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Li S, Wang Z, Wang X, Wang Y, Pattarayan D, Zhang Y, Nguyen P, Bhuniya A, Chen Y, Huang H, Huang Y, Wang L, Wang J, Li S, Zhang M, Liu Y, Lee N, Yang D. Integrative characterization of MYC RNA-binding function. CELL GENOMICS 2025:100878. [PMID: 40378850 DOI: 10.1016/j.xgen.2025.100878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2024] [Revised: 02/05/2025] [Accepted: 04/17/2025] [Indexed: 05/19/2025]
Abstract
Emerging evidence suggests that MYC interacts with RNAs. Here, we performed an integrative characterization of MYC as an RNA-binding protein in six cell lines. We found that MYC binds to a myriad of RNAs with high affinity for guanosine-rich RNAs. Global and specific depletion of RNAs reduces MYC chromatin occupancy. Mechanistically, two highly conserved sequences, amino acids 355-357 KRR and 364-367 RQRR, within the basic region of MYC are necessary for its RNA binding. Notably, alanine substitution of KRR abolishes MYC's RNA-binding ability both in vitro and in vivo, without affecting its ability to bind E-box DNA as part of the MYC:MAX dimer in vitro. The loss of RNA-binding function decreases MYC chromatin binding in vivo and attenuates its ability to promote gene expression, cell-cycle progression, and proliferation. Our study lays a foundation for future investigation into the role of RNAs in MYC-mediated transcriptional activation and oncogenic functions.
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Affiliation(s)
- Sihan Li
- Center for Pharmacogenetics and Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Zehua Wang
- Center for Pharmacogenetics and Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Xiaofei Wang
- Center for Pharmacogenetics and Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yifei Wang
- Center for Pharmacogenetics and Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Dhamotharan Pattarayan
- Center for Pharmacogenetics and Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yu Zhang
- Center for Pharmacogenetics and Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Phuong Nguyen
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA; UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA; Department of Bioengineering, Department of Electrical and Computer Engineering, Cancer Center at Illinois, Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Avishek Bhuniya
- Center for Pharmacogenetics and Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yuang Chen
- Center for Pharmacogenetics and Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Haozhe Huang
- Center for Pharmacogenetics and Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yixian Huang
- Center for Pharmacogenetics and Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Luxuan Wang
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA, USA
| | - Junmei Wang
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA, USA
| | - Song Li
- Center for Pharmacogenetics and Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Min Zhang
- Center for Pharmacogenetics and Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yang Liu
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA; UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA; Department of Bioengineering, Department of Electrical and Computer Engineering, Cancer Center at Illinois, Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Nara Lee
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Da Yang
- Center for Pharmacogenetics and Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA, USA; UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA; Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA.
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2
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Hyle J, Qi W, Djekidel MN, Rosikiewicz W, Xu B, Li C. Deciphering the role of RNA in regulating CTCF's DNA binding affinity in leukemia cells. Genome Biol 2025; 26:126. [PMID: 40355969 PMCID: PMC12067947 DOI: 10.1186/s13059-025-03582-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Accepted: 04/20/2025] [Indexed: 05/15/2025] Open
Abstract
BACKGROUND CTCF, a highly studied transcription factor, is essential for chromatin interaction maintenance. Several independent studies report that CTCF interacts with RNAs in vitro and in cells. Yet continuous debates about the authenticity of the RNA-binding affinity of CTCF and its biological role remain in large part due to limited research techniques available, such as CLIP-seq. RESULT Here, we investigate RNA's role in CTCF's transcription factor function through its chromatin occupancy. To systematically explore whether RNAs affect CTCF's ability to bind DNA, we perturb CTCF-RNA interactions by three independent approaches and examine CTCF genome occupancy by ChIP-seq. Although RNase A and triptolide treatment each affect a certain number of CTCF-binding peaks, few peaks overlap between treatment groups indicating the effect of RNA in regulating CTCF's DNA binding affinity is variable between loci. In addition, limited transcriptional or chromatin accessibility changes occur between cells expressing wild-type CTCF or CTCF lacking the RNA binding region. CONCLUSION Our data provide a complementary approach and in silico evidence to consider the significance of RNA affecting CTCF's DNA binding affinity globally.
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Affiliation(s)
- Judith Hyle
- Department of Tumor Cell Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Wenjie Qi
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Mohamed Nadhir Djekidel
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Wojciech Rosikiewicz
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Beisi Xu
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA.
| | - Chunliang Li
- Department of Tumor Cell Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA.
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3
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Turvey GL, López de Alba E, Stewart E, Cook H, Alalti A, Gawne RT, Ainscough JFX, Mason AS, Coverley D. Epigenetic deprogramming by disruption of CIZ1-RNA nuclear assemblies in early-stage breast cancers. J Cell Biol 2025; 224:e202409123. [PMID: 40067149 PMCID: PMC11895699 DOI: 10.1083/jcb.202409123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2024] [Revised: 01/11/2025] [Accepted: 02/17/2025] [Indexed: 03/15/2025] Open
Abstract
CIZ1 is part of the RNA-dependent supramolecular assemblies that form around the inactive X-chromosome (Xi) in female cells and smaller assemblies throughout the nucleus in both sexes. Here, we show that CIZ1 C-terminal anchor domain (AD) is elevated in human breast tumor transcriptomes, even at stage I. Elevation correlates with deprotection of chromatin and upregulation of lncRNA-containing gene clusters in ∼10 Mb regions enriched in cancer-associated genes. We modeled the effect of AD on endogenous CIZ1-Xi assemblies and observed dominant-negative interference with their reformation after mitosis, leading to abnormal assemblies similar to those in breast cancer cells, and depletion of H2AK119ub1, H3K27me3, and Xist. Consistent alterations in gene expression were evident across the genome, showing that AD-mediated interference has a destabilizing effect, likely by unscheduled exposure of underlying chromatin to modifying enzymes. The data argue for a dominant, potent, and rapid effect of CIZ1 AD that can deprogram gene expression patterns and which may predispose incipient tumors to epigenetic instability.
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Affiliation(s)
- Gabrielle L. Turvey
- Mammalian Cell Cycle Research Group, Department of Biology, University of York, York, UK
- York Biomedical Research Institute, University of York, York, UK
| | - Ernesto López de Alba
- Mammalian Cell Cycle Research Group, Department of Biology, University of York, York, UK
| | - Emma Stewart
- Mammalian Cell Cycle Research Group, Department of Biology, University of York, York, UK
- York Biomedical Research Institute, University of York, York, UK
| | - Heather Cook
- Mammalian Cell Cycle Research Group, Department of Biology, University of York, York, UK
| | - Ahmad Alalti
- Mammalian Cell Cycle Research Group, Department of Biology, University of York, York, UK
| | - Richard T. Gawne
- York Biomedical Research Institute, University of York, York, UK
- Jack Birch Unit for Molecular Carcinogenesis, Department of Biology, University of York, York, UK
| | - Justin F.-X. Ainscough
- Mammalian Cell Cycle Research Group, Department of Biology, University of York, York, UK
- York Biomedical Research Institute, University of York, York, UK
| | - Andrew S. Mason
- York Biomedical Research Institute, University of York, York, UK
- Jack Birch Unit for Molecular Carcinogenesis, Department of Biology, University of York, York, UK
| | - Dawn Coverley
- Mammalian Cell Cycle Research Group, Department of Biology, University of York, York, UK
- York Biomedical Research Institute, University of York, York, UK
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4
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Aguilar R, Rosenberg M, Levy V, Lee JT. An evolving landscape of PRC2-RNA interactions in chromatin regulation. Nat Rev Mol Cell Biol 2025:10.1038/s41580-025-00850-3. [PMID: 40307460 DOI: 10.1038/s41580-025-00850-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/24/2025] [Indexed: 05/02/2025]
Abstract
A major unsolved problem in epigenetics is how RNA regulates Polycomb repressive complex 2 (PRC2), a complex that trimethylates histone H3 Lys27 (H3K27me3) to form repressive chromatin. Key questions include how PRC2 binds RNA in vivo and what the functional consequences of binding are. In this Perspective, we expound on the viewpoint that RNA is integral to the stepwise regulation of PRC2 activity. Using the long non-coding RNA XIST and X chromosome inactivation as a model, we discuss evidence indicating that RNA is involved in PRC2 recruitment onto chromatin, in induction of its catalytic activity and in its eviction from chromatin. Studies have also implicated RNA in controlling promoter-proximal pausing of RNA polymerase II. The cumulative data argue that the functional consequences of PRC2-RNA interactions crucially depend on RNA conformation. We recognize that alternative hypotheses exist and therefore we attempt to integrate contrary data. Thus, although an RNA-rich landscape is emerging for Polycomb complexes, additional work is required to resolve a broad range of data interpretations.
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Affiliation(s)
- Rodrigo Aguilar
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Genetics, The Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Institute of Biomedical Sciences (ICB), Faculty of Medicine & Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile
| | - Michael Rosenberg
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Genetics, The Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Institute of Nanotechnology and Advanced Materials, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Vered Levy
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Genetics, The Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Jeannie T Lee
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.
- Department of Genetics, The Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
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5
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Bresser K, Popović B, Wolkers MC. What's in a name: the multifaceted function of DNA- and RNA-binding proteins in T cell responses. FEBS J 2025; 292:1853-1867. [PMID: 39304985 PMCID: PMC12001178 DOI: 10.1111/febs.17273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 06/12/2024] [Accepted: 09/02/2024] [Indexed: 04/17/2025]
Abstract
Cellular differentiation allows cells to transition between different functional states and adapt to various environmental cues. The diversity and plasticity of this process is beautifully exemplified by T cells responding to pathogens, which undergo highly specialized differentiation tailored to the ongoing infection. Such antigen-induced T cell differentiation is regulated at the transcriptional level by DNA-binding proteins and at the post-transcriptional level by RNA-binding proteins. Although traditionally defined as separate protein classes, a growing body of evidence indicates an overlap between these two groups of proteins, collectively coined DNA/RNA-binding proteins (DRBPs). In this review, we describe how DRBPs might bind both DNA and RNA, discuss the putative functional relevance of this dual binding, and provide an exploratory analysis into characteristics that are associated with DRBPs. To exemplify the significance of DRBPs in T cell biology, we detail the activity of several established and putative DRBPs during the T cell response. Finally, we highlight several methodologies that allow untangling of the distinct functionalities of DRBPs at the DNA and RNA level, including key considerations to take into account when applying such methods.
