1
|
Bhatt T, Dey R, Hegde A, Ketkar AA, Pulianmackal AJ, Deb AP, Rampalli S, Jamora C. Initiation of wound healing is regulated by the convergence of mechanical and epigenetic cues. PLoS Biol 2022; 20:e3001777. [PMID: 36112666 PMCID: PMC9522318 DOI: 10.1371/journal.pbio.3001777] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 09/29/2022] [Accepted: 08/02/2022] [Indexed: 11/24/2022] Open
Abstract
Wound healing in the skin is a complex physiological process that is a product of a cell state transition from homeostasis to repair. Mechanical cues are increasingly being recognized as important regulators of cellular reprogramming, but the mechanism by which it is translated to changes in gene expression and ultimately cellular behavior remains largely a mystery. To probe the molecular underpinnings of this phenomenon further, we used the down-regulation of caspase-8 as a biomarker of a cell entering the wound healing program. We found that the wound-induced release of tension within the epidermis leads to the alteration of gene expression via the nuclear translocation of the DNA methyltransferase 3A (DNMT3a). This enzyme then methylates promoters of genes that are known to be down-regulated in response to wound stimuli as well as potentially novel players in the repair program. Overall, these findings illuminate the convergence of mechanical and epigenetic signaling modules that are important regulators of the transcriptome landscape required to initiate the tissue repair process in the differentiated layers of the epidermis. Wound healing in the skin is a complex physiological process that entails a cell state transition from homeostasis to repair. This study reveals a mechanism involving nuclear translocation of DNA methyltransferase 3A (DNMT3a) that initiates the wound-healing process and is perturbed in skin diseases such as psoriasis.
Collapse
Affiliation(s)
- Tanay Bhatt
- IFOM-inStem Joint Research Laboratory, Center for Inflammation and Tissue Homeostasis, Institute for Stem Cell Science and Regenerative Medicine, Bangalore, India
- National Centre for Biological Sciences, Bangalore, India
| | - Rakesh Dey
- IFOM-inStem Joint Research Laboratory, Center for Inflammation and Tissue Homeostasis, Institute for Stem Cell Science and Regenerative Medicine, Bangalore, India
| | - Akshay Hegde
- IFOM-inStem Joint Research Laboratory, Center for Inflammation and Tissue Homeostasis, Institute for Stem Cell Science and Regenerative Medicine, Bangalore, India
- School of Chemical and Biotechnology, SASTRA University, Thanjavur, Tamil Nadu, India
| | - Alhad Ashok Ketkar
- Center for Inflammation and Tissue Homeostasis, Institute for Stem Cell Science and Regenerative Medicine, Bangalore, India
| | - Ajai J. Pulianmackal
- IFOM-inStem Joint Research Laboratory, Center for Inflammation and Tissue Homeostasis, Institute for Stem Cell Science and Regenerative Medicine, Bangalore, India
| | - Ashim P. Deb
- IFOM-inStem Joint Research Laboratory, Center for Inflammation and Tissue Homeostasis, Institute for Stem Cell Science and Regenerative Medicine, Bangalore, India
| | - Shravanti Rampalli
- Center for Inflammation and Tissue Homeostasis, Institute for Stem Cell Science and Regenerative Medicine, Bangalore, India
| | - Colin Jamora
- IFOM-inStem Joint Research Laboratory, Center for Inflammation and Tissue Homeostasis, Institute for Stem Cell Science and Regenerative Medicine, Bangalore, India
- * E-mail:
| |
Collapse
|
2
|
Arasala RR, Jayaram M, Chattai J, Kumarasamy T, Sambasivan R, Rampalli S. Characterization of new variant human ES line VH9 hESC (INSTEMe001-a): a tool for human stem cell and cancer research. Stem Cell Res 2019; 37:101444. [PMID: 31075691 DOI: 10.1016/j.scr.2019.101444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 04/03/2019] [Accepted: 04/16/2019] [Indexed: 11/29/2022] Open
Abstract
Human pluripotent stem cells (hPSCs) acquire changes at the genomic level upon proliferation and differentiation (Peterson and Loring, 2014). Studies from International Stem Cell Initiative and independent laboratories identified a copy number variant (CNV) in hES cell lines displaying a normal karyotype, which provided a selective advantage to hES cells in culture. In our laboratory we have identified variant H9-hESC (derived from H9-hESC) with normal karyotype, pluripotency expression, differentiation profile but with altered traits of high cell survival and low E-CADHERIN expression.
