |
Collapse
|
6
|
Wu Z, Li H, Xu H, Feng F, Zhang F, Zhang S, Wang L, Li Y. ChIP-seq analysis found IL21R, a target gene of GTF2I-the susceptibility gene for primary biliary cholangitis in Chinese Han. Hepatol Int 2024; 18:509-516. [PMID: 37713154 DOI: 10.1007/s12072-023-10586-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 08/17/2023] [Indexed: 09/16/2023]
Abstract
AIMS Aimed to identify a new susceptibility gene associated with primary biliary cholangitis (PBC) in Chinese Han and investigate the possible mechanism of that gene in PBC. METHODS A total of 466 PBC and 694 healthy controls (HC) were included in our study, and genotyping GTF2I gene variants by Sequenom. CD19 + B cells were isolated for Chromatin immunoprecipitation sequencing (ChIP-seq). Additionally, MEME-ChIP was utilized to perform searches for known motifs and de novo motif discovery. The GTF2I ChIP-seq of hematopoietic cell line (K562) results were obtained from ENCODE (GSE176987, GSE177691). The Genomic HyperBrowser was used to determine overlap and hierarchal clustering between ours and ENCODE datasets. RESULTS The frequency of the rs117026326 variant T allele was significantly higher in PBC patients than that in HC (20.26% compared with 13.89%, Pc = 1.09E-04). Furthermore, we observed an elevated proportion of GTF2I binding site located in the upstream and 5' UTR of genes in PBC in comparison with HC. Additionally, an in-depth analysis of IL21R region revealed that GTF2I might bind to the IL21R promoter to regulate the expression of the IL21R, with four peaks of GTF2I binding sites, including three increased binding sites in upstream, one increased binding site in 5' UTR. Motif analysis by MEME-ChIP uncovered five significant motifs. A significant overlap between our ChIP and GSE176987, GSE17769 were found by the Genomic HyperBroswer. CONCLUSIONS Our study confirmed that GTF2I was associated with PBC in Chinese Han. Furthermore, our gene function analysis indicated that IL21R may be the target gene regulated by GTF2I.
Collapse
Affiliation(s)
- Ziyan Wu
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 1 Shuaifuyuan Hutong, Dongcheng District, Beijing, 100730, China
| | - Haolong Li
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 1 Shuaifuyuan Hutong, Dongcheng District, Beijing, 100730, China
| | - Honglin Xu
- Department of Rheumatology and Clinical Immunology, Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Futai Feng
- Department of Rheumatology and Clinical Immunology, Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Fengchun Zhang
- Department of Rheumatology and Clinical Immunology, Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Shulan Zhang
- Department of Rheumatology and Clinical Immunology, Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
| | - Li Wang
- Department of Rheumatology and Clinical Immunology, Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
| | - Yongzhe Li
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 1 Shuaifuyuan Hutong, Dongcheng District, Beijing, 100730, China.
| |
Collapse
|
7
|
Feng D, Zhao H, Wang Q, Wu J, Ouyang L, Jia S, Lu Q, Zhao M. Aberrant H3K4me3 modification of immune response genes in CD4 + T cells of patients with systemic lupus erythematosus. Int Immunopharmacol 2024; 130:111748. [PMID: 38432146 DOI: 10.1016/j.intimp.2024.111748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 01/17/2024] [Accepted: 02/21/2024] [Indexed: 03/05/2024]
Abstract
BACKGROUND Increasing evidence has highlighted the significant role of histone modifications in pathogenesis of systemic lupus erythematosus (SLE). However, few studies have comprehensively analyzed trimethylation of histone H3 lysine 4 (H3K4me3) features at specific immune gene loci in SLE patients. METHODS We conducted H3K4me3 chromatin immunoprecipitation sequencing (ChIP-seq) on CD4+ T cells from SLE patients and healthy controls (HC). Differential H3K4me3 peaks were identified, followed by enrichment analysis. We integrated online RNA-seq and DNA methylation datasets to explore the relationship between H3K4me3 modification, DNA methylation and gene expression. We validated several upregulated peak regions by ChIP-qPCR and confirmed their impact on gene expression using RT-qPCR. Finally, we investigated the impact of H3K4 methyltransferases KMT2A on the expression of immune response genes. RESULTS we identified 147 downregulated and 2701 upregulated H3K4me3 peaks in CD4+ T cells of SLE. The upregulated peaks primarily classified as gained peaks and enriched in immune response genes such as FCGR2A, C5AR1, SERPING1 and OASL. Genes with upregulated H3K4me3 and downregulated DNA methylations in the promoter were highly expressed in SLE patients. These genes, including OAS1, IFI27 and IFI44L, were enriched in immune response pathways. The IFI44L locus also showed increased H3K27ac modification, chromatin accessibility and chromatin interactions in SLE. Moreover, knockdown of KMT2A can downregulate the expression of immune response genes in T cells. CONCLUSION Our study uncovers dysregulated H3K4me3 modification patterns in immune response genes loci, which also exhibit downregulated DNA methylation and higher mRNA expression in CD4+ T cells of SLE patients.
Collapse
Affiliation(s)
- Delong Feng
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Hongjun Zhao
- Department of Rheumatology, Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Qian Wang
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Jiali Wu
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Lianlian Ouyang
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Sujie Jia
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, Jiangsu, China
| | - Qianjin Lu
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China; Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, Jiangsu, China; Key Laboratory of Basic and Translational Research on Immune-Mediated Skin Diseases, Institute of Dermatology, Chinese Academy of Medical Sciences, Nanjing, Jiangsu, China
| | - Ming Zhao
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China; Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, Jiangsu, China; Key Laboratory of Basic and Translational Research on Immune-Mediated Skin Diseases, Institute of Dermatology, Chinese Academy of Medical Sciences, Nanjing, Jiangsu, China.
| |
Collapse
|
8
|
Healy E, Zhang Q, Gail EH, Agius SC, Sun G, Bullen M, Pandey V, Das PP, Polo JM, Davidovich C. The apparent loss of PRC2 chromatin occupancy as an artifact of RNA depletion. Cell Rep 2024; 43:113858. [PMID: 38416645 DOI: 10.1016/j.celrep.2024.113858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/08/2023] [Accepted: 02/08/2024] [Indexed: 03/01/2024] Open
Abstract
RNA has been implicated in the recruitment of chromatin modifiers, and previous studies have provided evidence in favor and against this idea. RNase treatment of chromatin is commonly used to study RNA-mediated regulation of chromatin modifiers, but the limitations of this approach remain unclear. RNase A treatment during chromatin immunoprecipitation (ChIP) reduces chromatin occupancy of the H3K27me3 methyltransferase Polycomb repressive complex 2 (PRC2). This led to suggestions of an "RNA bridge" between PRC2 and chromatin. Here, we show that RNase A treatment during ChIP causes the apparent loss of all facultative heterochromatin, including both PRC2 and H3K27me3 genome-wide. We track this observation to a gain of DNA from non-targeted chromatin, sequenced at the expense of DNA from facultative heterochromatin, which reduces ChIP signals. Our results emphasize substantial limitations in using RNase A treatment for mapping RNA-dependent chromatin occupancy and invalidate conclusions that were previously established for PRC2 based on this assay.
Collapse
Affiliation(s)
- Evan Healy
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC, Australia
| | - Qi Zhang
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC, Australia; South Australian immunoGENomics Cancer Institute (SAiGENCI), Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, Australia; EMBL-Australia at SAiGENCI, Adelaide, SA, Australia
| | - Emma H Gail
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC, Australia
| | - Samuel C Agius
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC, Australia
| | - Guizhi Sun
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Wellington Road, Clayton, VIC 3800, Australia
| | - Michael Bullen
- Department of Anatomy and Developmental Biology, Monash University, Wellington Road, Clayton, VIC 3800, Australia
| | - Varun Pandey
- Department of Anatomy and Developmental Biology, Monash University, Wellington Road, Clayton, VIC 3800, Australia
| | - Partha Pratim Das
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Wellington Road, Clayton, VIC 3800, Australia; Department of Anatomy and Developmental Biology, Monash University, Wellington Road, Clayton, VIC 3800, Australia
| | - Jose M Polo
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Wellington Road, Clayton, VIC 3800, Australia; Department of Anatomy and Developmental Biology, Monash University, Wellington Road, Clayton, VIC 3800, Australia; Adelaide Centre for Epigenetics and South Australian immunoGENomics Cancer Institute, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA, Australia
| | - Chen Davidovich
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC, Australia; EMBL-Australia, Clayton, VIC, Australia.
| |
Collapse
|
9
|
Hall Hickman A, Jenner RG. Apparent RNA bridging between PRC2 and chromatin is an artifact of non-specific chromatin precipitation upon RNA degradation. Cell Rep 2024; 43:113856. [PMID: 38416641 DOI: 10.1016/j.celrep.2024.113856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 01/26/2024] [Accepted: 02/08/2024] [Indexed: 03/01/2024] Open
Abstract
Polycomb repressive complex 2 (PRC2) modifies chromatin to maintain repression of genes specific for other cell lineages. In vitro, RNA inhibits PRC2 activity, but the effect of RNA on PRC2 in cells is less clear, with studies concluding that RNA either antagonizes or promotes PRC2 chromatin association. The addition of RNase A to chromatin immunoprecipitation reactions has been reported to reduce detection of PRC2 target sites, suggesting the existence of RNA bridges connecting PRC2 to chromatin. Here, we show that the apparent loss of PRC2 chromatin association after RNase A treatment is due to non-specific chromatin precipitation. RNA degradation precipitates chromatin out of solution, thereby masking enrichment of specific DNA sequences in chromatin immunoprecipitation reactions. Maintaining chromatin solubility by the addition of poly-L-glutamic acid rescues detection of PRC2 chromatin occupancy upon RNA degradation. These findings undermine support for the model that RNA bridges PRC2 and chromatin in cells.
Collapse
Affiliation(s)
- Alexander Hall Hickman
- UCL Cancer Institute, University College London, London WC1E 6BT, UK; CRUK City of London Centre, University College London, London WC1E 6BT, UK
| | - Richard G Jenner
- UCL Cancer Institute, University College London, London WC1E 6BT, UK; CRUK City of London Centre, University College London, London WC1E 6BT, UK.
| |
Collapse
|
10
|
Lykke-Andersen S, Rouvière JO, Schmid M, Gockert M, Jensen TH. Protocol for generating customizable and reproducible plots of sequencing coverage data using the seqNdisplayR package. STAR Protoc 2024; 5:102960. [PMID: 38502686 DOI: 10.1016/j.xpro.2024.102960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 12/11/2023] [Accepted: 02/29/2024] [Indexed: 03/21/2024] Open
Abstract
The widespread usage of next-generation sequencing methods for functional genomics studies requires standardized tools for consistent visualization of the associated data. Here, we present seqNdisplayR, an R package for plotting standard sequencing data coverage within a genomic region of interest in a customizable and reproducible manner. We describe steps for installing software, preparing data files, choosing options, and plotting data. This tool is readily available for users with no prior experience with R through the "Shiny app" interface. For complete details on the use and execution of this protocol, please refer to Lykke-Andersen et al.,1 Gockert et al.,2 and Rouviere et al.3.
Collapse
Affiliation(s)
- Søren Lykke-Andersen
- Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, 8000 Aarhus C, Denmark.
| | - Jérôme O Rouvière
- Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, 8000 Aarhus C, Denmark
| | - Manfred Schmid
- Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, 8000 Aarhus C, Denmark
| | - Maria Gockert
- Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, 8000 Aarhus C, Denmark
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, 8000 Aarhus C, Denmark.
| |
Collapse
|
11
|
Scholz R, Brösamle D, Yuan X, Beyer M, Neher JJ. Epigenetic control of microglial immune responses. Immunol Rev 2024. [PMID: 38491845 DOI: 10.1111/imr.13317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 03/02/2024] [Indexed: 03/18/2024]
Abstract
Microglia, the major population of brain-resident macrophages, are now recognized as a heterogeneous population comprising several cell subtypes with different (so far mostly supposed) functions in health and disease. A number of studies have performed molecular characterization of these different microglial activation states over the last years making use of "omics" technologies, that is transcriptomics, proteomics and, less frequently, epigenomics profiling. These approaches offer the possibility to identify disease mechanisms, discover novel diagnostic biomarkers, and develop new therapeutic strategies. Here, we focus on epigenetic profiling as a means to understand microglial immune responses beyond what other omics methods can offer, that is, revealing past and present molecular responses, gene regulatory networks and potential future response trajectories, and defining cell subtype-specific disease relevance through mapping non-coding genetic variants. We review the current knowledge in the field regarding epigenetic regulation of microglial identity and function, provide an exemplary analysis that demonstrates the advantages of performing joint transcriptomic and epigenomic profiling of single microglial cells and discuss how comprehensive epigenetic analyses may enhance our understanding of microglial pathophysiology.
Collapse
Affiliation(s)
- Rebekka Scholz
- Immunogenomics & Neurodegeneration, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
- Systems Medicine, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Desirée Brösamle
- Biomedical Center (BMC), Biochemistry, Faculty of Medicine, LMU Munich, Munich, Germany
- Neuroimmunology and Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Department of Cellular Neurology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Xidi Yuan
- Biomedical Center (BMC), Biochemistry, Faculty of Medicine, LMU Munich, Munich, Germany
- Neuroimmunology and Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Department of Cellular Neurology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Marc Beyer
- Immunogenomics & Neurodegeneration, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
- Systems Medicine, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
- Platform for Single Cell Genomics and Epigenomics, German Center for Neurodegenerative Diseases (DZNE) and University of Bonn and West German Genome Center, Bonn, Germany
| | - Jonas J Neher
- Biomedical Center (BMC), Biochemistry, Faculty of Medicine, LMU Munich, Munich, Germany
- Neuroimmunology and Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Department of Cellular Neurology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| |
Collapse
|
12
|
Katznelson A, Zaret K. A fluorescence-based protocol to quantitatively titrate CUT&RUN buffer components. STAR Protoc 2024; 5:102866. [PMID: 38329880 PMCID: PMC10862407 DOI: 10.1016/j.xpro.2024.102866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 12/04/2023] [Accepted: 01/18/2024] [Indexed: 02/10/2024] Open
Abstract
Cleavage under targets & release using nuclease (CUT&RUN) is a technique for identifying genomic sites where proteins or histone modifications are present in chromatin in permeabilized cells. Here, we present a fluorescence-based protocol to quantitatively titrate CUT&RUN buffer components, for efficient cell permeabilization and retention of target epitopes on chromatin. We describe steps for capturing cells on concanavalin A beads and using a fluorescently labeled secondary antibody to titrate concentrations of digitonin and NaCl in CUT&RUN buffers. We then detail procedures for fluorescence imaging to identify optimal conditions. For complete details on the use and execution of this protocol, please refer to Lerner et al.1.
