1
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Nickerson JA, Momen-Heravi F. Long non-coding RNAs: roles in cellular stress responses and epigenetic mechanisms regulating chromatin. Nucleus 2024; 15:2350180. [PMID: 38773934 PMCID: PMC11123517 DOI: 10.1080/19491034.2024.2350180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 04/22/2024] [Indexed: 05/24/2024] Open
Abstract
Most of the genome is transcribed into RNA but only 2% of the sequence codes for proteins. Non-coding RNA transcripts include a very large number of long noncoding RNAs (lncRNAs). A growing number of identified lncRNAs operate in cellular stress responses, for example in response to hypoxia, genotoxic stress, and oxidative stress. Additionally, lncRNA plays important roles in epigenetic mechanisms operating at chromatin and in maintaining chromatin architecture. Here, we address three lncRNA topics that have had significant recent advances. The first is an emerging role for many lncRNAs in cellular stress responses. The second is the development of high throughput screening assays to develop causal relationships between lncRNAs across the genome with cellular functions. Finally, we turn to recent advances in understanding the role of lncRNAs in regulating chromatin architecture and epigenetics, advances that build on some of the earliest work linking RNA to chromatin architecture.
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Affiliation(s)
- Jeffrey A Nickerson
- Division of Genes & Development, Department of Pediatrics, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Fatemeh Momen-Heravi
- College of Dental Medicine, Columbia University Medical Center, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
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2
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Palihati M, Saitoh N. RNA in chromatin organization and nuclear architecture. Curr Opin Genet Dev 2024; 86:102176. [PMID: 38490161 DOI: 10.1016/j.gde.2024.102176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 02/08/2024] [Accepted: 02/11/2024] [Indexed: 03/17/2024]
Abstract
In the cell nucleus, genomic DNA is surrounded by nonmembranous nuclear bodies. This might result from specific regions of the genome being transcribed into long noncoding RNAs (lncRNAs), which tend to remain at the sites of their own transcription. The lncRNAs seed the nuclear bodies by recruiting and concentrating proteins and RNAs, which undergo liquid-liquid-phase separation, and form molecular condensates, the so-called nuclear bodies. These nuclear bodies may provide appropriate environments for gene activation or repression. Notably, lncRNAs also contribute to three-dimensional genome structure by mediating long-range chromatin interactions. In this review, we discuss the mechanisms by which lncRNAs regulate gene expression through shaping chromatin and nuclear architectures. We also explore lncRNAs' potential as a therapeutic target for cancer, because lncRNAs are often expressed in a disease-specific manner.
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Affiliation(s)
- Maierdan Palihati
- Division of Cancer Biology, The Cancer Institute of JFCR, 3-8-31 Ariake, Koto-ku, Tokyo 135-8550, Japan
| | - Noriko Saitoh
- Division of Cancer Biology, The Cancer Institute of JFCR, 3-8-31 Ariake, Koto-ku, Tokyo 135-8550, Japan.
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3
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Willemin A, Szabó D, Pombo A. Epigenetic regulatory layers in the 3D nucleus. Mol Cell 2024; 84:415-428. [PMID: 38242127 PMCID: PMC10872226 DOI: 10.1016/j.molcel.2023.12.032] [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: 07/26/2023] [Revised: 11/21/2023] [Accepted: 12/15/2023] [Indexed: 01/21/2024]
Abstract
Nearly 7 decades have elapsed since Francis Crick introduced the central dogma of molecular biology, as part of his ideas on protein synthesis, setting the fundamental rules of sequence information transfer from DNA to RNAs and proteins. We have since learned that gene expression is finely tuned in time and space, due to the activities of RNAs and proteins on regulatory DNA elements, and through cell-type-specific three-dimensional conformations of the genome. Here, we review major advances in genome biology and discuss a set of ideas on gene regulation and highlight how various biomolecular assemblies lead to the formation of structural and regulatory features within the nucleus, with roles in transcriptional control. We conclude by suggesting further developments that will help capture the complex, dynamic, and often spatially restricted events that govern gene expression in mammalian cells.
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Affiliation(s)
- Andréa Willemin
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetic Regulation and Chromatin Architecture Group, Berlin, Germany; Humboldt-Universität zu Berlin, Institute for Biology, Berlin, Germany.
| | - Dominik Szabó
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetic Regulation and Chromatin Architecture Group, Berlin, Germany; Humboldt-Universität zu Berlin, Institute for Biology, Berlin, Germany
| | - Ana Pombo
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetic Regulation and Chromatin Architecture Group, Berlin, Germany; Humboldt-Universität zu Berlin, Institute for Biology, Berlin, Germany.
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4
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Hall LL, Creamer KM, Byron M, Lawrence JB. Differences in Alu vs L1-rich chromosome bands underpin architectural reorganization of the inactive-X chromosome and SAHFs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.09.574742. [PMID: 38260534 PMCID: PMC10802495 DOI: 10.1101/2024.01.09.574742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
The linear DNA sequence of mammalian chromosomes is organized in large blocks of DNA with similar sequence properties, producing a pattern of dark and light staining bands on mitotic chromosomes. Cytogenetic banding is essentially invariant between people and cell-types and thus may be assumed unrelated to genome regulation. We investigate whether large blocks of Alu-rich R-bands and L1-rich G-bands provide a framework upon which functional genome architecture is built. We examine two models of large-scale chromatin condensation: X-chromosome inactivation and formation of senescence-associated heterochromatin foci (SAHFs). XIST RNA triggers gene silencing but also formation of the condensed Barr Body (BB), thought to reflect cumulative gene silencing. However, we find Alu-rich regions are depleted from the L1-rich BB, supporting it is a dense core but not the entire chromosome. Alu-rich bands are also gene-rich, affirming our earlier findings that genes localize at the outer periphery of the BB. SAHFs similarly form within each territory by coalescence of syntenic L1 regions depleted for highly Alu-rich DNA. Analysis of senescent cell Hi-C data also shows large contiguous blocks of G-band and R-band DNA remodel as a segmental unit. Entire dark-bands gain distal intrachromosomal interactions as L1-rich regions form the SAHF. Most striking is that sharp Alu peaks within R-bands resist these changes in condensation. We further show that Chr19, which is exceptionally Alu rich, fails to form a SAHF. Collective results show regulation of genome architecture corresponding to large blocks of DNA and demonstrate resistance of segments with high Alu to chromosome condensation.
