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Button AC, Hall SD, Ashley EL, McHugh CA. Dissection of protein and RNA regions required for SPEN binding to XIST A-repeat RNA. RNA (NEW YORK, N.Y.) 2024; 30:240-255. [PMID: 38164599 PMCID: PMC10870365 DOI: 10.1261/rna.079713.123] [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: 08/24/2023] [Accepted: 12/06/2023] [Indexed: 01/03/2024]
Abstract
XIST noncoding RNA promotes the initiation of X chromosome silencing by recruiting the protein SPEN to one X chromosome in female mammals. The SPEN protein is also called SHARP (SMRT and HDAC-associated repressor protein) and MINT (Msx-2 interacting nuclear target) in humans. SPEN recruits N-CoR2 and HDAC3 to initiate histone deacetylation on the X chromosome, leading to the formation of repressive chromatin marks and silencing gene expression. We dissected the contributions of different RNA and protein regions to the formation of a human XIST-SPEN complex in vitro and identified novel sequence and structure determinants that may contribute to X chromosome silencing initiation. Binding of SPEN to XIST RNA requires RRM 4 of the protein, in contrast to the requirement of RRM 3 and RRM 4 for specific binding to SRA RNA. Measurements of SPEN binding to full-length, dimeric, trimeric, or other truncated versions of the A-repeat region revealed that high-affinity binding of XIST to SPEN in vitro requires a minimum of four A-repeat segments. SPEN binding to XIST A-repeat RNA changes the accessibility of the RNA at specific nucleotide sequences, as indicated by changes in RNA reactivity through chemical structure probing. Based on computational modeling, we found that inter-repeat duplexes formed by multiple A-repeats can present an unpaired adenosine in the context of a double-stranded region of RNA. The presence of this specific combination of sequence and structural motifs correlates with high-affinity SPEN binding in vitro. These data provide new information on the molecular basis of the XIST and SPEN interaction.
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Affiliation(s)
- Aileen C Button
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA
| | - Simone D Hall
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA
| | - Ethan L Ashley
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA
| | - Colleen A McHugh
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA
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2
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Yuan C, Hu Y, Liu Q, Xu J, Zhou W, Yu H, Shen L, Qin C. MED8 regulates floral transition in Arabidopsis by interacting with FPA. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:1234-1247. [PMID: 37565662 DOI: 10.1111/tpj.16419] [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: 05/18/2023] [Revised: 07/04/2023] [Accepted: 07/31/2023] [Indexed: 08/12/2023]
Abstract
Success in plant reproduction is highly dependent on the correct timing of the floral transition, which is tightly regulated by the flowering pathways. In the model plant Arabidopsis thaliana, the central flowering repressor FLOWERING LOCUS C (FLC) is precisely regulated by multiple flowering time regulators in the vernalization pathway and autonomous pathway, including FPA. Here we report that Arabidopsis MEDIATOR SUBUNIT 8 (MED8) promotes floral transition in Arabidopsis by recruiting FPA to the FLC locus to repress FLC expression. Loss of MED8 function leads to a significant late-flowering phenotype due to increased FLC expression. We further show that MED8 directly interacts with FPA in the nucleus and recruits FPA to the FLC locus. Moreover, MED8 is indispensable for FPA's function in controlling flowering time and regulating FLC expression. Our study thus reveals a flowering mechanism by which the Mediator subunit MED8 represses FLC expression by facilitating the binding of FPA to the FLC locus to ensure appropriate timing of flowering for reproductive success.
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Affiliation(s)
- Chen Yuan
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Yikai Hu
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Qinggang Liu
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Jingya Xu
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Wei Zhou
- Temasek Life Sciences Laboratory, National University of Singapore, 117604, Singapore
| | - Hao Yu
- Temasek Life Sciences Laboratory, National University of Singapore, 117604, Singapore
- Department of Biological Sciences, Faculty of Science, National University of Singapore, 117543, Singapore
| | - Lisha Shen
- Temasek Life Sciences Laboratory, National University of Singapore, 117604, Singapore
| | - Cheng Qin
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China
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3
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Kaufmann C, Wutz A. IndiSPENsable for X Chromosome Inactivation and Gene Silencing. EPIGENOMES 2023; 7:28. [PMID: 37987303 PMCID: PMC10660550 DOI: 10.3390/epigenomes7040028] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 10/23/2023] [Accepted: 10/30/2023] [Indexed: 11/22/2023] Open
Abstract
For about 30 years, SPEN has been the subject of research in many different fields due to its variety of functions and its conservation throughout a wide spectrum of species, like worms, arthropods, and vertebrates. To date, 216 orthologues have been documented. SPEN had been studied for its role in gene regulation in the context of cell signaling, including the NOTCH or nuclear hormone receptor signaling pathways. More recently, SPEN has been identified as a major regulator of initiation of chromosome-wide gene silencing during X chromosome inactivation (XCI) in mammals, where its function remains to be fully understood. Dependent on the biological context, SPEN functions via mechanisms which include different domains. While some domains of SPEN are highly conserved in sequence and secondary structure, species-to-species differences exist that might lead to mechanistic differences. Initiation of XCI appears to be different between humans and mice, which raises additional questions about the extent of generalization of SPEN's function in XCI. In this review, we dissect the mechanism of SPEN in XCI. We discuss its subregions and domains, focusing on its role as a major regulator. We further highlight species-related research, specifically of mouse and human SPEN, with the aim to reveal and clarify potential species-to-species differences in SPEN's function.
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Affiliation(s)
| | - Anton Wutz
- Institute of Molecular Health Sciences, Department of Biology, Swiss Federal Institute of Technology ETH Hönggerberg, 8093 Zurich, Switzerland;
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4
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Yang ZY, Yan XC, Zhang JYL, Liang L, Gao CC, Zhang PR, Liu Y, Sun JX, Ruan B, Duan JL, Wang RN, Feng XX, Che B, Xiao T, Han H. Repression of rRNA gene transcription by endothelial SPEN deficiency normalizes tumor vasculature via nucleolar stress. J Clin Invest 2023; 133:e159860. [PMID: 37607001 PMCID: PMC10575731 DOI: 10.1172/jci159860] [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: 03/03/2022] [Accepted: 08/17/2023] [Indexed: 08/23/2023] Open
Abstract
Human cancers induce a chaotic, dysfunctional vasculature that promotes tumor growth and blunts most current therapies; however, the mechanisms underlying the induction of a dysfunctional vasculature have been unclear. Here, we show that split end (SPEN), a transcription repressor, coordinates rRNA synthesis in endothelial cells (ECs) and is required for physiological and tumor angiogenesis. SPEN deficiency attenuated EC proliferation and blunted retinal angiogenesis, which was attributed to p53 activation. Furthermore, SPEN knockdown activated p53 by upregulating noncoding promoter RNA (pRNA), which represses rRNA transcription and triggers p53-mediated nucleolar stress. In human cancer biopsies, a low endothelial SPEN level correlated with extended overall survival. In mice, endothelial SPEN deficiency compromised rRNA expression and repressed tumor growth and metastasis by normalizing tumor vessels, and this was abrogated by p53 haploinsufficiency. rRNA gene transcription is driven by RNA polymerase I (RNPI). We found that CX-5461, an RNPI inhibitor, recapitulated the effect of Spen ablation on tumor vessel normalization and combining CX-5461 with cisplatin substantially improved the efficacy of treating tumors in mice. Together, these results demonstrate that SPEN is required for angiogenesis by repressing pRNA to enable rRNA gene transcription and ribosomal biogenesis and that RNPI represents a target for tumor vessel normalization therapy of cancer.
