1
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Bhat P, Chow A, Emert B, Ettlin O, Quinodoz SA, Strehle M, Takei Y, Burr A, Goronzy IN, Chen AW, Huang W, Ferrer JLM, Soehalim E, Goh ST, Chari T, Sullivan DK, Blanco MR, Guttman M. Genome organization around nuclear speckles drives mRNA splicing efficiency. Nature 2024; 629:1165-1173. [PMID: 38720076 PMCID: PMC11164319 DOI: 10.1038/s41586-024-07429-6] [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: 03/12/2023] [Accepted: 04/16/2024] [Indexed: 05/21/2024]
Abstract
The nucleus is highly organized, such that factors involved in the transcription and processing of distinct classes of RNA are confined within specific nuclear bodies1,2. One example is the nuclear speckle, which is defined by high concentrations of protein and noncoding RNA regulators of pre-mRNA splicing3. What functional role, if any, speckles might play in the process of mRNA splicing is unclear4,5. Here we show that genes localized near nuclear speckles display higher spliceosome concentrations, increased spliceosome binding to their pre-mRNAs and higher co-transcriptional splicing levels than genes that are located farther from nuclear speckles. Gene organization around nuclear speckles is dynamic between cell types, and changes in speckle proximity lead to differences in splicing efficiency. Finally, directed recruitment of a pre-mRNA to nuclear speckles is sufficient to increase mRNA splicing levels. Together, our results integrate the long-standing observations of nuclear speckles with the biochemistry of mRNA splicing and demonstrate a crucial role for dynamic three-dimensional spatial organization of genomic DNA in driving spliceosome concentrations and controlling the efficiency of mRNA splicing.
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Affiliation(s)
- Prashant Bhat
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Amy Chow
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Benjamin Emert
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Olivia Ettlin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Sofia A Quinodoz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
| | - Mackenzie Strehle
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Yodai Takei
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Alex Burr
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Isabel N Goronzy
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Allen W Chen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Wesley Huang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Jose Lorenzo M Ferrer
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Elizabeth Soehalim
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Say-Tar Goh
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Tara Chari
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Delaney K Sullivan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Mario R Blanco
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Mitchell Guttman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
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2
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Hall Hickman A, Jenner RG. Apparent RNA bridging between PRC2 and chromatin is an artifact of non-specific chromatin precipitation upon RNA degradation. Cell Rep 2024; 43:113856. [PMID: 38416641 DOI: 10.1016/j.celrep.2024.113856] [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: 10/27/2023] [Revised: 01/26/2024] [Accepted: 02/08/2024] [Indexed: 03/01/2024] Open
Abstract
Polycomb repressive complex 2 (PRC2) modifies chromatin to maintain repression of genes specific for other cell lineages. In vitro, RNA inhibits PRC2 activity, but the effect of RNA on PRC2 in cells is less clear, with studies concluding that RNA either antagonizes or promotes PRC2 chromatin association. The addition of RNase A to chromatin immunoprecipitation reactions has been reported to reduce detection of PRC2 target sites, suggesting the existence of RNA bridges connecting PRC2 to chromatin. Here, we show that the apparent loss of PRC2 chromatin association after RNase A treatment is due to non-specific chromatin precipitation. RNA degradation precipitates chromatin out of solution, thereby masking enrichment of specific DNA sequences in chromatin immunoprecipitation reactions. Maintaining chromatin solubility by the addition of poly-L-glutamic acid rescues detection of PRC2 chromatin occupancy upon RNA degradation. These findings undermine support for the model that RNA bridges PRC2 and chromatin in cells.
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Affiliation(s)
- Alexander Hall Hickman
- UCL Cancer Institute, University College London, London WC1E 6BT, UK; CRUK City of London Centre, University College London, London WC1E 6BT, UK
| | - 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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3
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Pourmorady AD, Bashkirova EV, Chiariello AM, Belagzhal H, Kodra A, Duffié R, Kahiapo J, Monahan K, Pulupa J, Schieren I, Osterhoudt A, Dekker J, Nicodemi M, Lomvardas S. RNA-mediated symmetry breaking enables singular olfactory receptor choice. Nature 2024; 625:181-188. [PMID: 38123679 PMCID: PMC10765522 DOI: 10.1038/s41586-023-06845-4] [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: 03/20/2023] [Accepted: 11/07/2023] [Indexed: 12/23/2023]
Abstract
Olfactory receptor (OR) choice provides an extreme example of allelic competition for transcriptional dominance, where every olfactory neuron stably transcribes one of approximately 2,000 or more OR alleles1,2. OR gene choice is mediated by a multichromosomal enhancer hub that activates transcription at a single OR3,4, followed by OR-translation-dependent feedback that stabilizes this choice5,6. Here, using single-cell genomics, we show formation of many competing hubs with variable enhancer composition, only one of which retains euchromatic features and transcriptional competence. Furthermore, we provide evidence that OR transcription recruits enhancers and reinforces enhancer hub activity locally, whereas OR RNA inhibits transcription of competing ORs over distance, promoting transition to transcriptional singularity. Whereas OR transcription is sufficient to break the symmetry between equipotent enhancer hubs, OR translation stabilizes transcription at the prevailing hub, indicating that there may be sequential non-coding and coding mechanisms that are implemented by OR alleles for transcriptional prevalence. We propose that coding OR mRNAs possess non-coding functions that influence nuclear architecture, enhance their own transcription and inhibit transcription from their competitors, with generalizable implications for probabilistic cell fate decisions.