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Affiliation(s)
- Lisa L. Hall
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Kevin M. Creamer
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Meg Byron
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Jeanne B. Lawrence
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
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5
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Alexander KA, Yu R, Skuli N, Coffey NJ, Nguyen S, Faunce C, Huang H, Dardani IP, Good AL, Lim J, Li C, Biddle N, Joyce EF, Raj A, Lee D, Keith B, Simon MC, Berger SL. Nuclear speckles regulate HIF-2α programs and correlate with patient survival in kidney cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.14.557228. [PMID: 37745397 PMCID: PMC10515914 DOI: 10.1101/2023.09.14.557228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Nuclear speckles are membrane-less bodies within the cell nucleus enriched in RNA biogenesis, processing, and export factors. In this study we investigated speckle phenotype variation in human cancer, finding a reproducible speckle signature, based on RNA expression of speckle-resident proteins, across >20 cancer types. Of these, clear cell renal cell carcinoma (ccRCC) exhibited a clear correlation between the presence of this speckle expression signature, imaging-based speckle phenotype, and clinical outcomes. ccRCC is typified by hyperactivation of the HIF-2α transcription factor, and we demonstrate here that HIF-2α drives physical association of a select subset of its target genes with nuclear speckles. Disruption of HIF-2α-driven speckle association via deletion of its speckle targeting motifs (STMs)-defined in this study-led to defective induction of speckle-associating HIF-2α target genes without impacting non-speckle-associating HIF-2α target genes. We further identify the RNA export complex, TREX, as being specifically altered in speckle signature, and knockdown of key TREX component, ALYREF, also compromises speckle-associated gene expression. By integrating tissue culture functional studies with tumor genomic and imaging analysis, we show that HIF-2α gene regulatory programs are impacted by specific manipulation of speckle phenotype and by abrogation of speckle targeting abilities of HIF-2α. These findings suggest that, in ccRCC, a key biological function of nuclear speckles is to modulate expression of a specific subset of HIF-2α-regulated target genes that, in turn, influence patient outcomes. We also identify STMs in other transcription factors, suggesting that DNA-speckle targeting may be a general mechanism of gene regulation.
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Affiliation(s)
- Katherine A. Alexander
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Cell and Developmental Biology, Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Ruofan Yu
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Cell and Developmental Biology, Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Nicolas Skuli
- Department of Cell and Developmental Biology, Perelman School of Medicine, Philadelphia, PA 19104, USA
- Stem Cell and Xenograft Core, Department of Medicine – Division of Hematology and Oncology, University of Pennsylvania, Philadelphia, PA 19104, USA
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Nathan J. Coffey
- Department of Cell and Developmental Biology, Perelman School of Medicine, Philadelphia, PA 19104, USA
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Son Nguyen
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Christine Faunce
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Cell and Developmental Biology, Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Hua Huang
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Cell and Developmental Biology, Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Ian P. Dardani
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Austin L. Good
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Joan Lim
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Cell and Developmental Biology, Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Catherine Li
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Cell and Developmental Biology, Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Nicholas Biddle
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Cell and Developmental Biology, Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Eric F. Joyce
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Arjun Raj
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Daniel Lee
- Division of Urology, Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA 19104, USA
| | - Brian Keith
- Department of Cell and Developmental Biology, Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - M. Celeste Simon
- Department of Cell and Developmental Biology, Perelman School of Medicine, Philadelphia, PA 19104, USA
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Shelley L. Berger
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Cell and Developmental Biology, Perelman School of Medicine, Philadelphia, PA 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
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6
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Valledor M, Byron M, Dumas B, Carone DM, Hall LL, Lawrence JB. Early chromosome condensation by XIST builds A-repeat RNA density that facilitates gene silencing. Cell Rep 2023; 42:112686. [PMID: 37384527 PMCID: PMC10461597 DOI: 10.1016/j.celrep.2023.112686] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 10/31/2022] [Accepted: 06/08/2023] [Indexed: 07/01/2023] Open
Abstract
XIST RNA triggers chromosome-wide gene silencing and condenses an active chromosome into a Barr body. Here, we use inducible human XIST to examine early steps in the process, showing that XIST modifies cytoarchitecture before widespread gene silencing. In just 2-4 h, barely visible transcripts populate the large "sparse zone" surrounding the smaller "dense zone"; importantly, density zones exhibit different chromatin impacts. Sparse transcripts immediately trigger immunofluorescence for H2AK119ub and CIZ1, a matrix protein. H3K27me3 appears hours later in the dense zone, which enlarges with chromosome condensation. Genes examined are silenced after compaction of the RNA/DNA territory. Insights into this come from the findings that the A-repeat alone can silence genes and rapidly, but only where dense RNA supports sustained histone deacetylation. We propose that sparse XIST RNA quickly impacts architectural elements to condense the largely non-coding chromosome, coalescing RNA density that facilitates an unstable, A-repeat-dependent step required for gene silencing.
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Affiliation(s)
- Melvys Valledor
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Meg Byron
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Brett Dumas
- Department of Medicine, Boston University Medical Center, Boston, MA 02118, USA
| | - Dawn M Carone
- Department of Biology, Swarthmore College, Swarthmore, PA 19081, USA
| | - Lisa L Hall
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA.
| | - Jeanne B Lawrence
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA; Department of Pediatrics, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA.
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7
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Ilık İA, Aktaş T. Nuclear speckles: dynamic hubs of gene expression regulation. FEBS J 2022; 289:7234-7245. [PMID: 34245118 DOI: 10.1111/febs.16117] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 06/13/2021] [Accepted: 07/08/2021] [Indexed: 01/13/2023]
Abstract
Complex, multistep biochemical reactions that routinely take place in our cells require high concentrations of enzymes, substrates, and other structural components to proceed efficiently and typically require chemical environments that can inhibit other reactions in their immediate vicinity. Eukaryotic cells solve these problems by restricting such reactions into diffusion-restricted compartments within the cell called organelles that can be separated from their environment by a lipid membrane, or into membrane-less compartments that form through liquid-liquid phase separation (LLPS). One of the most easily noticeable and the earliest discovered organelle is the nucleus, which harbors the genetic material in cells where transcription by RNA polymerases produces most of the messenger RNAs and a plethora of noncoding RNAs, which in turn are required for translation of mRNAs in the cytoplasm. The interior of the nucleus is not a uniform soup of biomolecules and rather consists of a variety of membrane-less bodies, such as the nucleolus, nuclear speckles (NS), paraspeckles, Cajal bodies, histone locus bodies, and more. In this review, we will focus on NS with an emphasis on recent developments including our own findings about the formation of NS by two large IDR-rich proteins SON and SRRM2.
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Affiliation(s)
| | - Tuğçe Aktaş
- Max Planck Institute for Molecular Genetics, Berlin, Germany
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8
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Nair SJ, Suter T, Wang S, Yang L, Yang F, Rosenfeld MG. Transcriptional enhancers at 40: evolution of a viral DNA element to nuclear architectural structures. Trends Genet 2022; 38:1019-1047. [PMID: 35811173 PMCID: PMC9474616 DOI: 10.1016/j.tig.2022.05.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 05/05/2022] [Accepted: 05/31/2022] [Indexed: 02/08/2023]
Abstract
Gene regulation by transcriptional enhancers is the dominant mechanism driving cell type- and signal-specific transcriptional diversity in metazoans. However, over four decades since the original discovery, how enhancers operate in the nuclear space remains largely enigmatic. Recent multidisciplinary efforts combining real-time imaging, genome sequencing, and biophysical strategies provide insightful but conflicting models of enhancer-mediated gene control. Here, we review the discovery and progress in enhancer biology, emphasizing the recent findings that acutely activated enhancers assemble regulatory machinery as mesoscale architectural structures with distinct physical properties. These findings help formulate novel models that explain several mysterious features of the assembly of transcriptional enhancers and the mechanisms of spatial control of gene expression.
