1
|
Gui T, Fleming C, Manzato C, Bourgeois B, Sirati N, Heuer J, Papadionysiou I, Montfort DIV, Gijzen MV, Smits LMM, Burgering BMT, Madl T, Schuijers J. Targeted perturbation of signaling-driven condensates. Mol Cell 2023; 83:4141-4157.e11. [PMID: 37977121 DOI: 10.1016/j.molcel.2023.10.023] [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: 07/28/2023] [Revised: 09/27/2023] [Accepted: 10/17/2023] [Indexed: 11/19/2023]
Abstract
Biomolecular condensates have emerged as a major organizational principle in the cell. However, the formation, maintenance, and dissolution of condensates are still poorly understood. Transcriptional machinery partitions into biomolecular condensates at key cell identity genes to activate these. Here, we report a specific perturbation of WNT-activated β-catenin condensates that disrupts oncogenic signaling. We use a live-cell condensate imaging method in human cancer cells to discover FOXO and TCF-derived peptides that specifically inhibit β-catenin condensate formation on DNA, perturb nuclear β-catenin condensates in cells, and inhibit β-catenin-driven transcriptional activation and colorectal cancer cell growth. We show that these peptides compete with homotypic intermolecular interactions that normally drive condensate formation. Using this framework, we derive short peptides that specifically perturb condensates and transcriptional activation of YAP and TAZ in the Hippo pathway. We propose a "monomer saturation" model in which short interacting peptides can be used to specifically inhibit condensate-associated transcription in disease.
Collapse
Affiliation(s)
- Tianshu Gui
- Center for Molecular Medicine, University Medical Center Utrecht, 3584 CG Utrecht, the Netherlands; Oncode Institute, 3721 AL Utrecht, the Netherlands
| | - Cassio Fleming
- Center for Molecular Medicine, University Medical Center Utrecht, 3584 CG Utrecht, the Netherlands
| | - Caterina Manzato
- Center for Molecular Medicine, University Medical Center Utrecht, 3584 CG Utrecht, the Netherlands
| | - Benjamin Bourgeois
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, 8010 Graz, Austria
| | - Nafiseh Sirati
- Center for Molecular Medicine, University Medical Center Utrecht, 3584 CG Utrecht, the Netherlands
| | - Jasper Heuer
- Center for Molecular Medicine, University Medical Center Utrecht, 3584 CG Utrecht, the Netherlands
| | - Ioanna Papadionysiou
- Center for Molecular Medicine, University Medical Center Utrecht, 3584 CG Utrecht, the Netherlands
| | - Daniel I van Montfort
- Center for Molecular Medicine, University Medical Center Utrecht, 3584 CG Utrecht, the Netherlands
| | - Merel van Gijzen
- Center for Molecular Medicine, University Medical Center Utrecht, 3584 CG Utrecht, the Netherlands
| | - Lydia M M Smits
- Center for Molecular Medicine, University Medical Center Utrecht, 3584 CG Utrecht, the Netherlands
| | - Boudewijn M T Burgering
- Center for Molecular Medicine, University Medical Center Utrecht, 3584 CG Utrecht, the Netherlands; Oncode Institute, 3721 AL Utrecht, the Netherlands
| | - Tobias Madl
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, 8010 Graz, Austria; BioTechMed-Graz, 8010 Graz, Austria
| | - Jurian Schuijers
- Center for Molecular Medicine, University Medical Center Utrecht, 3584 CG Utrecht, the Netherlands; Oncode Institute, 3721 AL Utrecht, the Netherlands.
| |
Collapse
|
2
|
Appelman MD, Hollaar EE, Schuijers J, van Mil SWC. Protein Condensation in the Nuclear Receptor Family; Implications for Transcriptional Output. Advances in Experimental Medicine and Biology 2022; 1390:243-253. [DOI: 10.1007/978-3-031-11836-4_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
|
3
|
Shrinivas K, Sabari BR, Coffey EL, Klein IA, Boija A, Zamudio AV, Schuijers J, Hannett NM, Sharp PA, Young RA, Chakraborty AK. Enhancer Features that Drive Formation of Transcriptional Condensates. Mol Cell 2020; 75:549-561.e7. [PMID: 31398323 DOI: 10.1016/j.molcel.2019.07.009] [Citation(s) in RCA: 212] [Impact Index Per Article: 53.0] [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: 12/15/2018] [Revised: 03/31/2019] [Accepted: 07/08/2019] [Indexed: 12/12/2022]
Abstract
Enhancers are DNA elements that are bound by transcription factors (TFs), which recruit coactivators and the transcriptional machinery to genes. Phase-separated condensates of TFs and coactivators have been implicated in assembling the transcription machinery at particular enhancers, yet the role of DNA sequence in this process has not been explored. We show that DNA sequences encoding TF binding site number, density, and affinity above sharply defined thresholds drive condensation of TFs and coactivators. A combination of specific structured (TF-DNA) and weak multivalent (TF-coactivator) interactions allows for condensates to form at particular genomic loci determined by the DNA sequence and the complement of expressed TFs. DNA features found to drive condensation promote enhancer activity and transcription in cells. Our study provides a framework to understand how the genome can scaffold transcriptional condensates at specific loci and how the universal phenomenon of phase separation might regulate this process.