Collapse
Affiliation(s)
- Radhika Rao Arasala
- Centre For Inflammation and Tissue Homeostasis, Institute For Stem Cell Biology and Regenerative Medicine, GKVK PO, Bellary Road, Bangalore 560065, India; Sastra University, Tirumalaisamudram, Thanjavur 613 401, TamilNadu, India
| | - Manjunath Jayaram
- Centre For Inflammation and Tissue Homeostasis, Institute For Stem Cell Biology and Regenerative Medicine, GKVK PO, Bellary Road, Bangalore 560065, India
| | - Jagamohan Chattai
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500007, India
| | | | - Ramkumar Sambasivan
- Centre For Inflammation and Tissue Homeostasis, Institute For Stem Cell Biology and Regenerative Medicine, GKVK PO, Bellary Road, Bangalore 560065, India
| | - Shravanti Rampalli
- Centre For Inflammation and Tissue Homeostasis, Institute For Stem Cell Biology and Regenerative Medicine, GKVK PO, Bellary Road, Bangalore 560065, India.
| |
Collapse
|
3
|
Rao RA, Ketkar AA, Kedia N, Krishnamoorthy VK, Lakshmanan V, Kumar P, Mohanty A, Kumar SD, Raja SO, Gulyani A, Chaturvedi CP, Brand M, Palakodeti D, Rampalli S. KMT1 family methyltransferases regulate heterochromatin-nuclear periphery tethering via histone and non-histone protein methylation. EMBO Rep 2019; 20:embr.201643260. [PMID: 30858340 PMCID: PMC6501005 DOI: 10.15252/embr.201643260] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 02/07/2019] [Accepted: 02/12/2019] [Indexed: 12/31/2022] Open
Abstract
Euchromatic histone methyltransferases (EHMTs), members of the KMT1 family, methylate histone and non-histone proteins. Here, we uncover a novel role for EHMTs in regulating heterochromatin anchorage to the nuclear periphery (NP) via non-histone methylation. We show that EHMTs methylate and stabilize LaminB1 (LMNB1), which associates with the H3K9me2-marked peripheral heterochromatin. Loss of LMNB1 methylation or EHMTs abrogates heterochromatin anchorage at the NP We further demonstrate that the loss of EHMTs induces many hallmarks of aging including global reduction of H3K27methyl marks and altered nuclear morphology. Consistent with this, we observe a gradual depletion of EHMTs, which correlates with loss of methylated LMNB1 and peripheral heterochromatin in aging human fibroblasts. Restoration of EHMT expression reverts peripheral heterochromatin defects in aged cells. Collectively, our work elucidates a new mechanism by which EHMTs regulate heterochromatin domain organization and reveals their impact on fundamental changes associated with the intrinsic aging process.
Collapse
Affiliation(s)
- Radhika Arasala Rao
- Centre For Inflammation and Tissue Homeostasis, Institute for Stem Cell Biology and Regenerative Medicine (inStem), Bangalore, Karnataka, India.,Sastra University, Tirumalaisamudram, Thanjavur, Tamilnadu, India
| | - Alhad Ashok Ketkar
- Centre For Inflammation and Tissue Homeostasis, Institute for Stem Cell Biology and Regenerative Medicine (inStem), Bangalore, Karnataka, India
| | - Neelam Kedia
- Centre For Inflammation and Tissue Homeostasis, Institute for Stem Cell Biology and Regenerative Medicine (inStem), Bangalore, Karnataka, India
| | - Vignesh K Krishnamoorthy
- Centre For Inflammation and Tissue Homeostasis, Institute for Stem Cell Biology and Regenerative Medicine (inStem), Bangalore, Karnataka, India
| | - Vairavan Lakshmanan
- Sastra University, Tirumalaisamudram, Thanjavur, Tamilnadu, India.,Technologies for the Advancement of Science, Institute for Stem Cell Biology and Regenerative Medicine (inStem), Bangalore, Karnataka, India
| | - Pankaj Kumar
- Centre For Inflammation and Tissue Homeostasis, Institute for Stem Cell Biology and Regenerative Medicine (inStem), Bangalore, Karnataka, India
| | - Abhishek Mohanty
- Centre For Inflammation and Tissue Homeostasis, Institute for Stem Cell Biology and Regenerative Medicine (inStem), Bangalore, Karnataka, India
| | - Shilpa Dilip Kumar
- Technologies for the Advancement of Science, Institute for Stem Cell Biology and Regenerative Medicine (inStem), Bangalore, Karnataka, India
| | - Sufi O Raja
- Technologies for the Advancement of Science, Institute for Stem Cell Biology and Regenerative Medicine (inStem), Bangalore, Karnataka, India
| | - Akash Gulyani
- Technologies for the Advancement of Science, Institute for Stem Cell Biology and Regenerative Medicine (inStem), Bangalore, Karnataka, India
| | - Chandra Prakash Chaturvedi
- Department of Hematology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - Marjorie Brand
- Sprott Centre for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Dasaradhi Palakodeti
- Technologies for the Advancement of Science, Institute for Stem Cell Biology and Regenerative Medicine (inStem), Bangalore, Karnataka, India
| | - Shravanti Rampalli
- Centre For Inflammation and Tissue Homeostasis, Institute for Stem Cell Biology and Regenerative Medicine (inStem), Bangalore, Karnataka, India
| |
Collapse
|
4
|
Szabo E, Rampalli S, Risueño RM, Schnerch A, Mitchell R, Fiebig-Comyn A, Levadoux-Martin M, Bhatia M. Author Correction: Direct conversion of human fibroblasts to multilineage blood progenitors. Nature 2018; 560:E32. [PMID: 30042505 DOI: 10.1038/s41586-018-0402-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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
In this Article, there were duplicated empty lanes in Supplementary Figs. 2e and 3b. The corrected figures are presented in the Supplementary Information to the accompanying Amendment. The original Article has not been corrected.