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Hamilton JS, Piria M, Gavrilović A, Mrkonjić Fuka M, Svečnjak L, Nikolić S, Bakiu R, Gardner JPA. Limited population genetic variation but pronounced seascape genetic structuring in populations of the Mediterranean mussel ( Mytilus galloprovincialis) from the eastern Adriatic Sea. Ecol Evol 2023; 13:e9729. [PMID: 36713489 PMCID: PMC9873513 DOI: 10.1002/ece3.9729] [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: 08/25/2022] [Revised: 12/15/2022] [Accepted: 12/23/2022] [Indexed: 01/26/2023] Open
Abstract
Population genetic analysis of variation at five neutral microsatellite loci for Mediterranean mussels (Mytilus galloprovincialis) from 18 sites along the eastern Adriatic Sea revealed little or no spatial variation. In contrast, seascape genetics analysis revealed a pronounced locus-specific gradient in allelic and genotypic frequencies across the study region. At a sixth locus, MGE7, the frequencies of two alleles, MGE7243 and MGE7249, were strongly associated, negatively and positively, respectively, with a single environmental variable - minimum salinity (minSAL). The frequency of the MGE7243/243 homozygous genotype was strongly negatively associated with minSAL, whereas the frequencies of the MGE7246/249 and the MGE7249/249 genotypes were strongly positively correlated with minSAL. Interpretation of these pronounced gradients is confounded by the fact that minSAL and another environmental variable, maximum sea surface temperature (maxSST), are highly correlated (R = -.911) and are therefore not necessarily acting independently. BLAST searches of the MGE7 locus against M. galloprovincialis whole genome shotgun sequence returned an alignment with contig mg10_S01094 (accession UYJE01010330.1) and 7 predicted M. galloprovincialis proteins VDI82194.1 - VDI82200.1. Conserved domain searches revealed a similar structure to the transcriptional regulator Msx2-interacting protein. The BLASTp search also returned significant alignments to Msx2-interacting proteins in Mytilus coruscus, Crassostrea virginica, and Haliotis rubra. The existence of the MGE7 gradient highlights the role that environmental variation may play in retarding gene flow among wild M. galloprovincialis populations, and also how the success of collection of young mussels (spat) from one site and their transfer to another site (the farm) may be influenced by a single factor such as minSAL or maxSST on a localized scale.
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Affiliation(s)
- Joanna S. Hamilton
- School of Biological SciencesVictoria University of WellingtonWellingtonNew Zealand
| | - Marina Piria
- Department of Fisheries, Apiculture, Faculty of Agriculture, Wildlife Management and Special ZoologyUniversity of ZagrebZagrebCroatia,Department of Ecology and Vertebrate Zoology, Faculty of Biology and Environmental ProtectionUniversity of ŁódźŁódźPoland
| | - Ana Gavrilović
- Department of Fisheries, Apiculture, Faculty of Agriculture, Wildlife Management and Special ZoologyUniversity of ZagrebZagrebCroatia
| | - Mirna Mrkonjić Fuka
- Department of Microbiology, Faculty of AgricultureUniversity of ZagrebZagrebCroatia
| | - Lidija Svečnjak
- Department of Fisheries, Apiculture, Faculty of Agriculture, Wildlife Management and Special ZoologyUniversity of ZagrebZagrebCroatia
| | - Slađana Nikolić
- Institute of Marine BiologyUniversity of MontenegroKotorMontenegro
| | - Rigers Bakiu
- Department of Aquaculture and Fisheries, Faculty of Agriculture and EnvironmentAgricultural University of TiranaTiranaAlbania,Albanian Center for Environmental Protection and Sustainable DevelopmentTiranaAlbania
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Xist spatially amplifies SHARP/SPEN recruitment to balance chromosome-wide silencing and specificity to the X chromosome. Nat Struct Mol Biol 2022; 29:239-249. [PMID: 35301492 DOI: 10.1038/s41594-022-00739-1] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 01/28/2022] [Indexed: 11/08/2022]
Abstract
Although thousands of long non-coding RNAs (lncRNAs) are encoded in mammalian genomes, their mechanisms of action are poorly understood, in part because they are often expressed at lower levels than their proposed targets. One such lncRNA is Xist, which mediates chromosome-wide gene silencing on one of the two X chromosomes (X) to achieve gene expression balance between males and females. How a limited number of Xist molecules can mediate robust silencing of a much larger number of target genes while maintaining specificity exclusively to genes on the X within each cell is not well understood. Here, we show that Xist drives non-stoichiometric recruitment of the essential silencing protein SHARP (also known as SPEN) to amplify its abundance across the inactive X, including at regions not directly occupied by Xist. This amplification is achieved through concentration-dependent homotypic assemblies of SHARP on the X and is required for chromosome-wide silencing. Expression of Xist at higher levels leads to increased localization at autosomal regions, demonstrating that low levels of Xist are critical for ensuring its specificity to the X. We show that Xist (through SHARP) acts to suppress production of its own RNA which may act to constrain overall RNA levels and restrict its ability to spread beyond the X. Together, our results demonstrate a spatial amplification mechanism that allows Xist to achieve two essential but countervailing regulatory objectives: chromosome-wide gene silencing and specificity to the X. This suggests a more general mechanism by which other low-abundance lncRNAs could balance specificity to, and robust control of, their regulatory targets.
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7
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Sanbonmatsu K. Towards Molecular Mechanism in Long Non-coding RNAs: Linking Structure and Function. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1363:23-32. [DOI: 10.1007/978-3-030-92034-0_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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8
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Sanbonmatsu K. Getting to the bottom of lncRNA mechanism: structure-function relationships. Mamm Genome 2021; 33:343-353. [PMID: 34642784 PMCID: PMC8509902 DOI: 10.1007/s00335-021-09924-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 09/28/2021] [Indexed: 12/14/2022]
Abstract
While long non-coding RNAs are known to play key roles in disease and development, relatively few structural studies have been performed for this important class of RNAs. Here, we review functional studies of long non-coding RNAs and expose the need for high-resolution 3-D structural studies, discussing the roles of long non-coding RNAs in the cell and how structure–function relationships might be used to elucidate further understanding. We then describe structural studies of other classes of RNAs using chemical probing, nuclear magnetic resonance, small-angle X-ray scattering, X-ray crystallography, and cryogenic electron microscopy (cryo-EM). Next, we review early structural studies of long non-coding RNAs to date and describe the way forward for the structural biology of long non-coding RNAs in terms of cryo-EM.