Collapse
Affiliation(s)
- Krishna Shrinivas
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Benjamin R Sabari
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA
| | - Eliot L Coffey
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Isaac A Klein
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Ann Boija
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA
| | - Alicia V Zamudio
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jurian Schuijers
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA
| | - Nancy M Hannett
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA
| | - Phillip A Sharp
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Richard A Young
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Arup K Chakraborty
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, USA; Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| |
Collapse
|
4
|
Zamudio AV, Dall'Agnese A, Henninger JE, Manteiga JC, Afeyan LK, Hannett NM, Coffey EL, Li CH, Oksuz O, Sabari BR, Boija A, Klein IA, Hawken SW, Spille JH, Decker TM, Cisse II, Abraham BJ, Lee TI, Taatjes DJ, Schuijers J, Young RA. Mediator Condensates Localize Signaling Factors to Key Cell Identity Genes. Mol Cell 2019; 76:753-766.e6. [PMID: 31563432 DOI: 10.1016/j.molcel.2019.08.016] [Citation(s) in RCA: 150] [Impact Index Per Article: 30.0] [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: 02/14/2019] [Revised: 06/14/2019] [Accepted: 08/16/2019] [Indexed: 01/09/2023]
Abstract
The gene expression programs that define the identity of each cell are controlled by master transcription factors (TFs) that bind cell-type-specific enhancers, as well as signaling factors, which bring extracellular stimuli to these enhancers. Recent studies have revealed that master TFs form phase-separated condensates with the Mediator coactivator at super-enhancers. Here, we present evidence that signaling factors for the WNT, TGF-β, and JAK/STAT pathways use their intrinsically disordered regions (IDRs) to enter and concentrate in Mediator condensates at super-enhancers. We show that the WNT coactivator β-catenin interacts both with components of condensates and DNA-binding factors to selectively occupy super-enhancer-associated genes. We propose that the cell-type specificity of the response to signaling is mediated in part by the IDRs of the signaling factors, which cause these factors to partition into condensates established by the master TFs and Mediator at genes with prominent roles in cell identity.
Collapse
Affiliation(s)
- Alicia V Zamudio
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | | | - John C Manteiga
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Lena K Afeyan
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Nancy M Hannett
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Eliot L Coffey
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Charles H Li
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ozgur Oksuz
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Benjamin R Sabari
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Ann Boija
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Isaac A Klein
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Susana W Hawken
- Program in Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jan-Hendrik Spille
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Tim-Michael Decker
- Department of Biochemistry, University of Colorado, Boulder, Boulder, CO 80303, USA
| | - Ibrahim I Cisse
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Brian J Abraham
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Tong I Lee
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Dylan J Taatjes
- Department of Biochemistry, University of Colorado, Boulder, Boulder, CO 80303, USA
| | - Jurian Schuijers
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.
| | - Richard A Young
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| |
Collapse
|
5
|
Boija A, Klein IA, Sabari BR, Dall'Agnese A, Coffey EL, Zamudio AV, Li CH, Shrinivas K, Manteiga JC, Hannett NM, Abraham BJ, Afeyan LK, Guo YE, Rimel JK, Fant CB, Schuijers J, Lee TI, Taatjes DJ, Young RA. Transcription Factors Activate Genes through the Phase-Separation Capacity of Their Activation Domains. Cell 2018; 175:1842-1855.e16. [PMID: 30449618 PMCID: PMC6295254 DOI: 10.1016/j.cell.2018.10.042] [Citation(s) in RCA: 952] [Impact Index Per Article: 158.7] [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: 06/12/2018] [Revised: 08/20/2018] [Accepted: 10/16/2018] [Indexed: 01/19/2023]
Abstract
Gene expression is controlled by transcription factors (TFs) that consist of DNA-binding domains (DBDs) and activation domains (ADs). The DBDs have been well characterized, but little is known about the mechanisms by which ADs effect gene activation. Here, we report that diverse ADs form phase-separated condensates with the Mediator coactivator. For the OCT4 and GCN4 TFs, we show that the ability to form phase-separated droplets with Mediator in vitro and the ability to activate genes in vivo are dependent on the same amino acid residues. For the estrogen receptor (ER), a ligand-dependent activator, we show that estrogen enhances phase separation with Mediator, again linking phase separation with gene activation. These results suggest that diverse TFs can interact with Mediator through the phase-separating capacity of their ADs and that formation of condensates with Mediator is involved in gene activation.