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Affiliation(s)
- Ariel D Pourmorady
- Vagelos College of Physicians and Surgeons, Columbia University New York, New York, NY, USA
- Department of Neuroscience, Columbia University, New York, NY, USA
- Mortimer B. Zuckerman Mind, Brain, and Behavior Institute, Columbia University New York, New York, NY, USA
| | - Elizaveta V Bashkirova
- Mortimer B. Zuckerman Mind, Brain, and Behavior Institute, Columbia University New York, New York, NY, USA
- Integrated Program in Cellular, Molecular and Biomedical Studies, Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Andrea M Chiariello
- Department of Physics 'Ettore Pancini', University of Naples, and INFN, Napoli, Italy
| | - Houda Belagzhal
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Albana Kodra
- Integrated Program in Cellular, Molecular and Biomedical Studies, Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Genetics and Development, Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Rachel Duffié
- Mortimer B. Zuckerman Mind, Brain, and Behavior Institute, Columbia University New York, New York, NY, USA
| | - Jerome Kahiapo
- Department of Molecular Biology & Biochemistry, Rutgers School of Arts and Sciences, Robert Wood Johnson Medical School, Piscataway, NJ, USA
| | - Kevin Monahan
- Department of Molecular Biology & Biochemistry, Rutgers School of Arts and Sciences, Robert Wood Johnson Medical School, Piscataway, NJ, USA
| | - Joan Pulupa
- Mortimer B. Zuckerman Mind, Brain, and Behavior Institute, Columbia University New York, New York, NY, USA
| | - Ira Schieren
- Mortimer B. Zuckerman Mind, Brain, and Behavior Institute, Columbia University New York, New York, NY, USA
| | - Alexa Osterhoudt
- Mortimer B. Zuckerman Mind, Brain, and Behavior Institute, Columbia University New York, New York, NY, USA
- Integrated Program in Cellular, Molecular and Biomedical Studies, Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Job Dekker
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Mario Nicodemi
- Department of Physics 'Ettore Pancini', University of Naples, and INFN, Napoli, Italy
| | - Stavros Lomvardas
- Mortimer B. Zuckerman Mind, Brain, and Behavior Institute, Columbia University New York, New York, NY, USA.
- Department of Biochemistry and Molecular Biophysics, Vagelos College of Physicians and Surgeons, New York, NY, USA.
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4
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Yan Y, Tian Y, Wu Z, Zhang K, Yang R. Interchromosomal Colocalization with Parental Genes Is Linked to the Function and Evolution of Mammalian Retrocopies. Mol Biol Evol 2023; 40:msad265. [PMID: 38060983 PMCID: PMC10733166 DOI: 10.1093/molbev/msad265] [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: 07/13/2023] [Revised: 10/25/2023] [Accepted: 11/29/2023] [Indexed: 12/22/2023] Open
Abstract
Retrocopies are gene duplicates arising from reverse transcription of mature mRNA transcripts and their insertion back into the genome. While long being regarded as processed pseudogenes, more and more functional retrocopies have been discovered. How the stripped-down retrocopies recover expression capability and become functional paralogs continually intrigues evolutionary biologists. Here, we investigated the function and evolution of retrocopies in the context of 3D genome organization. By mapping retrocopy-parent pairs onto sequencing-based and imaging-based chromatin contact maps in human and mouse cell lines and onto Hi-C interaction maps in 5 other mammals, we found that retrocopies and their parental genes show a higher-than-expected interchromosomal colocalization frequency. The spatial interactions between retrocopies and parental genes occur frequently at loci in active subcompartments and near nuclear speckles. Accordingly, colocalized retrocopies are more actively transcribed and translated and are more evolutionarily conserved than noncolocalized ones. The active transcription of colocalized retrocopies may result from their permissive epigenetic environment and shared regulatory elements with parental genes. Population genetic analysis of retroposed gene copy number variants in human populations revealed that retrocopy insertions are not entirely random in regard to interchromosomal interactions and that colocalized retroposed gene copy number variants are more likely to reach high frequencies, suggesting that both insertion bias and natural selection contribute to the colocalization of retrocopy-parent pairs. Further dissection implies that reduced selection efficacy, rather than positive selection, contributes to the elevated allele frequency of colocalized retroposed gene copy number variants. Overall, our results hint a role of interchromosomal colocalization in the "resurrection" of initially neutral retrocopies.