Collapse
Affiliation(s)
- Andrew Katznelson
- Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Kenneth Zaret
- Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| |
Collapse
|
13
|
Viel KCMF, Parameswaran S, Donmez OA, Forney CR, Hass MR, Yin C, Jones SH, Prosser HK, Diouf AA, Gittens OE, Edsall LE, Chen X, Rowden H, Dunn KA, Guo R, VonHandorf A, Leong MML, Ernst K, Kaufman KM, Lawson LP, Gewurz B, Zhao B, Kottyan LC, Weirauch MT. Shared and distinct interactions of type 1 and type 2 Epstein-Barr Nuclear Antigen 2 with the human genome. BMC Genomics 2024; 25:273. [PMID: 38475709 PMCID: PMC10935964 DOI: 10.1186/s12864-024-10183-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 03/04/2024] [Indexed: 03/14/2024] Open
Abstract
BACKGROUND There are two major genetic types of Epstein-Barr Virus (EBV): type 1 (EBV-1) and type 2 (EBV-2). EBV functions by manipulating gene expression in host B cells, using virus-encoded gene regulatory proteins including Epstein-Barr Nuclear Antigen 2 (EBNA2). While type 1 EBNA2 is known to interact with human transcription factors (hTFs) such as RBPJ, EBF1, and SPI1 (PU.1), type 2 EBNA2 shares only ~ 50% amino acid identity with type 1 and thus may have distinct binding partners, human genome binding locations, and functions. RESULTS In this study, we examined genome-wide EBNA2 binding in EBV-1 and EBV-2 transformed human B cells to identify shared and unique EBNA2 interactions with the human genome, revealing thousands of type-specific EBNA2 ChIP-seq peaks. Computational predictions based on hTF motifs and subsequent ChIP-seq experiments revealed that both type 1 and 2 EBNA2 co-occupy the genome with SPI1 and AP-1 (BATF and JUNB) hTFs. However, type 1 EBNA2 showed preferential co-occupancy with EBF1, and type 2 EBNA2 preferred RBPJ. These differences in hTF co-occupancy revealed possible mechanisms underlying type-specific gene expression of known EBNA2 human target genes: MYC (shared), CXCR7 (type 1 specific), and CD21 (type 2 specific). Both type 1 and 2 EBNA2 binding events were enriched at systemic lupus erythematosus (SLE) and multiple sclerosis (MS) risk loci, while primary biliary cholangitis (PBC) risk loci were specifically enriched for type 2 peaks. CONCLUSIONS This study reveals extensive type-specific EBNA2 interactions with the human genome, possible differences in EBNA2 interaction partners, and a possible new role for type 2 EBNA2 in autoimmune disorders. Our results highlight the importance of considering EBV type in the control of human gene expression and disease-related investigations.
Collapse
Affiliation(s)
- Kenyatta C M F Viel
- Molecular and Developmental Biology Graduate Program, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Sreeja Parameswaran
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Omer A Donmez
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Carmy R Forney
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Matthew R Hass
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Cailing Yin
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Sydney H Jones
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Hayley K Prosser
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Arame A Diouf
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Olivia E Gittens
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Lee E Edsall
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Xiaoting Chen
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Hope Rowden
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Katelyn A Dunn
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Rui Guo
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, 145 Harrison Ave, Boston, MA, 02111, USA
| | - Andrew VonHandorf
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Merrin Man Long Leong
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Kevin Ernst
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Kenneth M Kaufman
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Lucinda P Lawson
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Ben Gewurz
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Bo Zhao
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Leah C Kottyan
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA.
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA.
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA.
| | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA.
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA.
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA.
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA.
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA.
| |
Collapse
|
14
|
Jeppsson K, Pradhan B, Sutani T, Sakata T, Umeda Igarashi M, Berta DG, Kanno T, Nakato R, Shirahige K, Kim E, Björkegren C. Loop-extruding Smc5/6 organizes transcription-induced positive DNA supercoils. Mol Cell 2024; 84:867-882.e5. [PMID: 38295804 DOI: 10.1016/j.molcel.2024.01.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 11/16/2023] [Accepted: 01/08/2024] [Indexed: 03/10/2024]
Abstract
The structural maintenance of chromosomes (SMC) protein complexes-cohesin, condensin, and the Smc5/6 complex (Smc5/6)-are essential for chromosome function. At the molecular level, these complexes fold DNA by loop extrusion. Accordingly, cohesin creates chromosome loops in interphase, and condensin compacts mitotic chromosomes. However, the role of Smc5/6's recently discovered DNA loop extrusion activity is unknown. Here, we uncover that Smc5/6 associates with transcription-induced positively supercoiled DNA at cohesin-dependent loop boundaries on budding yeast (Saccharomyces cerevisiae) chromosomes. Mechanistically, single-molecule imaging reveals that dimers of Smc5/6 specifically recognize the tip of positively supercoiled DNA plectonemes and efficiently initiate loop extrusion to gather the supercoiled DNA into a large plectonemic loop. Finally, Hi-C analysis shows that Smc5/6 links chromosomal regions containing transcription-induced positive supercoiling in cis. Altogether, our findings indicate that Smc5/6 controls the three-dimensional organization of chromosomes by recognizing and initiating loop extrusion on positively supercoiled DNA.
Collapse
Affiliation(s)
- Kristian Jeppsson
- Karolinska Institutet, Department of Cell and Molecular Biology, Biomedicum, Tomtebodavägen 16, 171 77 Stockholm, Sweden; Karolinska Institutet, Department of Biosciences and Nutrition, Neo, Hälsovägen 7c, 141 83 Huddinge, Sweden; Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.
| | - Biswajit Pradhan
- Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Takashi Sutani
- Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Toyonori Sakata
- Karolinska Institutet, Department of Cell and Molecular Biology, Biomedicum, Tomtebodavägen 16, 171 77 Stockholm, Sweden; Karolinska Institutet, Department of Biosciences and Nutrition, Neo, Hälsovägen 7c, 141 83 Huddinge, Sweden; Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Miki Umeda Igarashi
- Karolinska Institutet, Department of Cell and Molecular Biology, Biomedicum, Tomtebodavägen 16, 171 77 Stockholm, Sweden; Karolinska Institutet, Department of Biosciences and Nutrition, Neo, Hälsovägen 7c, 141 83 Huddinge, Sweden
| | - Davide Giorgio Berta
- Karolinska Institutet, Department of Cell and Molecular Biology, Biomedicum, Tomtebodavägen 16, 171 77 Stockholm, Sweden
| | - Takaharu Kanno
- Karolinska Institutet, Department of Cell and Molecular Biology, Biomedicum, Tomtebodavägen 16, 171 77 Stockholm, Sweden; Karolinska Institutet, Department of Biosciences and Nutrition, Neo, Hälsovägen 7c, 141 83 Huddinge, Sweden
| | - Ryuichiro Nakato
- Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Katsuhiko Shirahige
- Karolinska Institutet, Department of Cell and Molecular Biology, Biomedicum, Tomtebodavägen 16, 171 77 Stockholm, Sweden; Karolinska Institutet, Department of Biosciences and Nutrition, Neo, Hälsovägen 7c, 141 83 Huddinge, Sweden; Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Eugene Kim
- Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany.
| | - Camilla Björkegren
- Karolinska Institutet, Department of Cell and Molecular Biology, Biomedicum, Tomtebodavägen 16, 171 77 Stockholm, Sweden; Karolinska Institutet, Department of Biosciences and Nutrition, Neo, Hälsovägen 7c, 141 83 Huddinge, Sweden.
| |
Collapse
|
15
|
Lasica C, de Carvalho Augusto R, Moné H, Mouahid G, Chaparro C, Veillard AC, Zelisko-Schmidt A, Grunau C. Automated ChIPmentation procedure on limited biological material of the human blood fluke Schistosoma mansoni. Wellcome Open Res 2024; 7:133. [PMID: 37521535 PMCID: PMC10372461 DOI: 10.12688/wellcomeopenres.17779.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/09/2024] [Indexed: 08/01/2023] Open
Abstract
In living cells, the genetic information stored in the DNA sequence is always associated with chromosomal and extra-chromosomal epigenetic information. Chromatin is formed by the DNA and associated proteins, in particular histones. Covalent histone modifications are important bearers of epigenetic information and as such have been increasingly studied since about the year 2000. One of the principal techniques to gather information about the association between DNA and modified histones is chromatin immunoprecipitation (ChIP), also combined with massive sequencing (ChIP-Seq). Automated ChIPmentation procedure is a convenient alternative to native chromatin immunoprecipitation (N-ChIP). It is now routinely used for ChIP-Seq in many model species, using in general roughly 10 6 cells per experiment. Such high cell numbers are sometimes difficult to produce. Using the human parasite Schistosoma mansoni, whose production requires sacrificing animals and should therefore be kept to a minimum, we show here that automated ChIPmentation is suitable for limited biological material. We define the operational limit as ≥20,000 Schistosoma cells with 30,000-300,000 cells as optimum. We also present a streamlined protocol for the preparation of ChIP input libraries.
Collapse
Affiliation(s)
- Chrystelle Lasica
- IHPE, Univ Perpignan Via Domitia, CNRS, IFREMER, Univ Montpellier, Perpignan, 66860, France
| | - Ronaldo de Carvalho Augusto
- IHPE, Univ Perpignan Via Domitia, CNRS, IFREMER, Univ Montpellier, Perpignan, 66860, France
- LBMC, Laboratoire de Biologie et Modélisation de la Cellule Univ Lyon, ENS de Lyon, Université Claude Bernard Lyon 1, CNRS, UMR 5239, INSERM, U1210,, Lyon, 69000, France
| | - Hélène Moné
- IHPE, Univ Perpignan Via Domitia, CNRS, IFREMER, Univ Montpellier, Perpignan, 66860, France
| | - Gabriel Mouahid
- IHPE, Univ Perpignan Via Domitia, CNRS, IFREMER, Univ Montpellier, Perpignan, 66860, France
| | - Cristian Chaparro
- IHPE, Univ Perpignan Via Domitia, CNRS, IFREMER, Univ Montpellier, Perpignan, 66860, France
| | | | | | - Christoph Grunau
- IHPE, Univ Perpignan Via Domitia, CNRS, IFREMER, Univ Montpellier, Perpignan, 66860, France
| |
Collapse
|
16
|
Nolan B, Harris HL, Kalluchi A, Reznicek TE, Cummings CT, Rowley MJ. HiCrayon reveals distinct layers of multi-state 3D chromatin organization. bioRxiv 2024:2024.02.11.579821. [PMID: 38405883 PMCID: PMC10888951 DOI: 10.1101/2024.02.11.579821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
The co-visualization of chromatin conformation with 1D 'omics data is key to the multi-omics driven data analysis of 3D genome organization. Chromatin contact maps are often shown as 2D heatmaps and visually compared to 1D genomic data by simple juxtaposition. While common, this strategy is imprecise, placing the onus on the reader to align features with each other. To remedy this, we developed HiCrayon, an interactive tool that facilitates the integration of 3D chromatin organization maps and 1D datasets. This visualization method integrates data from genomic assays directly into the chromatin contact map by coloring interactions according to 1D signal. HiCrayon is implemented using R shiny and python to create a graphical user interface (GUI) application, available in both web or containerized format to promote accessibility. HiCrayon is implemented in R, and includes a graphical user interface (GUI), as well as a slimmed-down web-based version that lets users quickly produce publication-ready images. We demonstrate the utility of HiCrayon in visualizing the effectiveness of compartment calling and the relationship between ChIP-seq and various features of chromatin organization. We also demonstrate the improved visualization of other 3D genomic phenomena, such as differences between loops associated with CTCF/cohesin vs. those associated with H3K27ac. We then demonstrate HiCrayon's visualization of organizational changes that occur during differentiation and use HiCrayon to detect compartment patterns that cannot be assigned to either A or B compartments, revealing a distinct 3rd chromatin compartment. Overall, we demonstrate the utility of co-visualizing 2D chromatin conformation with 1D genomic signals within the same matrix to reveal fundamental aspects of genome organization. Local version: https://github.com/JRowleyLab/HiCrayon Web version: https://jrowleylab.com/HiCrayon.
Collapse
Affiliation(s)
- Ben Nolan
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Emile St, Omaha, 68198, NE, USA
| | - Hannah L Harris
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Emile St, Omaha, 68198, NE, USA
| | - Achyuth Kalluchi
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Emile St, Omaha, 68198, NE, USA
| | - Timothy E Reznicek
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Emile St, Omaha, 68198, NE, USA
| | - Christopher T Cummings
- Department of Pediatrics, University of Nebraska Medical Center, Emile St, Omaha, 68198, NE, USA
| | - M Jordan Rowley
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Emile St, Omaha, 68198, NE, USA
| |
Collapse
|
17
|
Bakaric A, Cironi L, Praz V, Sanalkumar R, Broye LC, Favre-Bulle K, Letovanec I, Digklia A, Renella R, Stamenkovic I, Ott CJ, Nakamura T, Antonescu CR, Rivera MN, Riggi N. CIC-DUX4 Chromatin Profiling Reveals New Epigenetic Dependencies and Actionable Therapeutic Targets in CIC-Rearranged Sarcomas. Cancers (Basel) 2024; 16:457. [PMID: 38275898 PMCID: PMC10814785 DOI: 10.3390/cancers16020457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/16/2024] [Accepted: 01/18/2024] [Indexed: 01/27/2024] Open
Abstract
CIC-DUX4-rearranged sarcoma (CDS) is a rare and aggressive soft tissue tumor that occurs most frequently in young adults. The key oncogenic driver of this disease is the expression of the CIC-DUX4 fusion protein as a result of chromosomal rearrangements. CIC-DUX4 displays chromatin binding properties, and is therefore believed to function as an aberrant transcription factor. However, the chromatin remodeling events induced by CIC-DUX4 are not well understood, limiting our ability to identify new mechanism-based therapeutic strategies for these patients. Here, we generated a genome-wide profile of CIC-DUX4 DNA occupancy and associated chromatin states in human CDS cell models and primary tumors. Combining chromatin profiling, proximity ligation assays, as well as genetic and pharmacological perturbations, we show that CIC-DUX4 operates as a potent transcriptional activator at its binding sites. This property is in contrast with the repressive function of the wild-type CIC protein, and is mainly mediated through the direct interaction of CIC-DUX4 with the acetyltransferase p300. In keeping with this, we show p300 to be essential for CDS tumor cell proliferation; additionally, we find its pharmacological inhibition to significantly impact tumor growth in vitro and in vivo. Taken together, our study elucidates the mechanisms underpinning CIC-DUX4-mediated transcriptional regulation.
Collapse
Affiliation(s)
- Arnaud Bakaric
- Clinical Pathology Service, Department of Diagnostics, Geneva University Hospital, 1205 Geneva, Switzerland
| | - Luisa Cironi
- Pediatric Hematology-Oncology Research Laboratory, Woman-Mother-Child Department, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Viviane Praz
- Platform Genomics Technologies, Center for Integrative Genomics, Faculty of Biology and Medicine, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Rajendran Sanalkumar
- Experimental Pathology Service, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland (I.S.)
- Department of Cell and Tissue Genomics, Genentech. Inc., South San Francisco, CA 94103, USA
| | - Liliane C. Broye
- Experimental Pathology Service, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland (I.S.)
| | - Kerria Favre-Bulle
- Experimental Pathology Service, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland (I.S.)
| | - Igor Letovanec
- Department of Histopathology, Central Institute, Valais Hospital, 1951 Sion, Switzerland
| | - Antonia Digklia
- Department of Oncology, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Raffaele Renella
- Pediatric Hematology-Oncology Research Laboratory, Woman-Mother-Child Department, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Ivan Stamenkovic
- Experimental Pathology Service, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland (I.S.)
| | - Christopher J. Ott
- Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA; (C.J.O.)