Collapse
Affiliation(s)
- Ann Boija
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Isaac A Klein
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Benjamin R Sabari
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | | | - Eliot L Coffey
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Alicia V Zamudio
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Charles H Li
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Krishna Shrinivas
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Institute of Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - John C Manteiga
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Nancy M Hannett
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Brian J Abraham
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Lena K Afeyan
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Yang E Guo
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Jenna K Rimel
- Department of Biochemistry, University of Colorado, Boulder, CO 80303, USA
| | - Charli B Fant
- Department of Biochemistry, University of Colorado, Boulder, CO 80303, USA
| | - Jurian Schuijers
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Tong Ihn Lee
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Dylan J Taatjes
- Department of Biochemistry, University of Colorado, Boulder, CO 80303, USA
| | - Richard A Young
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| |
Collapse
|
6
|
Sabari BR, Dall'Agnese A, Boija A, Klein IA, Coffey EL, Shrinivas K, Abraham BJ, Hannett NM, Zamudio AV, Manteiga JC, Li CH, Guo YE, Day DS, Schuijers J, Vasile E, Malik S, Hnisz D, Lee TI, Cisse II, Roeder RG, Sharp PA, Chakraborty AK, Young RA. Coactivator condensation at super-enhancers links phase separation and gene control. Science 2018; 361:eaar3958. [PMID: 29930091 PMCID: PMC6092193 DOI: 10.1126/science.aar3958] [Citation(s) in RCA: 1356] [Impact Index Per Article: 226.0] [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] [Received: 11/04/2017] [Revised: 04/09/2018] [Accepted: 06/06/2018] [Indexed: 12/15/2022]
Abstract
Super-enhancers (SEs) are clusters of enhancers that cooperatively assemble a high density of the transcriptional apparatus to drive robust expression of genes with prominent roles in cell identity. Here we demonstrate that the SE-enriched transcriptional coactivators BRD4 and MED1 form nuclear puncta at SEs that exhibit properties of liquid-like condensates and are disrupted by chemicals that perturb condensates. The intrinsically disordered regions (IDRs) of BRD4 and MED1 can form phase-separated droplets, and MED1-IDR droplets can compartmentalize and concentrate the transcription apparatus from nuclear extracts. These results support the idea that coactivators form phase-separated condensates at SEs that compartmentalize and concentrate the transcription apparatus, suggest a role for coactivator IDRs in this process, and offer insights into mechanisms involved in the control of key cell-identity genes.
Collapse
Affiliation(s)
- Benjamin R Sabari
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA
| | | | - Ann Boija
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA
| | - Isaac A Klein
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Eliot L Coffey
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Krishna Shrinivas
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Brian J Abraham
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA
| | - Nancy M Hannett
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA
| | - Alicia V Zamudio
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - John C Manteiga
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Charles H Li
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Yang E Guo
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA
| | - Daniel S Day
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA
| | - Jurian Schuijers
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA
| | - Eliza Vasile
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sohail Malik
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA
| | - Denes Hnisz
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA
| | - Tong Ihn Lee
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA
| | - Ibrahim I Cisse
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Robert G Roeder
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA
| | - Phillip A Sharp
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Arup K Chakraborty
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard, Cambridge, MA 02139, USA
| | - Richard A Young
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| |
Collapse
|
7
|
Abraham BJ, Guo YE, Hnisz D, Li CH, Weintraub AS, Day DS, Schuijers J, Lee TI, Young RA. Abstract 971: Three-dimensional gene regulatory landscapes in normal and cancer cells. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-971] [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: 11/16/2022]
Abstract
Abstract
Key oncogenes can be misregulated in tumor cells by the acquisition of tumor-specific enhancers that direct gene expression through physical contacts (1,2). Identifying the full complement of enhancers regulating each oncogene could identify additional vulnerabilities in tumor expression programs, but remains challenging, because a given enhancer can regulate multiple genes and each of its targets may be genomically distant. Here we use DNA interaction data to construct gene regulatory landscapes for all expressed genes in a tumor cell and demonstrate that sets of enhancers can be assigned to these oncogenes using direct looping and insulated neighborhood data. A subset of these landscapes contains an exceptional amount of transcriptional apparatus, reminiscent of SEs (3), so we term this subset 3D-SEs. Well-characterized oncogenes, including c-Myc, acquire 3D-SEs in tumor cells where a c-Myc¬-associated linear SE was not identified, suggesting SE acquisition by c-Myc and other oncogenes has been underestimated. Each gene's regulatory network can also surprisingly extend beyond the confines of insulated neighborhoods and incorporate additional distal enhancers. Visualizing instances of 3D-SEs with microscopy demonstrates that they are components of liquid-liquid phase-separated bodies in cells, suggesting gene regulatory landscapes underpin these transcriptional condensates. The interactions comprising gene regulatory networks and their target genes thus extend previous interpretations of the targets of enhancers, signaling pathways, and disease-associated enhancer variants.
References: 1. Hnisz, Abraham, Lee, et al. and Young, Cell 2013. 2. Mansour, Abraham, et al. and Young and Look, Science 2014. 3. Whyte, Orlando, Hnisz, Abraham, et al. and Young, Cell 2013.
Citation Format: Brian J. Abraham, Yang Eric Guo, Denes Hnisz, Charles H. Li, Abraham S. Weintraub, Daniel S. Day, Jurian Schuijers, Tong Ihn Lee, Richard A. Young. Three-dimensional gene regulatory landscapes in normal and cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 971.