Collapse
Affiliation(s)
- Eva Szabo
- Stem Cell and Cancer Research Institute, McMaster University, Hamilton, Ontario, Canada, L8N 3Z5
| | - Shravanti Rampalli
- Stem Cell and Cancer Research Institute, McMaster University, Hamilton, Ontario, Canada, L8N 3Z5
| | - Ruth M Risueño
- Stem Cell and Cancer Research Institute, McMaster University, Hamilton, Ontario, Canada, L8N 3Z5
| | - Angelique Schnerch
- Stem Cell and Cancer Research Institute, McMaster University, Hamilton, Ontario, Canada, L8N 3Z5.,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada, L8N 3Z5
| | - Ryan Mitchell
- Stem Cell and Cancer Research Institute, McMaster University, Hamilton, Ontario, Canada, L8N 3Z5.,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada, L8N 3Z5
| | - Aline Fiebig-Comyn
- Stem Cell and Cancer Research Institute, McMaster University, Hamilton, Ontario, Canada, L8N 3Z5
| | - Marilyne Levadoux-Martin
- Stem Cell and Cancer Research Institute, McMaster University, Hamilton, Ontario, Canada, L8N 3Z5
| | - Mickie Bhatia
- Stem Cell and Cancer Research Institute, McMaster University, Hamilton, Ontario, Canada, L8N 3Z5. .,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada, L8N 3Z5.
| |
Collapse
|
5
|
Kaur R, Aiken C, Morrison LC, Rao R, Del Bigio MR, Rampalli S, Werbowetski-Ogilvie T. OTX2 exhibits cell-context-dependent effects on cellular and molecular properties of human embryonic neural precursors and medulloblastoma cells. Dis Model Mech 2015; 8:1295-309. [PMID: 26398939 PMCID: PMC4610233 DOI: 10.1242/dmm.020594] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 07/29/2015] [Indexed: 12/14/2022] Open
Abstract
Medulloblastoma (MB) is the most common malignant primary pediatric brain tumor and is currently divided into four subtypes based on different genomic alterations, gene expression profiles and response to treatment: WNT, Sonic Hedgehog (SHH), Group 3 and Group 4. This extensive heterogeneity has made it difficult to assess the functional relevance of genes to malignant progression. For example, expression of the transcription factor Orthodenticle homeobox2 (OTX2) is frequently dysregulated in multiple MB variants; however, its role may be subtype specific. We recently demonstrated that neural precursors derived from transformed human embryonic stem cells (trans-hENs), but not their normal counterparts (hENs), resemble Groups 3 and 4 MB in vitro and in vivo. Here, we tested the utility of this model system as a means of dissecting the role of OTX2 in MB using gain- and loss-of-function studies in hENs and trans-hENs, respectively. Parallel experiments with MB cells revealed that OTX2 exerts inhibitory effects on hEN and SHH MB cells by regulating growth, self-renewal and migration in vitro and tumor growth in vivo. This was accompanied by decreased expression of pluripotent genes, such as SOX2, and was supported by overexpression of SOX2 in OTX2+ SHH MB and hENs that resulted in significant rescue of self-renewal and cell migration. By contrast, OTX2 is oncogenic and promotes self-renewal of trans-hENs and Groups 3 and 4 MB independent of pluripotent gene expression. Our results demonstrate a novel role for OTX2 in self-renewal and migration of hENs and MB cells and reveal a cell-context-dependent link between OTX2 and pluripotent genes. Our study underscores the value of human embryonic stem cell derivatives as alternatives to cell lines and heterogeneous patient samples for investigating the contribution of key developmental regulators to MB progression. Summary: Human embryonic stem cell neural derivatives can be used to model the molecular and cellular properties of medulloblastoma.