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Takuro Nakamura
- Institute of Medical Science, Tokyo Medical University, Tokyo 160-0023, Japan
| | - Cristina R. Antonescu
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA;
| | - Miguel N. Rivera
- Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA; (C.J.O.)
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Nicolò Riggi
- Experimental Pathology Service, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland (I.S.)
- Department of Cell and Tissue Genomics, Genentech. Inc., South San Francisco, CA 94103, USA
| |
Collapse
|
18
|
Kawaguchi K, Kazama M, Hata T, Matsuo M, Obokata J, Satoh S. Inducible Expression of the Restriction Enzyme Uncovered Genome-Wide Distribution and Dynamic Behavior of Histones H4K16ac and H2A.Z at DNA Double-Strand Breaks in Arabidopsis. Plant Cell Physiol 2024; 65:142-155. [PMID: 37930797 DOI: 10.1093/pcp/pcad133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 10/23/2023] [Accepted: 10/24/2023] [Indexed: 11/07/2023]
Abstract
DNA double-strand breaks (DSBs) are among the most serious types of DNA damage, causing mutations and chromosomal rearrangements. In eukaryotes, DSBs are immediately repaired in coordination with chromatin remodeling for the deposition of DSB-related histone modifications and variants. To elucidate the details of DSB-dependent chromatin remodeling throughout the genome, artificial DSBs need to be reproducibly induced at various genomic loci. Recently, a comprehensive method for elucidating chromatin remodeling at multiple DSB loci via chemically induced expression of a restriction enzyme was developed in mammals. However, this DSB induction system is unsuitable for investigating chromatin remodeling during and after DSB repair, and such an approach has not been performed in plants. Here, we established a transgenic Arabidopsis plant harboring a restriction enzyme gene Sbf I driven by a heat-inducible promoter. Using this transgenic line, we performed chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) of histones H4K16ac and H2A.Z and investigated the dynamics of these histone marks around the endogenous 623 Sbf I recognition sites. We also precisely quantified DSB efficiency at all cleavage sites using the DNA resequencing data obtained by the ChIP-seq procedure. From the results, Sbf I-induced DSBs were detected at 360 loci, which induced the transient deposition of H4K16ac and H2A.Z around these regions. Interestingly, we also observed the co-localization of H4K16ac and H2A.Z at some DSB loci. Overall, DSB-dependent chromatin remodeling was found to be highly conserved between plants and animals. These findings provide new insights into chromatin remodeling that occurs in response to DSBs in Arabidopsis.
Collapse
Affiliation(s)
- Kohei Kawaguchi
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Sakyo-ku, Kyoto, Kyoto 606-8522, Japan
| | - Mei Kazama
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Sakyo-ku, Kyoto, Kyoto 606-8522, Japan
| | - Takayuki Hata
- Graduate School of Medicine, Hirosaki University, Hirosaki, Aomori 036-8560, Japan
| | - Mitsuhiro Matsuo
- Faculty of Agriculture, Setsunan University, Hirakata, Osaka 573-0101, Japan
| | - Junichi Obokata
- Faculty of Agriculture, Setsunan University, Hirakata, Osaka 573-0101, Japan
| | - Soichirou Satoh
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Sakyo-ku, Kyoto, Kyoto 606-8522, Japan
| |
Collapse
|
19
|
Jiang D, Zhang J. Ascertainment Bias in the Genomic Test of Positive Selection on Regulatory Sequences. Mol Biol Evol 2024; 41:msad284. [PMID: 38149460 PMCID: PMC10766478 DOI: 10.1093/molbev/msad284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 11/12/2023] [Accepted: 12/22/2023] [Indexed: 12/28/2023] Open
Abstract
Evolution of gene expression mediated by cis-regulatory changes is thought to be an important contributor to organismal adaptation, but identifying adaptive cis-regulatory changes is challenging due to the difficulty in knowing the expectation under no positive selection. A new approach for detecting positive selection on transcription factor binding sites (TFBSs) was recently developed, thanks to the application of machine learning in predicting transcription factor (TF) binding affinities of DNA sequences. Given a TFBS sequence from a focal species and the corresponding inferred ancestral sequence that differs from the former at n sites, one can predict the TF-binding affinities of many n-step mutational neighbors of the ancestral sequence and obtain a null distribution of the derived binding affinity, which allows testing whether the binding affinity of the real derived sequence deviates significantly from the null distribution. Applying this test genomically to all experimentally identified binding sites of 3 TFs in humans, a recent study reported positive selection for elevated binding affinities of TFBSs. Here, we show that this genomic test suffers from an ascertainment bias because, even in the absence of positive selection for strengthened binding, the binding affinities of known human TFBSs are more likely to have increased than decreased in evolution. We demonstrate by computer simulation that this bias inflates the false positive rate of the selection test. We propose several methods to mitigate the ascertainment bias and show that almost all previously reported positive selection signals disappear when these methods are applied.
Collapse
Affiliation(s)
- Daohan Jiang
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
- Present address: Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Jianzhi Zhang
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| |
Collapse
|
20
|
Chen H, Zhou S, Wang Y, Zhang Q, Leng L, Cao Z, Luan P, Li Y, Wang S, Li H, Cheng B. HBP1 promotes chicken preadipocyte proliferation via directly repressing SOCS3 transcription. Int J Biol Macromol 2024; 256:128414. [PMID: 38029903 DOI: 10.1016/j.ijbiomac.2023.128414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 11/13/2023] [Accepted: 11/22/2023] [Indexed: 12/01/2023]
Abstract
Preadipocyte proliferation is an essential process in adipose development. During proliferation of preadipocytes, transcription factors play crucial roles. HMG-box protein 1 (HBP1) is an important transcription factor of cellular proliferation. However, the function and underlying mechanisms of HBP1 in the proliferation of preadipocytes remain unclear. Here, we found that the expression level of HBP1 decreased first and then increased during the proliferation of chicken preadipocytes. Knockout of HBP1 could inhibit the proliferation of preadipocytes, while overexpression of HBP1 could promote the proliferation of preadipocytes. ChIP-seq data showed that HBP1 had the unique DNA binding motif in chicken preadipocytes. By integrating ChIP-Seq and RNA-Seq, we revealed a total of 3 candidate target genes of HBP1. Furthermore, the results of ChIP-qPCR, RT-qPCR, luciferase reporter assay and EMSA showed that HBP1 could inhibit the transcription of suppressor of cytokine signaling 3 (SOCS3) by binding to its promoter. Moreover, we confirmed that SOCS3 can mediate the regulation of HBP1 on the proliferation of preadipocytes through RNAi and rescue experiments. Altogether, these data demonstrated that HBP1 directly targets SOCS3 to regulate chicken preadipocyte proliferation. Our findings expand the transcriptional regulatory network of preadipocyte proliferation, and they will be helpful in formulating a molecular breeding scheme to control excessive abdominal fat deposition and to improve meat quality in chickens.
Collapse
Affiliation(s)
- Hongyan Chen
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin 150030, Heilongjiang, China; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin 150030, Heilongjiang, China; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, Heilongjiang, China; College of Life Science and Agriculture Forestry, Qiqihar University, Qiqihar 161006, Heilongjiang, China
| | - Sitong Zhou
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin 150030, Heilongjiang, China; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin 150030, Heilongjiang, China; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, Heilongjiang, China
| | - Youdong Wang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin 150030, Heilongjiang, China; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin 150030, Heilongjiang, China; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, Heilongjiang, China
| | - Qi Zhang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin 150030, Heilongjiang, China; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin 150030, Heilongjiang, China; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, Heilongjiang, China
| | - Li Leng
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin 150030, Heilongjiang, China; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin 150030, Heilongjiang, China; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, Heilongjiang, China
| | - Zhiping Cao
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin 150030, Heilongjiang, China; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin 150030, Heilongjiang, China; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, Heilongjiang, China
| | - Peng Luan
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin 150030, Heilongjiang, China; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin 150030, Heilongjiang, China; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, Heilongjiang, China
| | - Yumao Li
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin 150030, Heilongjiang, China; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin 150030, Heilongjiang, China; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, Heilongjiang, China
| | - Shouzhi Wang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin 150030, Heilongjiang, China; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin 150030, Heilongjiang, China; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, Heilongjiang, China
| | - Hui Li
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin 150030, Heilongjiang, China; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin 150030, Heilongjiang, China; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, Heilongjiang, China.
| | - Bohan Cheng
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin 150030, Heilongjiang, China; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin 150030, Heilongjiang, China; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, Heilongjiang, China.
| |
Collapse
|
21
|
Zhang ZN, Long L, Zhao XT, Shang SZ, Xu FC, Zhao JR, Hu GY, Mi LY, Song CP, Gao W. The dual role of GoPGF reveals that the pigment glands are synthetic sites of gossypol in aerial parts of cotton. New Phytol 2024; 241:314-328. [PMID: 37865884 DOI: 10.1111/nph.19331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 09/28/2023] [Indexed: 10/23/2023]
Abstract
Gossypol and the related terpenoids are stored in the pigment gland to protect cotton plants from biotic stresses, but little is known about the synthetic sites of these metabolites. Here, we showed that GoPGF, a key gene regulating gland formation, was expressed in gland cells and roots. The chromatin immunoprecipitation sequencing (ChIP-seq) analysis demonstrated that GoPGF targets GhJUB1 to regulate gland morphogenesis. RNA-sequencing (RNA-seq) showed high accumulation of gossypol biosynthetic genes in gland cells. Moreover, integrated analysis of the ChIP-seq and RNA-seq data revealed that GoPGF binds to the promoter of several gossypol biosynthetic genes. The cotton callus overexpressing GoPGF had dramatically increased the gossypol levels, indicating that GoPGF can directly activate the biosynthesis of gossypol. In addition, the gopgf mutant analysis revealed the existence of both GoPGF-dependent and -independent regulation of gossypol production in cotton roots. Our study revealed that the pigment glands are synthetic sites of gossypol in aerial parts of cotton and that GoPGF plays a dual role in regulating gland morphogenesis and gossypol biosynthesis. The study provides new insights for exploring the complex relationship between glands and the metabolites they store in cotton and other plant species.
Collapse
Affiliation(s)
- Zhen-Nan Zhang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization (Henan University), Kaifeng, Henan, 475004, China
| | - Lu Long
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization (Henan University), Kaifeng, Henan, 475004, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Science, Henan University, Kaifeng, Henan, 475004, China
| | - Xiao-Tong Zhao
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization (Henan University), Kaifeng, Henan, 475004, China
| | - Shen-Zhai Shang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization (Henan University), Kaifeng, Henan, 475004, China
| | - Fu-Chun Xu
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization (Henan University), Kaifeng, Henan, 475004, China
- Changzhi Medical College, Changzhi, Shanxi, 046000, China
| | - Jing-Ruo Zhao
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization (Henan University), Kaifeng, Henan, 475004, China
| | - Gai-Yuan Hu
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization (Henan University), Kaifeng, Henan, 475004, China
- Sanya Institute of Henan University, Sanya, Hainan, 572024, China
| | - Ling-Yu Mi
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization (Henan University), Kaifeng, Henan, 475004, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Science, Henan University, Kaifeng, Henan, 475004, China
| | - Chun-Peng Song
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization (Henan University), Kaifeng, Henan, 475004, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Science, Henan University, Kaifeng, Henan, 475004, China
| | - Wei Gao
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization (Henan University), Kaifeng, Henan, 475004, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Science, Henan University, Kaifeng, Henan, 475004, China
| |
Collapse
|
22
|
Di Giorgio E, Cortolezzis Y, Gualandi N, Agostini F, Rapozzi V, Xodo LE. NRF2 interacts with distal enhancer and inhibits nitric oxide synthase 2 expression in KRAS-driven pancreatic cancer cells. Biochim Biophys Acta Mol Cell Res 2024; 1871:119606. [PMID: 37852325 DOI: 10.1016/j.bbamcr.2023.119606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 10/07/2023] [Accepted: 10/10/2023] [Indexed: 10/20/2023]
Abstract
Nitric oxide is a pleiotropic free radical produced by three nitric oxide synthases (NOS1-3), of which inducible NOS2 is involved in tumor initiation and progression. In this study, RNA-seq, ChIP-seq and qRT-PCR experiments combined with bioinformatic analyses showed that NRF2 is a repressor of NOS2 gene by maintaining a distal enhancer located 22 kb downstream of TSS in an inactive state. Deletion of NRF2 leads to activation of the enhancer, which exerts a pioneering function before it is fully activated. Specifically, NRF2 controls the expression of NOS2 in response to intracellular oxidative stress and extracellular oxygen pressure. We found that abrogation of NOS2 expression by siRNAs partially reduced the ability of WT Panc-1 cells to form 3D spheroids, but strongly reduced the formation of 3D spheroids by NRF2-depleted Panc-1 cells. Mechanistically, this effect correlates with the finding that NOS2 and nitric oxide stimulate epithelial-to-mesenchymal transition in NRF2-depleted Panc-1 and MIA PaCa-2 cells. We also found that knockdown of NOS2 leads to blockade of 3D matrigel invasion of NRF2-depleted PDAC cells, demonstrating that a short-circuit in the reciprocal regulation of NOS2 and NRF2 attenuates the malignancy of PDAC cells. In summary, we show for the first time that: (i) NRF2 is a suppressor of NOS2 in pancreatic cancer cells; (ii) NRF2 binds to and inactivates an enhancer located 22 kb downstream of TSS of the NOS2 gene; (iii) activation of NOS2 requires suppression of NRF2; (iv) NOS2 is required for NRF2-depleted Panc-1 cells to maintain their malignancy and invasiveness.
Collapse
Affiliation(s)
- Eros Di Giorgio
- Department of Medicine, Laboratory of Biochemistry, P.le Kolbe 4, 33100 Udine, Italy.
| | - Ylenia Cortolezzis
- Department of Medicine, Laboratory of Biochemistry, P.le Kolbe 4, 33100 Udine, Italy
| | - Nicolò Gualandi
- Department of Medicine, Laboratory of Biochemistry, P.le Kolbe 4, 33100 Udine, Italy
| | - Francesca Agostini
- Department of Medicine, Laboratory of Biochemistry, P.le Kolbe 4, 33100 Udine, Italy
| | - Valentina Rapozzi
- Department of Medicine, Laboratory of Biochemistry, P.le Kolbe 4, 33100 Udine, Italy
| | - Luigi E Xodo
- Department of Medicine, Laboratory of Biochemistry, P.le Kolbe 4, 33100 Udine, Italy.
| |
Collapse
|
23
|
Mohorović P, Geldhof B, Holsteens K, Rinia M, Daems S, Reijnders T, Ceusters J, Van den Ende W, Van de Poel B. Ethylene inhibits photosynthesis via temporally distinct responses in tomato plants. Plant Physiol 2023:kiad685. [PMID: 38146839 DOI: 10.1093/plphys/kiad685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 10/24/2023] [Accepted: 11/19/2023] [Indexed: 12/27/2023]
Abstract
Ethylene is a volatile plant hormone that regulates many developmental processes and responses towards (a)biotic stress. Studies have shown that high levels of ethylene repress vegetative growth in many important crops, including tomato (Solanum lycopersicum), possibly by inhibiting photosynthesis. We investigated the temporal effects of ethylene on young tomato plants using an automated ethylene gassing system to monitor the physiological, biochemical, and molecular responses through time-course RNA-seq of a photosynthetically active source leaf. We found that ethylene evokes a dose-dependent inhibition of photosynthesis, which can be characterized by three temporally distinct phases. The earliest ethylene responses that marked the first phase and occurred a few hours after the start of the treatment were leaf epinasty and a decline in stomatal conductance, which led to lower light perception and CO2 uptake, respectively, resulting in a rapid decline of soluble sugar levels (glucose, fructose). The second phase of the ethylene effect was marked by low carbohydrate availability, which modulated plant energy metabolism to adapt by using alternative substrates (lipids and proteins) to fuel the TCA cycle. Long-term continuous exposure to ethylene led to the third phase, characterized by starch and chlorophyll breakdown, which further inhibited photosynthesis, leading to premature leaf senescence. To reveal early (3 h) ethylene-dependent regulators of photosynthesis, we performed a ChIP-seq experiment using anti-ETHYLENE INSENSITIVE 3-like 1 (EIL1) antibodies and found several candidate transcriptional regulators. Collectively, our study revealed a temporal sequence of events that led to the inhibition of photosynthesis by ethylene and identified potential transcriptional regulators responsible for this regulation.