Collapse
Affiliation(s)
| | - Yang Eric Guo
- MIT Whitehead Inst. for Biomedical Research, Cambridge, MA
| | - Denes Hnisz
- MIT Whitehead Inst. for Biomedical Research, Cambridge, MA
| | - Charles H. Li
- MIT Whitehead Inst. for Biomedical Research, Cambridge, MA
| | | | - Daniel S. Day
- MIT Whitehead Inst. for Biomedical Research, Cambridge, MA
| | | | - Tong Ihn Lee
- MIT Whitehead Inst. for Biomedical Research, Cambridge, MA
| | | |
Collapse
|
8
|
Abstract
Cancer arises from genetic alterations that produce dysregulated gene expression programs. Normal gene regulation occurs in the context of chromosome loop structures called insulated neighborhoods, and recent studies have shown that these structures are altered and can contribute to oncogene dysregulation in various cancer cells. We review the types of genetic and epigenetic alterations that influence neighborhood structures and contribute to gene dysregulation in cancer, present models for insulated neighborhoods associated with the most prominent human oncogenes, and discuss how such models may lead to further advances in cancer diagnosis and therapy.
Collapse
Affiliation(s)
- Denes Hnisz
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA;,
| | - Jurian Schuijers
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA;,
| | - Charles H. Li
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA;,
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Richard A. Young
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA;,
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| |
Collapse
|
9
|
Schuijers J, Day DS, Saint-Andre V, Young RA. Abstract PR01: 3D enhancer clusters in the response to Wnt-driven colorectal cancer. Mol Cancer Res 2016. [DOI: 10.1158/1557-3125.devbiolca15-pr01] [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: 11/16/2022]
Abstract
Abstract
Super-enhancers are clusters of enhancers that drive expression of genes key to development and cancer. We recently showed that super-enhancers and their target genes occur within DNA loops bounded by CTCF proteins. These chromosome structures constrain the activities of enhancers to genes that occur within the same loop, and were thus called insulated neighborhoods. Recent studies have shown that signaling pathways converge on super-enhancers, but the effect of signaling-mediated gene activation has yet to be investigated in the context of insulated neighborhood structure and function. We used a model of Wnt-pathway activation in colon cancer to investigate Wnt-mediated activation of target genes within insulated neighborhoods. When the Wnt-pathway was activated through genetic deletion of the tumor suppressor Apc in intestinal organoids, all enhancers within insulated neighborhoods that contained Tcf4 binding sites were activated, including enhancers that were not considered to contribute to super-enhancers. Thus, Wnt-stimulation co-activated multiple enhancers that are not in linear proximity, yet cluster in 3D space within insulated neighborhoods. We conclude that insulated neighborhoods allow the formation of 3D enhancer clusters whose constituents can operate concertedly, and thus expand the definition of super-enhancers to incorporate 3D chromatin organization.
This abstract is also presented as Poster A15.
Citation Format: Jurian Schuijers, Daniel S. Day, Violaine Saint-Andre, Richard A. Young. 3D enhancer clusters in the response to Wnt-driven colorectal cancer. [abstract]. In: Proceedings of the AACR Special Conference: Developmental Biology and Cancer; Nov 30-Dec 3, 2015; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Res 2016;14(4_Suppl):Abstract nr PR01.
Collapse
Affiliation(s)
| | - Daniel S. Day
- Whitehead Institute for Biomedical Research, Cambridge, MA
| | | | | |
Collapse
|
10
|
Hnisz D, Schuijers J, Lin CY, Weintraub AS, Abraham BJ, Lee TI, Bradner JE, Young RA. Convergence of developmental and oncogenic signaling pathways at transcriptional super-enhancers. Mol Cell 2015; 58:362-70. [PMID: 25801169 DOI: 10.1016/j.molcel.2015.02.014] [Citation(s) in RCA: 326] [Impact Index Per Article: 36.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Revised: 12/17/2014] [Accepted: 02/05/2015] [Indexed: 12/19/2022]
Abstract
Super-enhancers and stretch enhancers (SEs) drive expression of genes that play prominent roles in normal and disease cells, but the functional importance of these clustered enhancer elements is poorly understood, so it is not clear why genes key to cell identity have evolved regulation by such elements. Here, we show that SEs consist of functional constituent units that concentrate multiple developmental signaling pathways at key pluripotency genes in embryonic stem cells and confer enhanced responsiveness to signaling of their associated genes. Cancer cells frequently acquire SEs at genes that promote tumorigenesis, and we show that these genes are especially sensitive to perturbation of oncogenic signaling pathways. Super-enhancers thus provide a platform for signaling pathways to regulate genes that control cell identity during development and tumorigenesis.
