1
|
Thomas P, Srivastava S, Udayashankara AH, Damodaran S, Yadav L, Mathew B, Suresh SB, Mandal AK, Srikantia N. RhoC in association with TET2/WDR5 regulates cancer stem cells by epigenetically modifying the expression of pluripotency genes. Cell Mol Life Sci 2022; 80:1. [PMID: 36469134 PMCID: PMC11073244 DOI: 10.1007/s00018-022-04645-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 11/22/2022] [Accepted: 11/22/2022] [Indexed: 12/12/2022]
Abstract
Emerging evidence illustrates that RhoC has divergent roles in cervical cancer progression where it controls epithelial to mesenchymal transition (EMT), migration, angiogenesis, invasion, tumor growth, and radiation response. Cancer stem cells (CSCs) are the primary cause of recurrence and metastasis and exhibit all of the above phenotypes. It, therefore, becomes imperative to understand if RhoC regulates CSCs in cervical cancer. In this study, cell lines and clinical specimen-based findings demonstrate that RhoC regulates tumor phenotypes such as clonogenicity and anoikis resistance. Accordingly, inhibition of RhoC abrogated these phenotypes. RNA-seq analysis revealed that RhoC over-expression resulted in up-regulation of 27% of the transcriptome. Further, the Infinium MethylationEPIC array showed that RhoC over-expressing cells had a demethylated genome. Studies divulged that RhoC via TET2 signaling regulated the demethylation of the genome. Further investigations comprising ChIP-seq, reporter assays, and mass spectrometry revealed that RhoC associates with WDR5 in the nucleus and regulates the expression of pluripotency genes such as Nanog. Interestingly, clinical specimen-based investigations revealed the existence of a subset of tumor cells marked by RhoC+/Nanog+ expression. Finally, combinatorial inhibition (in vitro) of RhoC and its partners (WDR5 and TET2) resulted in increased sensitization of clinical specimen-derived cells to radiation. These findings collectively reveal a novel role for nuclear RhoC in the epigenetic regulation of Nanog and identify RhoC as a regulator of CSCs. The study nominates RhoC and associated signaling pathways as therapeutic targets.
Collapse
Affiliation(s)
- Pavana Thomas
- Translational and Molecular Biology Laboratory (TMBL), Division of Molecular Biology and Genetics, St. John's Research Institute (SJRI), St. John's Medical College, Bangalore, 560034, India
- School of Integrative Health Sciences, The University of Trans-Disciplinary Health Sciences and Technology (TDU), Bangalore, 560064, India
| | - Sweta Srivastava
- Translational and Molecular Biology Laboratory (TMBL), Division of Molecular Biology and Genetics, St. John's Medical College Hospital, Bangalore, 560034, India.
| | - Avinash H Udayashankara
- Department of Radiation Oncology, St John's Medical College Hospital, Bangalore, 560034, India
| | - Samyuktha Damodaran
- Translational and Molecular Biology Laboratory (TMBL), Division of Molecular Biology and Genetics, St. John's Research Institute (SJRI), St. John's Medical College, Bangalore, 560034, India
| | - Lokendra Yadav
- Translational and Molecular Biology Laboratory (TMBL), Division of Molecular Biology and Genetics, St. John's Medical College Hospital, Bangalore, 560034, India
| | - Boby Mathew
- Clinical Proteomics Unit, Division of Molecular Medicine, St. John's Research Institute (SJRI), St. John's Medical College, Bangalore, 560034, India
| | - Srinag Bangalore Suresh
- Translational and Molecular Biology Laboratory (TMBL), Division of Molecular Biology and Genetics, St. John's Research Institute (SJRI), St. John's Medical College, Bangalore, 560034, India
| | - Amit Kumar Mandal
- Clinical Proteomics Unit, Division of Molecular Medicine, St. John's Research Institute (SJRI), St. John's Medical College, Bangalore, 560034, India
| | - Nirmala Srikantia
- Department of Radiation Oncology, St John's Medical College Hospital, Bangalore, 560034, India
| |
Collapse
|
2
|