Collapse
Affiliation(s)
- Petar Mohorović
- Division of Crop Biotechnics, Department of Biosystems, KU Leuven, Willem de Croylaan 42, 3001 Leuven, Belgium
| | - Batist Geldhof
- Division of Crop Biotechnics, Department of Biosystems, KU Leuven, Willem de Croylaan 42, 3001 Leuven, Belgium
| | - Kristof Holsteens
- Division of Crop Biotechnics, Department of Biosystems, KU Leuven, Willem de Croylaan 42, 3001 Leuven, Belgium
| | - Marilien Rinia
- Division of Crop Biotechnics, Department of Biosystems, KU Leuven, Willem de Croylaan 42, 3001 Leuven, Belgium
| | - Stijn Daems
- Research Group for sustainable plant production and protection, Division of Crop Biotechnics, Department of Biosystems, KU Leuven, Campus Geel, Kleinhoefstraat 4, 2440 Geel, Belgium
| | - Timmy Reijnders
- Molecular Biotechnology of Plants and Microorganisms Lab, Department of Biology, KU Leuven, Kasteelpark Arenberg 31, 3001 Leuven, Belgium
| | - Johan Ceusters
- Research Group for sustainable plant production and protection, Division of Crop Biotechnics, Department of Biosystems, KU Leuven, Campus Geel, Kleinhoefstraat 4, 2440 Geel, Belgium
- Leuven Plant Institute (LPI), KU Leuven, Kasteelpark Arenberg 31, 3001 Leuven, Belgium
| | - Wim Van den Ende
- Molecular Biotechnology of Plants and Microorganisms Lab, Department of Biology, KU Leuven, Kasteelpark Arenberg 31, 3001 Leuven, Belgium
- Leuven Plant Institute (LPI), KU Leuven, Kasteelpark Arenberg 31, 3001 Leuven, Belgium
| | - Bram Van de Poel
- Division of Crop Biotechnics, Department of Biosystems, KU Leuven, Willem de Croylaan 42, 3001 Leuven, Belgium
- Leuven Plant Institute (LPI), KU Leuven, Kasteelpark Arenberg 31, 3001 Leuven, Belgium
| |
Collapse
|
24
|
Faltejsková K, Vondrášek J. PAPerFly: Partial Assembly-based Peak Finder for ab initio binding site reconstruction. BMC Bioinformatics 2023; 24:487. [PMID: 38114921 PMCID: PMC10731698 DOI: 10.1186/s12859-023-05613-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 12/11/2023] [Indexed: 12/21/2023] Open
Abstract
BACKGROUND The specific recognition of a DNA locus by a given transcription factor is a widely studied issue. It is generally agreed that the recognition can be influenced not only by the binding motif but by the larger context of the binding site. In this work, we present a novel heuristic algorithm that can reconstruct the unique binding sites captured in a sequencing experiment without using the reference genome. RESULTS We present PAPerFly, the Partial Assembly-based Peak Finder, a tool for the binding site and binding context reconstruction from the sequencing data without any prior knowledge. This tool operates without the need to know the reference genome of the respective organism. We employ algorithmic approaches that are used during genome assembly. The proposed algorithm constructs a de Bruijn graph from the sequencing data. Based on this graph, sequences and their enrichment are reconstructed using a novel heuristic algorithm. The reconstructed sequences are aligned and the peaks in the sequence enrichment are identified. Our approach was tested by processing several ChIP-seq experiments available in the ENCODE database and comparing the results of Paperfly and standard methods. CONCLUSIONS We show that PAPerFly, an algorithm tailored for experiment analysis without the reference genome, yields better results than an aggregation of ChIP-seq agnostic tools. Our tool is freely available at https://github.com/Caeph/paperfly/ or on Zenodo ( https://doi.org/10.5281/zenodo.7116424 ).
Collapse
Affiliation(s)
- Kateřina Faltejsková
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 542/2, 160 00, Prague, Czech Republic.
- Computer Science Institute, Faculty of Mathematics and Physics, Charles University, Malostranské náměstí 25, 118 00, Prague, Czech Republic.
| | - Jiří Vondrášek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 542/2, 160 00, Prague, Czech Republic.
| |
Collapse
|
25
|
Beauvais V, Moreau K, Žunar B, Hervouet-Coste N, Novačić A, Le Dantec A, Primig M, Mosrin-Huaman C, Stuparević I, Rahmouni AR. Tho2 is critical for the recruitment of Rrp6 to chromatin in response to perturbed mRNP biogenesis. RNA 2023; 30:89-98. [PMID: 37914399 PMCID: PMC10726162 DOI: 10.1261/rna.079707.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 10/24/2023] [Indexed: 11/03/2023]
Abstract
The eukaryotic THO complex coordinates the assembly of so-called messenger RNA-ribonucleoprotein particles (mRNPs), a process that involves cotranscriptional coating of nascent mRNAs with proteins. Once formed, mRNPs undergo a quality control step that marks them either for active transport to the cytoplasm, or Rrp6/RNA exosome-mediated degradation in the nucleus. However, the mechanism behind the quality control of nascent mRNPs is still unclear. We investigated the cotranscriptional quality control of mRNPs in budding yeast by expressing the bacterial Rho helicase, which globally perturbs yeast mRNP formation. We examined the genome-wide binding profiles of the THO complex subunits Tho2, Thp2, Hpr1, and Mft1 upon perturbation of the mRNP biogenesis, and found that Tho2 plays two roles. In addition to its function as a subunit of the THO complex, upon perturbation of mRNP biogenesis Tho2 targets Rrp6 to chromatin via its carboxy-terminal domain. Interestingly, other THO subunits are not enriched on chromatin upon perturbation of mRNP biogenesis and are not necessary for localizing Rrp6 at its target loci. Our study highlights the potential role of Tho2 in cotranscriptional mRNP quality control, which is independent of other THO subunits. Considering that both the THO complex and the RNA exosome are evolutionarily highly conserved, our findings are likely relevant for mRNP surveillance in mammals.
Collapse
Affiliation(s)
- Valentin Beauvais
- Centre de Biophysique Moléculaire, UPR 4301 du CNRS, 45071 Orléans, France
| | - Kévin Moreau
- Centre de Biophysique Moléculaire, UPR 4301 du CNRS, 45071 Orléans, France
| | - Bojan Žunar
- Laboratory of Biochemistry, Department of Chemistry and Biochemistry, Faculty of Food Technology and Biotechnology, University of Zagreb, Zagreb, Croatia
| | | | - Ana Novačić
- Laboratory of Biochemistry, Department of Chemistry and Biochemistry, Faculty of Food Technology and Biotechnology, University of Zagreb, Zagreb, Croatia
| | - Aurélia Le Dantec
- Centre de Biophysique Moléculaire, UPR 4301 du CNRS, 45071 Orléans, France
| | - Michael Primig
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail)-UMR_S 1085, F-2 Rennes, France
| | | | - Igor Stuparević
- Laboratory of Biochemistry, Department of Chemistry and Biochemistry, Faculty of Food Technology and Biotechnology, University of Zagreb, Zagreb, Croatia
| | - A Rachid Rahmouni
- Centre de Biophysique Moléculaire, UPR 4301 du CNRS, 45071 Orléans, France
| |
Collapse
|
26
|
Li X, Melo LAN, Bussemaker HJ. Benchmarking DNA binding affinity models using allele-specific transcription factor binding data. bioRxiv 2023:2023.12.15.571887. [PMID: 38168434 PMCID: PMC10760129 DOI: 10.1101/2023.12.15.571887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Transcription factors (TFs) bind to DNA in a highly sequence-specific manner. This specificity can manifest itself in vivo at heterozygous loci as a difference in TF occupancy between the two alleles. When applied on a genomic scale, functional genomic assays such as ChIP-seq typically lack the statistical power to detect allele-specific binding (ASB) at the level of individual variants. To address this, we propose a framework for benchmarking sequence-to-affinity models for TF binding in terms of their ability to predict allelic imbalances in ChIP-seq counts. We show that a likelihood function based on an over-dispersed binomial distribution can aggregate evidence for allelic preference across the genome without requiring statistical significance for individual variants. This allows us to systematically compare predictive performance when multiple binding models for the same TF are available. We introduce PyProBound, an easily extensible reimplementation of the ProBound biophysically interpretable machine learning framework. Configuring PyProBound to explicitly account for a confounding sequence-specific bias in DNA fragmentation rate yields improved TF binding models when training on ChIP-seq data. We also show how our likelihood function can be leveraged to perform de novo motif discovery on the raw allele-aware ChIP-seq counts.
Collapse
Affiliation(s)
- Xiaoting Li
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Lucas A. N. Melo
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Harmen J. Bussemaker
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
- Department of Systems Biology, Columbia University, New York, NY 10032, USA
| |
Collapse
|
27
|
Katsouda A, Valakos D, Vatsellas G, Thanos D, Papapetropoulos A. An optimized protocol for chromatin immunoprecipitation from murine inguinal white adipose tissue. STAR Protoc 2023; 4:102594. [PMID: 37742172 PMCID: PMC10520933 DOI: 10.1016/j.xpro.2023.102594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 08/17/2023] [Accepted: 09/05/2023] [Indexed: 09/26/2023] Open
Abstract
Chromatin immunoprecipitation (ChIP) protocols have been used to reveal protein-DNA interactions of various cell types and tissues; however, optimization is required for each specific type of sample. Here, we present a ChIP protocol from murine inguinal white adipose tissue. We describe steps for tissue harvesting, crosslinking, chromatin extraction, shearing, immunoprecipitation, and purification. We then detail procedures for analysis including library preparation, sequencing, and qRT-PCR validation. For complete details on the use and execution of this protocol, please refer to Antonia Katsouda et al. (2022).1.
Collapse
Affiliation(s)
- Antonia Katsouda
- Clinical, Experimental Surgery and Translational Research Center, Biomedical Research Foundation of the Academy of Athens, 11527, Athens, Greece; Laboratory of Pharmacology, Faculty of Pharmacy, National and Kapodistrian University of Athens, 15771, Athens, Greece
| | - Dimitrios Valakos
- Center of Basic Research, Biomedical Research Foundation of the Academy of Athens, 11527, Athens, Greece
| | - Giannis Vatsellas
- Center of Basic Research, Biomedical Research Foundation of the Academy of Athens, 11527, Athens, Greece
| | - Dimitris Thanos
- Center of Basic Research, Biomedical Research Foundation of the Academy of Athens, 11527, Athens, Greece
| | - Andreas Papapetropoulos
- Clinical, Experimental Surgery and Translational Research Center, Biomedical Research Foundation of the Academy of Athens, 11527, Athens, Greece; Laboratory of Pharmacology, Faculty of Pharmacy, National and Kapodistrian University of Athens, 15771, Athens, Greece.
| |
Collapse
|
28
|
Dutta S, Bhattacharya S, Harris H, Islam R, Bodas S, Polavaram N, Mishra J, Das D, Seshacharyulu P, Kalluchi A, Pal A, Kohli M, Lele S, Muders M, Batra S, Ghosh P, Datta K, Rowley M. Understanding the role of Pax5 in development of taxane-resistant neuroendocrine like prostate cancers. Res Sq 2023:rs.3.rs-3464475. [PMID: 38168280 PMCID: PMC10760218 DOI: 10.21203/rs.3.rs-3464475/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Resistance to the current Androgen Receptor Signaling Inhibitor (ARSI) therapies has led to higher incidences of therapy-induced neuroendocrine-like prostate cancer (t-NEPC). This highly aggressive subtype with predominant small cell-like characteristics is resistant to taxane chemotherapies and has a dismal overall survival. t-NEPCs are mostly treated with platinum-based drugs with a combination of etoposide or taxane and have less selectivity and high systemic toxicity, which often limit their clinical potential. During t-NEPC transformation, adenocarcinomas lose their luminal features and adopt neuro-basal characteristics. Whether the adaptive neuronal characteristics of t-NEPC are responsible for such taxane resistance remains unknown. Pathway analysis from patient gene-expression databases indicates that t-NEPC upregulates various neuronal pathways associated with enhanced cellular networks. To identify transcription factor(s) (TF) that could be important for promoting the gene expression for neuronal characters in t-NEPC, we performed ATAC-Seq, acetylated-histone ChIP-seq, and RNA-seq in our NE-like cell line models and analyzed the promoters of transcriptionally active and significantly enriched neuroendocrine-like (NE-like) cancer-specific genes. Our results indicate that Pax5 could be an important transcription factor for neuronal gene expression and specific to t-NEPC. Pathway analysis revealed that Pax5 expression is involved in axonal guidance, neurotransmitter regulation, and neuronal adhesion, which are critical for strong cellular communications. Further results suggest that depletion of Pax5 disrupts cellular interaction in NE-like cells and reduces surface growth factor receptor activation, thereby, sensitizing them to taxane therapies. Moreover, t-NEPC specific hydroxymethylation of Pax5 promoter CpG islands favors Pbx1 binding to induce Pax5 expression. Based on our study, we concluded that continuous exposure to ARSI therapies leads to epigenetic modifications and Pax5 activation in t-NEPC, which promotes the expression of genes necessary to adopt taxane-resistant NE-like cancer. Thus, targeting the Pax5 axis can be beneficial for reverting their taxane sensitivity.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - Michael Muders
- Rudolf Becker Laboratory for Prostate Cancer Research, Center of Pathology, University of Bonn Medical Center
| | - Surinder Batra
- University of Nebraska Medical Center, Buffett Cancer Center, Eppley Institute for Research in Cancer and Allied Diseases
| | | | | | | |
Collapse
|
29
|
Allu PKR, Cardamone MD, Gomes AS, Dall'agnese A, Cederquist C, Pan H, Dreyfuss JM, Enerbäck S, Kahn CR. FoxK1 associated gene regulatory network in hepatic insulin action and its relationship to FoxO1 and insulin receptor mediated transcriptional regulation. Mol Metab 2023; 78:101825. [PMID: 37852413 PMCID: PMC10641274 DOI: 10.1016/j.molmet.2023.101825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 09/28/2023] [Accepted: 10/12/2023] [Indexed: 10/20/2023] Open
Abstract
OBJECTIVE Insulin acts on the liver via changes in gene expression to maintain glucose and lipid homeostasis. This study aimed to the Forkhead box protein K1 (FOXK1) associated gene regulatory network as a transcriptional regulator of hepatic insulin action and to determine its role versus FoxO1 and possible actions of the insulin receptor at the DNA level. METHODS Genome-wide analysis of FoxK1 binding were studied by chromatin immunoprecipitation sequencing and compared to those for IR and FoxO1. These were validated by knockdown experiments and gene expression analysis. RESULTS Chromatin immunoprecipitation (ChIP) sequencing shows that FoxK1 binds to the proximal promoters and enhancers of over 4000 genes, and insulin enhances this interaction for about 75% of them. These include genes involved in cell cycle, senescence, steroid biosynthesis, autophagy, and metabolic regulation, including glucose metabolism and mitochondrial function and are enriched in a TGTTTAC consensus motif. Some of these genes are also bound by FoxO1. Comparing this FoxK1 ChIP-seq data to that of the insulin receptor (IR) reveals that FoxK1 may act as the transcription factor partner for some of the previously reported roles of IR in gene regulation, including for LARS1 and TIMM22, which are involved in rRNA processing and cell cycle. CONCLUSION These data demonstrate that FoxK1 is an important regulator of gene expression in response to insulin in liver and may act in concert with FoxO1 and IR in regulation of genes in metabolism and other important biological pathways.