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Affiliation(s)
- Kaspar Bresser
- T Cell Differentiation Lab, Department of ResearchSanquin Blood Supply FoundationAmsterdamThe Netherlands
- Landsteiner LaboratoryAmsterdam UMC, University of AmsterdamThe Netherlands
- Cancer Immunology, Cancer Center AmsterdamAmsterdam Institute for Infection & ImmunityThe Netherlands
- Oncode InstituteUtrechtThe Netherlands
| | - Branka Popović
- T Cell Differentiation Lab, Department of ResearchSanquin Blood Supply FoundationAmsterdamThe Netherlands
- Landsteiner LaboratoryAmsterdam UMC, University of AmsterdamThe Netherlands
- Cancer Immunology, Cancer Center AmsterdamAmsterdam Institute for Infection & ImmunityThe Netherlands
- Oncode InstituteUtrechtThe Netherlands
| | - Monika C. Wolkers
- T Cell Differentiation Lab, Department of ResearchSanquin Blood Supply FoundationAmsterdamThe Netherlands
- Landsteiner LaboratoryAmsterdam UMC, University of AmsterdamThe Netherlands
- Cancer Immunology, Cancer Center AmsterdamAmsterdam Institute for Infection & ImmunityThe Netherlands
- Oncode InstituteUtrechtThe Netherlands
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6
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Raina K, Modak K, Premkumar C, Joshi G, Palani D, Nandy K, Sivamani Y, Velayudhan SR, Thummer RP. UTF1 Expression is Important for the Generation and Maintenance of Human iPSCs. Stem Cell Rev Rep 2025; 21:859-871. [PMID: 39754619 DOI: 10.1007/s12015-024-10836-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/21/2024] [Indexed: 01/06/2025]
Abstract
BACKGROUND Undifferentiated embryonic cell transcription factor 1 (UTF1) is predominantly expressed in pluripotent stem cells and plays a vital role in embryonic development and pluripotency maintenance. Despite its established importance in murine models, the role of UTF1 on human induced pluripotent stem cells (iPSCs) has not been comprehensively studied. METHODS This study utilized CRISPR/Cas9 gene editing to create UTF1 knockout in human fibroblasts and iPSCs. We employed episomal vectors for reprogramming UTF1 knockout fibroblasts into iPSCs and analyzed the effects of UTF1 depletion on cellular morphology, pluripotency, and viability through Western blotting, PCR, and flow cytometry. In addition, we integrated an shRNA that downregulated the expression of UTF1 for mechanistic studies to understand the impact of UTF1 depletion in iPSC pluripotency and differentiation. RESULTS UTF1 knockout resulted in significantly reduced reprogramming efficiency and increased spontaneous differentiation, indicating its crucial role in maintaining human iPSC identity and stability. In knockdown experiments, gradual loss of UTF1 led to change in cellular morphologies and decreased expression of core pluripotency markers OCT4 and SOX2. Interestingly, unlike complete UTF1 knockout, the gradual downregulation of UTF1 in iPSCs did not result in apoptosis, suggesting that the loss of pluripotency can occur independently of the apoptotic pathways. CONCLUSIONS UTF1 is essential for maintaining the pluripotency and viability of human iPSCs. Its depletion affects the fundamental properties of stem cells, underscoring the potential challenges in using UTF1-deficient cells for therapeutic applications. Future studies should explore the mechanistic pathways through which UTF1 controls pluripotency and differentiation, which could provide insights into improving iPSC stability for clinical applications.
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Affiliation(s)
- Khyati Raina
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Kirti Modak
- Department of Hematology, Christian Medical College, Vellore, India
| | - Chitra Premkumar
- Center for Stem Cell Research, Christian Medical College, Vellore, India
| | - Gaurav Joshi
- Department of Hematology, Christian Medical College, Vellore, India
| | - Dhavapriya Palani
- Center for Stem Cell Research, Christian Medical College, Vellore, India
| | - Krittika Nandy
- Center for Stem Cell Research, Christian Medical College, Vellore, India
| | - Yazhini Sivamani
- Center for Stem Cell Research, Christian Medical College, Vellore, India
| | - Shaji R Velayudhan
- Department of Hematology, Christian Medical College, Vellore, India
- Center for Stem Cell Research, Christian Medical College, Vellore, India
| | - Rajkumar P Thummer
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India.
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7
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Xie B, Dean A. A Super Enhancer-Derived Enhancer RNA Acts Together with CTCF/Cohesin in Trans to Regulate Erythropoiesis. Genes (Basel) 2025; 16:389. [PMID: 40282349 PMCID: PMC12026470 DOI: 10.3390/genes16040389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2025] [Revised: 03/14/2025] [Accepted: 03/24/2025] [Indexed: 04/29/2025] Open
Abstract
Background/Objectives: Enhancer RNAs (eRNAs) function in diverse modes and increasing studies have shown that they play important roles in normal development and disease. However, their role in erythropoiesis is not fully understood. Methods: We analyzed published RNA-seq and Promoter Capture Hi-C data from mouse E14.5 fetal liver cells to identify enhancer RNAs in erythroid cells with long-range interactions. Results: We discovered an erythroid-specific enhancer RNA (CpoxeRNA) transcribed from an enhancer region upstream of Cpox, an enzyme important for heme synthesis. CpoxeRNA is important for erythropoiesis, as the knockdown of CpoxeRNA by shRNA results in impaired enucleation and cell proliferation during terminal differentiation. CpoxeRNA interacts with cohesin and acts both in cis and trans to regulate erythroid genes. Conclusions: we have identified a trans-acting eRNA, CpoxeRNA, as a potential regulator of terminal erythropoiesis.
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Affiliation(s)
- Bingning Xie
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ann Dean
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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8
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Trotman JB, Abrash EW, Murvin MM, Braceros AK, Li S, Boyson SP, Salcido RT, Cherney RE, Bischoff SR, Kaufmann K, Eberhard QE, Zhang Z, Cowley DO, Calabrese JM. Isogenic comparison of Airn and Xist reveals core principles of Polycomb recruitment by lncRNAs. Mol Cell 2025; 85:1117-1133.e14. [PMID: 40118040 PMCID: PMC11932450 DOI: 10.1016/j.molcel.2025.02.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2024] [Revised: 01/15/2025] [Accepted: 02/19/2025] [Indexed: 03/23/2025]
Abstract
The mechanisms and biological roles of Polycomb repressive complex (PRC) recruitment by long noncoding RNAs (lncRNAs) remain unclear. To gain insight, we expressed two lncRNAs that recruit PRCs to multi-megabase domains, Airn and Xist, from an ectopic locus in mouse stem cells and compared effects. Unexpectedly, ectopic Airn recruited PRC1 and PRC2 to chromatin with a potency resembling Xist yet did not repress genes. Compared with PRC2, PRC1 was more proximal to Airn and Xist, where its enrichment over C-rich elements required the RNA-binding protein HNRNPK. Fusing Airn to Repeat A, the domain required for gene silencing by Xist, enabled gene silencing and altered local patterns but not relative levels of PRC-directed modifications. Our data suggest that, endogenously, Airn recruits PRCs to maintain rather than initiate gene silencing, that PRC recruitment occurs independently of Repeat A, and that protein-bridged interactions, not direct RNA contacts, underlie PRC recruitment by Airn, Xist, and other lncRNAs.
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Affiliation(s)
- Jackson B Trotman
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27599, USA; RNA Discovery Center, University of North Carolina, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Elizabeth W Abrash
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27599, USA; RNA Discovery Center, University of North Carolina, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA; Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - McKenzie M Murvin
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27599, USA; RNA Discovery Center, University of North Carolina, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA; Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599, USA; Curriculum in Mechanistic, Interdisciplinary Studies of Biological Systems, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Aki K Braceros
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27599, USA; RNA Discovery Center, University of North Carolina, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA; Curriculum in Mechanistic, Interdisciplinary Studies of Biological Systems, University of North Carolina, Chapel Hill, NC 27599, USA; Curriculum in Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Shuang Li
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27599, USA; RNA Discovery Center, University of North Carolina, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Samuel P Boyson
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27599, USA; RNA Discovery Center, University of North Carolina, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA; Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Ryan T Salcido
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27599, USA; RNA Discovery Center, University of North Carolina, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA; Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Rachel E Cherney
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27599, USA; RNA Discovery Center, University of North Carolina, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA; Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Steven R Bischoff
- Animal Models Core, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Kyle Kaufmann
- Animal Models Core, University of North Carolina, Chapel Hill, NC 27599, USA; Transviragen, Inc., Chapel Hill, NC 27599, USA
| | - Quinn E Eberhard
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27599, USA; RNA Discovery Center, University of North Carolina, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA; Curriculum in Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Zhiyue Zhang
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Dale O Cowley
- Animal Models Core, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; Transviragen, Inc., Chapel Hill, NC 27599, USA
| | - J Mauro Calabrese
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27599, USA; RNA Discovery Center, University of North Carolina, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA.
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9
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Rajagopal V, Seiler J, Nasa I, Cantarella S, Theiss J, Herget F, Kaifer B, Klostermann M, Will R, Schneider M, Helm D, König J, Zarnack K, Diederichs S, Kettenbach AN, Caudron-Herger M. An atlas of RNA-dependent proteins in cell division reveals the riboregulation of mitotic protein-protein interactions. Nat Commun 2025; 16:2325. [PMID: 40057470 PMCID: PMC11890761 DOI: 10.1038/s41467-025-57671-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2024] [Accepted: 02/28/2025] [Indexed: 05/13/2025] Open
Abstract
Ribonucleoprotein complexes are dynamic assemblies of RNA with RNA-binding proteins, which modulate the fate of RNA. Inversely, RNA riboregulates the interactions and functions of the associated proteins. Dysregulation of ribonucleoprotein functions is linked to diseases such as cancer and neurological disorders. In dividing cells, RNA and RNA-binding proteins are present in mitotic structures, but their impact on cell division remains unclear. By applying the proteome-wide R-DeeP strategy to cells synchronized in mitosis versus interphase integrated with the RBP2GO knowledge, we provided an atlas of RNA-dependent proteins in cell division, accessible at R-DeeP3.dkfz.de. We uncovered AURKA, KIFC1 and TPX2 as unconventional RNA-binding proteins. KIFC1 was identified as a new substrate of AURKA, and new TPX2-interacting protein. Their pair-wise interactions were RNA dependent. In addition, RNA stimulated AURKA kinase activity and stabilized its conformation. In this work, we highlighted riboregulation of major mitotic factors as an additional complexity level of cell division.
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Affiliation(s)
- Varshni Rajagopal
- Research Group "RNA-Protein Complexes & Cell Proliferation", German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jeanette Seiler
- Research Group "RNA-Protein Complexes & Cell Proliferation", German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Isha Nasa
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
- Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Simona Cantarella
- Research Group "RNA-Protein Complexes & Cell Proliferation", German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jana Theiss
- Research Group "RNA-Protein Complexes & Cell Proliferation", German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Franziska Herget
- Research Group "RNA-Protein Complexes & Cell Proliferation", German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Bianca Kaifer
- Research Group "RNA-Protein Complexes & Cell Proliferation", German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Melina Klostermann
- Buchmann Institute for Molecular Life Sciences, Frankfurt, Germany
- Department of Bioinformatics, University of Würzburg, Würzburg, Germany
| | - Rainer Will
- Cellular Tools Core Facility, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Martin Schneider
- Proteomics Core Facility, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dominic Helm
- Proteomics Core Facility, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Julian König
- Institute of Molecular Biology (IMB), Mainz, Germany
- Theodor Boveri Institute, Biocenter, University of Würzburg, Würzburg, Germany
| | - Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences, Frankfurt, Germany
- Department of Bioinformatics, University of Würzburg, Würzburg, Germany
| | - Sven Diederichs
- Division of Cancer Research, Department of Thoracic Surgery, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
- German Cancer Consortium (DKTK), partner site Freiburg, a partnership between DKFZ and University Medical Center Freiburg, Freiburg, Germany.
| | - Arminja N Kettenbach
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA.
- Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA.
| | - Maïwen Caudron-Herger
- Research Group "RNA-Protein Complexes & Cell Proliferation", German Cancer Research Center (DKFZ), Heidelberg, Germany.
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10
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Peyda P, Lin CH, Onwuzurike K, Black DL. The Rbfox1/LASR complex controls alternative pre-mRNA splicing by recognition of multipart RNA regulatory modules. Genes Dev 2025; 39:364-383. [PMID: 39880658 PMCID: PMC11874969 DOI: 10.1101/gad.352105.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2024] [Accepted: 01/06/2025] [Indexed: 01/31/2025]
Abstract
The Rbfox proteins regulate alternative pre-mRNA splicing by binding to the RNA element GCAUG. In the nucleus, most of Rbfox is bound to the large assembly of splicing regulators (LASR), a complex of RNA-binding proteins that recognize additional RNA motifs. However, it remains unclear how the different subunits of the Rbfox/LASR complex act together to bind RNA and regulate splicing. We used a nuclease protection assay to map the transcriptome-wide footprints of Rbfox1/LASR on nascent cellular RNA. In addition to GCAUG, Rbfox1/LASR binds RNA motifs for LASR subunits hnRNPs M, H/F, and C and Matrin3. These elements are often arranged in tandem, forming multipart modules of RNA motifs. To distinguish contact sites of Rbfox1 from the LASR subunits, we analyzed a mutant Rbfox1(F125A) that has lost RNA binding but remains associated with LASR. Rbfox1(F125A)/LASR complexes no longer interact with GCAUG but retain binding to RNA elements for LASR. Splicing analyses reveal that in addition to activating exons through adjacent GCAUG elements, Rbfox can also stimulate exons near binding sites for LASR subunits. Minigene experiments demonstrate that these diverse elements produce a combined regulatory effect on a target exon. These findings illuminate how a complex of RNA-binding proteins can decode combinatorial splicing regulatory signals by recognizing groups of tandem RNA elements.
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Affiliation(s)
- Parham Peyda
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California 90095, USA
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California 90095, USA
- Medical Scientist Training Program, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California 90095, USA
| | - Chia-Ho Lin
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California 90095, USA
| | - Kelechi Onwuzurike
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California 90095, USA
| | - Douglas L Black
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California 90095, USA;
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California 90095, USA
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, California 90095, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, California 90095, USA
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11
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Lee Y, Das P, Kesner B, Rosenberg M, Blum R, Lee JT. Re-analysis of CLAP data affirms PRC2 as an RNA binding protein. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2024.09.19.613009. [PMID: 39345380 PMCID: PMC11429800 DOI: 10.1101/2024.09.19.613009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
Abstract
Using CLAP methodology, Guo et al. recently concluded that PRC2 is not an RNA binding protein (RBP). They suggest that prior findings were CLIP artifacts and argue against RNA's direct role in PRC2 regulation. Here, we re-analyze their raw datasets and reach contrary conclusions. Through an independent computational pipeline, we observe significant PRC2 enrichment throughout the transcriptome, including XIST. Applying the authors' published computational pipeline also reaffirms PRC2 as an RBP. Detailed investigation of the authors' pipeline reveals several unconventional practices. First, Guo et al. retained reads from foreign species and other unmappable reads to obtain a normalization factor. Second, they selectively removed read duplicates from the mappable fraction, while retaining them in the unmappable fraction. Finally, the authors applied an arbitrary cutoff for enrichment values in XIST. Their pipeline thereby inflated PRC2's background reads and suppressed mappable signals, creating the impression that PRC2 is not a robust RBP.
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Affiliation(s)
- YongWoo Lee
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA; and Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Priyojit Das
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA; and Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Barry Kesner
- Institute of Nanotechnology and Advanced Materials, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Michael Rosenberg
- Institute of Nanotechnology and Advanced Materials, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Roy Blum
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA; and Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Jeannie T Lee
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA; and Department of Genetics, Harvard Medical School, Boston, MA, USA
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12
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Corin A, Nora EP, Ramani V. Beyond genomic weaving: molecular roles for CTCF outside cohesin loop extrusion. Curr Opin Genet Dev 2025; 90:102298. [PMID: 39709822 PMCID: PMC12058310 DOI: 10.1016/j.gde.2024.102298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2024] [Revised: 11/22/2024] [Accepted: 11/29/2024] [Indexed: 12/24/2024]
Abstract
CCCTC-binding factor (CTCF) is a key regulator of 3D genome organization and transcriptional activity. Beyond its well-characterized role in facilitating cohesin-mediated loop extrusion, CTCF exhibits several cohesin-independent activities relevant to chromatin structure and various nuclear processes. These functions include patterning of nucleosome arrangement and chromatin accessibility through interactions with ATP-dependent chromatin remodelers. In addition to influencing transcription, DNA replication, and DNA repair in ways that are separable from its role in loop extrusion, CTCF also interacts with RNA and contributes to RNA splicing and condensation of transcriptional activators. Here, we review recent insight into cohesin-independent activities of CTCF, highlighting its multifaceted roles in chromatin biology and transcriptional regulation.
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Affiliation(s)
- Aaron Corin
- Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute for Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Elphège P Nora
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA; Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA; Chan-Zuckerberg Biohub, San Francisco, CA, USA.
| | - Vijay Ramani
- Gladstone Institute for Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA.
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13
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Mangoni D, Mazzetti A, Ansaloni F, Simi A, Tartaglia GG, Pandolfini L, Gustincich S, Sanges R. From the genome's perspective: Bearing somatic retrotransposition to leverage the regulatory potential of L1 RNAs. Bioessays 2025; 47:e2400125. [PMID: 39520370 PMCID: PMC11755705 DOI: 10.1002/bies.202400125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Revised: 10/16/2024] [Accepted: 10/23/2024] [Indexed: 11/16/2024]
Abstract
Transposable elements (TEs) are mobile genomic elements constituting a big fraction of eukaryotic genomes. They ignite an evolutionary arms race with host genomes, which in turn evolve strategies to restrict their activity. Despite being tightly repressed, TEs display precisely regulated expression patterns during specific stages of mammalian development, suggesting potential benefits for the host. Among TEs, the long interspersed nuclear element (LINE-1 or L1) has been found to be active in neurons. This activity prompted extensive research into its possible role in cognition. So far, no specific cause-effect relationship between L1 retrotransposition and brain functions has been conclusively identified. Nevertheless, accumulating evidence suggests that interactions between L1 RNAs and RNA/DNA binding proteins encode specific messages that cells utilize to activate or repress entire transcriptional programs. We summarize recent findings highlighting the activity of L1 RNAs at the non-coding level during early embryonic and brain development. We propose a hypothesis suggesting a mutualistic relationship between L1 mRNAs and the host cell. In this scenario, cells tolerate a certain rate of retrotransposition to leverage the regulatory effects of L1s as non-coding RNAs on potentiating their mitotic potential. In turn, L1s benefit from the cell's proliferative state to increase their chance to mobilize.
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Affiliation(s)
- Damiano Mangoni
- Center for Human Technologies, Non‐Coding RNAs and RNA‐Based TherapeuticsIstituto Italiano di Tecnologia (IIT)GenovaItaly
| | - Aurora Mazzetti
- Area of NeuroscienceInternational School for Advanced Studies (SISSA)TriesteItaly
| | - Federico Ansaloni
- Center for Human Technologies, Non‐Coding RNAs and RNA‐Based TherapeuticsIstituto Italiano di Tecnologia (IIT)GenovaItaly
| | - Alessandro Simi
- Center for Human Technologies, Non‐Coding RNAs and RNA‐Based TherapeuticsIstituto Italiano di Tecnologia (IIT)GenovaItaly
| | - Gian Gaetano Tartaglia
- Center for Human Technologies, RNA Systems BiologyIstituto Italiano di Tecnologia (IIT)GenovaItaly
| | - Luca Pandolfini
- Center for Human Technologies, Non‐Coding RNAs and RNA‐Based TherapeuticsIstituto Italiano di Tecnologia (IIT)GenovaItaly
| | - Stefano Gustincich
- Center for Human Technologies, Non‐Coding RNAs and RNA‐Based TherapeuticsIstituto Italiano di Tecnologia (IIT)GenovaItaly
| | - Remo Sanges
- Center for Human Technologies, Non‐Coding RNAs and RNA‐Based TherapeuticsIstituto Italiano di Tecnologia (IIT)GenovaItaly
- Area of NeuroscienceInternational School for Advanced Studies (SISSA)TriesteItaly
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14
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Ebot-Ojong F, Ferraro AR, Kaddar F, Hull-Crew C, Scadden AW, Klocko AD, Lewis ZA. Histone deacetylase-1 is required for epigenome stability in Neurospora crassa. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.01.17.633486. [PMID: 39896537 PMCID: PMC11785058 DOI: 10.1101/2025.01.17.633486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/04/2025]
Abstract
Polycomb group (PcG) proteins form chromatin modifying complexes that stably repress lineage- or context-specific genes in animals, plants, and some fungi. Polycomb Repressive Complex 2 (PRC2) catalyzes trimethylation of lysine 27 on histone H3 (H3K27me3) to assemble repressive chromatin. In the model fungus Neurospora crassa, H3K27me3 deposition is controlled by the H3K36 methyltransferase ASH1 and components of constitutive heterochromatin including the H3K9me3-binding protein HETEROCHROMATIN PROTEIN 1 (HP1). Hypoacetylated histones are a defining feature of both constitutive heterochromatin and PcG-repressed chromatin, but how histone deacetylases (HDACs) contribute to normal H3K27me3 and transcriptional repression within PcG-repressed chromatin is poorly understood. We performed a genetic screen to identify HDACs required for repression of PRC2-methylated genes. In the absence of HISTONE DEACETYLASE-1 (HDA-1), PRC2-methylated genes were activated and H3K27me3 was depleted from typical PRC2-targeted regions. At constitutive heterochromatin, HDA-1 deficient cells displayed reduced H3K9me3, hyperacetylation, and aberrant enrichment of H3K27me3 and H3K36me3. CHROMODOMAIN PROTEIN-2 (CDP-2) is required to target HDA-1 to constitutive heterochromatin and was also required for normal H3K27me3 patterns. Patterns of aberrant H3K27me3 were distinct in isogenic Δhda-1 strains, suggesting that loss of HDA-1 causes stochastic or progressive epigenome dysfunction. To test this, we constructed a new Δhda-1 strain and performed a laboratory evolution experiment. Deletion of hda-1 led to progressive epigenome decay over hundreds of nuclear divisions. Together, our data indicate that HDA-1 is a critical regulator of epigenome stability in N. crassa.