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Affiliation(s)
- Sreejith J Nair
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, USA.
| | - Tom Suter
- Howard Hughes Medical Institute, Department and School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Susan Wang
- Howard Hughes Medical Institute, Department and School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Cellular and Molecular Medicine Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Lu Yang
- Howard Hughes Medical Institute, Department and School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Feng Yang
- Howard Hughes Medical Institute, Department and School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Michael G Rosenfeld
- Howard Hughes Medical Institute, Department and School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
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9
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Gamliel A, Meluzzi D, Oh S, Jiang N, Destici E, Rosenfeld MG, Nair SJ. Long-distance association of topological boundaries through nuclear condensates. Proc Natl Acad Sci U S A 2022; 119:e2206216119. [PMID: 35914133 PMCID: PMC9371644 DOI: 10.1073/pnas.2206216119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 05/24/2022] [Indexed: 01/09/2023] Open
Abstract
The eukaryotic genome is partitioned into distinct topological domains separated by boundary elements. Emerging data support the concept that several well-established nuclear compartments are ribonucleoprotein condensates assembled through the physical process of phase separation. Here, based on our demonstration that chemical disruption of nuclear condensate assembly weakens the insulation properties of a specific subset (∼20%) of topologically associated domain (TAD) boundaries, we report that the disrupted boundaries are characterized by a high level of transcription and striking spatial clustering. These topological boundary regions tend to be spatially associated, even interchromosomally, segregate with nuclear speckles, and harbor a specific subset of "housekeeping" genes widely expressed in diverse cell types. These observations reveal a previously unappreciated mode of genome organization mediated by conserved boundary elements harboring highly and widely expressed transcription units and associated transcriptional condensates.
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Affiliation(s)
- Amir Gamliel
- Department of Medicine, University of California San Diego, La Jolla, CA 92093
- HHMI, University of California San Diego, La Jolla, CA 92093
| | - Dario Meluzzi
- Department of Medicine, University of California San Diego, La Jolla, CA 92093
- HHMI, University of California San Diego, La Jolla, CA 92093
| | - Soohwan Oh
- Department of Medicine, University of California San Diego, La Jolla, CA 92093
- HHMI, University of California San Diego, La Jolla, CA 92093
| | - Nan Jiang
- Department of Neurosciences, University of California San Diego, La Jolla, CA 92093
| | - Eugin Destici
- Department of Neurosciences, University of California San Diego, La Jolla, CA 92093
| | - Michael G Rosenfeld
- Department of Medicine, University of California San Diego, La Jolla, CA 92093
- HHMI, University of California San Diego, La Jolla, CA 92093
| | - Sreejith J Nair
- Department of Medicine, University of California San Diego, La Jolla, CA 92093
- HHMI, University of California San Diego, La Jolla, CA 92093
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10
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Nickerson JA. The ribonucleoprotein network of the nucleus: a historical perspective. Curr Opin Genet Dev 2022; 75:101940. [PMID: 35777349 DOI: 10.1016/j.gde.2022.101940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 05/16/2022] [Accepted: 05/24/2022] [Indexed: 11/28/2022]
Abstract
There is a long experimental history supporting the principle that RNA is essential for normal nuclear and chromatin architecture. Most of the genome is transcribed into RNA but only 2% of the sequence codes for proteins. In the nucleus, most non-coding RNA, packaged in proteins, is bound into structures including chromatin and a non-chromatin scaffolding, the nuclear matrix, which was first observed by electron microscopy. Removing nuclear RNA or inhibiting its transcription causes the condensation of chromatin, showing the importance of RNA in spatially and functionally organizing the genome. Today, powerful techniques for the molecular characterization of RNA and for mapping its spatial organization in the nucleus have provided molecular detail to these principles.
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Affiliation(s)
- Jeffrey A Nickerson
- Division of Genes & Development, Department of Pediatrics, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA.
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11
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Raina K, Rao BJ. Mammalian nuclear speckles exhibit stable association with chromatin: a biochemical study. Nucleus 2022; 13:58-73. [PMID: 35220893 PMCID: PMC8890396 DOI: 10.1080/19491034.2021.2024948] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Nuclear Speckles (NS) are phase-separated condensates of protein and RNA whose components dynamically coordinate RNA transcription, splicing, transport and DNA repair. NS, probed largely by imaging studies, remained historically well known as Interchromatin Granule Clusters, and biochemical properties, especially their association with Chromatin have been largely unexplored. In this study, we tested whether NS exhibit any stable association with chromatin and show that limited DNAse-1 nicking of chromatin leads to the collapse of NS into isotropic distribution or aggregates of constituent proteins without affecting other nuclear structures. Further biochemical probing revealed that NS proteins were tightly associated with chromatin, extractable only by high-salt treatment just like histone proteins. NS were also co-released with solubilised mono-dinucleosomal chromatin fraction following the MNase digestion of chromatin. We propose a model that NS-chromatin constitutes a “putative stable association” whose coupling might be subject to the combined regulation from both chromatin and NS changes. Abbreviations: NS: Nuclear speckles; DSB: double strand breaks; PTM: posttranslational modifications; DDR: DNA damage repair; RBP-RNA binding proteins; TAD: topologically associated domains; LCR: low complexity regions; IDR: intrinsically disordered regions.
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Affiliation(s)
- Komal Raina
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
- Department of Biology, Indian Institute of Science Education and Research (Iiser) Tirupati, Transit Campus: Sree Rama Engineering College, Tirupati, India
| | - Basuthkar J Rao
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
- Department of Biology, Indian Institute of Science Education and Research (Iiser) Tirupati, Transit Campus: Sree Rama Engineering College, Tirupati, India
- Department of Animal Biology, University of Hyderabad, Hyderabad, India
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12
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Bridger JM, Pereira RT, Pina C, Tosi S, Lewis A. Alterations to Genome Organisation in Stem Cells, Their Differentiation and Associated Diseases. Results Probl Cell Differ 2022; 70:71-102. [PMID: 36348105 DOI: 10.1007/978-3-031-06573-6_3] [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] [Indexed: 06/16/2023]
Abstract
The organisation of the genome in its home, the cell nucleus, is reliant on a number of different aspects to establish, maintain and alter its functional non-random positioning. The genome is dispersed throughout a cell nucleus in specific chromosome territories which are further divided into topologically associated domains (TADs), where regions of the genome from different and the same chromosomes come together. This organisation is both controlled by DNA and chromatin epigenetic modification and the association of the genome with nuclear structures such as the nuclear lamina, the nucleolus and nuclear bodies and speckles. Indeed, sequences that are associated with the first two structures mentioned are termed lamina-associated domains (LADs) and nucleolar-associated domains (NADs), respectively. The modifications and nuclear structures that regulate genome function are altered through a cell's life from stem cell to differentiated cell through to reversible quiescence and irreversible senescence, and hence impacting on genome organisation, altering it to silence specific genes and permit others to be expressed in a controlled way in different cell types and cell cycle statuses. The structures and enzymes and thus the organisation of the genome can also be deleteriously affected, leading to disease and/or premature ageing.