Collapse
Affiliation(s)
- Ravinder Kaur
- Regenerative Medicine Program, Departments of Biochemistry & Medical Genetics and Physiology & Pathophysiology, University of Manitoba, Winnipeg, Manitoba, Canada, R3E 0J9
| | - Christopher Aiken
- Regenerative Medicine Program, Departments of Biochemistry & Medical Genetics and Physiology & Pathophysiology, University of Manitoba, Winnipeg, Manitoba, Canada, R3E 0J9
| | - Ludivine Coudière Morrison
- Regenerative Medicine Program, Departments of Biochemistry & Medical Genetics and Physiology & Pathophysiology, University of Manitoba, Winnipeg, Manitoba, Canada, R3E 0J9
| | - Radhika Rao
- Centre for Inflammation and Tissue Homeostasis, Institute for Stem Cell Biology and Regenerative Medicine (inStem), NCBS-TIFR Campus, GKVK PO, Bellary Road, Bangalore 560065, India
| | - Marc R Del Bigio
- Department of Pathology, University of Manitoba, 401 Brodie Centre, 727 McDermot Avenue, Winnipeg, Manitoba, Canada, R3E 3P5 Children's Hospital Research Institute of Manitoba, Winnipeg, Manitoba, Canada
| | - Shravanti Rampalli
- Centre for Inflammation and Tissue Homeostasis, Institute for Stem Cell Biology and Regenerative Medicine (inStem), NCBS-TIFR Campus, GKVK PO, Bellary Road, Bangalore 560065, India
| | - Tamra Werbowetski-Ogilvie
- Regenerative Medicine Program, Departments of Biochemistry & Medical Genetics and Physiology & Pathophysiology, University of Manitoba, Winnipeg, Manitoba, Canada, R3E 0J9
| |
Collapse
|
6
|
Kaur R, Aiken C, Morrison LC, Rao R, Del Bigio M, Rampalli S, Werbowetski-Ogilvie T. PM-01 * NEURAL DERIVATIVES FROM HUMAN EMBRYONIC STEM CELLS: A CELLULAR SYSTEM TO STUDY THE ROLE OF Otx2 IN MEDULLOBLASTOMA PROGRESSION. Neuro Oncol 2015. [DOI: 10.1093/neuonc/nov061.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
|
7
|
Abstract
Comment on: Hong SH, et al. Cell Stem Cell 2011; 9:24-36.
Collapse
|
8
|
Hong SH, Rampalli S, Lee JB, McNicol J, Collins T, Draper JS, Bhatia M. Cell fate potential of human pluripotent stem cells is encoded by histone modifications. Cell Stem Cell 2012; 9:24-36. [PMID: 21726831 DOI: 10.1016/j.stem.2011.06.002] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2010] [Revised: 05/09/2011] [Accepted: 06/02/2011] [Indexed: 02/02/2023]
Abstract
Human embryonic stem cells (hESCs) expressing pluripotency markers are assumed to possess equipotent developmental potential. However, disparate responses to differentiation stimuli functionally illustrate that hESCs generate a spectrum of differentiated cell types, suggestive of lineage bias. Here, we reveal specific cell surface markers that allow subfractionation of hESCs expressing hallmark markers of pluripotency. By direct de novo isolation of these subsets, we demonstrate that propensities for lineage differentiation are balanced with reduced clonogenic self-renewal. Histone modification marks of gene loci associated with pluripotency versus lineage specificity predicted cell fate potential of these subfractions, thereby supporting the absence of uniform bivalency as a molecular paradigm to describe cell fate determination of pluripotent cells. Our study reveals that cell fate potential is encoded within cells comprising hESC cultures, highlighting them as a means to understand the mechanisms of lineage specification of pluripotent cells.