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Affiliation(s)
- Felicia Ebot-Ojong
- Department of Microbiology, University of Georgia, Athens, GA, 30602 USA
| | - Aileen R. Ferraro
- Department of Microbiology, University of Georgia, Athens, GA, 30602 USA
| | - Farh Kaddar
- Department of Chemistry & Biochemistry, University of Colorado Colorado Springs, Colorado Springs, CO, 80918, USA
| | - Clayton Hull-Crew
- Department of Chemistry & Biochemistry, University of Colorado Colorado Springs, Colorado Springs, CO, 80918, USA
| | - Ashley W. Scadden
- Department of Chemistry & Biochemistry, University of Colorado Colorado Springs, Colorado Springs, CO, 80918, USA
| | - Andrew D. Klocko
- Department of Chemistry & Biochemistry, University of Colorado Colorado Springs, Colorado Springs, CO, 80918, USA
| | - Zachary A. Lewis
- Department of Microbiology, University of Georgia, Athens, GA, 30602 USA
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15
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Zhang J, Ataei L, Mittal K, Wu L, Caldwell L, Huynh L, Sarajideen S, Tse K, Simon MM, Mazid MA, Cook DP, Trcka D, Kwan T, Hoffman MM, Wrana JL, Esteban MA, Ramalho-Santos M. LINE1 and PRC2 control nucleolar organization and repression of the 8C state in human ESCs. Dev Cell 2025; 60:186-203.e13. [PMID: 39413784 DOI: 10.1016/j.devcel.2024.09.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 08/02/2024] [Accepted: 09/19/2024] [Indexed: 10/18/2024]
Abstract
The mechanisms that ensure developmental progression in the early human embryo remain largely unknown. Here, we show that the family of long interspersed nuclear element 1 (LINE1) transposons prevents the reversion of naive human embryonic stem cells (hESCs) to 8-cell-like cells (8CLCs). LINE1 RNA contributes to maintenance of H3K27me3 levels, particularly at chromosome 19 (Chr19). Chr19 is enriched for key 8C regulators, H3K27me3, and genes derepressed upon LINE1 knockdown or PRC2 inhibition. Moreover, Chr19 is strongly associated with the nucleolus in hESCs but less in 8CLCs. Direct inhibition of PRC2 activity induces the 8C program and leads to a relocalization of Chr19 away from the nucleolus. LINE1 KD or PRC2 inhibition induces nucleolar stress, and disruption of nucleolar architecture is sufficient to de-repress the 8C program. These results indicate that LINE1 RNA and PRC2 maintain H3K27me3-mediated gene repression and 3D nuclear organization to prevent developmental reversion of hESCs.
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Affiliation(s)
- Juan Zhang
- Lunenfeld-Tanenbaum Research Institute and Department of Molecular Genetics, University of Toronto, Toronto, ON M5T 3H7, Canada.
| | - Lamisa Ataei
- Lunenfeld-Tanenbaum Research Institute and Department of Molecular Genetics, University of Toronto, Toronto, ON M5T 3H7, Canada
| | - Kirti Mittal
- Lunenfeld-Tanenbaum Research Institute and Department of Molecular Genetics, University of Toronto, Toronto, ON M5T 3H7, Canada
| | - Liang Wu
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Lauren Caldwell
- Lunenfeld-Tanenbaum Research Institute and Department of Molecular Genetics, University of Toronto, Toronto, ON M5T 3H7, Canada
| | - Linh Huynh
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2M9, Canada
| | - Shahil Sarajideen
- Department of Biological Sciences, University of Toronto Scarborough, Scarborough, ON M1C 1A4, Canada
| | - Kevin Tse
- Lunenfeld-Tanenbaum Research Institute and Department of Molecular Genetics, University of Toronto, Toronto, ON M5T 3H7, Canada
| | | | - Md Abdul Mazid
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - David P Cook
- Lunenfeld-Tanenbaum Research Institute and Department of Molecular Genetics, University of Toronto, Toronto, ON M5T 3H7, Canada
| | - Daniel Trcka
- Lunenfeld-Tanenbaum Research Institute and Department of Molecular Genetics, University of Toronto, Toronto, ON M5T 3H7, Canada
| | - Tony Kwan
- McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Michael M Hoffman
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2M9, Canada; Departments of Medical Biophysics and Computer Science, University of Toronto, Toronto, ON M5G 1L7, Canada; Vector Institute for Artificial Intelligence, Toronto, ON M5G 1M1, Canada
| | - Jeffrey L Wrana
- Lunenfeld-Tanenbaum Research Institute and Department of Molecular Genetics, University of Toronto, Toronto, ON M5T 3H7, Canada
| | - Miguel A Esteban
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; BGI-Shenzhen, Shenzhen, China
| | - Miguel Ramalho-Santos
- Lunenfeld-Tanenbaum Research Institute and Department of Molecular Genetics, University of Toronto, Toronto, ON M5T 3H7, Canada.
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16
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Oo JA, Warwick T, Pálfi K, Lam F, McNicoll F, Prieto-Garcia C, Günther S, Cao C, Zhou Y, Gavrilov AA, Razin SV, Cabrera-Orefice A, Wittig I, Pullamsetti SS, Kurian L, Gilsbach R, Schulz MH, Dikic I, Müller-McNicoll M, Brandes RP, Leisegang MS. Long non-coding RNAs direct the SWI/SNF complex to cell type-specific enhancers. Nat Commun 2025; 16:131. [PMID: 39747144 PMCID: PMC11695977 DOI: 10.1038/s41467-024-55539-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Accepted: 12/16/2024] [Indexed: 01/04/2025] Open
Abstract
The coordination of chromatin remodeling is essential for DNA accessibility and gene expression control. The highly conserved and ubiquitously expressed SWItch/Sucrose Non-Fermentable (SWI/SNF) chromatin remodeling complex plays a central role in cell type- and context-dependent gene expression. Despite the absence of a defined DNA recognition motif, SWI/SNF binds lineage specific enhancers genome-wide where it actively maintains open chromatin state. It does so while retaining the ability to respond dynamically to cellular signals. However, the mechanisms that guide SWI/SNF to specific genomic targets have remained elusive. Here we demonstrate that trans-acting long non-coding RNAs (lncRNAs) direct the SWI/SNF complex to cell type-specific enhancers. SWI/SNF preferentially binds lncRNAs and these predominantly bind DNA targets in trans. Together they localize to enhancers, many of which are cell type-specific. Knockdown of SWI/SNF- and enhancer-bound lncRNAs causes the genome-wide redistribution of SWI/SNF away from enhancers and a concomitant differential expression of spatially connected target genes. These lncRNA-SWI/SNF-enhancer networks support an enhancer hub model of SWI/SNF genomic targeting. Our findings reveal that lncRNAs competitively recruit SWI/SNF, providing a specific and dynamic layer of control over chromatin accessibility, and reinforcing their role in mediating enhancer activity and gene expression.
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Affiliation(s)
- James A Oo
- Goethe University Frankfurt, Institute for Cardiovascular Physiology, Frankfurt, Germany
- German Center of Cardiovascular Research (DZHK), Partner site Rhein/Main, Frankfurt, Germany
- Cardio-Pulmonary Institute (CPI), Goethe University Frankfurt, Frankfurt, Germany
| | - Timothy Warwick
- Goethe University Frankfurt, Institute for Cardiovascular Physiology, Frankfurt, Germany
- German Center of Cardiovascular Research (DZHK), Partner site Rhein/Main, Frankfurt, Germany
- Cardio-Pulmonary Institute (CPI), Goethe University Frankfurt, Frankfurt, Germany
| | - Katalin Pálfi
- Goethe University Frankfurt, Institute for Cardiovascular Physiology, Frankfurt, Germany
| | - Frederike Lam
- Goethe University Frankfurt, Institute for Cardiovascular Physiology, Frankfurt, Germany
- German Center of Cardiovascular Research (DZHK), Partner site Rhein/Main, Frankfurt, Germany
- Cardio-Pulmonary Institute (CPI), Goethe University Frankfurt, Frankfurt, Germany
| | - Francois McNicoll
- Goethe University Frankfurt, Institute for Molecular Biosciences, Frankfurt, Germany
| | - Cristian Prieto-Garcia
- Goethe University Frankfurt, Institute of Biochemistry II, Faculty of Medicine, Frankfurt, Germany
- Goethe University Frankfurt, Buchmann Institute for Molecular Life Sciences, Frankfurt, Germany
| | - Stefan Günther
- Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Can Cao
- Goethe University Frankfurt, Institute for Cardiovascular Physiology, Frankfurt, Germany
- Institute of Experimental Cardiology, Heidelberg University Hospital, Heidelberg, Germany
- German Center of Cardiovascular Research (DZHK), Partner site Heidelberg/Mannheim, Heidelberg, Germany
| | - Yinuo Zhou
- Goethe University Frankfurt, Institute for Cardiovascular Physiology, Frankfurt, Germany
- German Center of Cardiovascular Research (DZHK), Partner site Rhein/Main, Frankfurt, Germany
- Cardio-Pulmonary Institute (CPI), Goethe University Frankfurt, Frankfurt, Germany
| | - Alexey A Gavrilov
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Sergey V Razin
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Alfredo Cabrera-Orefice
- Goethe University Frankfurt, Institute for Cardiovascular Physiology, Frankfurt, Germany
- Goethe University Frankfurt, Functional Proteomics Center, Frankfurt, Germany
| | - Ilka Wittig
- Goethe University Frankfurt, Institute for Cardiovascular Physiology, Frankfurt, Germany
- Goethe University Frankfurt, Functional Proteomics Center, Frankfurt, Germany
| | - Soni Savai Pullamsetti
- Department of Internal Medicine, Justus Liebig University, Giessen, Germany
- Cardio-Pulmonary Institute (CPI), University of Giessen, Giessen, Germany
| | - Leo Kurian
- Goethe University Frankfurt, Institute for Cardiovascular Physiology, Frankfurt, Germany
- German Center of Cardiovascular Research (DZHK), Partner site Rhein/Main, Frankfurt, Germany
- Cardio-Pulmonary Institute (CPI), Goethe University Frankfurt, Frankfurt, Germany
| | - Ralf Gilsbach
- Goethe University Frankfurt, Institute for Cardiovascular Physiology, Frankfurt, Germany
- Institute of Experimental Cardiology, Heidelberg University Hospital, Heidelberg, Germany
- German Center of Cardiovascular Research (DZHK), Partner site Heidelberg/Mannheim, Heidelberg, Germany
| | - Marcel H Schulz
- German Center of Cardiovascular Research (DZHK), Partner site Rhein/Main, Frankfurt, Germany
- Cardio-Pulmonary Institute (CPI), Goethe University Frankfurt, Frankfurt, Germany
- Goethe University Frankfurt, Institute for Computational Genomic Medicine, Frankfurt, Germany
| | - Ivan Dikic
- Cardio-Pulmonary Institute (CPI), Goethe University Frankfurt, Frankfurt, Germany
- Goethe University Frankfurt, Institute of Biochemistry II, Faculty of Medicine, Frankfurt, Germany
- Goethe University Frankfurt, Buchmann Institute for Molecular Life Sciences, Frankfurt, Germany
| | - Michaela Müller-McNicoll
- Cardio-Pulmonary Institute (CPI), Goethe University Frankfurt, Frankfurt, Germany
- Goethe University Frankfurt, Institute for Molecular Biosciences, Frankfurt, Germany
- Max Planck Institute for Biophysics, Frankfurt, Germany
| | - Ralf P Brandes
- Goethe University Frankfurt, Institute for Cardiovascular Physiology, Frankfurt, Germany
- German Center of Cardiovascular Research (DZHK), Partner site Rhein/Main, Frankfurt, Germany
- Cardio-Pulmonary Institute (CPI), Goethe University Frankfurt, Frankfurt, Germany
| | - Matthias S Leisegang
- Goethe University Frankfurt, Institute for Cardiovascular Physiology, Frankfurt, Germany.