Collapse
Affiliation(s)
- Denes Hnisz
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
| | - Jurian Schuijers
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
| | - Charles Y Lin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Abraham S Weintraub
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Brian J Abraham
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
| | - Tong Ihn Lee
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
| | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Richard A Young
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| |
Collapse
|
11
|
Schuijers J, Junker JP, Mokry M, Hatzis P, Koo BK, Sasselli V, van der Flier LG, Cuppen E, van Oudenaarden A, Clevers H. Ascl2 acts as an R-spondin/Wnt-responsive switch to control stemness in intestinal crypts. Cell Stem Cell 2015; 16:158-70. [PMID: 25620640 DOI: 10.1016/j.stem.2014.12.006] [Citation(s) in RCA: 182] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 11/18/2014] [Accepted: 12/17/2014] [Indexed: 01/14/2023]
Abstract
The Wnt signaling pathway controls stem cell identity in the intestinal epithelium and in many other adult organs. The transcription factor Ascl2 (a Wnt target gene) is a master regulator of intestinal stem cell identity. It is unclear how the continuous Wnt gradient along the crypt axis is translated into discrete expression of Ascl2 and discrete specification of stem cells at crypt bottoms. We show that (1) Ascl2 is regulated in a direct autoactivatory loop, leading to a distinct on/off expression pattern, and (2) Wnt/R-spondin can activate this regulatory loop. This mechanism interprets the Wnt levels in the intestinal crypt and translates the continuous Wnt signal into a discrete Ascl2 "on" or "off" decision. In turn, Ascl2, together with β-catenin/Tcf, activates the genes fundamental to the stem cell state. In this manner, Ascl2 forms a transcriptional switch that is both Wnt responsive and Wnt dependent to define stem cell identity.
Collapse
Affiliation(s)
- Jurian Schuijers
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), University Medical Centre Utrecht, CancerGenomiCs.nl, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Jan Philipp Junker
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), University Medical Centre Utrecht, CancerGenomiCs.nl, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Michal Mokry
- Department of Pediatric Gastroenterology, Wilhelmina Children's Hospital, University Medical Centre Utrecht, 3508 AB Utrecht, the Netherlands
| | - Pantelis Hatzis
- Biomedical Sciences Research Center "Alexander Fleming," 16672 Vari, Greece
| | - Bon-Kyoung Koo
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), University Medical Centre Utrecht, CancerGenomiCs.nl, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands; Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK; Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - Valentina Sasselli
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), University Medical Centre Utrecht, CancerGenomiCs.nl, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Laurens G van der Flier
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), University Medical Centre Utrecht, CancerGenomiCs.nl, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands; SomantiX B.V., Utrecht, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Edwin Cuppen
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), University Medical Centre Utrecht, CancerGenomiCs.nl, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Alexander van Oudenaarden
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), University Medical Centre Utrecht, CancerGenomiCs.nl, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Hans Clevers
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), University Medical Centre Utrecht, CancerGenomiCs.nl, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands.
| |
Collapse
|
12
|
Cichello SA, Weisinger RS, Schuijers J, Jois M. 1-Sarcosine-angiotensin II infusion effects on food intake, weight loss, energy expenditure, and skeletal muscle UCP3 gene expression in a rat model. J Cachexia Sarcopenia Muscle 2014; 5:239-46. [PMID: 24614996 PMCID: PMC4159489 DOI: 10.1007/s13539-014-0133-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Accepted: 01/27/2014] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND There are a myriad of proteins responsible for modulation of expenditure of energy. Angiotensin II (Ang II) is a vital component of renin-angiotensin system that affects blood pressure and also linked to both cachexia and obesity via fat and muscle metabolism. Previous research suggests that the direct action of Ang II is on the brain, via angiotensin II type 1 receptor protein, affecting food intake and energy expenditure. The objective of the study is to investigate the effect of 1-sarcosine (SAR)-Ang II infusion on energy expenditure and metabolism in a rat model of congestive heart failure cachexia. METHODS Adult female rats of the Sprague Dawley strain (n = 33) were used (11 pair-fed control, 12 ad libitum and 10, 1-sarcosine-angiotensin II-infused rats). Body weight, faecal excretion, feed intake (in grams), water intake (in milliliters) and urine excreted were recorded daily. The measurements were recorded in three different periods (4 days prior to surgery, "pre-infusion"; day of surgery and 5 days postsurgery, "infusion period"; days 7 to 14, "recovery" period). Different analytical methods were used to measure energy expenditure per period, uncoupling protein 3 mRNA expression, crude protein and adipose tissue body composition. RESULTS During the infusion period, the SAR-Ang II group experienced rapid weight loss (p < 0.05) in comparison to the ad libitum and pair-fed groups. The SAR-Ang II group displayed lower (p < 0.05) body fat content (in percent) than the controls. There was also increased (p < 0.05) uncoupling protein 3 (UCP3) mRNA expression in the SAR-Ang II group and pair-fed group when compared to the controls. CONCLUSION In summary, the results suggest that SAR-Ang II infusion impairs appetite and decreases body weight by wasting predominantly adipose tissue, which may be due to elevated energy expenditure via mitochondrial uncoupling (UCP3 protein activity).