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Affiliation(s)
- Yubin Yan
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Yuhan Tian
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Zefeng Wu
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Kunling Zhang
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Ruolin Yang
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
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5
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Soroczynski J, Risca VI. Technological advances in probing 4D genome organization. Curr Opin Cell Biol 2023; 84:102211. [PMID: 37556867 PMCID: PMC10588670 DOI: 10.1016/j.ceb.2023.102211] [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: 04/01/2023] [Revised: 05/13/2023] [Accepted: 06/29/2023] [Indexed: 08/11/2023]
Abstract
The last two decades of work on chromosome conformation in eukaryotic nuclei have revealed a complex and highly regulated hierarchy of architectural features, from self-associating domains and compartmental interactions to locus-specific loops. Recent findings have shown that these structures are dynamic and heterogeneous, with emerging insights into the factors that shape them and implications for the control of transcription and other nuclear processes. Here, we review the latest advances in the DNA sequencing- and microscopy-based technologies for probing these features in space and time (4D) and discuss how they have been combined with complementary approaches such as genetic perturbations, protein and RNA measurements, and modeling to gain mechanistic insights about genome regulation across space and time.
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Affiliation(s)
- Jan Soroczynski
- Laboratory of Genome Architecture and Dynamics, The Rockefeller University, 1230 York Ave., Box 176, New York, NY 10065, USA; David Rockefeller Graduate Program in Bioscience, The Rockefeller University, 1230 York Ave., New York, NY 10065, USA
| | - Viviana I Risca
- Laboratory of Genome Architecture and Dynamics, The Rockefeller University, 1230 York Ave., Box 176, New York, NY 10065, USA.
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6
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Hertzog M, Erdel F. The Material Properties of the Cell Nucleus: A Matter of Scale. Cells 2023; 12:1958. [PMID: 37566037 PMCID: PMC10416959 DOI: 10.3390/cells12151958] [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: 06/30/2023] [Revised: 07/26/2023] [Accepted: 07/26/2023] [Indexed: 08/12/2023] Open
Abstract
Chromatin regulatory processes physically take place in the environment of the cell nucleus, which is filled with the chromosomes and a plethora of smaller biomolecules. The nucleus contains macromolecular assemblies of different sizes, from nanometer-sized protein complexes to micrometer-sized biomolecular condensates, chromosome territories, and nuclear bodies. This multiscale organization impacts the transport processes within the nuclear interior, the global mechanical properties of the nucleus, and the way the nucleus senses and reacts to mechanical stimuli. Here, we discuss recent work on these aspects, including microrheology and micromanipulation experiments assessing the material properties of the nucleus and its subcomponents. We summarize how the properties of multiscale media depend on the time and length scales probed in the experiment, and we reconcile seemingly contradictory observations made on different scales. We also revisit the concept of liquid-like and solid-like material properties for complex media such as the nucleus. We propose that the nucleus can be considered a multiscale viscoelastic medium composed of three major components with distinct properties: the lamina, the chromatin network, and the nucleoplasmic fluid. This multicomponent organization enables the nucleus to serve its different functions as a reaction medium on the nanoscale and as a mechanosensor and structural scaffold on the microscale.