- German Center of Cardiovascular Research (DZHK), Partner site Rhein/Main, Frankfurt, Germany.
- Cardio-Pulmonary Institute (CPI), Goethe University Frankfurt, Frankfurt, Germany.
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17
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Li J, Xu S, Liu Z, Yang L, Ming Z, Zhang R, Zhao W, Peng H, Quinn JJ, Wu M, Geng Y, Zhang Y, He J, Chen M, Li N, Shao NY, Ma Q. A noncanonical role of roX RNAs in autosomal epigenetic repression. Nat Commun 2025; 16:155. [PMID: 39747148 PMCID: PMC11696496 DOI: 10.1038/s41467-024-55711-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 12/19/2024] [Indexed: 01/04/2025] Open
Abstract
Long noncoding RNAs known as roX (RNA on the X) are crucial for male development in Drosophila, as their loss leads to male lethality from the late larval stages. While roX RNAs are recognized for their role in sex-chromosome dosage compensation, ensuring balanced expression of X-linked genes in both sexes, their potential influence on autosomal gene regulation remains unexplored. Here, using an integrative multi-omics approach, we show that roX RNAs not only govern the X chromosome but also target genes on autosomes that lack male-specific lethal (MSL) complex occupancy, together with Polycomb repressive complexes (PRCs). We observed that roX RNAs colocalize with MSL proteins on the X chromosome and PRC components on autosomes. Intriguingly, loss of roX function reduces X-chromosomal H4K16ac levels and autosomal H3K27me3 levels. Correspondingly, X-linked genes display reduced expression, whereas many autosomal genes exhibit elevated expression upon roX loss. Our findings propose a dual role for roX RNAs: activators of X-linked genes and repressors of autosomal genes, achieved through interactions with MSL and PRC complexes, respectively. This study uncovers the unconventional epigenetic repressive function of roX RNAs with PRC interaction.
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Affiliation(s)
- Jianjian Li
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Faculty of Synthetic Biology, Shenzhen University of Advanced Technology, Shenzhen, China
| | - Shuyang Xu
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Zicong Liu
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Liuyi Yang
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Zhe Ming
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Faculty of Health Sciences, University of Macau, Macau, Macau SAR, China
| | - Rui Zhang
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Wenjuan Zhao
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Huipai Peng
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Jeffrey J Quinn
- Center for Personal Dynamic Regulomes and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Manyin Wu
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Yushan Geng
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Yuying Zhang
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Jiazhi He
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Minghai Chen
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Nan Li
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Ning-Yi Shao
- Faculty of Health Sciences, University of Macau, Macau, Macau SAR, China
| | - Qing Ma
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
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18
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Alnefaie GO. A review of the complex interplay between chemoresistance and lncRNAs in lung cancer. J Transl Med 2024; 22:1109. [PMID: 39639388 PMCID: PMC11619437 DOI: 10.1186/s12967-024-05877-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2024] [Accepted: 11/11/2024] [Indexed: 12/07/2024] Open
Abstract
Lung Cancer (LC) is characterized by chemoresistance, which poses a significant clinical challenge and results in a poor prognosis for patients. Long non-coding RNAs (lncRNAs) have recently gained recognition as crucial mediators of chemoresistance in LC. Through the regulation of key cellular processes, these molecules play important roles in the progression of LC and response to therapy. The mechanisms by which lncRNAs affect chemoresistance include the modulation of gene expression, chromatin structure, microRNA interactions, and signaling pathways. Exosomes have emerged as key mediators of lncRNA-driven chemoresistance, facilitating the transfer of resistance-associated lncRNAs between cancer cells and contributing to tumor development. Consequently, exosomal lncRNAs may serve as biomarkers and therapeutic targets for the treatment of LC. Therapeutic strategies targeting lncRNAs offer novel approaches to circumvent chemoresistance. Different approaches, including RNA interference (RNAi) and antisense oligonucleotides (ASOs), are available to degrade lncRNAs or alter their function. ASO-based therapies are effective at reducing lncRNA expression levels, increasing chemotherapy sensitivity, and improving clinical outcomes. The use of these strategies can facilitate the development of targeted interventions designed to disrupt lncRNA-mediated mechanisms of chemoresistance. An important aspect of this review is the discussion of the complex relationship between lncRNAs and drug resistance in LC, particularly through exosomal pathways, and the development of innovative therapeutic strategies to enhance drug efficacy by targeting lncRNAs. The development of new pathways and interventions for treating LC holds promise in overcoming this resistance.
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Affiliation(s)
- Ghaliah Obaid Alnefaie
- Department of Pathology, College of Medicine, Taif University, P.O. Box 11099, Taif, 21944, Saudi Arabia.
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19
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Montano C, Flores-Arenas C, Carpenter S. LncRNAs, nuclear architecture and the immune response. Nucleus 2024; 15:2350182. [PMID: 38738760 PMCID: PMC11093052 DOI: 10.1080/19491034.2024.2350182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 04/22/2024] [Indexed: 05/14/2024] Open
Abstract
Long noncoding RNAs (LncRNAs) are key regulators of gene expression and can mediate their effects in both the nucleus and cytoplasm. Some of the best-characterized lncRNAs are localized within the nucleus, where they modulate the nuclear architecture and influence gene expression. In this review, we discuss the role of lncRNAs in nuclear architecture in the context of their gene regulatory functions in innate immunity. Here, we discuss various approaches to functionally characterize nuclear-localized lncRNAs and the challenges faced in the field.
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Affiliation(s)
- Christy Montano
- Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, CA, USA
| | - Cristina Flores-Arenas
- Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, CA, USA
| | - Susan Carpenter
- Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, CA, USA
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20
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Gao L, Li S, Chang HS, Kim YJ. Sequencing CURLY LEAF-associated RNAs in Arabidopsis revealed prevalent intergenic RNAs from the nuclear mitochondrial sequence. Mol Cells 2024; 47:100131. [PMID: 39427743 PMCID: PMC11605418 DOI: 10.1016/j.mocell.2024.100131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2024] [Revised: 09/29/2024] [Accepted: 10/15/2024] [Indexed: 10/22/2024] Open
Abstract
Polycomb group (PcG) proteins play key roles in development by repressing thousands of targets through histone modifications. However, how PcG is recruited to specific targets is poorly understood. In Arabidopsis, certain noncoding RNAs are necessary for recruiting the PcG protein CURLY LEAF (CLF) to its target sites. However, RNAs associated with CLF have not been analyzed on a genomic scale; thus, it is unknown whether long noncoding RNA (lncRNA)-mediated PcG recruitment is a widespread mechanism. Here, we systematically searched for CLF-associated RNAs by RNA immunoprecipitation followed by deep sequencing. We identified 1,299 genic and 138 intergenic regions that produced CLF-associated mRNAs and putative lncRNAs, respectively. The genes producing CLF-associated RNAs are depleted in PcG targets, carry active chromatin marks, and are highly expressed, suggesting that CLF may have a nonspecific or promiscuous RNA-binding affinity, similar to animal PcG proteins. Notably, a significant portion of the CLF-associated lncRNAs is derived from the nuclear mitochondrial sequence, which is extensively marked by H3K27me3. These findings indicate that, while CLF-RNA interactions are widespread, they may not always correlate with PcG target sites, highlighting the complexity of PcG recruitment mechanisms in Arabidopsis.
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Affiliation(s)
- Lei Gao
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China; Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Shengben Li
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Hyun Suh Chang
- Department of Systems Biology, Yonsei University, Seoul 03722, Republic of Korea
| | - Yun Ju Kim
- Department of Systems Biology, Yonsei University, Seoul 03722, Republic of Korea.
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21
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Krautwurst S, Lamkiewicz K. RNA-protein interaction prediction without high-throughput data: An overview and benchmark of in silico tools. Comput Struct Biotechnol J 2024; 23:4036-4046. [PMID: 39610906 PMCID: PMC11603007 DOI: 10.1016/j.csbj.2024.11.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2024] [Revised: 11/05/2024] [Accepted: 11/05/2024] [Indexed: 11/30/2024] Open
Abstract
RNA-protein interactions (RPIs) are crucial for accurately operating various processes in and between organisms across kingdoms of life. Mutual detection of RPI partner molecules depends on distinct sequential, structural, or thermodynamic features, which can be determined via experimental and bioinformatic methods. Still, the underlying molecular mechanisms of many RPIs are poorly understood. It is further hypothesized that many RPIs are not even described yet. Computational RPI prediction is continuously challenged by the lack of data and detailed research of very specific examples. With the discovery of novel RPI complexes in all kingdoms of life, adaptations of existing RPI prediction methods are necessary. Continuously improving computational RPI prediction is key in advancing the understanding of RPIs in detail and supplementing experimental RPI determination. The growing amount of data covering more species and detailed mechanisms support the accuracy of prediction tools, which in turn support specific experimental research on RPIs. Here, we give an overview of RPI prediction tools that do not use high-throughput data as the user's input. We review the tools according to their input, usability, and output. We then apply the tools to known RPI examples across different kingdoms of life. Our comparison shows that the investigated prediction tools do not favor a certain species and equip the user with results varying in degree of information, from an overall RPI score to detailed interacting residues. Furthermore, we provide a guide tree to assist users which RPI prediction tool is appropriate for their available input data and desired output.