Collapse
Affiliation(s)
- S A Cichello
- School of Life Sciences, La Trobe University, Bundoora, VIC, 3086, Australia,
| | | | | | | |
Collapse
|
13
|
Schuijers J, van der Flier LG, van Es J, Clevers H. Robust cre-mediated recombination in small intestinal stem cells utilizing the olfm4 locus. Stem Cell Reports 2014; 3:234-41. [PMID: 25254337 PMCID: PMC4175542 DOI: 10.1016/j.stemcr.2014.05.018] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Revised: 05/22/2014] [Accepted: 05/23/2014] [Indexed: 02/08/2023] Open
Abstract
The epithelium of the small intestine is the most rapidly self-renewing tissue in mammals. We previously demonstrated the existence of a long-lived pool of cycling stem cells defined by Lgr5 expression at the bottom of intestinal crypts. An Lgr5-eGFP-IRES-CreERT2 knockin allele has been instrumental in characterizing and profiling these cells, yet its low level expression and its silencing in patches of adjacent crypts have not allowed quantitative gene deletion. Olfactomedin-4 (Olfm4) has emerged from a gene signature of Lgr5 stem cells as a robust marker for murine small intestinal stem cells. We observe that Olfm4(null) animals show no phenotype and report the generation of an Olfm4-IRES-eGFPCreERT2 knockin mouse model that allows visualization and genetic manipulation of Lgr5+ stem cells in the epithelium of the small intestine. The eGFPCreERT2 fusion protein faithfully marks all stem cells in the small intestine and induces the activation of a conditional LacZ reporter with robust efficiency.
Collapse
Affiliation(s)
- Jurian Schuijers
- Hubrecht Institute for Developmental Biology and Stem Cells, University Medical Centre Utrecht, University of Utrecht, Utrecht, Uppsalalaan 8, 3584CT Utrecht, the Netherlands
| | - Laurens G van der Flier
- Hubrecht Institute for Developmental Biology and Stem Cells, University Medical Centre Utrecht, University of Utrecht, Utrecht, Uppsalalaan 8, 3584CT Utrecht, the Netherlands
| | - Johan van Es
- Hubrecht Institute for Developmental Biology and Stem Cells, University Medical Centre Utrecht, University of Utrecht, Utrecht, Uppsalalaan 8, 3584CT Utrecht, the Netherlands
| | - Hans Clevers
- Hubrecht Institute for Developmental Biology and Stem Cells, University Medical Centre Utrecht, University of Utrecht, Utrecht, Uppsalalaan 8, 3584CT Utrecht, the Netherlands.
| |
Collapse
|
14
|
Schuijers J, Mokry M, Hatzis P, Cuppen E, Clevers H. Wnt-induced transcriptional activation is exclusively mediated by TCF/LEF. EMBO J 2014; 33:146-56. [PMID: 24413017 DOI: 10.1002/embj.201385358] [Citation(s) in RCA: 134] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Active canonical Wnt signaling results in recruitment of β-catenin to DNA by TCF/LEF family members, leading to transcriptional activation of TCF target genes. However, additional transcription factors have been suggested to recruit β-catenin and tether it to DNA. Here, we describe the genome-wide pattern of β-catenin DNA binding in murine intestinal epithelium, Wnt-responsive colorectal cancer (CRC) cells and HEK293 embryonic kidney cells. We identify two classes of β-catenin binding sites. The first class represents the majority of the DNA-bound β-catenin and co-localizes with TCF4, the prominent TCF/LEF family member in these cells. The second class consists of β-catenin binding sites that co-localize with a minimal amount of TCF4. The latter consists of lower affinity β-catenin binding events, does not drive transcription and often does not contain a consensus TCF binding motif. Surprisingly, a dominant-negative form of TCF4 abrogates the β-catenin/DNA interaction of both classes of binding sites, implying that the second class comprises low affinity TCF-DNA complexes. Our results indicate that β-catenin is tethered to chromatin overwhelmingly through the TCF/LEF transcription factors in these three systems.
Collapse
Affiliation(s)
- Jurian Schuijers
- Hubrecht Institute-KNAW, University Medical Centre Utrecht, Utrecht, The Netherlands
| | | | | | | | | |
Collapse
|
15
|
Huch M, Bonfanti P, Boj SF, Sato T, Loomans CJM, van de Wetering M, Sojoodi M, Li VSW, Schuijers J, Gracanin A, Ringnalda F, Begthel H, Hamer K, Mulder J, van Es JH, de Koning E, Vries RGJ, Heimberg H, Clevers H. Unlimited in vitro expansion of adult bi-potent pancreas progenitors through the Lgr5/R-spondin axis. EMBO J 2013; 32:2708-21. [PMID: 24045232 PMCID: PMC3801438 DOI: 10.1038/emboj.2013.204] [Citation(s) in RCA: 477] [Impact Index Per Article: 43.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2013] [Accepted: 08/16/2013] [Indexed: 02/06/2023] Open
Abstract
Lgr5 marks adult stem cells in multiple adult organs and is a receptor for the Wnt-agonistic R-spondins (RSPOs). Intestinal, stomach and liver Lgr5+ stem cells grow in 3D cultures to form ever-expanding organoids, which resemble the tissues of origin. Wnt signalling is inactive and Lgr5 is not expressed under physiological conditions in the adult pancreas. However, we now report that the Wnt pathway is robustly activated upon injury by partial duct ligation (PDL), concomitant with the appearance of Lgr5 expression in regenerating pancreatic ducts. In vitro, duct fragments from mouse pancreas initiate Lgr5 expression in RSPO1-based cultures, and develop into budding cyst-like structures (organoids) that expand five-fold weekly for >40 weeks. Single isolated duct cells can also be cultured into pancreatic organoids, containing Lgr5 stem/progenitor cells that can be clonally expanded. Clonal pancreas organoids can be induced to differentiate into duct as well as endocrine cells upon transplantation, thus proving their bi-potentiality. The establishment of conditions for long-term culture and expansion of adult, bi-potent pancreas progenitors may facilitate novel and tailored therapeutic approaches.