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Affiliation(s)
- Joanna M Bridger
- Division of Biosciences, Department of Life Sciences, Centre for Genome Engineering and Maintenance (cenGEM), College of Health, Medicine and Life Sciences, Brunel University London, Uxbridge, UK.
| | - Rita Torres Pereira
- Division of Biosciences, Department of Life Sciences, Centre for Genome Engineering and Maintenance (cenGEM), College of Health, Medicine and Life Sciences, Brunel University London, Uxbridge, UK
| | - Cristina Pina
- Division of Biosciences, Department of Life Sciences, Centre for Genome Engineering and Maintenance (cenGEM), College of Health, Medicine and Life Sciences, Brunel University London, Uxbridge, UK
| | - Sabrina Tosi
- Division of Biosciences, Department of Life Sciences, Centre for Genome Engineering and Maintenance (cenGEM), College of Health, Medicine and Life Sciences, Brunel University London, Uxbridge, UK
| | - Annabelle Lewis
- Division of Biosciences, Department of Life Sciences, Centre for Genome Engineering and Maintenance (cenGEM), College of Health, Medicine and Life Sciences, Brunel University London, Uxbridge, UK
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13
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Nuclear compartmentalization as a mechanism of quantitative control of gene expression. Nat Rev Mol Cell Biol 2021; 22:653-670. [PMID: 34341548 DOI: 10.1038/s41580-021-00387-1] [Citation(s) in RCA: 115] [Impact Index Per Article: 38.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/28/2021] [Indexed: 01/08/2023]
Abstract
Gene regulation requires the dynamic coordination of hundreds of regulatory factors at precise genomic and RNA targets. Although many regulatory factors have specific affinity for their nucleic acid targets, molecular diffusion and affinity models alone cannot explain many of the quantitative features of gene regulation in the nucleus. One emerging explanation for these quantitative properties is that DNA, RNA and proteins organize within precise, 3D compartments in the nucleus to concentrate groups of functionally related molecules. Recently, nucleic acids and proteins involved in many important nuclear processes have been shown to engage in cooperative interactions, which lead to the formation of condensates that partition the nucleus. In this Review, we discuss an emerging perspective of gene regulation, which moves away from classic models of stoichiometric interactions towards an understanding of how spatial compartmentalization can lead to non-stoichiometric molecular interactions and non-linear regulatory behaviours. We describe key mechanisms of nuclear compartment formation, including emerging roles for non-coding RNAs in facilitating their formation, and discuss the functional role of nuclear compartments in transcription regulation, co-transcriptional and post-transcriptional RNA processing, and higher-order chromatin regulation. More generally, we discuss how compartmentalization may explain important quantitative aspects of gene regulation.
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14
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Liu S, Wang T, Shi Y, Bai L, Wang S, Guo D, Zhang Y, Qi Y, Chen C, Zhang J, Zhang Y, Liu Q, Yang Q, Wang Y, Liu H. USP42 drives nuclear speckle mRNA splicing via directing dynamic phase separation to promote tumorigenesis. Cell Death Differ 2021; 28:2482-2498. [PMID: 33731873 PMCID: PMC8329168 DOI: 10.1038/s41418-021-00763-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Revised: 02/20/2021] [Accepted: 02/24/2021] [Indexed: 01/31/2023] Open
Abstract
Liquid-liquid phase separation is considered a generic approach to organize membrane-less compartments, enabling the dynamic regulation of phase-separated assemblies to be investigated and pivotal roles of protein posttranslational modifications to be demonstrated. By surveying the subcellular localizations of human deubiquitylases, USP42 was identified to form nuclear punctate structures that are associated with phase separation properties. Bioinformatic analysis demonstrated that the USP42 C-terminal sequence was intrinsically disordered, which was further experimentally confirmed to confer phase separation features. USP42 is distributed to SC35-positive nuclear speckles in a positively charged C-terminal residue- and enzymatic activity-dependent manner. Notably, USP42 directs the integration of the spliceosome component PLRG1 into nuclear speckles, and its depletion interferes with the conformation of SC35 foci. Functionally, USP42 downregulation deregulates multiple mRNA splicing events and leads to deterred cancer cell growth, which is consistent with the impact of PLRG1 repression. Finally, USP42 expression is strongly correlated with that of PLRG1 in non-small-cell lung cancer samples and predicts adverse prognosis in overall survival. As a deubiquitylase capable of dynamically guiding nuclear speckle phase separation and mRNA splicing, USP42 inhibition presents a novel anticancer strategy by targeting phase separation.
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Affiliation(s)
- Shuyan Liu
- grid.411971.b0000 0000 9558 1426The Second Affiliated Hospital, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, Liaoning Province China
| | - Taishu Wang
- grid.411971.b0000 0000 9558 1426The Second Affiliated Hospital, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, Liaoning Province China
| | - Yulin Shi
- grid.411971.b0000 0000 9558 1426The Second Affiliated Hospital, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, Liaoning Province China
| | - Lu Bai
- grid.411971.b0000 0000 9558 1426The Second Affiliated Hospital, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, Liaoning Province China
| | - Shanshan Wang
- grid.411971.b0000 0000 9558 1426The Second Affiliated Hospital, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, Liaoning Province China
| | - Dong Guo
- grid.411971.b0000 0000 9558 1426The Second Affiliated Hospital, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, Liaoning Province China
| | - Yang Zhang
- grid.411971.b0000 0000 9558 1426The Second Affiliated Hospital, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, Liaoning Province China
| | - Yangfan Qi
- grid.411971.b0000 0000 9558 1426The Second Affiliated Hospital, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, Liaoning Province China
| | - Chaoqun Chen
- grid.411971.b0000 0000 9558 1426The Second Affiliated Hospital, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, Liaoning Province China
| | - Jinrui Zhang
- grid.411971.b0000 0000 9558 1426The Second Affiliated Hospital, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, Liaoning Province China
| | - Yingqiu Zhang
- grid.411971.b0000 0000 9558 1426The Second Affiliated Hospital, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, Liaoning Province China
| | - Quentin Liu
- grid.411971.b0000 0000 9558 1426The Second Affiliated Hospital, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, Liaoning Province China
| | - Qingkai Yang
- grid.411971.b0000 0000 9558 1426The Second Affiliated Hospital, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, Liaoning Province China
| | - Yang Wang
- grid.411971.b0000 0000 9558 1426The Second Affiliated Hospital, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, Liaoning Province China
| | - Han Liu
- grid.411971.b0000 0000 9558 1426The Second Affiliated Hospital, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, Liaoning Province China
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15
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Pathak RU, Soujanya M, Mishra RK. Deterioration of nuclear morphology and architecture: A hallmark of senescence and aging. Ageing Res Rev 2021; 67:101264. [PMID: 33540043 DOI: 10.1016/j.arr.2021.101264] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 01/04/2021] [Accepted: 01/26/2021] [Indexed: 12/15/2022]
Abstract
The metazoan nucleus is a highly structured organelle containing several well-defined sub-organelles. It is the largest organelle inside a cell taking up from one tenth to half of entire cell volume. This makes it one of the easiest organelles to identify and study under the microscope. Abnormalities in the nuclear morphology and architecture are commonly observed in an aged and senescent cell. For example, the nuclei enlarge, loose their shape, appear lobulated, harbour nuclear membrane invaginations, carry enlarged/fragmented nucleolus, loose heterochromatin, etc. In this review we discuss about the age-related changes in nuclear features and elaborate upon the molecular reasons driving the change. Many of these changes can be easily imaged under a microscope and analysed in silico. Thus, computational image analysis of nuclear features appears to be a promising tool to evaluate physiological age of a cell and offers to be a legitimate biomarker. It can be used to examine progression of age-related diseases and evaluate therapies.