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Affiliation(s)
- Sarah Krautwurst
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, Leutragraben 1, 07743 Jena, Germany
- European Virus Bioinformatics Center, Leutragraben 1, 07743 Jena, Germany
| | - Kevin Lamkiewicz
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, Leutragraben 1, 07743 Jena, Germany
- European Virus Bioinformatics Center, Leutragraben 1, 07743 Jena, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstr. 4, 04103 Leipzig, Germany
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22
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Deforzh E, Kharel P, Zhang Y, Karelin A, El Khayari A, Ivanov P, Krichevsky AM. HOXDeRNA activates a cancerous transcription program and super enhancers via genome-wide binding. Mol Cell 2024; 84:3950-3966.e6. [PMID: 39383879 PMCID: PMC11490371 DOI: 10.1016/j.molcel.2024.09.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 06/24/2024] [Accepted: 09/13/2024] [Indexed: 10/11/2024]
Abstract
The role of long non-coding RNAs (lncRNAs) in malignant cell transformation remains elusive. We previously identified an enhancer-associated lncRNA, LINC01116 (named HOXDeRNA), as a transformative factor converting human astrocytes into glioma-like cells. Employing a combination of CRISPR editing, chromatin isolation by RNA purification coupled with sequencing (ChIRP-seq), in situ mapping RNA-genome interactions (iMARGI), chromatin immunoprecipitation sequencing (ChIP-seq), HiC, and RNA/DNA FISH, we found that HOXDeRNA directly binds to CpG islands within the promoters of 35 glioma-specific transcription factors (TFs) distributed throughout the genome, including key stem cell TFs SOX2, OLIG2, POU3F2, and ASCL1, liberating them from PRC2 repression. This process requires a distinct RNA quadruplex structure and other segments of HOXDeRNA, interacting with EZH2 and CpGs, respectively. Subsequent transformation activates multiple oncogenes (e.g., EGFR, miR-21, and WEE1), driven by the SOX2- and OLIG2-dependent glioma-specific super enhancers. These results help reconstruct the sequence of events underlying the process of astrocyte transformation, highlighting HOXDeRNA's central genome-wide activity and suggesting a shared RNA-dependent mechanism in otherwise heterogeneous and multifactorial gliomagenesis.
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Affiliation(s)
- Evgeny Deforzh
- Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Prakash Kharel
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Yanhong Zhang
- Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Anton Karelin
- Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Abdellatif El Khayari
- Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Institute of Biological Sciences (ISSB-P), UM6P Faculty of Medical Sciences, Mohammed VI Polytechnic University, Ben-Guerir 43150, Morocco
| | - Pavel Ivanov
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Anna M Krichevsky
- Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.
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23
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Lee Y, Lee JT. PRC2-RNA interactions: Viewpoint from YongWoo Lee and Jeannie T. Lee. Mol Cell 2024; 84:3586-3592. [PMID: 39366347 DOI: 10.1016/j.molcel.2024.09.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2024] [Revised: 09/06/2024] [Accepted: 09/06/2024] [Indexed: 10/06/2024]
Abstract
Here, we expound on the view that Xist RNA directly controls Polycomb repressive complex 2 (PRC2) recruitment, off-loading to chromatin, catalytic activity, and eviction from chromatin. RNA-PRC2 interactions also control RNA polymerase II transcription pausing. Dynamic RNA folding determines PRC2 activity. Disparate studies and interpretations abound but can be reconciled.
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Affiliation(s)
- YongWoo Lee
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA; Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Jeannie T Lee
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA; Department of Genetics, Harvard Medical School, Boston, MA, USA.
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24
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Cech TR, Davidovich C, Jenner RG. PRC2-RNA interactions: Viewpoint from Tom Cech, Chen Davidovich, and Richard Jenner. Mol Cell 2024; 84:3593-3595. [PMID: 39366348 DOI: 10.1016/j.molcel.2024.09.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2024] [Revised: 09/09/2024] [Accepted: 09/09/2024] [Indexed: 10/06/2024]
Abstract
Diverse biochemical, structural, and in vivo data support models for the regulation of polycomb repressive complex 2 (PRC2) activity by RNAs, which may contribute to the maintenance of epigenetic states. Here, we summarize this research and also suggest why it can be difficult to capture biologically relevant PRC2-RNA interactions in living cells.
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Affiliation(s)
- Thomas R Cech
- Department of Biochemistry, BioFrontiers Institute, and Howard Hughes Medical Institute, University of Colorado, Boulder, CO 80309, USA.
| | - Chen Davidovich
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton 3800 VIC, Australia; EMBL-Australia, Clayton 3800 VIC, Australia.
| | - Richard G Jenner
- UCL Cancer Institute, University College London, London WC1E 6BT, UK; CRUK City of London Centre, University College London, London WC1E 6BT, UK.
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25
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Henninger JE, Young RA. An RNA-centric view of transcription and genome organization. Mol Cell 2024; 84:3627-3643. [PMID: 39366351 PMCID: PMC11495847 DOI: 10.1016/j.molcel.2024.08.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 08/13/2024] [Accepted: 08/16/2024] [Indexed: 10/06/2024]
Abstract
Foundational models of transcriptional regulation involve the assembly of protein complexes at DNA elements associated with specific genes. These assemblies, which can include transcription factors, cofactors, RNA polymerase, and various chromatin regulators, form dynamic spatial compartments that contribute to both gene regulation and local genome architecture. This DNA-protein-centric view has been modified with recent evidence that RNA molecules have important roles to play in gene regulation and genome structure. Here, we discuss evidence that gene regulation by RNA occurs at multiple levels that include assembly of transcriptional complexes and genome compartments, feedback regulation of active genes, silencing of genes, and control of protein kinases. We thus provide an RNA-centric view of transcriptional regulation that must reside alongside the more traditional DNA-protein-centric perspectives on gene regulation and genome architecture.
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Affiliation(s)
- Jonathan E Henninger
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
| | - Richard A Young
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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26
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Nabeel-Shah S, Pu S, Burns JD, Braunschweig U, Ahmed N, Burke GL, Lee H, Radovani E, Zhong G, Tang H, Marcon E, Zhang Z, Hughes TR, Blencowe BJ, Greenblatt JF. C2H2-zinc-finger transcription factors bind RNA and function in diverse post-transcriptional regulatory processes. Mol Cell 2024; 84:3810-3825.e10. [PMID: 39303720 DOI: 10.1016/j.molcel.2024.08.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 06/13/2024] [Accepted: 08/30/2024] [Indexed: 09/22/2024]
Abstract
Cys2-His2 zinc-finger proteins (C2H2-ZNFs) constitute the largest class of DNA-binding transcription factors (TFs) yet remain largely uncharacterized. Although certain family members, e.g., GTF3A, have been shown to bind both DNA and RNA, the extent to which C2H2-ZNFs interact with-and regulate-RNA-associated processes is not known. Using UV crosslinking and immunoprecipitation (CLIP), we observe that 148 of 150 analyzed C2H2-ZNFs bind directly to RNA in human cells. By integrating CLIP sequencing (CLIP-seq) RNA-binding maps for 50 of these C2H2-ZNFs with data from chromatin immunoprecipitation sequencing (ChIP-seq), protein-protein interaction assays, and transcriptome profiling experiments, we observe that the RNA-binding profiles of C2H2-ZNFs are generally distinct from their DNA-binding preferences and that they regulate a variety of post-transcriptional processes, including pre-mRNA splicing, cleavage and polyadenylation, and m6A modification of mRNA. Our results thus define a substantially expanded repertoire of C2H2-ZNFs that bind RNA and provide an important resource for elucidating post-transcriptional regulatory programs.
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Affiliation(s)
- Syed Nabeel-Shah
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Shuye Pu
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - James D Burns
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | | | - Nujhat Ahmed
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Giovanni L Burke
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Hyunmin Lee
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Computer Sciences, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Ernest Radovani
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Guoqing Zhong
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Hua Tang
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Edyta Marcon
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Zhaolei Zhang
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Computer Sciences, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Timothy R Hughes
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Benjamin J Blencowe
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Jack F Greenblatt
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
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27
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Guo JK, Blanco MR, Guttman M. PRC2-RNA interactions: Viewpoint from Jimmy K. Guo, Mario R. Blanco, and Mitchell Guttman. Mol Cell 2024; 84:3578-3585. [PMID: 39366346 DOI: 10.1016/j.molcel.2024.09.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2024] [Revised: 09/06/2024] [Accepted: 09/06/2024] [Indexed: 10/06/2024]
Abstract
Many reported PRC2-RNA interactions have been shown to be functionally dispensable, raising questions about whether they occur in vivo. Here, we lay out technical issues with existing evidence for direct binding and argue that there is currently a lack of biochemical or functional evidence for direct PRC2-RNA binding in vivo.
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Affiliation(s)
- Jimmy K Guo
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Mario R Blanco
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Mitchell Guttman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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28
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Herbert A. A Compendium of G-Flipon Biological Functions That Have Experimental Validation. Int J Mol Sci 2024; 25:10299. [PMID: 39408629 PMCID: PMC11477331 DOI: 10.3390/ijms251910299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2024] [Revised: 09/16/2024] [Accepted: 09/18/2024] [Indexed: 10/20/2024] Open
Abstract
As with all new fields of discovery, work on the biological role of G-quadruplexes (GQs) has produced a number of results that at first glance are quite baffling, sometimes because they do not fit well together, but mostly because they are different from commonly held expectations. Like other classes of flipons, those that form G-quadruplexes have a repeat sequence motif that enables the fold. The canonical DNA motif (G3N1-7)3G3, where N is any nucleotide and G is guanine, is a feature that is under active selection in avian and mammalian genomes. The involvement of G-flipons in genome maintenance traces back to the invertebrate Caenorhabditis elegans and to ancient DNA repair pathways. The role of GQs in transcription is supported by the observation that yeast Rap1 protein binds both B-DNA, in a sequence-specific manner, and GQs, in a structure-specific manner, through the same helix. Other sequence-specific transcription factors (TFs) also engage both conformations to actuate cellular transactions. Noncoding RNAs can also modulate GQ formation in a sequence-specific manner and engage the same cellular machinery as localized by TFs, linking the ancient RNA world with the modern protein world. The coevolution of noncoding RNAs and sequence-specific proteins is supported by studies of early embryonic development, where the transient formation of G-quadruplexes coordinates the epigenetic specification of cell fate.
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Affiliation(s)
- Alan Herbert
- Discovery, InsideOutBio, 42 8th Street, Unit 3412, Charlestown, MA 02129, USA
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29
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Sharp JA, Sparago E, Thomas R, Alimenti K, Wang W, Blower MD. Role of the SAF-A SAP domain in X inactivation, transcription, splicing, and cell proliferation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.09.612041. [PMID: 39314300 PMCID: PMC11419091 DOI: 10.1101/2024.09.09.612041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
SAF-A is conserved throughout vertebrates and has emerged as an important factor regulating a multitude of nuclear functions, including lncRNA localization, gene expression, and splicing. SAF-A has several functional domains, including an N-terminal SAP domain that binds directly to DNA. Phosphorylation of SAP domain serines S14 and S26 are important for SAF-A localization and function during mitosis, however whether these serines are involved in interphase functions of SAF-A is not known. In this study we tested for the role of the SAP domain, and SAP domain serines S14 and S26 in X chromosome inactivation, protein dynamics, gene expression, splicing, and cell proliferation. Here we show that the SAP domain serines S14 and S26 are required to maintain XIST RNA localization and polycomb-dependent histone modifications on the inactive X chromosome in female cells. In addition, we present evidence that an Xi localization signal resides in the SAP domain. We found that that the SAP domain is not required to maintain gene expression and plays only a minor role in mRNA splicing. In contrast, the SAF-A SAP domain, in particular serines S14 and S26, are required for normal protein dynamics, and to maintain normal cell proliferation. We propose a model whereby dynamic phosphorylation of SAF-A serines S14 and S26 mediates rapid turnover of SAF-A interactions with DNA during interphase.