Collapse
Affiliation(s)
- Seok-Ho Hong
- McMaster Stem Cell and Cancer Research Institute, Michael G. DeGroote School of Medicine, McMaster University, Hamilton, ON, Canada
| | | | | | | | | | | | | |
Collapse
|
9
|
Werbowetski-Ogilvie TE, Schnerch A, Rampalli S, Mills CE, Lee JB, Hong SH, Levadoux-Martin M, Bhatia M. Evidence for the transmission of neoplastic properties from transformed to normal human stem cells. Oncogene 2011; 30:4632-44. [PMID: 21625212 DOI: 10.1038/onc.2011.175] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The in vivo relationship between human tumor cells and interacting normal cells in their local environment is poorly understood. Here, using a uniquely developed in vitro co-culture system for human embryonic stem cells (hESCs), we examined the interactions between transformed and normal human stem cells. Co-culture of transformed-hESCs (t-hESCs) with normal hESCs led to enhanced self-renewal and niche independence in normal hESCs. Global gene expression analysis of normal hESCs after timed exposure to t-hESCs indicated a transition of the molecular network controlling the hESC state, which included epigenetic changes, towards neoplastic features. These included enhanced pluripotent marker expression and a differentiation blockade as major hallmark changes. Functional studies revealed a loss in normal terminal differentiation programs for both hematopoiesis and neural lineages after normal stem cell co-culture with transformed variants. This transmission of neoplastic properties from t-hESCs to normal hESCs was dependent on direct cell-cell contact. Our study indicates that normal human stem cells can co-opt neoplastic cancer stem cell properties, raising the possibility that assimilation of healthy cells towards neoplastic behavior maybe a contributing feature of sustained tumorigenesis in vivo.
Collapse
Affiliation(s)
- T E Werbowetski-Ogilvie
- McMaster Stem Cell and Cancer Research Institute, Michael G. Degroote School of Medicine, Department of Biochemistry, McMaster University, Hamilton, Ontario, Canada
| | | | | | | | | | | | | | | |
Collapse
|
10
|
Malonia SK, Sinha S, Lakshminarasimhan P, Singh K, Jalota-Badhwar A, Rampalli S, Kaul-Ghanekar R, Chattopadhyay S. Gene regulation by SMAR1: Role in cellular homeostasis and cancer. Biochim Biophys Acta Rev Cancer 2010; 1815:1-12. [PMID: 20709157 DOI: 10.1016/j.bbcan.2010.08.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2010] [Revised: 08/04/2010] [Accepted: 08/06/2010] [Indexed: 12/22/2022]
Abstract
Changes in the composition of nuclear matrix associated proteins contribute to alterations in nuclear structure, one of the major phenotypes of malignant cancer cells. The malignancy-induced changes in this structure lead to alterations in chromatin folding, the fidelity of genome replication and gene expression programs. The nuclear matrix forms a scaffold upon which the chromatin is organized into periodic loop domains called matrix attachment regions (MAR) by binding to various MAR binding proteins (MARBPs). Aberrant expression of MARBPs modulates the chromatin organization and disrupt transcriptional network that leads to oncogenesis. Dysregulation of nuclear matrix associated MARBPs has been reported in different types of cancers. Some of these proteins have tumor specific expression and are therefore considered as promising diagnostic or prognostic markers in few cancers. SMAR1 (scaffold/matrix attachment region binding protein 1), is one such nuclear matrix associated protein whose expression is drastically reduced in higher grades of breast cancer. SMAR1 gene is located on human chromosome 16q24.3 locus, the loss of heterozygosity (LOH) of which has been reported in several types of cancers. This review elaborates on the multiple roles of nuclear matrix associated protein SMAR1 in regulating various cellular target genes involved in cell growth, apoptosis and tumorigenesis.
Collapse
|
11
|
Seenundun S, Rampalli S, Liu QC, Aziz A, Palii C, Hong S, Blais A, Brand M, Ge K, Dilworth FJ. UTX mediates demethylation of H3K27me3 at muscle-specific genes during myogenesis. EMBO J 2010; 29:1401-11. [PMID: 20300060 PMCID: PMC2868576 DOI: 10.1038/emboj.2010.37] [Citation(s) in RCA: 168] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2009] [Accepted: 02/19/2010] [Indexed: 01/03/2023] Open
Abstract
Polycomb (PcG) and Trithorax (TrxG) group proteins act antagonistically to establish tissue-specific patterns of gene expression. The PcG protein Ezh2 facilitates repression by catalysing histone H3-Lys27 trimethylation (H3K27me3). For expression, H3K27me3 marks are removed and replaced by TrxG protein catalysed histone H3-Lys4 trimethylation (H3K4me3). Although H3K27 demethylases have been identified, the mechanism by which these enzymes are targeted to specific genomic regions to remove H3K27me3 marks has not been established. Here, we demonstrate a two-step mechanism for UTX-mediated demethylation at muscle-specific genes during myogenesis. Although the transactivator Six4 initially recruits UTX to the regulatory region of muscle genes, the resulting loss of H3K27me3 marks is limited to the region upstream of the transcriptional start site. Removal of the repressive H3K27me3 mark within the coding region then requires RNA Polymerase II (Pol II) elongation. Interestingly, blocking Pol II elongation on transcribed genes leads to increased H3K27me3 within the coding region, and formation of bivalent (H3K27me3/H3K4me3) chromatin domains. Thus, removal of repressive H3K27me3 marks by UTX occurs through targeted recruitment followed by spreading across the gene.