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Affiliation(s)
| | - Mamilla Soujanya
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, 500007, Telangana, India
| | - Rakesh Kumar Mishra
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, 500007, Telangana, India.
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16
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p53 mediates target gene association with nuclear speckles for amplified RNA expression. Mol Cell 2021; 81:1666-1681.e6. [PMID: 33823140 DOI: 10.1016/j.molcel.2021.03.006] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 01/05/2021] [Accepted: 03/03/2021] [Indexed: 01/01/2023]
Abstract
Nuclear speckles are prominent nuclear bodies that contain proteins and RNA involved in gene expression. Although links between nuclear speckles and gene activation are emerging, the mechanisms regulating association of genes with speckles are unclear. We find that speckle association of p53 target genes is driven by the p53 transcription factor. Focusing on p21, a key p53 target, we demonstrate that speckle association boosts expression by elevating nascent RNA amounts. p53-regulated speckle association did not depend on p53 transactivation functions but required an intact proline-rich domain and direct DNA binding, providing mechanisms within p53 for regulating gene-speckle association. Beyond p21, a substantial subset of p53 targets have p53-regulated speckle association. Strikingly, speckle-associating p53 targets are more robustly activated and occupy a distinct niche of p53 biology compared with non-speckle-associating p53 targets. Together, our findings illuminate regulated speckle association as a mechanism used by a transcription factor to boost gene expression.
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17
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Liao SE, Regev O. Splicing at the phase-separated nuclear speckle interface: a model. Nucleic Acids Res 2021; 49:636-645. [PMID: 33337476 PMCID: PMC7826271 DOI: 10.1093/nar/gkaa1209] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 11/24/2020] [Accepted: 12/03/2020] [Indexed: 02/07/2023] Open
Abstract
Phase-separated membraneless bodies play important roles in nucleic acid biology. While current models for the roles of phase separation largely focus on the compartmentalization of constituent proteins, we reason that other properties of phase separation may play functional roles. Specifically, we propose that interfaces of phase-separated membraneless bodies could have functional roles in spatially organizing biochemical reactions. Here we propose such a model for the nuclear speckle, a membraneless body implicated in RNA splicing. In our model, sequence-dependent RNA positioning along the nuclear speckle interface coordinates RNA splicing. Our model asserts that exons are preferentially sequestered into nuclear speckles through binding by SR proteins, while introns are excluded through binding by nucleoplasmic hnRNP proteins. As a result, splice sites at exon-intron boundaries are preferentially positioned at nuclear speckle interfaces. This positioning exposes splice sites to interface-localized spliceosomes, enabling the subsequent splicing reaction. Our model provides a simple mechanism that seamlessly explains much of the complex logic of splicing. This logic includes experimental results such as the antagonistic duality between splicing factors, the position dependence of splicing sequence motifs, and the collective contribution of many motifs to splicing decisions. Similar functional roles for phase-separated interfaces may exist for other membraneless bodies.
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Affiliation(s)
- Susan E Liao
- Computer Science Department, Courant Institute of Mathematical Sciences, New York University, New York, NY, USA
| | - Oded Regev
- Computer Science Department, Courant Institute of Mathematical Sciences, New York University, New York, NY, USA
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18
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Zhang L, Zhang Y, Chen Y, Gholamalamdari O, Wang Y, Ma J, Belmont AS. TSA-seq reveals a largely conserved genome organization relative to nuclear speckles with small position changes tightly correlated with gene expression changes. Genome Res 2021; 31:251-264. [PMID: 33355299 PMCID: PMC7849416 DOI: 10.1101/gr.266239.120] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 12/17/2020] [Indexed: 12/31/2022]
Abstract
TSA-seq mapping suggests that gene distance to nuclear speckles is more deterministic and predictive of gene expression levels than gene radial positioning. Gene expression correlates inversely with distance to nuclear speckles, with chromosome regions of unusually high expression located at the apex of chromosome loops protruding from the nuclear periphery into the interior. Genomic distances to the nearest lamina-associated domain are larger for loop apexes mapping closest to nuclear speckles, suggesting the possibility of conservation of speckle-associated regions. To facilitate comparison of genome organization by TSA-seq, we reduced required cell numbers 10- to 20-fold for TSA-seq by deliberately saturating protein-labeling while preserving distance mapping by the still unsaturated DNA-labeling. Only ∼10% of the genome shows statistically significant shifts in relative nuclear speckle distances in pair-wise comparisons between human cell lines (H1, HFF, HCT116, K562); however, these moderate shifts in nuclear speckle distances tightly correlate with changes in cell type-specific gene expression. Similarly, half of heat shock-induced gene loci already preposition very close to nuclear speckles, with the remaining positioned near or at intermediate distance (HSPH1) to nuclear speckles but shifting even closer with transcriptional induction. Speckle association together with chromatin decondensation correlates with expression amplification upon HSPH1 activation. Our results demonstrate a largely "hardwired" genome organization with specific genes moving small mean distances relative to speckles during cell differentiation or a physiological transition, suggesting an important role of nuclear speckles in gene expression regulation.
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Affiliation(s)
- Liguo Zhang
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Yang Zhang
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - Yu Chen
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Omid Gholamalamdari
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Yuchuan Wang
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - Jian Ma
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - Andrew S Belmont
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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19
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Hasenson SE, Shav‐Tal Y. Speculating on the Roles of Nuclear Speckles: How RNA‐Protein Nuclear Assemblies Affect Gene Expression. Bioessays 2020; 42:e2000104. [DOI: 10.1002/bies.202000104] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 06/17/2020] [Indexed: 02/06/2023]
Affiliation(s)
- Sarah E. Hasenson
- The Mina & Everard Goodman Faculty of Life Sciences and the Institute of Nanotechnology and Advanced Materials Bar‐Ilan University Ramat Gan 4481400 Israel
| | - Yaron Shav‐Tal
- The Mina & Everard Goodman Faculty of Life Sciences and the Institute of Nanotechnology and Advanced Materials Bar‐Ilan University Ramat Gan 4481400 Israel
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20
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Kim J, Venkata NC, Hernandez Gonzalez GA, Khanna N, Belmont AS. Gene expression amplification by nuclear speckle association. J Cell Biol 2020; 219:jcb.201904046. [PMID: 31757787 PMCID: PMC7039209 DOI: 10.1083/jcb.201904046] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 08/31/2019] [Accepted: 10/23/2019] [Indexed: 11/22/2022] Open
Abstract
Many active genes reproducibly position near nuclear speckles, but the functional significance of this positioning is unknown. Here we show that HSPA1B BAC transgenes and endogenous Hsp70 genes turn on 2-4 min after heat shock (HS), irrespective of their distance to speckles. However, both total HSPA1B mRNA counts and nascent transcript levels measured adjacent to the transgene are approximately twofold higher for speckle-associated alleles 15 min after HS. Nascent transcript level fold-increases for speckle-associated alleles are 12-56-fold and 3-7-fold higher 1-2 h after HS for HSPA1B transgenes and endogenous genes, respectively. Severalfold higher nascent transcript levels for several Hsp70 flanking genes also correlate with speckle association at 37°C. Live-cell imaging reveals that HSPA1B nascent transcript levels increase/decrease with speckle association/disassociation. Initial investigation reveals that increased nascent transcript levels accompanying speckle association correlate with reduced exosome RNA degradation and larger Ser2p CTD-modified RNA polymerase II foci. Our results demonstrate stochastic gene expression dependent on positioning relative to a liquid-droplet nuclear compartment through "gene expression amplification."