Collapse
Affiliation(s)
- Prasanna K R Allu
- Section on Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, MA, USA
| | | | - Antonio S Gomes
- Section on Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, MA, USA
| | | | - Carly Cederquist
- Section on Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, MA, USA
| | - Hui Pan
- Bioinformatics and Biostatistics Core, Joslin Diabetes Center, Harvard Medical School, Boston, MA, USA
| | - Jonathan M Dreyfuss
- Bioinformatics and Biostatistics Core, Joslin Diabetes Center, Harvard Medical School, Boston, MA, USA
| | - Sven Enerbäck
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - C Ronald Kahn
- Section on Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
30
|
Schmidt CA, Hodkinson LJ, Comstra HS, Khan S, Torres H, Rieder LE. A cost-free CURE: using bioinformatics to identify DNA-binding factors at a specific genomic locus. J Microbiol Biol Educ 2023; 24:e00120-23. [PMID: 38107989 PMCID: PMC10720551 DOI: 10.1128/jmbe.00120-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 09/14/2023] [Indexed: 12/19/2023]
Abstract
Research experiences provide diverse benefits for undergraduates. Many academic institutions have adopted course-based undergraduate research experiences (CUREs) to improve student access to research opportunities. However, potential instructors of a CURE might still face financial or practical hurdles that prevent implementation. Bioinformatics research offers an alternative that is free, safe, compatible with remote learning, and may be more accessible for students with disabilities. Here, we describe a bioinformatics CURE that leverages publicly available datasets to discover novel proteins that target an instructor-determined genomic locus of interest. We use the free, user-friendly bioinformatics platform Galaxy to map ChIP-seq datasets to a genome, which removes the computing burden from students. Both faculty and students directly benefit from this CURE, as faculty can perform candidate screens and publish CURE results. Students gain not only basic bioinformatics knowledge, but also transferable skills, including scientific communication, database navigation, and primary literature experience. The CURE is flexible and can be expanded to analyze different types of high-throughput data or to investigate different genomic loci in any species.
Collapse
Affiliation(s)
| | - Lauren J. Hodkinson
- Graduate Program in Genetics and Molecular Biology, Emory University, Atlanta, Georgia, USA
| | - H. Skye Comstra
- Department of Biology, Emory University, Atlanta, Georgia, USA
| | - Samia Khan
- Department of Biology, Emory University, Atlanta, Georgia, USA
| | | | - Leila E. Rieder
- Department of Biology, Emory University, Atlanta, Georgia, USA
- Graduate Program in Genetics and Molecular Biology, Emory University, Atlanta, Georgia, USA
| |
Collapse
|
31
|
Birgersson M, Indukuri R, Lindquist L, Stepanauskaite L, Luo Q, Deng Q, Archer A, Williams C. Ovarian ERβ cistrome and transcriptome reveal chromatin interaction with LRH-1. BMC Biol 2023; 21:277. [PMID: 38031019 PMCID: PMC10688478 DOI: 10.1186/s12915-023-01773-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 11/21/2023] [Indexed: 12/01/2023] Open
Abstract
BACKGROUND Estrogen receptor beta (ERβ, Esr2) plays a pivotal role in folliculogenesis and ovulation, yet its exact mechanism of action is mainly uncharacterized. RESULTS We here performed ERβ ChIP-sequencing of mouse ovaries followed by complementary RNA-sequencing of wild-type and ERβ knockout ovaries. By integrating the ERβ cistrome and transcriptome, we identified its direct target genes and enriched biological functions in the ovary. This demonstrated its strong impact on genes regulating organism development, cell migration, lipid metabolism, response to hypoxia, and response to estrogen. Cell-type deconvolution analysis of the bulk RNA-seq data revealed a decrease in luteal cells and an increased proportion of theca cells and a specific type of cumulus cells upon ERβ loss. Moreover, we identified a significant overlap with the gene regulatory network of liver receptor homolog 1 (LRH-1, Nr5a2) and showed that ERβ and LRH-1 extensively bound to the same chromatin locations in granulosa cells. Using ChIP-reChIP, we corroborated simultaneous ERβ and LRH-1 co-binding at the ERβ-repressed gene Greb1 but not at the ERβ-upregulated genes Cyp11a1 and Fkbp5. Transactivation assay experimentation further showed that ERβ and LRH-1 can inhibit their respective transcriptional activity at classical response elements. CONCLUSIONS By characterizing the genome-wide endogenous ERβ chromatin binding, gene regulations, and extensive crosstalk between ERβ and LRH-1, along with experimental corroborations, our data offer genome-wide mechanistic underpinnings of ovarian physiology and fertility.
Collapse
Affiliation(s)
- Madeleine Birgersson
- Science for Life Laboratory (SciLifeLab), Department of Protein Science, KTH Royal Institute of Technology, 171 21, Solna, Sweden
- Department of Biosciences and Nutrition, Karolinska Institutet, 141 83, Huddinge, Sweden
| | - Rajitha Indukuri
- Science for Life Laboratory (SciLifeLab), Department of Protein Science, KTH Royal Institute of Technology, 171 21, Solna, Sweden
| | - Linnéa Lindquist
- Science for Life Laboratory (SciLifeLab), Department of Protein Science, KTH Royal Institute of Technology, 171 21, Solna, Sweden
- Department of Biosciences and Nutrition, Karolinska Institutet, 141 83, Huddinge, Sweden
| | - Lina Stepanauskaite
- Science for Life Laboratory (SciLifeLab), Department of Protein Science, KTH Royal Institute of Technology, 171 21, Solna, Sweden
- Department of Biosciences and Nutrition, Karolinska Institutet, 141 83, Huddinge, Sweden
| | - Qing Luo
- Department of Physiology and Pharmacology, Karolinska Institutet, 141 83, Huddinge, Sweden
| | - Qiaolin Deng
- Department of Physiology and Pharmacology, Karolinska Institutet, 141 83, Huddinge, Sweden
| | - Amena Archer
- Science for Life Laboratory (SciLifeLab), Department of Protein Science, KTH Royal Institute of Technology, 171 21, Solna, Sweden
- Department of Biosciences and Nutrition, Karolinska Institutet, 141 83, Huddinge, Sweden
| | - Cecilia Williams
- Science for Life Laboratory (SciLifeLab), Department of Protein Science, KTH Royal Institute of Technology, 171 21, Solna, Sweden.
- Department of Biosciences and Nutrition, Karolinska Institutet, 141 83, Huddinge, Sweden.
| |
Collapse
|
32
|
Yoo SS, Lee S, Choi JE, Hong MJ, Do SK, Lee JH, Lee WK, Park JE, Lee YH, Choi SH, Seo H, Lee J, Lee SY, Cha SI, Kim CH, Kang HG, Park JY. Promoter-Specific Variants in NeuroD1 and H3K4me3 Coincident Regions and Clinical Outcomes of Small Cell Lung Cancer. J Korean Med Sci 2023; 38:e381. [PMID: 37987107 PMCID: PMC10659920 DOI: 10.3346/jkms.2023.38.e381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 08/11/2023] [Indexed: 11/22/2023] Open
Abstract
BACKGROUND Neurogenic differentiation 1 (NeuroD1) is a representative small cell lung cancer (SCLC) transcription regulator involved in the carcinogenesis and behavior of SCLC. Histone modifications play an important role in transcription, and H3 lysine 4 trimethylation (H3K4me3) is primarily associated with promoter regions. METHODS We investigated the association between single nucleotide polymorphisms (SNPs) in NeuroD1 and H3K4me3 coincident regions, selected using ChIP sequencing (ChIP-seq), and the clinical outcomes of 261 patients with SCLC. RESULTS Among 230 SNPs, two were significantly associated with both the chemotherapy response and overall survival (OS) of patients with SCLC. RNF145 rs2043268A>G was associated with worse chemotherapy response and OS (under a recessive model, adjusted odds ratio [aOR], 0.50, 95% confidence interval [CI], 0.26-0.94, P = 0.031, and adjusted hazard ratio [aHR], 1.88, 95% CI, 1.38-2.57, P < 0.001). CINP rs762105A>G was also associated with worse chemotherapy response and OS (under a dominant model, aOR, 0.47, 95% CI, 0.23-0.99, P = 0.046, and aHR, 2.03, 95% CI, 1.47-2.82, P < 0.001). ChIP-quantitative polymerase chain reaction and luciferase assay confirmed that the two SNPs were located in the active promoter regions and influenced the promoter activity of each gene. CONCLUSION To summarize, among SNPs selected using ChIP-seq in promoter regions with high peaks in both NeuroD1 and H3K4me3, RNF145 rs2043268A>G and CINP rs762105A>G were associated with clinical outcomes in patients with SCLC and also affected the promoter activity of each gene.
Collapse
Affiliation(s)
- Seung Soo Yoo
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Daegu, Korea
| | - Sunwoong Lee
- Department of Biochemistry and Cell Biology, School of Medicine, Kyungpook National University, Daegu, Korea
- BK21 Plus KNU Biomedical Convergence Program, Department of Biomedical Science, Kyungpook National University, Daegu, Korea
| | - Jin Eun Choi
- Department of Biochemistry and Cell Biology, School of Medicine, Kyungpook National University, Daegu, Korea
- Cell and Matrix Research Institute, School of Medicine, Kyungpook National University, Daegu, Korea
| | - Mi Jeong Hong
- Department of Biochemistry and Cell Biology, School of Medicine, Kyungpook National University, Daegu, Korea
- Cell and Matrix Research Institute, School of Medicine, Kyungpook National University, Daegu, Korea
| | - Sook Kyung Do
- Department of Biochemistry and Cell Biology, School of Medicine, Kyungpook National University, Daegu, Korea
- Cell and Matrix Research Institute, School of Medicine, Kyungpook National University, Daegu, Korea
| | - Jang Hyuck Lee
- Department of Biochemistry and Cell Biology, School of Medicine, Kyungpook National University, Daegu, Korea
- Cell and Matrix Research Institute, School of Medicine, Kyungpook National University, Daegu, Korea
| | - Won Kee Lee
- Medical Research Collaboration Center in Kyungpook National University Hospital and School of Medicine, Kyungpook National University, Daegu, Korea
| | - Ji Eun Park
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Daegu, Korea
| | - Yong Hoon Lee
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Daegu, Korea
| | - Sun Ha Choi
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Daegu, Korea
| | - Hyewon Seo
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Daegu, Korea
| | - Jaehee Lee
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Daegu, Korea
| | - Shin Yup Lee
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Daegu, Korea
| | - Seung Ick Cha
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Daegu, Korea
| | - Chang Ho Kim
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Daegu, Korea
| | - Hyo-Gyoung Kang
- Department of Biochemistry and Cell Biology, School of Medicine, Kyungpook National University, Daegu, Korea
- Cell and Matrix Research Institute, School of Medicine, Kyungpook National University, Daegu, Korea.
| | - Jae Yong Park
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Daegu, Korea
- Department of Biochemistry and Cell Biology, School of Medicine, Kyungpook National University, Daegu, Korea
- BK21 Plus KNU Biomedical Convergence Program, Department of Biomedical Science, Kyungpook National University, Daegu, Korea
- Cell and Matrix Research Institute, School of Medicine, Kyungpook National University, Daegu, Korea.
| |
Collapse
|
33
|
Sreenivas P, Wang L, Wang M, Challa A, Modi P, Hensch NR, Gryder B, Chou HC, Zhao XR, Sunkel B, Moreno-Campos R, Khan J, Stanton BZ, Ignatius MS. A SNAI2/CTCF Interaction is Required for NOTCH1 Expression in Rhabdomyosarcoma. Mol Cell Biol 2023; 43:547-565. [PMID: 37882064 PMCID: PMC10761179 DOI: 10.1080/10985549.2023.2256640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 08/30/2023] [Indexed: 10/27/2023] Open
Abstract
Rhabdomyosarcoma (RMS) is a pediatric malignancy of the muscle with characteristics of cells blocked in differentiation. NOTCH1 is an oncogene that promotes self-renewal and blocks differentiation in the fusion negative-RMS sub-type. However, how NOTCH1 expression is transcriptionally maintained in tumors is unknown. Analyses of SNAI2 and CTCF chromatin binding and HiC analyses revealed a conserved SNAI2/CTCF overlapping peak downstream of the NOTCH1 locus marking a sub-topologically associating domain (TAD) boundary. Deletion of the SNAI2-CTCF peak showed that it is essential for NOTCH1 expression and viability of FN-RMS cells. Reintroducing constitutively activated NOTCH1-ΔE in cells with the SNAI2-CTCF peak deleted restored cell-viability. Ablation of SNAI2 using CRISPR/Cas9 reagents resulted in the loss of majority of RD and SMS-CTR FN-RMS cells. However, the few surviving clones that repopulate cultures have recovered NOTCH1. Cells that re-establish NOTCH1 expression after SNAI2 ablation are unable to differentiate robustly as SNAI2 shRNA knockdown cells; yet, SNAI2-ablated cells continued to be exquisitely sensitive to ionizing radiation. Thus, we have uncovered a novel mechanism by which SNAI2 and CTCF maintenance of a sub-TAD boundary promotes rather than represses NOTCH1 expression. Further, we demonstrate that SNAI2 suppression of apoptosis post-radiation is independent of SNAI2/NOTCH1 effects on self-renewal and differentiation.