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Affiliation(s)
- Judith A. Sharp
- Department of Biochemistry and Cell Biology, Chobanian and Avedisian School of Medicine, Boston University, 72 E. Concord St, K112, Boston, MA 02118
| | - Emily Sparago
- Department of Biochemistry and Cell Biology, Chobanian and Avedisian School of Medicine, Boston University, 72 E. Concord St, K112, Boston, MA 02118
| | - Rachael Thomas
- Department of Biochemistry and Cell Biology, Chobanian and Avedisian School of Medicine, Boston University, 72 E. Concord St, K112, Boston, MA 02118
| | - Kaitlyn Alimenti
- Department of Biochemistry and Cell Biology, Chobanian and Avedisian School of Medicine, Boston University, 72 E. Concord St, K112, Boston, MA 02118
| | - Wei Wang
- Department of Biochemistry and Cell Biology, Chobanian and Avedisian School of Medicine, Boston University, 72 E. Concord St, K112, Boston, MA 02118
| | - Michael D. Blower
- Department of Biochemistry and Cell Biology, Chobanian and Avedisian School of Medicine, Boston University, 72 E. Concord St, K112, Boston, MA 02118
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30
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Makino S, Fukaya T. Dynamic modulation of enhancer-promoter and promoter-promoter connectivity in gene regulation. Bioessays 2024; 46:e2400101. [PMID: 38922969 DOI: 10.1002/bies.202400101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 05/28/2024] [Accepted: 06/04/2024] [Indexed: 06/28/2024]
Abstract
Enhancers are short segments of regulatory DNA that control when and in which cell-type genes should be turned on in response to a variety of extrinsic and intrinsic signals. At the molecular level, enhancers serve as a genomic scaffold that recruits sequence-specific transcription factors and co-activators to facilitate transcription from linked promoters. However, it remains largely unclear how enhancers communicate with appropriate target promoters in the context of higher-order genome topology. In this review, we discuss recent progress in our understanding of the functional interplay between enhancers, genome topology, and the molecular properties of transcription machineries in gene regulation. We suggest that the activities of transcription hubs are highly regulated through the dynamic rearrangement of enhancer-promoter and promoter-promoter connectivity during animal development.
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Affiliation(s)
- Shiho Makino
- Laboratory of Transcription Dynamics, Research Center for Biological Visualization, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Takashi Fukaya
- Laboratory of Transcription Dynamics, Research Center for Biological Visualization, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
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31
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Song J, Yao L, Gooding AR, Thron V, Kasinath V, Cech TR. Diverse RNA Structures Induce PRC2 Dimerization and Inhibit Histone Methyltransferase Activity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.29.610323. [PMID: 39257770 PMCID: PMC11383989 DOI: 10.1101/2024.08.29.610323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2024]
Abstract
Methyltransferase PRC2 (Polycomb Repressive Complex 2) introduces histone H3K27 trimethylation, a repressive chromatin mark, to tune the differential expression of genes. PRC2 is precisely regulated by accessory proteins, histone post-translational modifications and, notably, RNA. Research on PRC2-associated RNA has mostly focused on the tight-binding G-quadruplex (G4) RNAs, which inhibit PRC2 enzymatic activity in vitro and in cells. Our recent cryo-EM structure provided a molecular mechanism for G4 RNA inactivating PRC2 via dimerization, but it remained unclear how diverse RNAs associate with and regulate PRC2. Here, we show that a single-stranded G-rich RNA and an atypical G4 structure called pUG-fold unexpectedly also mediate near-identical PRC2 dimerization resulting in inhibition of PRC2 methyltransferase activity. The conformational flexibility of arginine-rich loops within subunits EZH2 and AEBP2 of PRC2 can accommodate diverse RNA secondary structures, resulting in protein-RNA and protein-protein interfaces similar to those observed previously with G4 RNA. Furthermore, we address a recent report that failed to detect PRC2-associated RNAs in living cells by demonstrating the insensitivity of PRC2-RNA interaction to photochemical crosslinking. Our results support the significance of RNA-mediated PRC2 regulation by showing that this interaction is not limited to a single RNA secondary structure, consistent with the broad PRC2 transcriptome containing many G-tract RNAs incapable of folding into G4 structures.
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32
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Ozbulut HC, Hilgers V. Neuronal RNA processing: cross-talk between transcriptional regulation and RNA-binding proteins. Front Mol Neurosci 2024; 17:1426410. [PMID: 39149613 PMCID: PMC11324583 DOI: 10.3389/fnmol.2024.1426410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Accepted: 07/22/2024] [Indexed: 08/17/2024] Open
Abstract
In the nervous system, alternative RNA processing is particularly prevalent, which results in the expression of thousands of transcript variants found in no other tissue. Neuron-specific RNA-binding proteins co-transcriptionally regulate alternative splicing, alternative polyadenylation, and RNA editing, thereby shaping the RNA identity of nervous system cells. Recent evidence suggests that interactions between RNA-binding proteins and cis-regulatory elements such as promoters and enhancers play a role in the determination of neuron-specific expression profiles. Here, we discuss possible mechanisms through which transcription and RNA processing cross-talk to generate the uniquely complex neuronal transcriptome, with a focus on alternative 3'-end formation.
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Affiliation(s)
- Hasan Can Ozbulut
- Max-Planck-Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Faculty of Biology, Albert Ludwig University, Freiburg, Germany
- International Max Planck Research School for Immunobiology, Epigenetics, and Metabolism (IMPRS-IEM), Freiburg, Germany
| | - Valérie Hilgers
- Max-Planck-Institute of Immunobiology and Epigenetics, Freiburg, Germany
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33
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Jiang L, Huang L, Jiang W. H3K27me3-mediated epigenetic regulation in pluripotency maintenance and lineage differentiation. CELL INSIGHT 2024; 3:100180. [PMID: 39072246 PMCID: PMC11278802 DOI: 10.1016/j.cellin.2024.100180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Revised: 06/20/2024] [Accepted: 06/26/2024] [Indexed: 07/30/2024]
Abstract
Cell fate determination is an intricate process which is orchestrated by multiple regulatory layers including signal pathways, transcriptional factors, epigenetic modifications, and metabolic rewiring. Among the sophisticated epigenetic modulations, the repressive mark H3K27me3, deposited by PRC2 (polycomb repressive complex 2) and removed by demethylase KDM6, plays a pivotal role in mediating the cellular identity transition through its dynamic and precise alterations. Herein, we overview and discuss how H3K27me3 and its modifiers regulate pluripotency maintenance and early lineage differentiation. We primarily highlight the following four aspects: 1) the two subcomplexes PRC2.1 and PRC2.2 and the distribution of genomic H3K27 methylation; 2) PRC2 as a critical regulator in pluripotency maintenance and exit; 3) the emerging role of the eraser KDM6 in early differentiation; 4) newly identified additional factors influencing H3K27me3. We present a comprehensive insight into the molecular principles of the dynamic regulation of H3K27me3, as well as how this epigenetic mark participates in pluripotent stem cell-centered cell fate determination.
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Affiliation(s)
- Liwen Jiang
- Department of Biological Repositories, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430071, China
| | - Linfeng Huang
- Wang-Cai Biochemistry Lab, Division of Natural and Applied Sciences, Duke Kunshan University, Kunshan, Jiangsu, China
| | - Wei Jiang
- Department of Biological Repositories, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430071, China
- Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan, 430071, China
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34
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Thurm AR, Finkel Y, Andrews C, Cai XS, Benko C, Bintu L. High-throughput discovery of regulatory effector domains in human RNA-binding proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.19.604317. [PMID: 39071298 PMCID: PMC11275849 DOI: 10.1101/2024.07.19.604317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
RNA regulation plays an integral role in tuning gene expression and is controlled by thousands of RNA-binding proteins (RBPs). We develop and use a high-throughput recruitment assay (HT-RNA-Recruit) to identify regulatory domains within human RBPs by recruiting over 30,000 protein tiles from 367 RBPs to a reporter mRNA. We discover over 100 unique RNA-regulatory effectors in 86 distinct RBPs, presenting evidence that RBPs contain functionally separable domains that dictate their post-transcriptional control of gene expression, and identify some with unique activity at 5' or 3'UTRs. We identify some domains that downregulate gene expression both when recruited to DNA and RNA, and dissect their mechanisms of regulation. Finally, we build a synthetic RNA regulator that can stably maintain gene expression at desired levels that are predictable by a mathematical model. This work serves as a resource for human RNA-regulatory effectors and expands the synthetic repertoire of RNA-based genetic control tools. Highlights HT-RNA-Recruit identifies hundreds of RNA-regulatory effectors in human proteins.Recruitment to 5' and 3' UTRs identifies regulatory domains unique to each position.Some protein domains have both transcriptional and post-transcriptional regulatory activity.We develop a synthetic RNA regulator and a mathematical model to describe its behavior.
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35
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Hemphill WO, Steiner HR, Kominsky JR, Wuttke DS, Cech TR. Transcription factors ERα and Sox2 have differing multiphasic DNA- and RNA-binding mechanisms. RNA (NEW YORK, N.Y.) 2024; 30:1089-1105. [PMID: 38760076 PMCID: PMC11251522 DOI: 10.1261/rna.080027.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 05/01/2024] [Indexed: 05/19/2024]
Abstract
Many transcription factors (TFs) have been shown to bind RNA, leading to open questions regarding the mechanism(s) of this RNA binding and its role in regulating TF activities. Here, we use biophysical assays to interrogate the k on, k off, and K d for DNA and RNA binding of two model human TFs, ERα and Sox2. Unexpectedly, we found that both proteins exhibit multiphasic nucleic acid-binding kinetics. We propose that Sox2 RNA and DNA multiphasic binding kinetics can be explained by a conventional model for sequential Sox2 monomer association and dissociation. In contrast, ERα nucleic acid binding exhibited biphasic dissociation paired with novel triphasic association behavior, in which two apparent binding transitions are separated by a 10-20 min "lag" phase depending on protein concentration. We considered several conventional models for the observed kinetic behavior, none of which adequately explained all the ERα nucleic acid-binding data. Instead, simulations with a model incorporating sequential ERα monomer association, ERα nucleic acid complex isomerization, and product "feedback" on isomerization rate recapitulated the general kinetic trends for both ERα DNA and RNA binding. Collectively, our findings reveal that Sox2 and ERα bind RNA and DNA with previously unappreciated multiphasic binding kinetics, and that their reaction mechanisms differ with ERα binding nucleic acids via a novel reaction mechanism.