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Affiliation(s)
- Jiah Kim
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL
| | - Neha Chivukula Venkata
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL
| | | | - Nimish Khanna
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL
| | - Andrew S Belmont
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL.,Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL
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21
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Matsui M, Sakasai R, Abe M, Kimura Y, Kajita S, Torii W, Katsuki Y, Ishiai M, Iwabuchi K, Takata M, Nishi R. USP42 enhances homologous recombination repair by promoting R-loop resolution with a DNA-RNA helicase DHX9. Oncogenesis 2020; 9:60. [PMID: 32541651 PMCID: PMC7296013 DOI: 10.1038/s41389-020-00244-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 05/21/2020] [Accepted: 05/29/2020] [Indexed: 01/05/2023] Open
Abstract
The nucleus of mammalian cells is compartmentalized by nuclear bodies such as nuclear speckles, however, involvement of nuclear bodies, especially nuclear speckles, in DNA repair has not been actively investigated. Here, our focused screen for nuclear speckle factors involved in homologous recombination (HR), which is a faithful DNA double-strand break (DSB) repair mechanism, identified transcription-related nuclear speckle factors as potential HR regulators. Among the top hits, we provide evidence showing that USP42, which is a hitherto unidentified nuclear speckles protein, promotes HR by facilitating BRCA1 recruitment to DSB sites and DNA-end resection. We further showed that USP42 localization to nuclear speckles is required for efficient HR. Furthermore, we established that USP42 interacts with DHX9, which possesses DNA-RNA helicase activity, and is required for efficient resolution of DSB-induced R-loop. In conclusion, our data propose a model in which USP42 facilitates BRCA1 loading to DSB sites, resolution of DSB-induced R-loop and preferential DSB repair by HR, indicating the importance of nuclear speckle-mediated regulation of DSB repair.
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Affiliation(s)
- Misaki Matsui
- Department of Biomedical Sciences, Ritsumeikan University, Kusatsu, Shiga, 525-8577, Japan
| | - Ryo Sakasai
- Department of Biochemistry I, Kanazawa Medical University, Kahoku, Ishikawa, 920-0293, Japan
| | - Masako Abe
- Department of Late Effects Studies, Radiation Biology Centre, Graduate School of Biostudies, Kyoto University, Kyoto, Kyoto, 606-8501, Japan
| | - Yusuke Kimura
- Department of Biomedical Sciences, Ritsumeikan University, Kusatsu, Shiga, 525-8577, Japan
| | - Shoki Kajita
- Department of Biomedical Sciences, Ritsumeikan University, Kusatsu, Shiga, 525-8577, Japan
| | - Wakana Torii
- Department of Biomedical Sciences, Ritsumeikan University, Kusatsu, Shiga, 525-8577, Japan
| | - Yoko Katsuki
- Department of Late Effects Studies, Radiation Biology Centre, Graduate School of Biostudies, Kyoto University, Kyoto, Kyoto, 606-8501, Japan
| | - Masamichi Ishiai
- Central Radioisotope Division, National Cancer Centre Research Institute, Chuoku, Tokyo, 104-0045, Japan
| | - Kuniyoshi Iwabuchi
- Department of Biochemistry I, Kanazawa Medical University, Kahoku, Ishikawa, 920-0293, Japan
| | - Minoru Takata
- Department of Late Effects Studies, Radiation Biology Centre, Graduate School of Biostudies, Kyoto University, Kyoto, Kyoto, 606-8501, Japan
| | - Ryotaro Nishi
- Department of Biomedical Sciences, Ritsumeikan University, Kusatsu, Shiga, 525-8577, Japan. .,School of Bioscience and Biotechnology, Tokyo University of Technology, Hachioji, Tokyo, 192-0982, Japan.
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22
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Smith KP, Hall LL, Lawrence JB. Nuclear hubs built on RNAs and clustered organization of the genome. Curr Opin Cell Biol 2020; 64:67-76. [PMID: 32259767 DOI: 10.1016/j.ceb.2020.02.015] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 02/13/2020] [Accepted: 02/22/2020] [Indexed: 12/18/2022]
Abstract
RNAs play diverse roles in formation and function of subnuclear compartments, most of which are associated with active genes. NEAT1 and NEAT2/MALAT1 exemplify long non-coding RNAs (lncRNAs) known to function in nuclear bodies; however, we suggest that RNA biogenesis itself may underpin much nuclear compartmentalization. Recent studies show that active genes cluster with nuclear speckles on a genome-wide scale, significantly advancing earlier cytological evidence that speckles (aka SC-35 domains) are hubs of concentrated pre-mRNA metabolism. We propose the 'karyotype to hub' hypothesis to explain this organization: clustering of genes in the human karyotype may have evolved to facilitate the formation of efficient nuclear hubs, driven in part by the propensity of ribonucleoproteins (RNPs) to form large-scale condensates. The special capacity of highly repetitive RNAs to impact architecture is highlighted by recent findings that human satellite II RNA sequesters factors into abnormal nuclear bodies in disease, potentially co-opting a normal developmental mechanism.
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Affiliation(s)
- Kelly P Smith
- Department of Neurology, University of Massachusetts Medical School, 55 Lake Ave. North, Worcester, MA, 01655, USA
| | - Lisa L Hall
- Department of Neurology, University of Massachusetts Medical School, 55 Lake Ave. North, Worcester, MA, 01655, USA
| | - Jeanne B Lawrence
- Department of Neurology, University of Massachusetts Medical School, 55 Lake Ave. North, Worcester, MA, 01655, USA.