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9
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Giaimo BD, Robert-Finestra T, Oswald F, Gribnau J, Borggrefe T. Chromatin Regulator SPEN/SHARP in X Inactivation and Disease. Cancers (Basel) 2021; 13:cancers13071665. [PMID: 33916248 PMCID: PMC8036811 DOI: 10.3390/cancers13071665] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 03/26/2021] [Accepted: 03/26/2021] [Indexed: 12/14/2022] Open
Abstract
Simple Summary Carcinogenesis is a multistep process involving not only the activation of oncogenes and disabling tumor suppressor genes, but also epigenetic modulation of gene expression. X chromosome inactivation (XCI) is a paradigm to study heterochromatin formation and maintenance. The double dosage of X chromosomal genes in female mammals is incompatible with early development. XCI is an excellent model system for understanding the establishment of facultative heterochromatin initiated by the expression of a 17,000 nt long non-coding RNA, known as Xinactivespecifictranscript (Xist), on the X chromosome. This review focuses on the molecular mechanisms of how epigenetic modulators act in a step-wise manner to establish facultative heterochromatin, and we put these in the context of cancer biology and disease. An in depth understanding of XCI will allow a better characterization of particular types of cancer and hopefully facilitate the development of novel epigenetic therapies. Abstract Enzymes, such as histone methyltransferases and demethylases, histone acetyltransferases and deacetylases, and DNA methyltransferases are known as epigenetic modifiers that are often implicated in tumorigenesis and disease. One of the best-studied chromatin-based mechanism is X chromosome inactivation (XCI), a process that establishes facultative heterochromatin on only one X chromosome in females and establishes the right dosage of gene expression. The specificity factor for this process is the long non-coding RNA Xinactivespecifictranscript (Xist), which is upregulated from one X chromosome in female cells. Subsequently, Xist is bound by the corepressor SHARP/SPEN, recruiting and/or activating histone deacetylases (HDACs), leading to the loss of active chromatin marks such as H3K27ac. In addition, polycomb complexes PRC1 and PRC2 establish wide-spread accumulation of H3K27me3 and H2AK119ub1 chromatin marks. The lack of active marks and establishment of repressive marks set the stage for DNA methyltransferases (DNMTs) to stably silence the X chromosome. Here, we will review the recent advances in understanding the molecular mechanisms of how heterochromatin formation is established and put this into the context of carcinogenesis and disease.
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Affiliation(s)
- Benedetto Daniele Giaimo
- Institute of Biochemistry, University of Giessen, Friedrichstrasse 24, 35392 Giessen, Germany
- Correspondence: (B.D.G.); (T.B.); Tel.: +49-641-9947-400 (T.B.)
| | - Teresa Robert-Finestra
- Department of Developmental Biology, Erasmus MC, Oncode Institute, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands; (T.R.-F.); (J.G.)
| | - Franz Oswald
- Center for Internal Medicine, Department of Internal Medicine I, University Medical Center Ulm, Albert-Einstein-Allee 23, 89081 Ulm, Germany;
| | - Joost Gribnau
- Department of Developmental Biology, Erasmus MC, Oncode Institute, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands; (T.R.-F.); (J.G.)
| | - Tilman Borggrefe
- Institute of Biochemistry, University of Giessen, Friedrichstrasse 24, 35392 Giessen, Germany
- Correspondence: (B.D.G.); (T.B.); Tel.: +49-641-9947-400 (T.B.)
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10
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Rambout X, Maquat LE. NCBP3: A Multifaceted Adaptive Regulator of Gene Expression. Trends Biochem Sci 2020; 46:87-96. [PMID: 33032857 DOI: 10.1016/j.tibs.2020.09.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 08/31/2020] [Accepted: 09/08/2020] [Indexed: 12/29/2022]
Abstract
Eukaryotic cells have divided the steps of gene expression between their nucleus and cytoplasm. Protein-encoding genes generate mRNAs in the nucleus and mRNAs undergo transport to the cytoplasm for the purpose of producing proteins. Cap-binding protein (CBP)20 and its binding partner CBP80 have been thought to constitute the cap-binding complex (CBC) that is acquired co-transcriptionally by the precursors of all mRNAs. However, this principle has recently been challenged by studies of nuclear cap-binding protein 3 (NCBP3). Here we submit how NCBP3, as an alternative to CBP20, an accessory to the canonical CBP20-CBP80 CBC, and/or an RNA-binding protein - possibly in association with the exon-junction complex (EJC) - expands the capacity of cells to regulate gene expression.
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Affiliation(s)
- Xavier Rambout
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA; Center for RNA Biology, University of Rochester, Rochester, NY 14642, USA
| | - Lynne E Maquat
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA; Center for RNA Biology, University of Rochester, Rochester, NY 14642, USA.
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11
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Jones AN, Sattler M. Challenges and perspectives for structural biology of lncRNAs-the example of the Xist lncRNA A-repeats. J Mol Cell Biol 2020; 11:845-859. [PMID: 31336384 PMCID: PMC6917512 DOI: 10.1093/jmcb/mjz086] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 06/30/2019] [Accepted: 07/02/2019] [Indexed: 12/21/2022] Open
Abstract
Following the discovery of numerous long non-coding RNA (lncRNA) transcripts in the human genome, their important roles in biology and human disease are emerging. Recent progress in experimental methods has enabled the identification of structural features of lncRNAs. However, determining high-resolution structures is challenging as lncRNAs are expected to be dynamic and adopt multiple conformations, which may be modulated by interaction with protein binding partners. The X-inactive specific transcript (Xist) is necessary for X inactivation during dosage compensation in female placental mammals and one of the best-studied lncRNAs. Recent progress has provided new insights into the domain organization, molecular features, and RNA binding proteins that interact with distinct regions of Xist. The A-repeats located at the 5′ end of the transcript are of particular interest as they are essential for mediating silencing of the inactive X chromosome. Here, we discuss recent progress with elucidating structural features of the Xist lncRNA, focusing on the A-repeats. We discuss the experimental and computational approaches employed that have led to distinct structural models, likely reflecting the intrinsic dynamics of this RNA. The presence of multiple dynamic conformations may also play an important role in the formation of the associated RNPs, thus influencing the molecular mechanism underlying the biological function of the Xist A-repeats. We propose that integrative approaches that combine biochemical experiments and high-resolution structural biology in vitro with chemical probing and functional studies in vivo are required to unravel the molecular mechanisms of lncRNAs.