Collapse
Affiliation(s)
- Shayesta Seenundun
- Regenerative Medicine Program, Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
| | | | | | | | | | | | | | | | | | | |
Collapse
|
12
|
Rampalli S, Li L, Mak E, Ge K, Brand M, Tapscott SJ, Dilworth FJ. p38 MAPK signaling regulates recruitment of Ash2L-containing methyltransferase complexes to specific genes during differentiation. Nat Struct Mol Biol 2007; 14:1150-6. [PMID: 18026121 DOI: 10.1038/nsmb1316] [Citation(s) in RCA: 177] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2007] [Accepted: 09/19/2007] [Indexed: 02/07/2023]
Abstract
Cell-specific patterns of gene expression are established through the antagonistic functions of trithorax group (TrxG) and Polycomb group (PcG) proteins. Several muscle-specific genes have previously been shown to be epigenetically marked for repression by PcG proteins in muscle progenitor cells. Here we demonstrate that these developmentally regulated genes become epigenetically marked for gene expression (trimethylated on histone H3 Lys4, H3K4me3) during muscle differentiation through specific recruitment of Ash2L-containing methyltransferase complexes. Targeting of Ash2L to specific genes is mediated by the transcriptional regulator Mef2d. Furthermore, this interaction is modulated during differentiation through activation of the p38 MAPK signaling pathway via phosphorylation of Mef2d. Thus, we provide evidence that signaling pathways regulate the targeting of TrxG-mediated epigenetic modifications at specific promoters during cellular differentiation.
Collapse
Affiliation(s)
- Shravanti Rampalli
- Sprott Center for Stem Cell Research, Ottawa Health Research Institute, Ottawa, Ontario K1H 8L6, Canada
| | | | | | | | | | | | | |
Collapse
|
13
|
Pavithra L, Rampalli S, Sinha S, Sreenath K, Pestell RG, Chattopadhyay S. Stabilization of SMAR1 mRNA by PGA2 involves a stem loop structure in the 5' UTR. Nucleic Acids Res 2007; 35:6004-16. [PMID: 17726044 PMCID: PMC2094063 DOI: 10.1093/nar/gkm649] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2007] [Revised: 08/03/2007] [Accepted: 08/03/2007] [Indexed: 02/06/2023] Open
Abstract
Prostaglandins are anticancer agents known to inhibit tumor cell proliferation both in vitro and in vivo by affecting the mRNA stability. Here we report that a MAR-binding protein SMAR1 is a target of Prostaglandin A2 (PGA2) induced growth arrest. We identify a regulatory mechanism leading to stabilization of SMAR1 transcript. Our results show that a minor stem and loop structure present in the 5' UTR of SMAR1 (1-UTR) is critical for nucleoprotein complex formation that leads to SMAR1 stabilization in response to PGA2. This results in an increased SMAR1 transcript and altered protein levels, that in turn causes downregulation of Cyclin D1 gene, essential for G1/S phase transition. We also provide evidence for the presence of a variant 5' UTR SMAR1 (17-UTR) in breast cancer-derived cell lines. This form lacks the minor stem and loop structure required for mRNA stabilization in response to PGA2. As a consequence of this, there is a low level of endogenous tumor suppressor protein SMAR1 in breast cancer-derived cell lines. Our studies provide a mechanistic insight into the regulation of tumor suppressor protein SMAR1 by a cancer therapeutic PGA2, that leads to repression of Cyclin D1 gene.