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23
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Abstract
In the nucleus, genomic DNA is wrapped around histone octamers to form nucleosomes. In principle, nucleosomes are substantial barriers to transcriptional activities. Nuclear non-coding RNAs (ncRNAs) are proposed to function in chromatin conformation modulation and transcriptional regulation. However, it remains unclear how ncRNAs affect the nucleosome structure. Eleanors are clusters of ncRNAs that accumulate around the estrogen receptor-α (ESR1) gene locus in long-term estrogen deprivation (LTED) breast cancer cells, and markedly enhance the transcription of the ESR1 gene. Here we detected nucleosome depletion around the transcription site of Eleanor2, the most highly expressed Eleanor in the LTED cells. We found that the purified Eleanor2 RNA fragment drastically destabilized the nucleosome in vitro. This activity was also exerted by other ncRNAs, but not by poly(U) RNA or DNA. The RNA-mediated nucleosome destabilization may be a common feature among natural nuclear RNAs, and may function in transcription regulation in chromatin. The Eleanor cluster of non-coding RNAs is localised upstream of estrogen receptor-α (ESR1) gene locus in estrogen-deprived breast cancer cells. Fujita et al find that RNA fragments of Eleanor2 and of other non-coding RNAs are able to destabilise nucleosomes in vitro, suggesting a role in transcriptional regulation.
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24
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Kempfer R, Pombo A. Methods for mapping 3D chromosome architecture. Nat Rev Genet 2019; 21:207-226. [PMID: 31848476 DOI: 10.1038/s41576-019-0195-2] [Citation(s) in RCA: 288] [Impact Index Per Article: 57.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/04/2019] [Indexed: 12/12/2022]
Abstract
Determining how chromosomes are positioned and folded within the nucleus is critical to understanding the role of chromatin topology in gene regulation. Several methods are available for studying chromosome architecture, each with different strengths and limitations. Established imaging approaches and proximity ligation-based chromosome conformation capture (3C) techniques (such as DNA-FISH and Hi-C, respectively) have revealed the existence of chromosome territories, functional nuclear landmarks (such as splicing speckles and the nuclear lamina) and topologically associating domains. Improvements to these methods and the recent development of ligation-free approaches, including GAM, SPRITE and ChIA-Drop, are now helping to uncover new aspects of 3D genome topology that confirm the nucleus to be a complex, highly organized organelle.
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Affiliation(s)
- Rieke Kempfer
- Epigenetic Regulation and Chromatin Architecture Group, Berlin Institute for Medical Systems Biology, Max-Delbrück Centre for Molecular Medicine, Berlin, Germany. .,Institute for Biology, Humboldt University of Berlin, Berlin, Germany.
| | - Ana Pombo
- Epigenetic Regulation and Chromatin Architecture Group, Berlin Institute for Medical Systems Biology, Max-Delbrück Centre for Molecular Medicine, Berlin, Germany. .,Institute for Biology, Humboldt University of Berlin, Berlin, Germany.
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25
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Lemaire S, Fontrodona N, Aubé F, Claude JB, Polvèche H, Modolo L, Bourgeois CF, Mortreux F, Auboeuf D. Characterizing the interplay between gene nucleotide composition bias and splicing. Genome Biol 2019; 20:259. [PMID: 31783898 PMCID: PMC6883713 DOI: 10.1186/s13059-019-1869-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 10/28/2019] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Nucleotide composition bias plays an important role in the 1D and 3D organization of the human genome. Here, we investigate the potential interplay between nucleotide composition bias and the regulation of exon recognition during splicing. RESULTS By analyzing dozens of RNA-seq datasets, we identify two groups of splicing factors that activate either about 3200 GC-rich exons or about 4000 AT-rich exons. We show that splicing factor-dependent GC-rich exons have predicted RNA secondary structures at 5' ss and are dependent on U1 snRNP-associated proteins. In contrast, splicing factor-dependent AT-rich exons have a large number of decoy branch points, SF1- or U2AF2-binding sites and are dependent on U2 snRNP-associated proteins. Nucleotide composition bias also influences local chromatin organization, with consequences for exon recognition during splicing. Interestingly, the GC content of exons correlates with that of their hosting genes, isochores, and topologically associated domains. CONCLUSIONS We propose that regional nucleotide composition bias over several dozens of kilobase pairs leaves a local footprint at the exon level and induces constraints during splicing that can be alleviated by local chromatin organization at the DNA level and recruitment of specific splicing factors at the RNA level. Therefore, nucleotide composition bias establishes a direct link between genome organization and local regulatory processes, like alternative splicing.
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Affiliation(s)
- Sébastien Lemaire
- Laboratory of Biology and Modelling of the Cell, Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, 46 Allée d'Italie Site Jacques Monod, F-69007, Lyon, France
| | - Nicolas Fontrodona
- Laboratory of Biology and Modelling of the Cell, Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, 46 Allée d'Italie Site Jacques Monod, F-69007, Lyon, France
| | - Fabien Aubé
- Laboratory of Biology and Modelling of the Cell, Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, 46 Allée d'Italie Site Jacques Monod, F-69007, Lyon, France
| | - Jean-Baptiste Claude
- Laboratory of Biology and Modelling of the Cell, Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, 46 Allée d'Italie Site Jacques Monod, F-69007, Lyon, France
| | | | - Laurent Modolo
- LBMC Biocomputing Center, CNRS UMR 5239, INSERM U1210, 46 Allée d'Italie Site Jacques Monod, F-69007, Lyon, France
| | - Cyril F Bourgeois
- Laboratory of Biology and Modelling of the Cell, Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, 46 Allée d'Italie Site Jacques Monod, F-69007, Lyon, France
| | - Franck Mortreux
- Laboratory of Biology and Modelling of the Cell, Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, 46 Allée d'Italie Site Jacques Monod, F-69007, Lyon, France
| | - Didier Auboeuf
- Laboratory of Biology and Modelling of the Cell, Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, 46 Allée d'Italie Site Jacques Monod, F-69007, Lyon, France.
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26
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Bera M, Kalyana Sundaram RV. Chromosome Territorial Organization Drives Efficient Protein Complex Formation: A Hypothesis. THE YALE JOURNAL OF BIOLOGY AND MEDICINE 2019; 92:541-548. [PMID: 31543715 PMCID: PMC6747946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
In eukaryotes, chromosomes often form a transcriptional kissing loop during interphase. We propose that these kissing loops facilitate the formation of protein complexes. mRNA transcripts from these loops could cluster together into phase-separated nuclear granules. Their export into the ER could be ensured by guided diffusion through the inter-chromatin space followed by association with nuclear baskets and export factors. Inside the ER, these mRNAs would form a translation hub. Juxtaposed translation of these mRNAs would increase the cis/trans protein complex assembly among the nascent protein chains. Eukaryotes might employ this pathway to increase complex formation efficiency.