Collapse
Affiliation(s)
- Prethish Sreenivas
- Greehey Children’s Cancer Research Institute, Department of Molecular Medicine, University of Texas Health Sciences Center, San Antonio, Texas, USA
| | - Long Wang
- Greehey Children’s Cancer Research Institute, Department of Molecular Medicine, University of Texas Health Sciences Center, San Antonio, Texas, USA
| | - Meng Wang
- Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children’s Hospital, The Ohio State University, Columbus, Ohio, USA
| | - Anil Challa
- Greehey Children’s Cancer Research Institute, Department of Molecular Medicine, University of Texas Health Sciences Center, San Antonio, Texas, USA
- Department of Biology, University of Alabama at Birmingham, Birmingham, USA
| | - Paulomi Modi
- Greehey Children’s Cancer Research Institute, Department of Molecular Medicine, University of Texas Health Sciences Center, San Antonio, Texas, USA
| | - Nicole Rae Hensch
- Greehey Children’s Cancer Research Institute, Department of Molecular Medicine, University of Texas Health Sciences Center, San Antonio, Texas, USA
| | - Berkley Gryder
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| | | | - Xiang R. Zhao
- Greehey Children’s Cancer Research Institute, Department of Molecular Medicine, University of Texas Health Sciences Center, San Antonio, Texas, USA
| | - Benjamin Sunkel
- Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children’s Hospital, The Ohio State University, Columbus, Ohio, USA
| | - Rodrigo Moreno-Campos
- Greehey Children’s Cancer Research Institute, Department of Molecular Medicine, University of Texas Health Sciences Center, San Antonio, Texas, USA
| | - Javed Khan
- Pediatric Oncology Branch, NCI, NIH, Bethesda, Maryland, USA
| | - Benjamin Z. Stanton
- Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children’s Hospital, The Ohio State University, Columbus, Ohio, USA
| | - Myron S. Ignatius
- Greehey Children’s Cancer Research Institute, Department of Molecular Medicine, University of Texas Health Sciences Center, San Antonio, Texas, USA
| |
Collapse
|
34
|
Oleksiewicz U, Machnik M, Sobocińska J, Molenda S, Olechnowicz A, Florczak A, Mierzejewska J, Adamczak D, Smolibowski M, Kaczmarek M, Mackiewicz A. ZNF643/ZFP69B Exerts Oncogenic Properties and Associates with Cell Adhesion and Immune Processes. Int J Mol Sci 2023; 24:16380. [PMID: 38003570 PMCID: PMC10671213 DOI: 10.3390/ijms242216380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 11/03/2023] [Accepted: 11/09/2023] [Indexed: 11/26/2023] Open
Abstract
The global cancer burden remains high; thus, a better understanding of the molecular mechanisms driving carcinogenesis is needed to improve current prevention and treatment options. We previously detected the ZNF643/ZFP69B gene upregulated in multiple tumors, and we speculated it may play a role in tumor biology. To test this hypothesis, we employed TCGA-centered databases to correlate ZNF643 status with various clinicopathological parameters. We also performed RNA-seq analysis and in vitro studies assessing cancer cell phenotypes, and we searched for ZNF643-bound genomic loci. Our data indicated higher levels of ZNF643 in most analyzed tumors compared to normal samples, possibly due to copy number variations. ZNF643 mRNA correlated with diverse molecular and immune subtypes and clinicopathological features (tumor stage, grade, patient survival). RNA-seq analysis revealed that ZNF643 silencing triggers the deregulation of the genes implicated in various cancer-related processes, such as growth, adhesion, and immune system. Moreover, we observed that ZNF643 positively influences cell cycle, migration, and invasion. Finally, our ChIP-seq analysis indicated that the genes associated with ZNF643 binding are linked to adhesion and immune signaling. In conclusion, our data confirm the oncogenic properties of ZNF643 and pinpoint its impact on cell adhesion and immune processes.
Collapse
Affiliation(s)
- Urszula Oleksiewicz
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland; (U.O.)
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Center, 15 Garbary Street, 61-866 Poznan, Poland
| | - Marta Machnik
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland; (U.O.)
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Center, 15 Garbary Street, 61-866 Poznan, Poland
| | - Joanna Sobocińska
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland; (U.O.)
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Center, 15 Garbary Street, 61-866 Poznan, Poland
| | - Sara Molenda
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland; (U.O.)
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Center, 15 Garbary Street, 61-866 Poznan, Poland
- Doctoral School, Poznan University of Medical Sciences, 70 Bukowska Street, 60-812 Poznan, Poland
| | - Anna Olechnowicz
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland; (U.O.)
- Doctoral School, Poznan University of Medical Sciences, 70 Bukowska Street, 60-812 Poznan, Poland
- Department of Histology and Embryology, Poznan University of Medical Sciences, 6 Święcickiego Street, 60-781 Poznan, Poland
| | - Anna Florczak
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland; (U.O.)
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Center, 15 Garbary Street, 61-866 Poznan, Poland
| | - Julia Mierzejewska
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland; (U.O.)
| | - Dominika Adamczak
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland; (U.O.)
| | - Mikołaj Smolibowski
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland; (U.O.)
| | - Mariusz Kaczmarek
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland; (U.O.)
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Center, 15 Garbary Street, 61-866 Poznan, Poland
| | - Andrzej Mackiewicz
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland; (U.O.)
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Center, 15 Garbary Street, 61-866 Poznan, Poland
| |
Collapse
|
35
|
van der Sande M, Frölich S, Schäfers T, Smits JG, Snabel RR, Rinzema S, van Heeringen SJ. Seq2science: an end-to-end workflow for functional genomics analysis. PeerJ 2023; 11:e16380. [PMID: 38025697 PMCID: PMC10656911 DOI: 10.7717/peerj.16380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 10/09/2023] [Indexed: 12/01/2023] Open
Abstract
Sequencing databases contain enormous amounts of functional genomics data, making them an extensive resource for genome-scale analysis. Reanalyzing publicly available data, and integrating it with new, project-specific data sets, can be invaluable. With current technologies, genomic experiments have become feasible for virtually any species of interest. However, using and integrating this data comes with its challenges, such as standardized and reproducible analysis. Seq2science is a multi-purpose workflow that covers preprocessing, quality control, visualization, and analysis of functional genomics sequencing data. It facilitates the downloading of sequencing data from all major databases, including NCBI SRA, EBI ENA, DDBJ, GSA, and ENCODE. Furthermore, it automates the retrieval of any genome assembly available from Ensembl, NCBI, and UCSC. It has been tested on a variety of species, and includes diverse workflows such as ATAC-, RNA-, and ChIP-seq. It consists of both generic as well as advanced steps, such as differential gene expression or peak accessibility analysis and differential motif analysis. Seq2science is built on the Snakemake workflow language and thus can be run on a range of computing infrastructures. It is available at https://github.com/vanheeringen-lab/seq2science.
Collapse
Affiliation(s)
- Maarten van der Sande
- Molecular Developmental Biology, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Siebren Frölich
- Molecular Developmental Biology, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Tilman Schäfers
- Molecular Developmental Biology, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Jos G.A. Smits
- Molecular Developmental Biology, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Rebecca R. Snabel
- Molecular Developmental Biology, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Sybren Rinzema
- Molecular Developmental Biology, Radboud University Nijmegen, Nijmegen, the Netherlands
| | | |
Collapse
|
36
|
Fahey L, Ali D, Donohoe G, Ó Broin P, Morris DW. Genes positively regulated by Mef2c in cortical neurons are enriched for common genetic variation associated with IQ and educational attainment. Hum Mol Genet 2023; 32:3194-3203. [PMID: 37672226 PMCID: PMC10630234 DOI: 10.1093/hmg/ddad142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 07/27/2023] [Accepted: 08/01/2023] [Indexed: 09/07/2023] Open
Abstract
The myocyte enhancer factor 2 C (MEF2C) gene encodes a transcription factor important for neurogenesis and synapse development and contains common variants associated with intelligence (IQ) and educational attainment (EA). Here, we took gene expression data from the mouse cortex of a Mef2c mouse model with a heterozygous DNA binding-deficient mutation of Mef2c (Mef2c-het) and combined these data with MEF2C ChIP-seq data from cortical neurons and single-cell data from the mouse brain. This enabled us to create a set of genes that were differentially regulated in Mef2c-het mice, represented direct target genes of MEF2C and had elevated in expression in cortical neurons. We found this gene-set to be enriched for genes containing common genetic variation associated with IQ and EA. Genes within this gene-set that were down-regulated, i.e. have reduced expression in Mef2c-het mice versus controls, were specifically significantly enriched for both EA and IQ associated genes. These down-regulated genes were enriched for functionality in the adenylyl cyclase signalling system, which is known to positively regulate synaptic transmission and has been linked to learning and memory. Within the adenylyl cyclase signalling system, three genes regulated by MEF2C, CRHR1, RGS6, and GABRG3, are associated at genome-wide significant levels with IQ and/or EA. Our results indicate that genetic variation in MEF2C and its direct target genes within cortical neurons contribute to variance in cognition within the general population, and the molecular mechanisms involved include the adenylyl cyclase signalling system's role in synaptic function.
Collapse
Affiliation(s)
- Laura Fahey
- Centre for Neuroimaging, Cognition and Genomics (NICOG), School of Biological and Chemical Sciences and School of Psychology, University of Galway, University Road, Galway, H91 CF50, Ireland
- Discipline of Bioinformatics, School of Mathematical and Statistical Sciences, University of Galway, University Road, Galway, H91 CF50, Ireland
| | - Deema Ali
- Centre for Neuroimaging, Cognition and Genomics (NICOG), School of Biological and Chemical Sciences and School of Psychology, University of Galway, University Road, Galway, H91 CF50, Ireland
| | - Gary Donohoe
- Centre for Neuroimaging, Cognition and Genomics (NICOG), School of Biological and Chemical Sciences and School of Psychology, University of Galway, University Road, Galway, H91 CF50, Ireland
| | - Pilib Ó Broin
- Discipline of Bioinformatics, School of Mathematical and Statistical Sciences, University of Galway, University Road, Galway, H91 CF50, Ireland
| | - Derek W Morris
- Centre for Neuroimaging, Cognition and Genomics (NICOG), School of Biological and Chemical Sciences and School of Psychology, University of Galway, University Road, Galway, H91 CF50, Ireland
| |
Collapse
|
37
|
Pascal C, Zonszain J, Hameiri O, Gargi-Levi C, Lev-Maor G, Tammer L, Levy T, Tarabeih A, Roy VR, Ben-Salmon S, Elbaz L, Eid M, Hakim T, Abu Rabe'a S, Shalev N, Jordan A, Meshorer E, Ast G. Human histone H1 variants impact splicing outcome by controlling RNA polymerase II elongation. Mol Cell 2023; 83:3801-3817.e8. [PMID: 37922872 DOI: 10.1016/j.molcel.2023.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 08/17/2023] [Accepted: 10/05/2023] [Indexed: 11/07/2023]
Abstract
Histones shape chromatin structure and the epigenetic landscape. H1, the most diverse histone in the human genome, has 11 variants. Due to the high structural similarity between the H1s, their unique functions in transferring information from the chromatin to mRNA-processing machineries have remained elusive. Here, we generated human cell lines lacking up to five H1 subtypes, allowing us to characterize the genomic binding profiles of six H1 variants. Most H1s bind to specific sites, and binding depends on multiple factors, including GC content. The highly expressed H1.2 has a high affinity for exons, whereas H1.3 binds intronic sequences. H1s are major splicing regulators, especially of exon skipping and intron retention events, through their effects on the elongation of RNA polymerase II (RNAPII). Thus, H1 variants determine splicing fate by modulating RNAPII elongation.
Collapse
Affiliation(s)
- Corina Pascal
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Jonathan Zonszain
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Ofir Hameiri
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Chen Gargi-Levi
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Galit Lev-Maor
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Luna Tammer
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Tamar Levy
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Anan Tarabeih
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Vanessa Rachel Roy
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Stav Ben-Salmon
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Liraz Elbaz
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Mireille Eid
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Tamar Hakim
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Salima Abu Rabe'a
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Nana Shalev
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Albert Jordan
- Instituto de Biologia Molecular de Barcelona (IBMB-CSIC), Carrer de Baldiri Reixac, 15, 08028 Barcelona, Spain
| | - Eran Meshorer
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, Jerusalem 91904, Israel; Edmond and Lily Center for Brain Sciences (ELSC), The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Gil Ast
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
| |
Collapse
|
38
|
von Stromberg K, Seddar L, Ip WH, Günther T, Gornott B, Weinert SC, Hüppner M, Bertzbach LD, Dobner T. The human adenovirus E1B-55K oncoprotein coordinates cell transformation through regulation of DNA-bound host transcription factors. Proc Natl Acad Sci U S A 2023; 120:e2310770120. [PMID: 37883435 PMCID: PMC10622919 DOI: 10.1073/pnas.2310770120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 09/13/2023] [Indexed: 10/28/2023] Open
Abstract
The multifunctional adenovirus E1B-55K oncoprotein can induce cell transformation in conjunction with adenovirus E1A gene products. Previous data from transient expression studies and in vitro experiments suggest that these growth-promoting activities correlate with E1B-55K-mediated transcriptional repression of p53-targeted genes. Here, we analyzed genome-wide occupancies and transcriptional consequences of species C5 and A12 E1B-55Ks in transformed mammalian cells by combinatory ChIP and RNA-seq analyses. E1B-55K-mediated repression correlates with tethering of the viral oncoprotein to p53-dependent promoters via DNA-bound p53. Moreover, we found that E1B-55K also interacts with and represses transcription of numerous p53-independent genes through interactions with transcription factors that play central roles in cancer and stress signaling. Our results demonstrate that E1B-55K oncoproteins function as promiscuous transcriptional repressors of both p53-dependent and -independent genes and further support the model that manipulation of cellular transcription is central to adenovirus-induced cell transformation and oncogenesis.
Collapse
Affiliation(s)
| | - Laura Seddar
- Department of Viral Transformation, Leibniz Institute of Virology, Hamburg20251, Germany
| | - Wing-Hang Ip
- Department of Viral Transformation, Leibniz Institute of Virology, Hamburg20251, Germany
| | - Thomas Günther
- Virus Genomics, Leibniz Institute of Virology, Hamburg20251, Germany
| | - Britta Gornott
- Department of Viral Transformation, Leibniz Institute of Virology, Hamburg20251, Germany
| | - Sophie-Celine Weinert
- Department of Viral Transformation, Leibniz Institute of Virology, Hamburg20251, Germany
| | - Max Hüppner
- Department of Viral Transformation, Leibniz Institute of Virology, Hamburg20251, Germany
| | - Luca D. Bertzbach
- Department of Viral Transformation, Leibniz Institute of Virology, Hamburg20251, Germany
| | - Thomas Dobner
- Department of Viral Transformation, Leibniz Institute of Virology, Hamburg20251, Germany
| |
Collapse
|
39
|
Molina M, Way LE, Ren Z, Liao Q, Guerra B, Shields B, Wang X, Kim H. A framework to validate fluorescently labeled DNA-binding proteins for single-molecule experiments. Cell Rep Methods 2023; 3:100614. [PMID: 37832544 PMCID: PMC10626211 DOI: 10.1016/j.crmeth.2023.100614] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 07/28/2023] [Accepted: 09/20/2023] [Indexed: 10/15/2023]
Abstract
Due to the enhanced labeling capability of maleimide-based fluorescent probes, lysine-cysteine-lysine (KCK) tags are frequently added to proteins for visualization. In this study, we employed an in vitro single-molecule DNA flow-stretching assay as a sensitive way to assess the impact of the KCK tag on the property of DNA-binding proteins. Using Bacillus subtilis ParB as an example, we show that, although no noticeable changes were detected by in vivo fluorescence imaging and chromatin immunoprecipitation (ChIP) assays, the KCK tag substantially altered ParB's DNA compaction rates and its response to nucleotide binding and to the presence of the specific sequence (parS) on the DNA. While it is typically assumed that short peptide tags minimally perturb protein function, our results urge researchers to carefully validate the use of tags for protein labeling. Our comprehensive analysis can be expanded and used as a guide to assess the impacts of other tags on DNA-binding proteins in single-molecule assays.