Collapse
Affiliation(s)
- Lakshminarasimhan Pavithra
- National Centre for Cell Science, Ganeshkhind, Pune 411007, Maharashtra, India and Department of Cancer Biology, Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, USA
| | - Shravanti Rampalli
- National Centre for Cell Science, Ganeshkhind, Pune 411007, Maharashtra, India and Department of Cancer Biology, Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, USA
| | - Surajit Sinha
- National Centre for Cell Science, Ganeshkhind, Pune 411007, Maharashtra, India and Department of Cancer Biology, Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, USA
| | - Kadreppa Sreenath
- National Centre for Cell Science, Ganeshkhind, Pune 411007, Maharashtra, India and Department of Cancer Biology, Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, USA
| | - Richard G. Pestell
- National Centre for Cell Science, Ganeshkhind, Pune 411007, Maharashtra, India and Department of Cancer Biology, Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, USA
| | - Samit Chattopadhyay
- National Centre for Cell Science, Ganeshkhind, Pune 411007, Maharashtra, India and Department of Cancer Biology, Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, USA
| |
Collapse
|
14
|
Rampalli S, Pavithra L, Bhatt A, Kundu TK, Chattopadhyay S. Tumor suppressor SMAR1 mediates cyclin D1 repression by recruitment of the SIN3/histone deacetylase 1 complex. Mol Cell Biol 2005; 25:8415-29. [PMID: 16166625 PMCID: PMC1265755 DOI: 10.1128/mcb.25.19.8415-8429.2005] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Matrix attachment region binding proteins have been shown to play an important role in gene regulation by altering chromatin in a stage- and tissue-specific manner. Our previous studies report that SMAR1, a matrix-associated protein, regresses B16-F1-induced tumors in mice. Here we show SMAR1 targets the cyclin D1 promoter, a gene product whose dysregulation is attributed to breast malignancies. Our studies reveal that SMAR1 represses cyclin D1 gene expression, which can be reversed by small interfering RNA specific to SMAR1. We demonstrate that SMAR1 interacts with histone deacetylation complex 1, SIN3, and pocket retinoblastomas to form a multiprotein repressor complex. This interaction is mediated by the SMAR1(160-350) domain. Our data suggest SMAR1 recruits a repressor complex to the cyclin D1 promoter that results in deacetylation of chromatin at that locus, which spreads to a distance of at least the 5 kb studied upstream of the cyclin D1 promoter. Interestingly, we find that the high induction of cyclin D1 in breast cancer cell lines can be correlated to the decreased levels of SMAR1 in these lines. Our results establish the molecular mechanism exhibited by SMAR1 to regulate cyclin D1 by modification of chromatin.
Collapse
Affiliation(s)
- Shravanti Rampalli
- National Center for Cell Science, Pune University Campus, Ganeshkhind, Pune 411007, India
| | | | | | | | | |
Collapse
|
15
|
Kulkarni A, Ravi DS, Singh K, Rampalli S, Parekh V, Mitra D, Chattopadhyay S. HIV-1 Tat modulates T-bet expression and induces Th1 type of immune response. Biochem Biophys Res Commun 2005; 329:706-12. [PMID: 15737643 DOI: 10.1016/j.bbrc.2005.02.042] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2004] [Indexed: 11/18/2022]
Abstract
The HIV-1 transactivator Tat performs various viral and cellular functions. Primarily, it induces processive transcription from the HIV-1 LTR promoter. However, Tat secreted from infected cells is known to activate uninfected lymphocytes through receptors. To further delineate the specific target genes, extracellular Tat was expressed on the cell membrane of stimulator cells and co-cultured with human PBMCs. Along with induced CD4(+) T cell proliferation and IFN-gamma secretion, there was strong upregulation of T-bet expression which is majorly implicated in generating T(H)1 type of immune response. To further delineate the effect of extracellular Tat on HIV replication, both p24 analysis and in vivo GFP expression were performed. There was a significant inhibition of HIV-1 replication in human CEM-GFP cell line and hPBMCs. Thus, for the first time we report that apart from its transactivation activity, extracellular Tat acts as a costimulatory molecule that affects viral replication by modulating host immune response through induction of T-bet expression and IFN-gamma secretion.
Collapse
Affiliation(s)
- Asavari Kulkarni
- National Center for Cell Science, Pune University Campus, Ganeshkhind, Pune 411 007, India
| | | | | | | | | | | | | |
Collapse
|
16
|
Kulkarni A, Pavithra L, Rampalli S, Mogare D, Babu K, Shiekh G, Ghosh S, Chattopadhyay S. HIV-1 integration sites are flanked by potential MARs that alone can act as promoters. Biochem Biophys Res Commun 2004; 322:672-7. [PMID: 15325282 DOI: 10.1016/j.bbrc.2004.07.170] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2004] [Indexed: 10/26/2022]
Abstract
Matrix attachment regions (MARs) are cis regulatory elements that modulate gene expression in a tissue and cell stage specific manner. Recent reports show that viral integration within the genome takes place at nonrandom active genes. We have checked for the presence of MARs in the vicinity of the reported 524 HIV-1 integration sites. Our studies show that in 92.5% cases, MARs flank the integration sites. Similarly, for adeno-associated virus, two potential MARs were present next to the integration site on the human chromosome. Earlier we have shown that short MAR sequences present upstream of HIV-1 LTR promote processive transcription at a distance. Here, using a well-studied IgH-MAR and another potential MAR from p53 promoter, we demonstrate that MARs alone can act as promoters. Thus, we propose that MAR elements near the HIV-1 integration sites can act as potential promoters, which may facilitate proviral integration and transcription.