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Affiliation(s)
- Alisha N Jones
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, 85764, Germany.,Center for Integrated Protein Science Munich and Bavarian NMR Center at Department of Chemistry, Technical University of Munich, Garching, 85747, Germany
| | - Michael Sattler
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, 85764, Germany.,Center for Integrated Protein Science Munich and Bavarian NMR Center at Department of Chemistry, Technical University of Munich, Garching, 85747, Germany
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12
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Abstract
The X inactive-specific transcript (Xist) gene is the master regulator of X chromosome inactivation in mammals. Xist produces a long noncoding (lnc)RNA that accumulates over the entire length of the chromosome from which it is transcribed, recruiting factors to modify underlying chromatin and silence X-linked genes in cis Recent years have seen significant progress in identifying important functional elements in Xist RNA, their associated RNA-binding proteins (RBPs), and the downstream pathways for chromatin modification and gene silencing. In this review, we summarize progress in understanding both how these pathways function in Xist-mediated silencing and the complex interplay between them.
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Affiliation(s)
- Neil Brockdorff
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Joseph S Bowness
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Guifeng Wei
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
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13
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Carter AC, Xu J, Nakamoto MY, Wei Y, Zarnegar BJ, Shi Q, Broughton JP, Ransom RC, Salhotra A, Nagaraja SD, Li R, Dou DR, Yost KE, Cho SW, Mistry A, Longaker MT, Khavari PA, Batey RT, Wuttke DS, Chang HY. Spen links RNA-mediated endogenous retrovirus silencing and X chromosome inactivation. eLife 2020; 9:e54508. [PMID: 32379046 PMCID: PMC7282817 DOI: 10.7554/elife.54508] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 05/05/2020] [Indexed: 12/12/2022] Open
Abstract
The Xist lncRNA mediates X chromosome inactivation (XCI). Here we show that Spen, an Xist-binding repressor protein essential for XCI , binds to ancient retroviral RNA, performing a surveillance role to recruit chromatin silencing machinery to these parasitic loci. Spen loss activates a subset of endogenous retroviral (ERV) elements in mouse embryonic stem cells, with gain of chromatin accessibility, active histone modifications, and ERV RNA transcription. Spen binds directly to ERV RNAs that show structural similarity to the A-repeat of Xist, a region critical for Xist-mediated gene silencing. ERV RNA and Xist A-repeat bind the RRM domains of Spen in a competitive manner. Insertion of an ERV into an A-repeat deficient Xist rescues binding of Xist RNA to Spen and results in strictly local gene silencing in cis. These results suggest that Xist may coopt transposable element RNA-protein interactions to repurpose powerful antiviral chromatin silencing machinery for sex chromosome dosage compensation.
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Affiliation(s)
- Ava C Carter
- Center for Personal Dynamic Regulomes, Stanford UniversityStanfordUnited States
| | - Jin Xu
- Center for Personal Dynamic Regulomes, Stanford UniversityStanfordUnited States
| | - Meagan Y Nakamoto
- Department of Biochemistry, University of ColoradoBoulderUnited States
| | - Yuning Wei
- Center for Personal Dynamic Regulomes, Stanford UniversityStanfordUnited States
| | - Brian J Zarnegar
- Department of Dermatology, Stanford University School of MedicineStanfordUnited States
| | - Quanming Shi
- Center for Personal Dynamic Regulomes, Stanford UniversityStanfordUnited States
| | - James P Broughton
- Center for Personal Dynamic Regulomes, Stanford UniversityStanfordUnited States
| | - Ryan C Ransom
- Department of Surgery, Division of Plastic and Reconstructive Surgery, Stanford University School of MedicineStanfordUnited States
| | - Ankit Salhotra
- Department of Surgery, Division of Plastic and Reconstructive Surgery, Stanford University School of MedicineStanfordUnited States
| | - Surya D Nagaraja
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford UniversityStanfordUnited States
| | - Rui Li
- Center for Personal Dynamic Regulomes, Stanford UniversityStanfordUnited States
| | - Diana R Dou
- Center for Personal Dynamic Regulomes, Stanford UniversityStanfordUnited States
| | - Kathryn E Yost
- Center for Personal Dynamic Regulomes, Stanford UniversityStanfordUnited States
| | - Seung-Woo Cho
- Center for Personal Dynamic Regulomes, Stanford UniversityStanfordUnited States
| | - Anil Mistry
- Novartis Institute for Biomedical ResearchCambridgeUnited States
| | - Michael T Longaker
- Department of Surgery, Division of Plastic and Reconstructive Surgery, Stanford University School of MedicineStanfordUnited States
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford UniversityStanfordUnited States
| | - Paul A Khavari
- Department of Dermatology, Stanford University School of MedicineStanfordUnited States
| | - Robert T Batey
- Department of Biochemistry, University of ColoradoBoulderUnited States
| | - Deborah S Wuttke
- Department of Biochemistry, University of ColoradoBoulderUnited States
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford UniversityStanfordUnited States
- Department of Dermatology, Stanford University School of MedicineStanfordUnited States
- Howard Hughes Medical Institute, Stanford UniversityStanfordUnited States
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14
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Zampetaki A, Albrecht A, Steinhofel K. Long Non-coding RNA Structure and Function: Is There a Link? Front Physiol 2018; 9:1201. [PMID: 30197605 PMCID: PMC6117379 DOI: 10.3389/fphys.2018.01201] [Citation(s) in RCA: 151] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 08/10/2018] [Indexed: 01/12/2023] Open
Abstract
RNA has emerged as the prime target for diagnostics, therapeutics and the development of personalized medicine. In particular, the non-coding RNAs (ncRNAs) that do not encode proteins, display remarkable biochemical versatility. They can fold into complex structures and interact with proteins, DNA and other RNAs, modulating the activity, DNA targets or partners of multiprotein complexes. Thus, ncRNAs confer regulatory plasticity and represent a new layer of epigenetic control that is dysregulated in disease. Intriguingly, for long non-coding RNAs (lncRNAs, >200 nucleotides length) structural conservation rather than nucleotide sequence conservation seems to be crucial for maintaining their function. LncRNAs tend to acquire complex secondary and tertiary structures and their functions only impose very subtle sequence constraints. In the present review we will discuss the biochemical assays that can be employed to determine the lncRNA structural configurations. The implications and challenges of linking function and lncRNA structure to design novel RNA therapeutic approaches will also be analyzed.