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Affiliation(s)
| | - Fabian Erdel
- MCD, Center for Integrative Biology (CBI), University of Toulouse, CNRS, 169 Avenue Marianne Grunberg-Manago, 31062 Toulouse, France
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7
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Schede HH, Natarajan P, Chakraborty AK, Shrinivas K. A model for organization and regulation of nuclear condensates by gene activity. Nat Commun 2023; 14:4152. [PMID: 37438363 DOI: 10.1038/s41467-023-39878-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 07/03/2023] [Indexed: 07/14/2023] Open
Abstract
Condensation by phase separation has recently emerged as a mechanism underlying many nuclear compartments essential for cellular functions. Nuclear condensates enrich nucleic acids and proteins, localize to specific genomic regions, and often promote gene expression. How diverse properties of nuclear condensates are shaped by gene organization and activity is poorly understood. Here, we develop a physics-based model to interrogate how spatially-varying transcription activity impacts condensate properties and dynamics. Our model predicts that spatial clustering of active genes can enable precise localization and de novo nucleation of condensates. Strong clustering and high activity results in aspherical condensate morphologies. Condensates can flow towards distant gene clusters and competition between multiple clusters lead to stretched morphologies and activity-dependent repositioning. Overall, our model predicts and recapitulates morphological and dynamical features of diverse nuclear condensates and offers a unified mechanistic framework to study the interplay between non-equilibrium processes, spatially-varying transcription, and multicomponent condensates in cell biology.
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Affiliation(s)
- Halima H Schede
- School of Life Sciences, École Polytechnique Fédérale Lausanne, CH-1015, Lausanne, Switzerland
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Pradeep Natarajan
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Arup K Chakraborty
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Krishna Shrinivas
- NSF-Simons Center for Mathematical & Statistical Analysis of Biology, Harvard University, Cambridge, MA, USA.
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8
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Mattick JS. RNA out of the mist. Trends Genet 2023; 39:187-207. [PMID: 36528415 DOI: 10.1016/j.tig.2022.11.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 11/08/2022] [Accepted: 11/27/2022] [Indexed: 12/23/2022]
Abstract
RNA has long been regarded primarily as the intermediate between genes and proteins. It was a surprise then to discover that eukaryotic genes are mosaics of mRNA sequences interrupted by large tracts of transcribed but untranslated sequences, and that multicellular organisms also express many long 'intergenic' and antisense noncoding RNAs (lncRNAs). The identification of small RNAs that regulate mRNA translation and half-life did not disturb the prevailing view that animals and plant genomes are full of evolutionary debris and that their development is mainly supervised by transcription factors. Gathering evidence to the contrary involved addressing the low conservation, expression, and genetic visibility of lncRNAs, demonstrating their cell-specific roles in cell and developmental biology, and their association with chromatin-modifying complexes and phase-separated domains. The emerging picture is that most lncRNAs are the products of genetic loci termed 'enhancers', which marshal generic effector proteins to their sites of action to control cell fate decisions during development.
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Affiliation(s)
- John S Mattick
- School of Biotechnology and Biomolecular Sciences, UNSW, Sydney, NSW 2052, Australia; UNSW RNA Institute, UNSW, Sydney, NSW 2052, Australia.
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9
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González L, Kolbin D, Trahan C, Jeronimo C, Robert F, Oeffinger M, Bloom K, Michnick SW. Adaptive partitioning of a gene locus to the nuclear envelope in Saccharomyces cerevisiae is driven by polymer-polymer phase separation. Nat Commun 2023; 14:1135. [PMID: 36854718 PMCID: PMC9975218 DOI: 10.1038/s41467-023-36391-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 01/30/2023] [Indexed: 03/03/2023] Open
Abstract
Partitioning of active gene loci to the nuclear envelope (NE) is a mechanism by which organisms increase the speed of adaptation and metabolic robustness to fluctuating resources in the environment. In the yeast Saccharomyces cerevisiae, adaptation to nutrient depletion or other stresses, manifests as relocalization of active gene loci from nucleoplasm to the NE, resulting in more efficient transport and translation of mRNA. The mechanism by which this partitioning occurs remains a mystery. Here, we demonstrate that the yeast inositol depletion-responsive gene locus INO1 partitions to the nuclear envelope, driven by local histone acetylation-induced polymer-polymer phase separation from the nucleoplasmic phase. This demixing is consistent with recent evidence for chromatin phase separation by acetylation-mediated dissolution of multivalent histone association and fits a physical model where increased bending stiffness of acetylated chromatin polymer causes its phase separation from de-acetylated chromatin. Increased chromatin spring stiffness could explain nucleation of transcriptional machinery at active gene loci.