Collapse
Affiliation(s)
- Miranda Molina
- Biochemistry and Molecular Biology Program, University of Texas Rio Grande Valley, Edinburg, TX 78539, USA; Department of Physics and Astronomy, University of Texas Rio Grande Valley, Edinburg, TX 78539, USA
| | - Lindsey E Way
- Department of Biology, Indiana University, 1001 E 3(rd) St., Bloomington, IN 47405, USA
| | - Zhongqing Ren
- Department of Biology, Indiana University, 1001 E 3(rd) St., Bloomington, IN 47405, USA
| | - Qin Liao
- Department of Biology, Indiana University, 1001 E 3(rd) St., Bloomington, IN 47405, USA
| | - Bianca Guerra
- Department of Physics and Astronomy, University of Texas Rio Grande Valley, Edinburg, TX 78539, USA
| | - Brandon Shields
- Department of Physics and Astronomy, University of Texas Rio Grande Valley, Edinburg, TX 78539, USA
| | - Xindan Wang
- Department of Biology, Indiana University, 1001 E 3(rd) St., Bloomington, IN 47405, USA.
| | - HyeongJun Kim
- Biochemistry and Molecular Biology Program, University of Texas Rio Grande Valley, Edinburg, TX 78539, USA; Department of Physics and Astronomy, University of Texas Rio Grande Valley, Edinburg, TX 78539, USA.
| |
Collapse
|
40
|
Trouillon J, Doubleday PF, Sauer U. Genomic footprinting uncovers global transcription factor responses to amino acids in Escherichia coli. Cell Syst 2023; 14:860-871.e4. [PMID: 37820729 DOI: 10.1016/j.cels.2023.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 09/01/2023] [Accepted: 09/19/2023] [Indexed: 10/13/2023]
Abstract
Our knowledge of transcriptional responses to changes in nutrient availability comes primarily from few well-studied transcription factors (TFs), often lacking an unbiased genome-wide perspective. Leveraging recent advances allowing bacterial genomic footprinting, we comprehensively mapped the genome-wide regulatory responses of Escherichia coli to exogenous leucine, methionine, alanine, and lysine. The global TF Lrp was found to individually sense three amino acids and mount three different target gene responses. Overall, 531 genes had altered RNA polymerase occupancy, and 32 TFs responded directly or indirectly to the presence of amino acids, including regulators of membrane and osmotic pressure homeostasis. About 70% of the detected TF-DNA interactions had not been reported before. We thus identified 682 previously unknown TF-binding locations, for a subset of which the involved TFs were identified by affinity purification. This comprehensive map of amino acid regulation illustrates the incompleteness of the known transcriptional regulation network, even in E. coli.
Collapse
Affiliation(s)
- Julian Trouillon
- Institute of Molecular Systems Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Peter F Doubleday
- Institute of Molecular Systems Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Uwe Sauer
- Institute of Molecular Systems Biology, ETH Zürich, 8093 Zürich, Switzerland.
| |
Collapse
|
41
|
Barton IS, Ren Z, Cribb CB, Pitzer JE, Baglivo I, Martin DW, Wang X, Roop RM. Brucella MucR acts as an H-NS-like protein to silence virulence genes and structure the nucleoid. mBio 2023; 14:e0220123. [PMID: 37847580 PMCID: PMC10746212 DOI: 10.1128/mbio.02201-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 08/21/2023] [Indexed: 10/19/2023] Open
Abstract
Histone-like nucleoid structuring (H-NS) and H-NS-like proteins serve as global gene silencers and work with antagonistic transcriptional activators (counter-silencers) to properly coordinate the expression of virulence genes in pathogenic bacteria. In Brucella, MucR has been proposed as a novel H-NS-like gene silencer, but direct experimental evidence is lacking. Here, we show that MucR serves as an H-NS-like silencer of the Brucella abortus genes encoding the polar autotransporter adhesins BtaE and BmaC, the c-di-GMP-specific phosphodiesterase BpdB, and the quorum-sensing regulator BabR. We also demonstrate that the MarR-type transcriptional activator MdrA can displace MucR from the btaE promoter, supporting the existence of MucR counter-silencers in Brucella. Moreover, our chromatin immunoprecipitation (ChIP)-seq analysis identified 546 MucR enrichment peaks along the genome, including in the promoters of the genes encoding the Type IV secretion machinery and effectors and the quorum-sensing regulator VjbR. Importantly, MucR ChIP-seq peaks overlap with the previously described binding sites for the transcriptional activators VjbR, BvrR, and CtrA suggesting that these regulators serve as MucR counter-silencers and work in concert with MucR to coordinate virulence gene expression in Brucella. In addition, using chromosome conformation capture (Hi-C), we show that like H-NS in Escherichia coli, MucR alters the global structure of the Brucella nucleoid. Finally, a copy of the E. coli hns rescues the distinctive growth defect and elevated btaE expression of a B. abortus mucR mutant. Together, these findings solidify the role of MucR as a novel type of H-NS-like protein and suggest that MucR's gene-silencing properties play a key role in virulence in Brucella. IMPORTANCE Histone-like nucleoid structuring (H-NS) and H-NS-like proteins coordinate host-associated behaviors in many pathogenic bacteria, often through forming silencer/counter-silencer pairs with signal-responsive transcriptional activators to tightly control gene expression. Brucella and related bacteria do not encode H-NS or homologs of known H-NS-like proteins, and it is unclear if they have other proteins that perform analogous functions during pathogenesis. In this work, we provide compelling evidence for the role of MucR as a novel H-NS-like protein in Brucella. We show that MucR possesses many of the known functions attributed to H-NS and H-NS-like proteins, including the formation of silencer/counter-silencer pairs to control virulence gene expression and global structuring of the nucleoid. These results uncover a new role for MucR as a nucleoid structuring protein and support the importance of temporal control of gene expression in Brucella and related bacteria.
Collapse
Affiliation(s)
- Ian S. Barton
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, USA
| | - Zhongqing Ren
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - Connor B. Cribb
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, USA
| | - Joshua E. Pitzer
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, USA
| | - Ilaria Baglivo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, Caserta, Italy
| | - Daniel W. Martin
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, USA
| | - Xindan Wang
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - R. Martin Roop
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, USA
| |
Collapse
|
42
|
Sharkey LKR, Guerillot R, Walsh CJ, Turner AM, Lee JYH, Neville SL, Klatt S, Baines SL, Pidot SJ, Rossello FJ, Seemann T, McWilliam HEG, Cho E, Carter GP, Howden BP, McDevitt CA, Hachani A, Stinear TP, Monk IR. The two-component system WalKR provides an essential link between cell wall homeostasis and DNA replication in Staphylococcus aureus. mBio 2023; 14:e0226223. [PMID: 37850732 PMCID: PMC10746227 DOI: 10.1128/mbio.02262-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 09/05/2023] [Indexed: 10/19/2023] Open
Abstract
Among the 16 two-component systems in the opportunistic human pathogen Staphylococcus aureus, only WalKR is essential. Like the orthologous systems in other Bacillota, S. aureus WalKR controls autolysins involved in peptidoglycan remodeling and is therefore intimately involved in cell division. However, despite the importance of WalKR in S. aureus, the basis for its essentiality is not understood and the regulon is poorly defined. Here, we defined a consensus WalR DNA-binding motif and the direct WalKR regulon by using functional genomics, including chromatin immunoprecipitation sequencing, with a panel of isogenic walKR mutants that had a spectrum of altered activities. Consistent with prior findings, the direct regulon includes multiple autolysin genes. However, this work also revealed that WalR directly regulates at least five essential genes involved in lipoteichoic acid synthesis (ltaS): translation (rplK), DNA compaction (hup), initiation of DNA replication (dnaA, hup) and purine nucleotide metabolism (prs). Thus, WalKR in S. aureus serves as a polyfunctional regulator that contributes to fundamental control over critical cell processes by coordinately linking cell wall homeostasis with purine biosynthesis, protein biosynthesis, and DNA replication. Our findings further address the essentiality of this locus and highlight the importance of WalKR as a bona fide target for novel anti-staphylococcal therapeutics. IMPORTANCE The opportunistic human pathogen Staphylococcus aureus uses an array of protein sensing systems called two-component systems (TCS) to sense environmental signals and adapt its physiology in response by regulating different genes. This sensory network is key to S. aureus versatility and success as a pathogen. Here, we reveal for the first time the full extent of the regulatory network of WalKR, the only staphylococcal TCS that is indispensable for survival under laboratory conditions. We found that WalKR is a master regulator of cell growth, coordinating the expression of genes from multiple, fundamental S. aureus cellular processes, including those involved in maintaining cell wall metabolism, protein biosynthesis, nucleotide metabolism, and the initiation of DNA replication.
Collapse
Affiliation(s)
- Liam K. R. Sharkey
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Romain Guerillot
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Calum J. Walsh
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Adrianna M. Turner
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Jean Y. H. Lee
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Stephanie L. Neville
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Stephan Klatt
- The Florey Institute of Neuroscience and Mental Health, Melbourne Dementia Research Centre, The University of Melbourne, Parkville, Victoria, Australia
| | - Sarah L. Baines
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Sacha J. Pidot
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Fernando J. Rossello
- University of Melbourne Centre for Cancer Research, The University of Melbourne, Melbourne, Victoria, Australia
- Australian Regenerative Medicine Institute, Monash University, Melbourne, Victoria, Australia
| | - Torsten Seemann
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
- Department of Microbiology and Immunology, Centre for Pathogen Genomics, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Hamish E. G. McWilliam
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Ellie Cho
- Biological Optical Microscopy Platform, University of Melbourne, Melbourne, Victoria, Australia
| | - Glen P. Carter
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Benjamin P. Howden
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
- Department of Microbiology and Immunology, Centre for Pathogen Genomics, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Christopher A. McDevitt
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Abderrahman Hachani
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Timothy P. Stinear
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
- Department of Microbiology and Immunology, Centre for Pathogen Genomics, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Ian R. Monk
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| |
Collapse
|
43
|
Gamberoni F, Borgese M, Pagiatakis C, Armenia I, Grazù V, Gornati R, Serio S, Papait R, Bernardini G. Iron Oxide Nanoparticles with and without Cobalt Functionalization Provoke Changes in the Transcription Profile via Epigenetic Modulation of Enhancer Activity. Nano Lett 2023; 23:9151-9159. [PMID: 37494138 PMCID: PMC10571150 DOI: 10.1021/acs.nanolett.3c01967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 07/22/2023] [Indexed: 07/28/2023]
Abstract
Despite the progress in the field of nanotoxicology, much about the cellular mechanisms that mediate the adverse effects of nanoparticles (NPs) and, in particular, the possible role of epigenetics in nanotoxicity, remains to be clarified. Therefore, we studied the changes occurring in the genome-wide distribution of H3K27ac, H3K4me1, H3K9me2, and H3K27me3 histone modifications and compared them with the transcriptome after exposing NIH3T3 cells to iron-based magnetic NPs (i.e., Fe2O3 and Fe2O3@Co NPs). We found that the transcription response is mainly due to changes in the genomic distribution of H3K27ac that can modulate the activity of enhancers. We propose that alteration of the epigenetic landscape is a key mechanism in defining the gene expression program changes resulting in nanotoxicity. With this approach, it is possible to construct a data set of genomic regions that could be useful for defining toxicity in a manner that is more comprehensive than what is possible with the present toxicology assays.
Collapse
Affiliation(s)
- Federica Gamberoni
- Department
of Biotechnology and Life Sciences, University
of Insubria, via J.H. Dunant 3, 21100 Varese, Italy
| | - Marina Borgese
- Department
of Medicine and Surgery, University of Insubria, via Guicciardini 9, 21100 Varese, Italy
| | - Christina Pagiatakis
- Department
of Biotechnology and Life Sciences, University
of Insubria, via J.H. Dunant 3, 21100 Varese, Italy
- IRCCS
Humanitas Research Hospital, via Manzoni 56, 20089 Rozzano, Milan, Italy
| | - Ilaria Armenia
- BioNanoSurf
Group, Instituto de Nanociencia y Materiales
de Aragón (INMA, CSIC-UNIZAR), Edificio I + D, 50018 Zaragoza, Spain
| | - Valeria Grazù
- BioNanoSurf
Group, Instituto de Nanociencia y Materiales
de Aragón (INMA, CSIC-UNIZAR), Edificio I + D, 50018 Zaragoza, Spain
| | - Rosalba Gornati
- Department
of Biotechnology and Life Sciences, University
of Insubria, via J.H. Dunant 3, 21100 Varese, Italy
| | - Simone Serio
- Department
of Biotechnology and Life Sciences, University
of Insubria, via J.H. Dunant 3, 21100 Varese, Italy
- IRCCS
Humanitas Research Hospital, via Manzoni 56, 20089 Rozzano, Milan, Italy
- Department
of Biomedical Sciences, Humanitas University, via Rita Levi Montalcini 4, 20072 Pieve Emanuele, MI, Italy
| | - Roberto Papait
- Department
of Biotechnology and Life Sciences, University
of Insubria, via J.H. Dunant 3, 21100 Varese, Italy
- IRCCS
Humanitas Research Hospital, via Manzoni 56, 20089 Rozzano, Milan, Italy
| | - Giovanni Bernardini
- Department
of Biotechnology and Life Sciences, University
of Insubria, via J.H. Dunant 3, 21100 Varese, Italy
| |
Collapse
|
44
|
Tahara S, Tsuchiya T, Matsumoto H, Ozaki H. Transcription factor-binding k-mer analysis clarifies the cell type dependency of binding specificities and cis-regulatory SNPs in humans. BMC Genomics 2023; 24:597. [PMID: 37805453 PMCID: PMC10560430 DOI: 10.1186/s12864-023-09692-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 09/21/2023] [Indexed: 10/09/2023] Open
Abstract
BACKGROUND Transcription factors (TFs) exhibit heterogeneous DNA-binding specificities in individual cells and whole organisms under natural conditions, and de novo motif discovery usually provides multiple motifs, even from a single chromatin immunoprecipitation-sequencing (ChIP-seq) sample. Despite the accumulation of ChIP-seq data and ChIP-seq-derived motifs, the diversity of DNA-binding specificities across different TFs and cell types remains largely unexplored. RESULTS Here, we applied MOCCS2, our k-mer-based motif discovery method, to a collection of human TF ChIP-seq samples across diverse TFs and cell types, and systematically computed profiles of TF-binding specificity scores for all k-mers. After quality control, we compiled a set of TF-binding specificity score profiles for 2,976 high-quality ChIP-seq samples, comprising 473 TFs and 398 cell types. Using these high-quality samples, we confirmed that the k-mer-based TF-binding specificity profiles reflected TF- or TF-family dependent DNA-binding specificities. We then compared the binding specificity scores of ChIP-seq samples with the same TFs but with different cell type classes and found that half of the analyzed TFs exhibited differences in DNA-binding specificities across cell type classes. Additionally, we devised a method to detect differentially bound k-mers between two ChIP-seq samples and detected k-mers exhibiting statistically significant differences in binding specificity scores. Moreover, we demonstrated that differences in the binding specificity scores between k-mers on the reference and alternative alleles could be used to predict the effect of variants on TF binding, as validated by in vitro and in vivo assay datasets. Finally, we demonstrated that binding specificity score differences can be used to interpret disease-associated non-coding single-nucleotide polymorphisms (SNPs) as TF-affecting SNPs and provide candidates responsible for TFs and cell types. CONCLUSIONS Our study provides a basis for investigating the regulation of gene expression in a TF-, TF family-, or cell-type-dependent manner. Furthermore, our differential analysis of binding-specificity scores highlights noncoding disease-associated variants in humans.