Collapse
Affiliation(s)
- Meritxell Huch
- Hubrecht Institute for Developmental Biology and Stem Cell Research, University Medical Centre Utrecht, Utrecht, The Netherlands
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
16
|
Kaaij LTJ, van de Wetering M, Fang F, Decato B, Molaro A, van de Werken HJG, van Es JH, Schuijers J, de Wit E, de Laat W, Hannon GJ, Clevers HC, Smith AD, Ketting RF. DNA methylation dynamics during intestinal stem cell differentiation reveals enhancers driving gene expression in the villus. Genome Biol 2013; 14:R50. [PMID: 23714178 PMCID: PMC4053812 DOI: 10.1186/gb-2013-14-5-r50] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Accepted: 05/28/2013] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND DNA methylation is of pivotal importance during development. Previous genome-wide studies identified numerous differentially methylated regions upon differentiation of stem cells, many of them associated with transcriptional start sites. RESULTS We present the first genome-wide, single-base-resolution view into DNA methylation dynamics during differentiation of a mammalian epithelial stem cell: the mouse small intestinal Lgr5+ stem cell. Very little change was observed at transcriptional start sites and our data suggest that differentiation-related genes are already primed for expression in the stem cell. Genome-wide, only 50 differentially methylated regions were identified. Almost all of these loci represent enhancers driving gene expression in the differentiated part of the small intestine. Finally, we show that binding of the transcription factor Tcf4 correlates with hypo-methylation and demonstrate that Tcf4 is one of the factors contributing to formation of differentially methylated regions. CONCLUSIONS Our results reveal limited DNA methylation dynamics during small intestine stem cell differentiation and an impact of transcription factor binding on shaping the DNA methylation landscape during differentiation of stem cells in vivo.
Collapse
|
17
|
Schuijers J, Clevers H. Adult mammalian stem cells: the role of Wnt, Lgr5 and R-spondins. EMBO J 2012; 31:2685-96. [PMID: 22617424 DOI: 10.1038/emboj.2012.149] [Citation(s) in RCA: 173] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Accepted: 04/26/2012] [Indexed: 12/12/2022] Open
Abstract
After its discovery as oncogen and morphogen, studies on Wnt focused initially on its role in animal development. With the finding that the colorectal tumour suppressor gene APC is a negative regulator of the Wnt pathway in (colorectal) cancer, attention gradually shifted to the study of the role of Wnt signalling in the adult. The first indication that adult Wnt signalling controls stem cells came from a Tcf4 knockout experiment: mutant mice failed to build crypt stem cell compartments. This observation was followed by similar findings in multiple other tissues. Recent studies have indicated that Wnt agonists of the R-spondin family provide potent growth stimuli for crypts in vivo and in vitro. Independently, Lgr5 was found as an exquisite marker for these crypt stem cells. The story has come full circle with the finding that the stem cell marker Lgr5 constitutes the receptor for R-spondins and occurs in complex with Frizzled/Lrp.
Collapse
Affiliation(s)
- Jurian Schuijers
- Hubrecht Institute-KNAW, University Medical Centre Utrecht, The Netherlands
| | | |
Collapse
|
18
|
Mokry M, Hatzis P, Schuijers J, Lansu N, Ruzius FP, Clevers H, Cuppen E. Integrated genome-wide analysis of transcription factor occupancy, RNA polymerase II binding and steady-state RNA levels identify differentially regulated functional gene classes. Nucleic Acids Res 2012; 40:148-58. [PMID: 21914722 PMCID: PMC3245935 DOI: 10.1093/nar/gkr720] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [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: 07/19/2011] [Revised: 08/22/2011] [Accepted: 08/22/2011] [Indexed: 12/15/2022] Open
Abstract
Routine methods for assaying steady-state mRNA levels such as RNA-seq and micro-arrays are commonly used as readouts to study the role of transcription factors (TFs) in gene expression regulation. However, cellular RNA levels do not solely depend on activity of TFs and subsequent transcription by RNA polymerase II (Pol II), but are also affected by RNA turnover rate. Here, we demonstrate that integrated analysis of genome-wide TF occupancy, Pol II binding and steady-state RNA levels provide important insights in gene regulatory mechanisms. Pol II occupancy, as detected by Pol II ChIP-seq, was found to correlate better with TF occupancy compared to steady-state RNA levels and is thus a more precise readout for the primary transcriptional mechanisms that are triggered by signal transduction. Furthermore, analysis of differential Pol II occupancy and RNA-seq levels identified genes with high Pol II occupancy and relatively low RNA levels and vice versa. These categories are strongly enriched for genes from different functional classes. Our results demonstrate a complementary value in Pol II chip-seq and RNA-seq approaches for better understanding of gene expression regulation.