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Affiliation(s)
- Anna Zampetaki
- King's British Heart Foundation Centre, King's College London, London, United Kingdom
| | - Andreas Albrecht
- Faculty of Science and Technology, Middlesex University, London, United Kingdom
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15
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Lu Z, Carter AC, Chang HY. Mechanistic insights in X-chromosome inactivation. Philos Trans R Soc Lond B Biol Sci 2018; 372:rstb.2016.0356. [PMID: 28947655 DOI: 10.1098/rstb.2016.0356] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/09/2017] [Indexed: 11/12/2022] Open
Abstract
X-chromosome inactivation (XCI) is a critical epigenetic mechanism for balancing gene dosage between XY males and XX females in eutherian mammals. A long non-coding RNA (lncRNA), XIST, and its associated proteins orchestrate this multi-step process, resulting in the inheritable silencing of one of the two X-chromosomes in females. The XIST RNA is large and complex, exemplifying the unique challenges associated with the structural and functional analysis of lncRNAs. Recent technological advances in the analysis of macromolecular structure and interactions have enabled us to systematically dissect the XIST ribonucleoprotein complex, which is larger than the ribosome, and its place of action, the inactive X-chromosome. These studies shed light on key mechanisms of XCI, such as XIST coating of the X-chromosome, recruitment of DNA, RNA and histone modification enzymes, and compaction and compartmentalization of the inactive X. Here, we summarize recent studies on XCI, highlight the critical contributions of new technologies and propose a unifying model for XIST function in XCI where modular domains serve as the structural and functional units in both lncRNA-protein complexes and DNA-protein complexes in chromatin.This article is part of the themed issue 'X-chromosome inactivation: a tribute to Mary Lyon'.
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Affiliation(s)
- Zhipeng Lu
- Center for Dynamic Personal Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Ava C Carter
- Center for Dynamic Personal Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Howard Y Chang
- Center for Dynamic Personal Regulomes, Stanford University, Stanford, CA 94305, USA
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16
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Hawkes EJ, Hennelly SP, Novikova IV, Irwin JA, Dean C, Sanbonmatsu KY. COOLAIR Antisense RNAs Form Evolutionarily Conserved Elaborate Secondary Structures. Cell Rep 2018; 16:3087-3096. [PMID: 27653675 DOI: 10.1016/j.celrep.2016.08.045] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Revised: 06/03/2016] [Accepted: 08/12/2016] [Indexed: 01/07/2023] Open
Abstract
There is considerable debate about the functionality of long non-coding RNAs (lncRNAs). Lack of sequence conservation has been used to argue against functional relevance. We investigated antisense lncRNAs, called COOLAIR, at the A. thaliana FLC locus and experimentally determined their secondary structure. The major COOLAIR variants are highly structured, organized by exon. The distally polyadenylated transcript has a complex multi-domain structure, altered by a single non-coding SNP defining a functionally distinct A. thaliana FLC haplotype. The A. thaliana COOLAIR secondary structure was used to predict COOLAIR exons in evolutionarily divergent Brassicaceae species. These predictions were validated through chemical probing and cloning. Despite the relatively low nucleotide sequence identity, the structures, including multi-helix junctions, show remarkable evolutionary conservation. In a number of places, the structure is conserved through covariation of a non-contiguous DNA sequence. This structural conservation supports a functional role for COOLAIR transcripts rather than, or in addition to, antisense transcription.
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Affiliation(s)
- Emily J Hawkes
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Scott P Hennelly
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA; New Mexico Consortium, Los Alamos, NM 87544, USA
| | - Irina V Novikova
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA; Pacific Northwest National Laboratory, Environmental Molecular Sciences Laboratory, Richland, WA 99354, USA
| | - Judith A Irwin
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Caroline Dean
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Karissa Y Sanbonmatsu
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA; New Mexico Consortium, Los Alamos, NM 87544, USA.
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17
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Pintacuda G, Young AN, Cerase A. Function by Structure: Spotlights on Xist Long Non-coding RNA. Front Mol Biosci 2017; 4:90. [PMID: 29302591 PMCID: PMC5742192 DOI: 10.3389/fmolb.2017.00090] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 12/05/2017] [Indexed: 12/29/2022] Open
Abstract
Recent experimental evidence indicates that lncRNAs can act as regulatory molecules in the context of development and disease. Xist, the master regulator of X chromosome inactivation, is a classic example of how lncRNAs can exert multi-layered and fine-tuned regulatory functions, by acting as a molecular scaffold for recruitment of distinct protein factors. In this review, we discuss the methodologies employed to define Xist RNA structures and the tight interplay between structural clues and functionality of lncRNAs. This model of modular function dictated by structure, can be also generalized to other lncRNAs, beyond the field of X chromosome inactivation, to explain common features of similarly folded RNAs.
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Affiliation(s)
- Greta Pintacuda
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | | | - Andrea Cerase
- European Molecular Biology Laboratory, Monterotondo, Italy
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18
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Expression of the RNA-binding protein RBP10 promotes the bloodstream-form differentiation state in Trypanosoma brucei. PLoS Pathog 2017; 13:e1006560. [PMID: 28800584 PMCID: PMC5568443 DOI: 10.1371/journal.ppat.1006560] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 08/23/2017] [Accepted: 07/29/2017] [Indexed: 01/06/2023] Open
Abstract
In nearly all eukaryotes, cellular differentiation is governed by changes in transcription, and stabilized by chromatin and DNA modification. Gene expression control in the pathogen Trypanosoma brucei, in contrast, relies almost exclusively on post-transcriptional mechanisms, so RNA binding proteins must assume the burden that is usually borne by transcription factors. T. brucei multiply in the blood of mammals as bloodstream forms, and in the midgut of Tsetse flies as procyclic forms. We show here that a single RNA-binding protein, RBP10, promotes the bloodstream-form trypanosome differentiation state. Depletion of RBP10 from bloodstream-form trypanosomes gives cells that can grow only as procyclic forms; conversely, expression of RBP10 in procyclic forms converts them to bloodstream forms. RBP10 binds to procyclic-specific mRNAs containing an UAUUUUUU motif, targeting them for translation repression and destruction. Products of RBP10 target mRNAs include not only the major procyclic surface protein and enzymes of energy metabolism, but also protein kinases and stage-specific RNA-binding proteins: this suggests that alterations in RBP10 trigger a regulatory cascade.