Collapse
Affiliation(s)
- Asavari Kulkarni
- National Center for Cell Science, Pune University Campus, Ganeshkhind, Pune-411 007, India
| | | | | | | | | | | | | | | |
Collapse
|
17
|
Jiang L, Rampalli S, George D, Press C, Bremer EG, O'Gorman MRG, Bohn MC. Tight regulation from a single tet-off rAAV vector as demonstrated by flow cytometry and quantitative, real-time PCR. Gene Ther 2004; 11:1057-67. [PMID: 15152187 DOI: 10.1038/sj.gt.3302245] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Vectors suitable for delivery of therapeutic genes to the CNS for chronic neurodegenerative diseases will require regulatable transgene expression. In this study, three self-regulating rAAV vectors encoding humanized green fluorescent protein (hGFP) were made using the tetracycline (tet)-off system. Elements were cloned in different orientations relative to each other and to the AAV internal terminal repeat (ITRs). The advantage of this vector system is that all infected cells will carry both the 'therapeutic' gene and the tet-regulator. To compare the efficiency of the vectors, 293T cells infected by each vector were grown in the presence or absence of the tet-analog doxycycline (dox). Cells were analyzed by flow cytometry for hGFP protein expression, and quantitative RT-PCR (QRT-PCR) for levels of hGFP mRNA and the tet-activator (tTA) mRNA. In the presence of dox, cells infected with one of the vectors, rAAVS3, showed less than 2% total fluorescent intensity and mRNA copy number than cells grown without dox. The other two vectors were significantly more leaky. Levels of tTA mRNA were not affected by dox. The S3 vector also displayed tight regulation in HeLa and HT1080 cells. To assess regulation in the brain, the S3 vector was injected into rat striatum and rats maintained on regular or dox-supplemented water. At 1 month after vector injection, numerous positive cells were observed in rats maintained on regular water whereas only rare positive cells with very low levels of fluorescence were observed in rats maintained on water containing dox. The QRT-PCR analysis showed that dox inhibited expression of hGFP mRNA in brain by greater than 99%. These results demonstrate that exceedingly tight regulation of transgene expression is possible using the tet-off system in the context of a self-regulating rAAV vector and that the specific orientation of two promoters relative to each other and to the ITRs is important. Regulatable vectors based on this design are ideal for therapeutic gene delivery to the CNS.
Collapse
Affiliation(s)
- L Jiang
- 1Department of Pediatrics, Children's Memorial Institute for Education & Research, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | | | | | | | | | | | | |
Collapse
|
18
|
Rampalli S, Kulkarni A, Kumar P, Mogare D, Galande S, Mitra D, Chattopadhyay S. Stimulation of Tat-independent transcriptional processivity from the HIV-1 LTR promoter by matrix attachment regions. Nucleic Acids Res 2003; 31:3248-56. [PMID: 12799452 PMCID: PMC162244 DOI: 10.1093/nar/gkg410] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The chromatin environment and the sites of integration in the host genome are critical determinants of human immunodeficiency virus (HIV) transcription and replication. Depending on the chromosomal location of provirus integration within the genome, HIV-1 long terminal repeat (LTR)-mediated transcription may vary from 0- to 70-fold. Cis-elements such as topoisomerase II cleavage sites, Alu repeats and matrix attachment regions (MARs) are thought to be targets for retroviral integration. Here we show that a novel MAR sequence from the T-cell receptor beta locus (MARbeta) and the IgH MAR mediate transcriptional augmentation when placed upstream of the HIV-1 LTR promoter. The effect of transcriptional augmentation is seen in both transient and stable transfection, indicating its effect even upon integration in the genome. MAR-mediated transcriptional elevation is independent of Tat, and occurs synergistically in the presence of Tat. Further, we show that MAR-mediated transcriptional elevation is specific to the HIV-1 LTR and the Moloney murine leukemia virus LTR promoter. In a transient transfection assay using over-expressed IkappaB, the inhibitor of NF-kappaB, we show that MAR-induced processive transcription is NF-kappaB dependent, signifying the role of local enhancers within the LTR promoter. Furthermore, by RNase protection experiments using proximal and distal probes, we show that MAR-mediated transcriptional upregulation is more prominent at the distal rather than the proximal end, thus indicating the potential role of MARs in promoting elongation.
Collapse
Affiliation(s)
- Shravanti Rampalli
- National Center for Cell Science, Pune University Campus, Ganeshkhind, Pune 411007, India
| | | | | | | | | | | | | |
Collapse
|
19
|
Bhowmick AK, Rampalli S, Gallagher K, Seeger R, McIntyre D. The degradation of guayule rubber and the effect of resin components on degradation at high temperature. J Appl Polym Sci 1987. [DOI: 10.1002/app.1987.070330407] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
20
|
|