Collapse
Affiliation(s)
- Michal Mokry
- Hubrecht Institute KNAW and University Medical Center, 3584 CT Utrecht, The Netherlands and Department of Medical Genetics, University Medical Center Utrecht (UMCU), 3584 CG Utrecht, The Netherlands
| | - Pantelis Hatzis
- Hubrecht Institute KNAW and University Medical Center, 3584 CT Utrecht, The Netherlands and Department of Medical Genetics, University Medical Center Utrecht (UMCU), 3584 CG Utrecht, The Netherlands
| | - Jurian Schuijers
- Hubrecht Institute KNAW and University Medical Center, 3584 CT Utrecht, The Netherlands and Department of Medical Genetics, University Medical Center Utrecht (UMCU), 3584 CG Utrecht, The Netherlands
| | - Nico Lansu
- Hubrecht Institute KNAW and University Medical Center, 3584 CT Utrecht, The Netherlands and Department of Medical Genetics, University Medical Center Utrecht (UMCU), 3584 CG Utrecht, The Netherlands
| | - Frans-Paul Ruzius
- Hubrecht Institute KNAW and University Medical Center, 3584 CT Utrecht, The Netherlands and Department of Medical Genetics, University Medical Center Utrecht (UMCU), 3584 CG Utrecht, The Netherlands
| | - Hans Clevers
- Hubrecht Institute KNAW and University Medical Center, 3584 CT Utrecht, The Netherlands and Department of Medical Genetics, University Medical Center Utrecht (UMCU), 3584 CG Utrecht, The Netherlands
| | - Edwin Cuppen
- Hubrecht Institute KNAW and University Medical Center, 3584 CT Utrecht, The Netherlands and Department of Medical Genetics, University Medical Center Utrecht (UMCU), 3584 CG Utrecht, The Netherlands
| |
Collapse
|
19
|
Verzi MP, Hatzis P, Sulahian R, Philips J, Schuijers J, Shin H, Freed E, Lynch JP, Dang DT, Brown M, Clevers H, Liu XS, Shivdasani RA. TCF4 and CDX2, major transcription factors for intestinal function, converge on the same cis-regulatory regions. Proc Natl Acad Sci U S A 2010; 107:15157-62. [PMID: 20696899 PMCID: PMC2930576 DOI: 10.1073/pnas.1003822107] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [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] [Indexed: 12/11/2022] Open
Abstract
Surprisingly few pathways signal between cells, raising questions about mechanisms for tissue-specific responses. In particular, Wnt ligands signal in many mammalian tissues, including the intestinal epithelium, where constitutive signaling causes cancer. Genome-wide analysis of DNA cis-regulatory regions bound by the intestine-restricted transcription factor CDX2 in colonic cells uncovered highly significant overrepresentation of sequences that bind TCF4, a transcriptional effector of intestinal Wnt signaling. Chromatin immunoprecipitation confirmed TCF4 occupancy at most such sites and co-occupancy of CDX2 and TCF4 across short distances. A region spanning the single nucleotide polymorphism rs6983267, which lies within a MYC enhancer and confers colorectal cancer risk in humans, represented one of many co-occupied sites. Co-occupancy correlated with intestine-specific gene expression and CDX2 loss reduced TCF4 binding. These results implicate CDX2 in directing TCF4 binding in intestinal cells. Co-occupancy of regulatory regions by signal-effector and tissue-restricted transcription factors may represent a general mechanism for ubiquitous signaling pathways to achieve tissue-specific outcomes.
Collapse
Affiliation(s)
- Michael P. Verzi
- Department of Medical Oncology and
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115
| | - Pantelis Hatzis
- Netherlands Institute of Developmental Biology and Hubrecht Institute, 3508 AD, Utrecht, The Netherlands
| | - Rita Sulahian
- Department of Medical Oncology and
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115
| | | | - Jurian Schuijers
- Netherlands Institute of Developmental Biology and Hubrecht Institute, 3508 AD, Utrecht, The Netherlands
| | - Hyunjin Shin
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02115
| | | | - John P. Lynch
- Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA 19104; and
| | - Duyen T. Dang
- Department of Medicine, University of Michigan School of Medicine, Ann Arbor, MI 48109
| | - Myles Brown
- Department of Medical Oncology and
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115
| | - Hans Clevers
- Netherlands Institute of Developmental Biology and Hubrecht Institute, 3508 AD, Utrecht, The Netherlands
| | - X. Shirley Liu
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02115
| | - Ramesh A. Shivdasani
- Department of Medical Oncology and
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115
| |
Collapse
|