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19
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Novel players in X inactivation: insights into Xist-mediated gene silencing and chromosome conformation. Nat Struct Mol Biol 2017; 24:197-204. [DOI: 10.1038/nsmb.3370] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 01/05/2017] [Indexed: 02/07/2023]
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20
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Eichhorn CD, Chug R, Feigon J. hLARP7 C-terminal domain contains an xRRM that binds the 3' hairpin of 7SK RNA. Nucleic Acids Res 2016; 44:9977-9989. [PMID: 27679474 PMCID: PMC5175362 DOI: 10.1093/nar/gkw833] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 09/02/2016] [Accepted: 09/10/2016] [Indexed: 12/21/2022] Open
Abstract
The 7SK small nuclear ribonucleoprotein (snRNP) sequesters and inactivates the positive transcription elongation factor b (P-TEFb), an essential eukaryotic mRNA transcription factor. The human La-related protein group 7 (hLARP7) is a constitutive component of the 7SK snRNP and localizes to the 3' terminus of the 7SK long noncoding RNA. hLARP7, and in particular its C-terminal domain (CTD), is essential for 7SK RNA stability and assembly with P-TEFb. The hLARP7 N-terminal La module binds and protects the 3' end from degradation, but the structural and functional role of its CTD is unclear. We report the solution NMR structure of the hLARP7 CTD and show that this domain contains an xRRM, a class of atypical RRM first identified in the Tetrahymena thermophila telomerase LARP7 protein p65. The xRRM binds the 3' end of 7SK RNA at the top of stem-loop 4 (SL4) and interacts with both unpaired and base-paired nucleotides. This study confirms that the xRRM is general to the LARP7 family of proteins and defines the binding site for hLARP7 on the 7SK RNA, providing insight into function.
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Affiliation(s)
- Catherine D Eichhorn
- Department of Chemistry and Biochemistry, P.O. Box 951569, University of California, Los Angeles, CA 90095-1569, USA
| | - Rahul Chug
- Department of Chemistry and Biochemistry, P.O. Box 951569, University of California, Los Angeles, CA 90095-1569, USA
| | - Juli Feigon
- Department of Chemistry and Biochemistry, P.O. Box 951569, University of California, Los Angeles, CA 90095-1569, USA
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21
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Zhang Y, Rataj K, Simpson GG, Tong L. Crystal Structure of the SPOC Domain of the Arabidopsis Flowering Regulator FPA. PLoS One 2016; 11:e0160694. [PMID: 27513867 PMCID: PMC4981400 DOI: 10.1371/journal.pone.0160694] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 07/23/2016] [Indexed: 11/18/2022] Open
Abstract
The Arabidopsis protein FPA controls flowering time by regulating the alternative 3′-end processing of the FLOWERING LOCUS (FLC) antisense RNA. FPA belongs to the split ends (SPEN) family of proteins, which contain N-terminal RNA recognition motifs (RRMs) and a SPEN paralog and ortholog C-terminal (SPOC) domain. The SPOC domain is highly conserved among FPA homologs in plants, but the conservation with the domain in other SPEN proteins is much lower. We have determined the crystal structure of Arabidopsis thaliana FPA SPOC domain at 2.7 Å resolution. The overall structure is similar to that of the SPOC domain in human SMRT/HDAC1 Associated Repressor Protein (SHARP), although there are also substantial conformational differences between them. Structural and sequence analyses identify a surface patch that is conserved among plant FPA homologs. Mutations of two residues in this surface patch did not disrupt FPA functions, suggesting that either the SPOC domain is not required for the role of FPA in regulating RNA 3′-end formation or the functions of the FPA SPOC domain cannot be disrupted by the combination of mutations, in contrast to observations with the SHARP SPOC domain.
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Affiliation(s)
- Yinglu Zhang
- Department of Biological Sciences, Columbia University, New York, NY, 10027, United States of America
| | - Katarzyna Rataj
- Division Plant Sciences & Centre for Gene Regulation & Expression, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, Scotland, United Kingdom
| | - Gordon G. Simpson
- Division Plant Sciences & Centre for Gene Regulation & Expression, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, Scotland, United Kingdom
- Cell & Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, Scotland, United Kingdom
| | - Liang Tong
- Department of Biological Sciences, Columbia University, New York, NY, 10027, United States of America
- * E-mail:
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22
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Steroid receptor RNA activator: Biologic function and role in disease. Clin Chim Acta 2016; 459:137-146. [DOI: 10.1016/j.cca.2016.06.004] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 06/05/2016] [Accepted: 06/05/2016] [Indexed: 12/25/2022]
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23
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Foulds CE, Panigrahi AK, Coarfa C, Lanz RB, O'Malley BW. Long Noncoding RNAs as Targets and Regulators of Nuclear Receptors. Curr Top Microbiol Immunol 2016; 394:143-76. [PMID: 26362934 DOI: 10.1007/82_2015_465] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Intensive research has been directed at the discovery, biogenesis, and expression patterns of long noncoding RNAs , yet their biochemical functions have remained elusive for the most part. Nuclear receptors that interpret signaling mediated by small molecule hormones play a role in regulating the expression of some long noncoding RNAs. More importantly, these RNAs have also been shown to effect hormone-affected gene transcription regulated by the nuclear receptors. In this chapter, we summarize the current knowledge that has been acquired on hormonal signaling inducing expression of long noncoding RNAs and how they then may act in trans or in cis to modulate gene transcription. We highlight a few of these noncoding RNA molecules in terms of how they may impact hormone-driven cancers. Future directions critical for moving this field forward are presented, with a clear emphasis on the need for better biochemical approaches to address the mechanism of action of these exciting RNAs.
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Affiliation(s)
- Charles E Foulds
- Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Anil K Panigrahi
- Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Cristian Coarfa
- Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Rainer B Lanz
- Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Bert W O'Malley
- Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
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24
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Légaré S, Basik M. Minireview: The Link Between ERα Corepressors and Histone Deacetylases in Tamoxifen Resistance in Breast Cancer. Mol Endocrinol 2016; 30:965-76. [PMID: 27581354 DOI: 10.1210/me.2016-1072] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Approximately 70% of breast cancers express the estrogen receptor (ER)α and are treated with the ERα antagonist, tamoxifen. However, resistance to tamoxifen frequently develops in advanced breast cancer, in part due to a down-regulation of ERα corepressors. Nuclear receptor corepressors function by attenuating hormone responses and have been shown to potentiate tamoxifen action in various biological systems. Recent genomic data on breast cancers has revealed that genetic and/or genomic events target ERα corepressors in the majority of breast tumors, suggesting that the loss of nuclear receptor corepressor activity may represent an important mechanism that contributes to intrinsic and acquired tamoxifen resistance. Here, the biological functions of ERα corepressors are critically reviewed to elucidate their role in modifying endocrine sensitivity in breast cancer. We highlight a mechanism of gene repression common to corepressors previously shown to enhance the antitumorigenic effects of tamoxifen, which involves the recruitment of histone deacetylases (HDACs) to DNA. As an indicator of epigenetic disequilibrium, the loss of ERα corepressors may predispose cancer cells to the cytotoxic effects of HDAC inhibitors, a class of drug that has been shown to effectively reverse tamoxifen resistance in numerous studies. HDAC inhibition thus appears as a promising therapeutic approach that deserves to be further explored as an avenue to restore drug sensitivity in corepressor-deficient and tamoxifen-resistant breast cancers.