Collapse
Affiliation(s)
- Saeko Tahara
- Bioinformatics Laboratory, Institute of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
- School of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
| | - Takaho Tsuchiya
- Bioinformatics Laboratory, Institute of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
- Center for Artificial Intelligence Research, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
| | - Hirotaka Matsumoto
- School of Information and Data Sciences, Nagasaki University, 1-14, Bunkyo-Machi, Nagasaki City, Nagasaki, 852-8521, Japan
- Laboratory for Bioinformatics Research, RIKEN Center for Biosystems Dynamics, Wako, Saitama, 351-0198, Japan
| | - Haruka Ozaki
- Bioinformatics Laboratory, Institute of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan.
- Center for Artificial Intelligence Research, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan.
- Laboratory for Bioinformatics Research, RIKEN Center for Biosystems Dynamics, Wako, Saitama, 351-0198, Japan.
| |
Collapse
|
45
|
Qiu L, Chen X, Zhu L, Yao R, Qi P. ChIP-seq identifies McSLC35E2 as a novel target gene of McNrf2 in Mytilus coruscus, highlighting its role in the regulation of oxidative stress response in marine mollusks. Front Physiol 2023; 14:1282900. [PMID: 37869713 PMCID: PMC10587546 DOI: 10.3389/fphys.2023.1282900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 09/25/2023] [Indexed: 10/24/2023] Open
Abstract
NF-E2-related factor 2 (Nrf2) plays a crucial role in the oxidative regulatory process, which could trigger hundreds of antioxidant elements to confront xenobiotics. In the previous study, we identified Nrf2 from the marine mussel Mytilus coruscus, and the findings demonstrated that McNrf2 effectively protected the mussels against oxidative stress induced by benzopyrene (Bap). In order to delve deeper into the underlying mechanism, we utilized Chromatin Immunoprecipitation followed by sequencing (ChIP-seq) technology to systematically identify potential novel target genes of McNrf2. A total of 3,465 potential target genes were screened, of which 219 owned binding sites located within the promoter region. During subsequent experimental verification, it was found that McSLC35E2, a candidate target gene of McNrf2, exhibited negative regulation by McNrf2, as confirmed through dual luciferase and qRT-PCR detection. Further, the enzyme activity tests demonstrated that McNrf2 could counteract Bap induced oxidative stress by inhibiting McSLC35E2. The current study provides valuable insights into the application of ChIP-seq technology in the research of marine mollusks, advancing our understanding of the key role of Nrf2 in antioxidant defense mechanisms, and highlighting the significance of SLC35E2 in the highly sophisticated regulation of oxidative stress response in marine invertebrates.
Collapse
Affiliation(s)
| | | | | | | | - Pengzhi Qi
- National Engineering Research Center of Marine Facilities Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, Zhejiang, China
| |
Collapse
|
46
|
Abstract
PURPOSE OF REVIEW Runt-related transcription factors (RUNX) play critical roles in skeletal development, metabolism, and diseases. In mammals, three RUNX members, namely RUNX1, RUNX2, and RUNX3, play distinct and redundant roles, although RUNX2 is a dominant factor in skeletal development and several skeletal diseases. This review is to provide an overview of the current understanding of RUNX-mediated transcriptional regulation in different skeletal cell types. RECENT FINDINGS Advances in chromatin immunoprecipitation and next-generation sequencing (ChIP-seq) have revealed genome-wide RUNX-mediated gene regulatory mechanisms, including their association with cis-regulatory elements and putative target genes. Further studies with genome-wide analysis and biochemical assays have shed light on RUNX-mediated pioneering action and involvements of RUNX2 in lipid-lipid phase separation. Emerging multi-layered mechanisms of RUNX-mediated gene regulations help us better understanding of skeletal development and diseases, which also provides clues to think how genome-wide studies can help develop therapeutic strategies for skeletal diseases.
Collapse
Affiliation(s)
- Hironori Hojo
- Division of Clinical Biotechnology, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-8655 Japan
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, Tokyo, 113-8655 Japan
| | - Shinsuke Ohba
- Department of Tissue and Developmental Biology, Graduate School of Dentistry, Osaka University, 1-8 Yamadaoka, Suita, Osaka 565-0871 Japan
| |
Collapse
|
47
|
Sutter CH, Azim S, Wang A, Bhuju J, Simpson AS, Uberoi A, Grice EA, Sutter TR. Ligand Activation of the Aryl Hydrocarbon Receptor Upregulates Epidermal Uridine Diphosphate Glucose Ceramide Glucosyltransferase and Glucosylceramides. J Invest Dermatol 2023; 143:1964-1972.e4. [PMID: 37004877 PMCID: PMC10529782 DOI: 10.1016/j.jid.2023.03.1662] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 03/08/2023] [Accepted: 03/14/2023] [Indexed: 04/03/2023]
Abstract
Ligand activation of the aryl hydrocarbon receptor (AHR) accelerates keratinocyte differentiation and the formation of the epidermal permeability barrier. Several classes of lipids, including ceramides, are critical to the epidermal permeability barrier. In normal human epidermal keratinocytes, the AHR ligand, 2,3,7,8-tetrachlorodibenzo-p-dioxin, increased RNA levels of ceramide metabolism and transport genes: uridine diphosphate glucose ceramide glucosyltransferase (UGCG), ABCA12, GBA1, and SMPD1. Levels of abundant skin ceramides were also increased by 2,3,7,8-tetrachlorodibenzo-p-dioxin. These included the metabolites synthesized by UGCG, glucosylceramides, and acyl glucosylceramides. Chromatin immunoprecipitation-sequence analysis and luciferase reporter assays identified UGCG as a direct AHR target. The AHR antagonist, GNF351, inhibited the 2,3,7,8-tetrachlorodibenzo-p-dioxin-mediated RNA and transcriptional increases. Tapinarof, an AHR ligand approved for the treatment of psoriasis, increased UGCG RNA, protein, and its lipid metabolites hexosylceramides as well as increased the RNA expression of ABCA12, GBA1, and SMPD1. In Ahr-null mice, Ugcg RNA and hexosylceramides were lower than those in the wild type. These results indicate that the AHR regulates the expression of UGCG, a ceramide-metabolizing enzyme required for ceramide trafficking, keratinocyte differentiation, and epidermal permeability barrier formation.
Collapse
Affiliation(s)
- Carrie Hayes Sutter
- Department of Biological Sciences, The University of Memphis, Memphis, Tennessee, USA
| | - Shafquat Azim
- Department of Biological Sciences, The University of Memphis, Memphis, Tennessee, USA; Department of Surgery, School of Medicine, University of Maryland, Baltimore, Maryland, USA
| | - Anyou Wang
- Department of Biological Sciences, The University of Memphis, Memphis, Tennessee, USA
| | - Jyoti Bhuju
- Department of Biological Sciences, The University of Memphis, Memphis, Tennessee, USA; Sanegene Bio USA, Cambridge, Massachusetts, USA
| | - Amelia S Simpson
- Department of Biological Sciences, The University of Memphis, Memphis, Tennessee, USA
| | - Aayushi Uberoi
- Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Elizabeth A Grice
- Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Thomas R Sutter
- Department of Biological Sciences, The University of Memphis, Memphis, Tennessee, USA; Department of Chemistry, The University of Memphis, Memphis, Tennessee, USA.
| |
Collapse
|
48
|
Zeng L, Zhang B. Exploring the Genomic Landscape: An In-depth ChIP-seq Analysis Protocol for Uncovering Protein-DNA Interactions. Curr Protoc 2023; 3:e909. [PMID: 37830781 DOI: 10.1002/cpz1.909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2023]
Abstract
Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is a widely employed technique for investigating protein-DNA interactions. However, the absence of a standardized and clear workflow necessitates researchers to independently assemble methodologies from diverse resources. This lack of uniformity hampers reproducibility and makes version control a complex endeavor, thereby limiting the accessibility of ChIP-seq analyses to individuals with extensive training in bioinformatics. In light of these challenges, we have developed an executable protocol that addresses these limitations. Our protocol encompasses all aspects of ChIP-seq analysis, ranging from quality control of raw reads to peak calling and downstream functional analyses. We have implemented two distinct approaches for peak calling, providing researchers with flexibility to choose the most suitable method for their specific experimental needs. This protocol will contribute to the scientific community by providing a standardized and clear resource that will enhance the reproducibility and accessibility of ChIP-seq analyses. © 2023 Wiley Periodicals LLC. Basic Protocol: ChIP-seq analysis workflow Alternative Protocol: Call differentially enriched peaks by using MACS3.
Collapse
Affiliation(s)
- Liping Zeng
- Institute for Integrative Genome Biology and Department of Botany and Plant Sciences, University of California, Riverside, California
| | - Bailong Zhang
- Institute for Integrative Genome Biology and Department of Botany and Plant Sciences, University of California, Riverside, California
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| |
Collapse
|
49
|
Wang G, Zhang G, Zhu N, Zhu C, Kang M, Zuo G, Niu Z, Ye W, Tian B, Cai R. Integrative analyses of RNA-seq and ChIP-seq Reveal MITF as a Target Gene of TFPI-2 in MDA231 Cells. Biochem Genet 2023; 61:1745-1757. [PMID: 36787085 DOI: 10.1007/s10528-023-10340-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 01/27/2023] [Indexed: 02/15/2023]
Abstract
Breast cancer is the most prevalent cancer in female patients worldwide. Tissue factor pathway inhibitor 2 (TFPI-2) is identified as an important tumor suppressor in various cancers. Recent studies have shown that TFPI-2 translocates into the nucleus, where it modulates the transcription of the matrix metalloproteinase-2 (MMP-2) gene. However, its biological role and molecular mechanisms in the progression of breast cancer remain unclear. In this study, we identified 5125 differentially expressed genes (DEGs) from RNA sequencing (RNA-seq) in TFPI-2-overexpressing MDA231 cells compared with control cells. Gene ontology and Kyoto encyclopedia of genes and genomes (KEGG) analysis shown that cell cycle, cell differentiation, proteoglycans in cancer, and pathways associated with cancer were highly enriched in downregulated DEGs. Integration of the RNA-seq and ChIP-sequencing (ChIP-seq) data identified 73 genes directly controlled by TFPI-2 in MDA231 cells. Among them, melanocyte inducing transcription factor (MITF) gene expression was repressed by TFPI-2, which was further verified by a luciferase reporter assay and ChIP-quantitative PCR. Our study provides evidence of a novel role of TFPI-2 in human breast cancer involving targeting of the MITF.
Collapse
Affiliation(s)
- Guangli Wang
- Department of Genetics and Precision Medicine Laboratory, Affiliated Hospital of Guilin Medical University, Guilin, 541001, Guangxi, People's Republic of China.
| | - Gaofeng Zhang
- Department of Radiation Oncology, Affiliated Hospital of Guilin Medical University, Guilin, 541001, Guangxi, People's Republic of China
| | - Ningxia Zhu
- Department of Pathology and Physiopathology, Guilin Medical University, Guilin, 541004, Guangxi, People's Republic of China.
| | - Chunjiang Zhu
- Department of Genetics and Precision Medicine Laboratory, Affiliated Hospital of Guilin Medical University, Guilin, 541001, Guangxi, People's Republic of China
| | - Mafei Kang
- Department of Medical Oncology, The Affiliated Hospital of Guilin Medical University, Guilin, 541001, Guangxi, People's Republic of China
| | - Guidan Zuo
- Department of Radiation Oncology, Affiliated Hospital of Guilin Medical University, Guilin, 541001, Guangxi, People's Republic of China
| | - Zhijie Niu
- Department of Radiation Oncology, Affiliated Hospital of Guilin Medical University, Guilin, 541001, Guangxi, People's Republic of China
| | - Wei Ye
- Department of Genetics and Precision Medicine Laboratory, Affiliated Hospital of Guilin Medical University, Guilin, 541001, Guangxi, People's Republic of China
| | - Baodong Tian
- Department of Genetics and Precision Medicine Laboratory, Affiliated Hospital of Guilin Medical University, Guilin, 541001, Guangxi, People's Republic of China
| | - Rui Cai
- Department of Radiation Oncology, Affiliated Hospital of Guilin Medical University, Guilin, 541001, Guangxi, People's Republic of China
| |
Collapse
|
50
|
Khan S, Pradhan SJ, Giraud G, Bleicher F, Paul R, Merabet S, Shashidhara LS. A Micro-evolutionary Change in Target Binding Sites as a Key Determinant of Ultrabithorax Function in Drosophila. J Mol Evol 2023; 91:616-627. [PMID: 37341745 DOI: 10.1007/s00239-023-10123-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 06/01/2023] [Indexed: 06/22/2023]
Abstract
Hox genes encode Homeodomain-containing transcription factors, which specify segmental identities along the anterior-posterior axis. Functional changes in Hox genes have been directly implicated in the evolution of body plans across the metazoan lineage. The Hox protein Ultrabithorax (Ubx) is expressed and required in developing third thoracic (T3) segments in holometabolous insects studied so far, particularly, of the order Coleoptera, Lepidoptera and Diptera. Ubx function is key to specify differential development of the second (T2) and T3 thoracic segments in these insects. While Ubx is expressed in the third thoracic segment in developing larvae of Hymenopteran Apis mellifera, the morphological differences between T2 and T3 are subtle. To identify evolutionary changes that are behind the differential function of Ubx in Drosophila and Apis, which are diverged for more than 350 million years, we performed comparative analyses of genome wide Ubx-binding sites between these two insects. Our studies reveal that a motif with a TAAAT core is a preferred binding site for Ubx in Drosophila, but not in Apis. Biochemical and transgenic assays suggest that in Drosophila, the TAAAT core sequence in the Ubx binding sites is required for Ubx-mediated regulation of two of its target genes studied here; CG13222, a gene that is normally upregulated by Ubx and vestigial (vg), whose expression is repressed by Ubx in T3. Interestingly, changing the TAAT site to a TAAAT site was sufficient to bring an otherwise unresponsive enhancer of the vg gene from Apis under the control of Ubx in a Drosophila transgenic assay. Taken together, our results suggest an evolutionary mechanism by which critical wing patterning genes might have come under the regulation of Ubx in the Dipteran lineage.
Collapse
Affiliation(s)
- Soumen Khan
- Indian Institute of Science Education and Research (IISER), Pune, 411008, India.
| | - Saurabh J Pradhan
- Indian Institute of Science Education and Research (IISER), Pune, 411008, India
| | - Guillaume Giraud
- IGFL, ENS Lyon, UMR5242, 32 Av. Tony Garnier, 69007, Lyon, France
| | | | - Rachel Paul
- IGFL, ENS Lyon, UMR5242, 32 Av. Tony Garnier, 69007, Lyon, France
| | - Samir Merabet
- IGFL, ENS Lyon, UMR5242, 32 Av. Tony Garnier, 69007, Lyon, France
| | - L S Shashidhara
- Indian Institute of Science Education and Research (IISER), Pune, 411008, India.
- Ashoka University, Sonipat, Haryana, 131029, India.
| |
Collapse
|