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Affiliation(s)
- Lidice González
- Département de Biochimie, Université de Montréal, C.P. 6128, Succursale centre-ville, Montréal, QC, H3C 3J7, Canada
| | - Daniel Kolbin
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Christian Trahan
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC, H2W 1R7, Canada
| | - Célia Jeronimo
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC, H2W 1R7, Canada
| | - François Robert
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC, H2W 1R7, Canada
- Faculty of Medicine, Division of Experimental Medicine, McGill University, Montréal, QC, H3A 1A3, Canada
- Département de Médecine, Faculté de Médecine, Université de Montréal, 2900 Boul. Édouard-Montpetit, Montréal, QC, H3T 1J4, Canada
| | - Marlene Oeffinger
- Département de Biochimie, Université de Montréal, C.P. 6128, Succursale centre-ville, Montréal, QC, H3C 3J7, Canada
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC, H2W 1R7, Canada
- Faculty of Medicine, Division of Experimental Medicine, McGill University, Montréal, QC, H3A 1A3, Canada
| | - Kerry Bloom
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Stephen W Michnick
- Département de Biochimie, Université de Montréal, C.P. 6128, Succursale centre-ville, Montréal, QC, H3C 3J7, Canada.
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10
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Chang HY, Qi LS. Reversing the Central Dogma: RNA-guided control of DNA in epigenetics and genome editing. Mol Cell 2023; 83:442-451. [PMID: 36736311 PMCID: PMC10044466 DOI: 10.1016/j.molcel.2023.01.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 12/15/2022] [Accepted: 01/05/2023] [Indexed: 02/05/2023]
Abstract
The Central Dogma of the flow of genetic information is arguably the crowning achievement of 20th century molecular biology. Reversing the flow of information from RNA to DNA or chromatin has come to the fore in recent years, from the convergence of fundamental discoveries and synthetic biology. Inspired by the example of long noncoding RNAs (lncRNAs) in mammalian genomes that direct chromatin modifications and gene expression, synthetic biologists have repurposed prokaryotic RNA-guided genome defense systems such as CRISPR to edit eukaryotic genomes and epigenomes. Here we explore the parallels of these two fields and highlight opportunities for synergy and future breakthroughs.
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Affiliation(s)
- Howard Y Chang
- Center for Personal Dynamic Regulome, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA.
| | - Lei S Qi
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Sarafan ChEM-H, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94080, USA.
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11
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Bhat P, Chow A, Emert B, Ettlin O, Quinodoz SA, Takei Y, Huang W, Blanco MR, Guttman M. 3D genome organization around nuclear speckles drives mRNA splicing efficiency. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.04.522632. [PMID: 36711853 PMCID: PMC9881923 DOI: 10.1101/2023.01.04.522632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The nucleus is highly organized such that factors involved in transcription and processing of distinct classes of RNA are organized within specific nuclear bodies. One such nuclear body is the nuclear speckle, which is defined by high concentrations of protein and non-coding RNA regulators of pre-mRNA splicing. What functional role, if any, speckles might play in the process of mRNA splicing remains unknown. Here we show that genes localized near nuclear speckles display higher spliceosome concentrations, increased spliceosome binding to their pre-mRNAs, and higher co-transcriptional splicing levels relative to genes that are located farther from nuclear speckles. We show that directed recruitment of a pre-mRNA to nuclear speckles is sufficient to drive increased mRNA splicing levels. Finally, we show that gene organization around nuclear speckles is highly dynamic with differential localization between cell types corresponding to differences in Pol II occupancy. Together, our results integrate the longstanding observations of nuclear speckles with the biochemistry of mRNA splicing and demonstrate a critical role for dynamic 3D spatial organization of genomic DNA in driving spliceosome concentrations and controlling the efficiency of mRNA splicing.
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12
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An in situ method for tagging chromatin-associated RNAs. Nat Methods 2022; 19:1351-1352. [PMID: 36192464 DOI: 10.1038/s41592-022-01619-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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13
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Trigiante G, Blanes Ruiz N, Cerase A. Emerging Roles of Repetitive and Repeat-Containing RNA in Nuclear and Chromatin Organization and Gene Expression. Front Cell Dev Biol 2021; 9:735527. [PMID: 34722514 PMCID: PMC8552494 DOI: 10.3389/fcell.2021.735527] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 09/09/2021] [Indexed: 12/14/2022] Open
Abstract
Genomic repeats have been intensely studied as regulatory elements controlling gene transcription, splicing and genome architecture. Our understanding of the role of the repetitive RNA such as the RNA coming from genomic repeats, or repetitive sequences embedded in mRNA/lncRNAs, in nuclear and cellular functions is instead still limited. In this review we discuss evidence supporting the multifaceted roles of repetitive RNA and RNA binding proteins in nuclear organization, gene regulation, and in the formation of dynamic membrane-less aggregates. We hope that our review will further stimulate research in the consolidating field of repetitive RNA biology.
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Affiliation(s)
| | | | - Andrea Cerase
- Centre for Genomics and Child Health, Barts and The London School of Medicine and Dentistry, Blizard Institute, Queen Mary University of London, London, United Kingdom
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