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Affiliation(s)
- Stéphanie Légaré
- Division of Experimental Medicine, Department of Oncology and Surgery, Segal Cancer Center, Lady Davis Institute for Medical Research, Sir Mortimer B. Davis Jewish General Hospital, McGill University, Montréal, Québec, Canada H3T 1E2
| | - Mark Basik
- Division of Experimental Medicine, Department of Oncology and Surgery, Segal Cancer Center, Lady Davis Institute for Medical Research, Sir Mortimer B. Davis Jewish General Hospital, McGill University, Montréal, Québec, Canada H3T 1E2
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25
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Obeid JP, Zafar N, El Hokayem J. Steroid Hormone Receptor Coregulators in Endocrine Cancers. IUBMB Life 2016; 68:504-15. [PMID: 27240871 DOI: 10.1002/iub.1517] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 05/11/2016] [Accepted: 05/11/2016] [Indexed: 01/14/2023]
Abstract
Coregulators span a broad and extensive domain in modulating cellular transcriptional activity. Studies have established a dynamic role for such coregulators in various endocrine cancers. Steroid hormone receptors (SHRs) play a pivotal role in such endocrine cancers, and interact abundantly with transcriptional coregulators in altering gene expression. Several families of coregulators have implications in propagating the development, progression and invasion of breast, prostate, and other hormone-responsive cancers. This mini-review aims to discuss different classes of coregulators involved in endocrine cancers and highlight unique information regarding each family with relevance to mechanism, intervention, and novel directions being investigated. © 2016 IUBMB Life, 68(7):504-515, 2016.
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Affiliation(s)
- Jean-Pierre Obeid
- Department of Biochemistry and Molecular Biology, University of Miami, FL, USA
| | - Nawal Zafar
- Department of Biochemistry and Molecular Biology, University of Miami, FL, USA
| | - Jimmy El Hokayem
- Department of Biochemistry and Molecular Biology, University of Miami, FL, USA
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26
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RNA Duplex Map in Living Cells Reveals Higher-Order Transcriptome Structure. Cell 2016; 165:1267-1279. [PMID: 27180905 DOI: 10.1016/j.cell.2016.04.028] [Citation(s) in RCA: 430] [Impact Index Per Article: 53.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 03/03/2016] [Accepted: 04/05/2016] [Indexed: 02/06/2023]
Abstract
RNA has the intrinsic property to base pair, forming complex structures fundamental to its diverse functions. Here, we develop PARIS, a method based on reversible psoralen crosslinking for global mapping of RNA duplexes with near base-pair resolution in living cells. PARIS analysis in three human and mouse cell types reveals frequent long-range structures, higher-order architectures, and RNA-RNA interactions in trans across the transcriptome. PARIS determines base-pairing interactions on an individual-molecule level, revealing pervasive alternative conformations. We used PARIS-determined helices to guide phylogenetic analysis of RNA structures and discovered conserved long-range and alternative structures. XIST, a long noncoding RNA (lncRNA) essential for X chromosome inactivation, folds into evolutionarily conserved RNA structural domains that span many kilobases. XIST A-repeat forms complex inter-repeat duplexes that nucleate higher-order assembly of the key epigenetic silencing protein SPEN. PARIS is a generally applicable and versatile method that provides novel insights into the RNA structurome and interactome. VIDEO ABSTRACT.
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27
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RNA binding proteins implicated in Xist-mediated chromosome silencing. Semin Cell Dev Biol 2016; 56:58-70. [PMID: 26816113 DOI: 10.1016/j.semcdb.2016.01.029] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 01/20/2016] [Accepted: 01/21/2016] [Indexed: 11/20/2022]
Abstract
Chromosome silencing by Xist RNA occurs in two steps; localisation in cis within the nuclear matrix to form a domain that corresponds to the territory of the inactive X chromosome elect, and transduction of silencing signals from Xist RNA to the underlying chromatin. Key factors that mediate these processes have been identified in a series of recent studies that harnessed comprehensive proteomic or genetic screening strategies. In this review we discuss these findings in light of prior knowledge both of Xist-mediated silencing and known functions/properties of the novel factors.
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28
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Towards structural classification of long non-coding RNAs. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1859:41-5. [PMID: 26537437 DOI: 10.1016/j.bbagrm.2015.09.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 09/10/2015] [Accepted: 09/28/2015] [Indexed: 01/16/2023]
Abstract
While long non-coding RNAs play key roles in disease and development, few structural studies have been performed to date for this emerging class of RNAs. Previous structural studies are reviewed, and a pipeline is presented to determine secondary structures of long non-coding RNAs. Similar to riboswitches, experimentally determined secondary structures of long non-coding RNAs for one species, may be used to improve sequence/structure alignments for other species. As riboswitches have been classified according to their secondary structure, a similar scheme could be used to classify long non-coding RNAs. This article is part of a Special Issue titled: Clues to long noncoding RNA taxonomy1, edited by Dr. Tetsuro Hirose and Dr. Shinichi Nakagawa.
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29
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Yue M, Charles Richard JL, Ogawa Y. Dynamic interplay and function of multiple noncoding genes governing X chromosome inactivation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1859:112-20. [PMID: 26260844 DOI: 10.1016/j.bbagrm.2015.07.015] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 07/07/2015] [Accepted: 07/14/2015] [Indexed: 12/17/2022]
Abstract
There is increasing evidence for the emergence of long noncoding RNAs (lncRNAs) as important components, especially in the regulation of gene expression. In the event of X chromosome inactivation, robust epigenetic marks are established in a long noncoding Xist RNA-dependent manner, giving rise to a distinct epigenetic landscape on the inactive X chromosome (Xi). The X inactivation center (Xic) is essential for induction of X chromosome inactivation and harbors two topologically associated domains (TADs) to regulate monoallelic Xist expression: one at the noncoding Xist gene and its upstream region, and the other at the antisense Tsix and its upstream region. The monoallelic expression of Xist is tightly regulated by these two functionally distinct TADs as well as their constituting lncRNAs and proteins. In this review, we summarize recent updates in our knowledge of lncRNAs found at the Xic and discuss their overall mechanisms of action. We also discuss our current understanding of the molecular mechanism behind Xist RNA-mediated induction of the repressive epigenetic landscape at the Xi. This article is part of a Special Issue entitled: Clues to long noncoding RNA taxonomy1, edited by Dr. Tetsuro Hirose and Dr. Shinichi Nakagawa.
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Affiliation(s)
- Minghui Yue
- Division of Reproductive Sciences, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - John Lalith Charles Richard
- Division of Reproductive Sciences, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Yuya Ogawa
- Division of Reproductive Sciences, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, 3333 Burnet Avenue, Cincinnati, OH 45229, USA.