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Affiliation(s)
- Wayne O Hemphill
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado 80303, USA
- Howard Hughes Medical Institute and BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado 80303, USA
| | - Halley R Steiner
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado 80303, USA
| | - Jackson R Kominsky
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado 80303, USA
- Howard Hughes Medical Institute and BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado 80303, USA
| | - Deborah S Wuttke
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado 80303, USA
| | - Thomas R Cech
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado 80303, USA
- Howard Hughes Medical Institute and BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado 80303, USA
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36
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Bracken CP, Goodall GJ, Gregory PA. RNA regulatory mechanisms controlling TGF-β signaling and EMT in cancer. Semin Cancer Biol 2024; 102-103:4-16. [PMID: 38917876 DOI: 10.1016/j.semcancer.2024.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 06/05/2024] [Accepted: 06/13/2024] [Indexed: 06/27/2024]
Abstract
Epithelial-mesenchymal transition (EMT) is a major contributor to metastatic progression and is prominently regulated by TGF-β signalling. Both EMT and TGF-β pathway components are tightly controlled by non-coding RNAs - including microRNAs (miRNAs), long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) - that collectively have major impacts on gene expression and resulting cellular states. While miRNAs are the best characterised regulators of EMT and TGF-β signaling and the miR-200-ZEB1/2 feedback loop plays a central role, important functions for lncRNAs and circRNAs are also now emerging. This review will summarise our current understanding of the roles of non-coding RNAs in EMT and TGF-β signaling with a focus on their functions in cancer progression.
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Affiliation(s)
- Cameron P Bracken
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA 5000, Australia; Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA 5000, Australia; School of Biological Sciences, Faculty of Sciences, Engineering and Technology, The University of Adelaide, Adelaide, SA 5000, Australia.
| | - Gregory J Goodall
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA 5000, Australia; Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA 5000, Australia; School of Biological Sciences, Faculty of Sciences, Engineering and Technology, The University of Adelaide, Adelaide, SA 5000, Australia.
| | - Philip A Gregory
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA 5000, Australia; Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA 5000, Australia.
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37
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Wulfridge P, Sarma K. Intertwining roles of R-loops and G-quadruplexes in DNA repair, transcription and genome organization. Nat Cell Biol 2024; 26:1025-1036. [PMID: 38914786 PMCID: PMC12044674 DOI: 10.1038/s41556-024-01437-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 05/10/2024] [Indexed: 06/26/2024]
Abstract
R-loops are three-stranded nucleic acid structures that are abundant and widespread across the genome and that have important physiological roles in many nuclear processes. Their accumulation is observed in cancers and neurodegenerative disorders. Recent studies have implicated a function for R-loops and G-quadruplex (G4) structures, which can form on the displaced single strand of R-loops, in three-dimensional genome organization in both physiological and pathological contexts. Here we discuss the interconnected functions of DNA:RNA hybrids and G4s within R-loops, their impact on DNA repair and gene regulatory networks, and their emerging roles in genome organization during development and disease.
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Affiliation(s)
- Phillip Wulfridge
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA, USA
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Kavitha Sarma
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA, USA.
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA.
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38
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Lee YH, Hass EP, Campodonico W, Lee YK, Lasda E, Shah J, Rinn J, Hwang T. Massively parallel dissection of RNA in RNA-protein interactions in vivo. Nucleic Acids Res 2024; 52:e48. [PMID: 38726866 PMCID: PMC11162807 DOI: 10.1093/nar/gkae334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 04/10/2024] [Accepted: 04/16/2024] [Indexed: 06/11/2024] Open
Abstract
Many of the biological functions performed by RNA are mediated by RNA-binding proteins (RBPs), and understanding the molecular basis of these interactions is fundamental to biology. Here, we present massively parallel RNA assay combined with immunoprecipitation (MPRNA-IP) for in vivo high-throughput dissection of RNA-protein interactions and describe statistical models for identifying RNA domains and parsing the structural contributions of RNA. By using custom pools of tens of thousands of RNA sequences containing systematically designed truncations and mutations, MPRNA-IP is able to identify RNA domains, sequences, and secondary structures necessary and sufficient for protein binding in a single experiment. We show that this approach is successful for multiple RNAs of interest, including the long noncoding RNA NORAD, bacteriophage MS2 RNA, and human telomerase RNA, and we use it to interrogate the hitherto unknown sequence or structural RNA-binding preferences of the DNA-looping factor CTCF. By integrating systematic mutation analysis with crosslinking immunoprecipitation, MPRNA-IP provides a novel high-throughput way to elucidate RNA-based mechanisms behind RNA-protein interactions in vivo.
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Affiliation(s)
- Yu Hsuan Lee
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
| | - Evan P Hass
- Department of Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, CO 80309, USA
| | - Will Campodonico
- Department of Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, CO 80309, USA
| | - Yong Kyu Lee
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
| | - Erika Lasda
- Department of Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, CO 80309, USA
| | - Jaynish S Shah
- Department of Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, CO 80309, USA
| | - John L Rinn
- Department of Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, CO 80309, USA
| | - Taeyoung Hwang
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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39
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Cantile M, Belli V, Scognamiglio G, Martorana A, De Pietro G, Tracey M, Budillon A. The role of HOTAIR in the modulation of resistance to anticancer therapy. Front Mol Biosci 2024; 11:1414651. [PMID: 38887279 PMCID: PMC11181001 DOI: 10.3389/fmolb.2024.1414651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Accepted: 05/10/2024] [Indexed: 06/20/2024] Open
Abstract
Leading anti-tumour therapeutic strategies typically involve surgery and radiotherapy for locally advanced (non-metastatic) cancers, while hormone therapy, chemotherapy, and molecular targeted therapy are the current treatment options for metastatic cancer. Despite the initially high sensitivity rate to anticancer therapies, a large number of patients develop resistance, leading to a poor prognosis. The mechanisms related to drug resistance are highly complex, and long non-coding RNAs appear to play a crucial role in these processes. Among these, the lncRNA homeobox transcript antisense intergenic RNA (HOTAIR), widely implicated in cancer initiation and progression, likewise plays a significant role in anticancer drug resistance. It can modulate cell activities such as proliferation, apoptosis, hypoxia, autophagy, as well as epithelial-mesenchymal transition, thereby contributing to the development of resistant tumour cells. In this manuscript, we describe different mechanisms of antitumor drug resistance in which HOTAIR is involved and suggest its potential as a therapeutic predictive biomarker for the management of cancer patients.
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Affiliation(s)
- Monica Cantile
- Scientific Directorate, Istituto Nazionale Tumori IRCCS Fondazione G. Pascale, Naples, Italy
| | - Valentina Belli
- Scientific Directorate, Istituto Nazionale Tumori IRCCS Fondazione G. Pascale, Naples, Italy
| | - Giosuè Scognamiglio
- Scientific Directorate, Istituto Nazionale Tumori IRCCS Fondazione G. Pascale, Naples, Italy
| | - Anna Martorana
- Scientific Directorate, Istituto Nazionale Tumori IRCCS Fondazione G. Pascale, Naples, Italy
| | - Giovanna De Pietro
- Scientific Directorate, Istituto Nazionale Tumori IRCCS Fondazione G. Pascale, Naples, Italy
| | - Maura Tracey
- Rehabilitation Medicine Unit, Istituto Nazionale Tumori IRCCS Fondazione G. Pascale, Naples, Italy
| | - Alfredo Budillon
- Scientific Directorate, Istituto Nazionale Tumori IRCCS Fondazione G. Pascale, Naples, Italy
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40
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Gibbons MD, Bungert J. GATA2: sense and (anti)sensibility. Blood 2024; 143:2224-2225. [PMID: 38814656 DOI: 10.1182/blood.2024024549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2024] Open
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41
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Lee YW, Weissbein U, Blum R, Lee JT. G-quadruplex folding in Xist RNA antagonizes PRC2 activity for stepwise regulation of X chromosome inactivation. Mol Cell 2024; 84:1870-1885.e9. [PMID: 38759625 PMCID: PMC11505738 DOI: 10.1016/j.molcel.2024.04.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 11/25/2023] [Accepted: 04/19/2024] [Indexed: 05/19/2024]
Abstract
How Polycomb repressive complex 2 (PRC2) is regulated by RNA remains an unsolved problem. Although PRC2 binds G-tracts with the potential to form RNA G-quadruplexes (rG4s), whether rG4s fold extensively in vivo and whether PRC2 binds folded or unfolded rG4 are unknown. Using the X-inactivation model in mouse embryonic stem cells, here we identify multiple folded rG4s in Xist RNA and demonstrate that PRC2 preferentially binds folded rG4s. High-affinity rG4 binding inhibits PRC2's histone methyltransferase activity, and stabilizing rG4 in vivo antagonizes H3 at lysine 27 (H3K27me3) enrichment on the inactive X chromosome. Surprisingly, mutagenizing the rG4 does not affect PRC2 recruitment but promotes its release and catalytic activation on chromatin. H3K27me3 marks are misplaced, however, and gene silencing is compromised. Xist-PRC2 complexes become entrapped in the S1 chromosome compartment, precluding the required translocation into the S2 compartment. Thus, Xist rG4 folding controls PRC2 activity, H3K27me3 enrichment, and the stepwise regulation of chromosome-wide gene silencing.
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Affiliation(s)
- Yong Woo Lee
- Department of Molecular Biology, Massachusetts General Hospital and Department of Genetics, Harvard Medical School, Boston, MA 02114, USA
| | - Uri Weissbein
- Department of Molecular Biology, Massachusetts General Hospital and Department of Genetics, Harvard Medical School, Boston, MA 02114, USA
| | - Roy Blum
- Department of Molecular Biology, Massachusetts General Hospital and Department of Genetics, Harvard Medical School, Boston, MA 02114, USA
| | - Jeannie T Lee
- Department of Molecular Biology, Massachusetts General Hospital and Department of Genetics, Harvard Medical School, Boston, MA 02114, USA.
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42
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Friedman MJ, Wagner T, Lee H, Rosenfeld MG, Oh S. Enhancer-promoter specificity in gene transcription: molecular mechanisms and disease associations. Exp Mol Med 2024; 56:772-787. [PMID: 38658702 PMCID: PMC11058250 DOI: 10.1038/s12276-024-01233-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 02/28/2024] [Accepted: 03/05/2024] [Indexed: 04/26/2024] Open
Abstract
Although often located at a distance from their target gene promoters, enhancers are the primary genomic determinants of temporal and spatial transcriptional specificity in metazoans. Since the discovery of the first enhancer element in simian virus 40, there has been substantial interest in unraveling the mechanism(s) by which enhancers communicate with their partner promoters to ensure proper gene expression. These research efforts have benefited considerably from the application of increasingly sophisticated sequencing- and imaging-based approaches in conjunction with innovative (epi)genome-editing technologies; however, despite various proposed models, the principles of enhancer-promoter interaction have still not been fully elucidated. In this review, we provide an overview of recent progress in the eukaryotic gene transcription field pertaining to enhancer-promoter specificity. A better understanding of the mechanistic basis of lineage- and context-dependent enhancer-promoter engagement, along with the continued identification of functional enhancers, will provide key insights into the spatiotemporal control of gene expression that can reveal therapeutic opportunities for a range of enhancer-related diseases.
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Affiliation(s)
- Meyer J Friedman
- Department and School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Tobias Wagner
- Department and School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Haram Lee
- College of Pharmacy Korea University, 2511 Sejong-ro, Sejong, 30019, Republic of Korea
| | - Michael G Rosenfeld
- Department and School of Medicine, University of California, San Diego, La Jolla, CA, USA.
| | - Soohwan Oh
- College of Pharmacy Korea University, 2511 Sejong-ro, Sejong, 30019, Republic of Korea.
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