Zhao H, Zhang W, Zhang T, Lin Y, Hu Y, Fang C, Jiang J. Genome-wide MNase hypersensitivity assay unveils distinct classes of open chromatin associated with H3K27me3 and DNA methylation in Arabidopsis thaliana. Genome Biol 2020; 21:24. [PMID: 32014062 PMCID: PMC6996174 DOI: 10.1186/s13059-020-1927-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 01/06/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Regulation of transcription depends on interactions between cis-regulatory elements (CREs) and regulatory proteins. Active CREs are imbedded in open chromatin that are accessible to nucleases. Several techniques, including DNase-seq, which is based on nuclease DNase I, and ATAC-seq, which is based on transposase Tn5, have been widely used to identify genomic regions associated with open chromatin. These techniques have played a key role in dissecting the regulatory networks in gene expression in both animal and plant species. RESULTS We develop a technique, named MNase hypersensitivity sequencing (MH-seq), to identify genomic regions associated with open chromatin in Arabidopsis thaliana. Genomic regions enriched with MH-seq reads are referred as MNase hypersensitive sites (MHSs). MHSs overlap with the majority (~ 90%) of the open chromatin identified previously by DNase-seq and ATAC-seq. Surprisingly, 22% MHSs are not covered by DNase-seq or ATAC-seq reads, which are referred to "specific MHSs" (sMHSs). sMHSs tend to be located away from promoters, and a substantial portion of sMHSs are derived from transposable elements. Most interestingly, genomic regions containing sMHSs are enriched with epigenetic marks, including H3K27me3 and DNA methylation. In addition, sMHSs show a number of distinct characteristics including association with transcriptional repressors. Thus, sMHSs span distinct classes of open chromatin that may not be accessible to DNase I or Tn5. We hypothesize that the small size of the MNase enzyme relative to DNase I or Tn5 allows its access to relatively more condensed chromatin domains. CONCLUSION MNase can be used to identify open chromatin regions that are not accessible to DNase I or Tn5. Thus, MH-seq provides an important tool to identify and catalog all classes of open chromatin in plants.
Collapse
Affiliation(s)
- Hainan Zhao
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
| | - Wenli Zhang
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA.
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agriculture University, Nanjing, 210095, Jiangsu, China.
| | - Tao Zhang
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Key Laboratory of Plant Functional Genomics of Ministry of Education, Yangzhou University, Yangzhou, 225009, China
| | - Yuan Lin
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
| | - Yaodong Hu
- Department of Animal Sciences, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Chao Fang
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
| | - Jiming Jiang
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA.
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA.
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA.
- Michigan State University AgBioResearch, East Lansing, MI, 48824, USA.
| |
Collapse
|
3
|
Enhancers and chromatin structures: regulatory hubs in gene expression and diseases. Biosci Rep 2017; 37:BSR20160183. [PMID: 28351896 PMCID: PMC5408663 DOI: 10.1042/bsr20160183] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 02/23/2017] [Accepted: 03/27/2017] [Indexed: 12/14/2022] Open
Abstract
Gene expression requires successful communication between enhancer and promoter regions, whose activities are regulated by a variety of factors and associated with distinct chromatin structures; in addition, functionally related genes and their regulatory repertoire tend to be arranged in the same subchromosomal regulatory domains. In this review, we discuss the importance of enhancers, especially clusters of enhancers (such as super-enhancers), as key regulatory hubs to integrate environmental cues and encode spatiotemporal instructions for genome expression, which are critical for a variety of biological processes governing mammalian development. Furthermore, we emphasize that the enhancer–promoter interaction landscape provides a critical context to understand the aetiologies and mechanisms behind numerous complex human diseases and provides new avenues for effective transcription-based interventions.
Collapse
|