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30
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Monfort A, Di Minin G, Postlmayr A, Freimann R, Arieti F, Thore S, Wutz A. Identification of Spen as a Crucial Factor for Xist Function through Forward Genetic Screening in Haploid Embryonic Stem Cells. Cell Rep 2015; 12:554-61. [PMID: 26190100 PMCID: PMC4530576 DOI: 10.1016/j.celrep.2015.06.067] [Citation(s) in RCA: 176] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 05/22/2015] [Accepted: 06/23/2015] [Indexed: 01/21/2023] Open
Abstract
In mammals, the noncoding Xist RNA triggers transcriptional silencing of one of the two X chromosomes in female cells. Here, we report a genetic screen for silencing factors in X chromosome inactivation using haploid mouse embryonic stem cells (ESCs) that carry an engineered selectable reporter system. This system was able to identify several candidate factors that are genetically required for chromosomal repression by Xist. Among the list of candidates, we identify the RNA-binding protein Spen, the homolog of split ends. Independent validation through gene deletion in ESCs confirms that Spen is required for gene repression by Xist. However, Spen is not required for Xist RNA localization and the recruitment of chromatin modifications, including Polycomb protein Ezh2. The identification of Spen opens avenues for further investigation into the gene-silencing pathway of Xist and shows the usefulness of haploid ESCs for genetic screening of epigenetic pathways.
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Affiliation(s)
- Asun Monfort
- Institute of Molecular Health Sciences, Swiss Federal Institute of Technology, ETH Hönggerberg, Otto-Stern-Weg 7, 8093 Zurich, Switzerland
| | - Giulio Di Minin
- Institute of Molecular Health Sciences, Swiss Federal Institute of Technology, ETH Hönggerberg, Otto-Stern-Weg 7, 8093 Zurich, Switzerland
| | - Andreas Postlmayr
- Institute of Molecular Health Sciences, Swiss Federal Institute of Technology, ETH Hönggerberg, Otto-Stern-Weg 7, 8093 Zurich, Switzerland
| | - Remo Freimann
- Institute of Molecular Health Sciences, Swiss Federal Institute of Technology, ETH Hönggerberg, Otto-Stern-Weg 7, 8093 Zurich, Switzerland
| | - Fabiana Arieti
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 753/5, Brno 62500, Czech Republic
| | - Stéphane Thore
- University of Bordeaux, European Institute for Chemistry and Biology (IECB), ARNA Laboratory, Bordeaux 33000, France; Institut National de la Sante et de la Recherche Medicale, INSERM, U869, ARNA Laboratory, Bordeaux 33000, France
| | - Anton Wutz
- Institute of Molecular Health Sciences, Swiss Federal Institute of Technology, ETH Hönggerberg, Otto-Stern-Weg 7, 8093 Zurich, Switzerland.
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31
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McHugh CA, Chen CK, Chow A, Surka CF, Tran C, McDonel P, Pandya-Jones A, Blanco M, Burghard C, Moradian A, Sweredoski MJ, Shishkin AA, Su J, Lander ES, Hess S, Plath K, Guttman M. The Xist lncRNA interacts directly with SHARP to silence transcription through HDAC3. Nature 2015; 521:232-6. [PMID: 25915022 PMCID: PMC4516396 DOI: 10.1038/nature14443] [Citation(s) in RCA: 808] [Impact Index Per Article: 89.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 04/02/2015] [Indexed: 12/14/2022]
Abstract
Many long non-coding RNAs (lncRNAs) affect gene expression, but the mechanisms by which they act are still largely unknown. One of the best-studied lncRNAs is Xist, which is required for transcriptional silencing of one X chromosome during development in female mammals. Despite extensive efforts to define the mechanism of Xist-mediated transcriptional silencing, we still do not know any proteins required for this role. The main challenge is that there are currently no methods to comprehensively define the proteins that directly interact with a lncRNA in the cell. Here we develop a method to purify a lncRNA from cells and identify proteins interacting with it directly using quantitative mass spectrometry. We identify ten proteins that specifically associate with Xist, three of these proteins--SHARP, SAF-A and LBR--are required for Xist-mediated transcriptional silencing. We show that SHARP, which interacts with the SMRT co-repressor that activates HDAC3, is not only essential for silencing, but is also required for the exclusion of RNA polymerase II (Pol II) from the inactive X. Both SMRT and HDAC3 are also required for silencing and Pol II exclusion. In addition to silencing transcription, SHARP and HDAC3 are required for Xist-mediated recruitment of the polycomb repressive complex 2 (PRC2) across the X chromosome. Our results suggest that Xist silences transcription by directly interacting with SHARP, recruiting SMRT, activating HDAC3, and deacetylating histones to exclude Pol II across the X chromosome.
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Affiliation(s)
- Colleen A. McHugh
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Chun-Kan Chen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Amy Chow
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Christine F. Surka
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Christina Tran
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | | | - Amy Pandya-Jones
- Department of Biological Chemistry, Jonsson Comprehensive Cancer Center, Molecular Biology Institute, and Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095
| | - Mario Blanco
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Christina Burghard
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Annie Moradian
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125
| | - Michael J. Sweredoski
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125
| | - Alexander A. Shishkin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Julia Su
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | | | - Sonja Hess
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125
| | - Kathrin Plath
- Department of Biological Chemistry, Jonsson Comprehensive Cancer Center, Molecular Biology Institute, and Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095
| | - Mitchell Guttman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
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Systematic discovery of Xist RNA binding proteins. Cell 2015; 161:404-16. [PMID: 25843628 DOI: 10.1016/j.cell.2015.03.025] [Citation(s) in RCA: 747] [Impact Index Per Article: 83.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2014] [Revised: 01/29/2015] [Accepted: 03/11/2015] [Indexed: 12/15/2022]
Abstract
Noncoding RNAs (ncRNAs) function with associated proteins to effect complex structural and regulatory outcomes. To reveal the composition and dynamics of specific noncoding RNA-protein complexes (RNPs) in vivo, we developed comprehensive identification of RNA binding proteins by mass spectrometry (ChIRP-MS). ChIRP-MS analysis of four ncRNAs captures key protein interactors, including a U1-specific link to the 3' RNA processing machinery. Xist, an essential lncRNA for X chromosome inactivation (XCI), interacts with 81 proteins from chromatin modification, nuclear matrix, and RNA remodeling pathways. The Xist RNA-protein particle assembles in two steps coupled with the transition from pluripotency to differentiation. Specific interactors include HnrnpK, which participates in Xist-mediated gene silencing and histone modifications but not Xist localization, and Drosophila Split ends homolog Spen, which interacts via the A-repeat domain of Xist and is required for gene silencing. Thus, Xist lncRNA engages with proteins in a modular and developmentally controlled manner to coordinate chromatin spreading and silencing.
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