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Affiliation(s)
- Manindra Bera
- To whom all correspondence should be addressed: Manindra Bera, Department of Cell Biology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT USA, 06520; Tel: 203-737-3269,
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27
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Tasan I, Sustackova G, Zhang L, Kim J, Sivaguru M, HamediRad M, Wang Y, Genova J, Ma J, Belmont AS, Zhao H. CRISPR/Cas9-mediated knock-in of an optimized TetO repeat for live cell imaging of endogenous loci. Nucleic Acids Res 2019; 46:e100. [PMID: 29912475 PMCID: PMC6158506 DOI: 10.1093/nar/gky501] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Accepted: 06/13/2018] [Indexed: 12/30/2022] Open
Abstract
Nuclear organization has an important role in determining genome function; however, it is not clear how spatiotemporal organization of the genome relates to functionality. To elucidate this relationship, a method for tracking any locus of interest is desirable. Recently clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) or transcription activator-like effectors were adapted for imaging endogenous loci; however, they are mostly limited to visualization of repetitive regions. Here, we report an efficient and scalable method named SHACKTeR (Short Homology and CRISPR/Cas9-mediated Knock-in of a TetO Repeat) for live cell imaging of specific chromosomal regions without the need for a pre-existing repetitive sequence. SHACKTeR requires only two modifications to the genome: CRISPR/Cas9-mediated knock-in of an optimized TetO repeat and its visualization by TetR-EGFP expression. Our simplified knock-in protocol, utilizing short homology arms integrated by polymerase chain reaction, was successful at labeling 10 different loci in HCT116 cells. We also showed the feasibility of knock-in into lamina-associated, heterochromatin regions, demonstrating that these regions prefer non-homologous end joining for knock-in. Using SHACKTeR, we were able to observe DNA replication at a specific locus by long-term live cell imaging. We anticipate the general applicability and scalability of our method will enhance causative analyses between gene function and compartmentalization in a high-throughput manner.
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Affiliation(s)
- Ipek Tasan
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Gabriela Sustackova
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Liguo Zhang
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Jiah Kim
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Mayandi Sivaguru
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Mohammad HamediRad
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.,Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Yuchuan Wang
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Justin Genova
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Jian Ma
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Andrew S Belmont
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.,Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Huimin Zhao
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.,Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.,Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.,Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.,Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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28
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Chen Y, Belmont AS. Genome organization around nuclear speckles. Curr Opin Genet Dev 2019; 55:91-99. [PMID: 31394307 DOI: 10.1016/j.gde.2019.06.008] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 06/05/2019] [Accepted: 06/11/2019] [Indexed: 01/08/2023]
Abstract
Higher eukaryotic cell nuclei are highly compartmentalized into bodies and structural assemblies of specialized functions. Nuclear speckles/IGCs are one of the most prominent nuclear bodies, yet their functional significance remains largely unknown. Recent advances in sequence-based mapping of nuclear genome organization now provide genome-wide analysis of chromosome organization relative to nuclear speckles. Here we review older microscopy-based studies on a small number of genes with the new genomic mapping data suggesting a significant fraction of the genome is almost deterministically positioned near nuclear speckles. Both microscopy and genomic-based approaches support the concept of the nuclear speckle periphery as a major active chromosomal compartment which may play an important role in fine-tuning gene regulation.
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Affiliation(s)
- Yu Chen
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, CIRM Center of Excellence, University of California, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, Berkeley, CA 94720, USA
| | - Andrew S Belmont
- Department of Cell and Developmental Biology, University of Illinois, Urbana-Champaign, B107 CLSL, 601 S. Goodwin Avenue, Urbana, IL 61801, USA.
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29
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Fritz AJ, Sehgal N, Pliss A, Xu J, Berezney R. Chromosome territories and the global regulation of the genome. Genes Chromosomes Cancer 2019; 58:407-426. [PMID: 30664301 DOI: 10.1002/gcc.22732] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 01/11/2019] [Accepted: 01/12/2019] [Indexed: 12/29/2022] Open
Abstract
Spatial positioning is a fundamental principle governing nuclear processes. Chromatin is organized as a hierarchy from nucleosomes to Mbp chromatin domains (CD) or topologically associating domains (TADs) to higher level compartments culminating in chromosome territories (CT). Microscopic and sequencing techniques have substantiated chromatin organization as a critical factor regulating gene expression. For example, enhancers loop back to interact with their target genes almost exclusively within TADs, distally located coregulated genes reposition into common transcription factories upon activation, and Mbp CDs exhibit dynamic motion and configurational changes in vivo. A longstanding question in the nucleus field is whether an interactive nuclear matrix provides a direct link between structure and function. The findings of nonrandom radial positioning of CT within the nucleus suggest the possibility of preferential interaction patterns among populations of CT. Sequential labeling up to 10 CT followed by application of computer imaging and geometric graph mining algorithms revealed cell-type specific interchromosomal networks (ICN) of CT that are altered during the cell cycle, differentiation, and cancer progression. It is proposed that the ICN correlate with the global level of genome regulation. These approaches also demonstrated that the large scale 3-D topology of CT is specific for each CT. The cell-type specific proximity of certain chromosomal regions in normal cells may explain the propensity of distinct translocations in cancer subtypes. Understanding how genes are dysregulated upon disruption of the normal "wiring" of the nucleus by translocations, deletions, and amplifications that are hallmarks of cancer, should enable more targeted therapeutic strategies.
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Affiliation(s)
- Andrew J Fritz
- Department of Biochemistry and University of Vermont Cancer Center, The University of Vermont Larner College of Medicine, Burlington, Vermont
| | - Nitasha Sehgal
- Department of Biological Sciences, University at Buffalo, Buffalo, New York
| | - Artem Pliss
- Institute for Lasers, Photonics and Biophotonics and the Department of Chemistry, University at Buffalo, Buffalo, New York
| | - Jinhui Xu
- Department of Computer Science and Engineering, University at Buffalo, Buffalo, New York
| | - Ronald Berezney
- Department of Biological Sciences, University at Buffalo, Buffalo, New York
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30
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Nair SJ, Yang L, Meluzzi D, Oh S, Yang F, Friedman MJ, Wang S, Suter T, Alshareedah I, Gamliel A, Ma Q, Zhang J, Hu Y, Tan Y, Ohgi KA, Jayani RS, Banerjee PR, Aggarwal AK, Rosenfeld MG. Phase separation of ligand-activated enhancers licenses cooperative chromosomal enhancer assembly. Nat Struct Mol Biol 2019; 26:193-203. [PMID: 30833784 PMCID: PMC6709854 DOI: 10.1038/s41594-019-0190-5] [Citation(s) in RCA: 210] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 01/18/2019] [Indexed: 12/16/2022]
Abstract
A crucial feature of differentiated cells is the rapid activation of enhancer-driven transcriptional programs in response to signals. The potential contributions of physicochemical properties of enhancer assembly in signaling events remain poorly understood. Here we report that in human breast cancer cells, the acute 17β-estradiol-dependent activation of functional enhancers requires assembly of an enhancer RNA-dependent ribonucleoprotein (eRNP) complex exhibiting properties of phase-separated condensates. Unexpectedly, while acute ligand-dependent assembly of eRNPs resulted in enhancer activation sensitive to chemical disruption of phase separation, chronically activated enhancers proved resistant to such disruption, with progressive maturation of eRNPs to a more gel-like state. Acute, but not chronic, stimulation resulted in ligand-induced, condensin-dependent changes in spatial chromatin conformation based on homotypic enhancer association, resulting in cooperative enhancer-activation events. Thus, distinct physicochemical properties of eRNP condensates on enhancers serve as determinants of rapid ligand-dependent alterations in chromosomal architecture and cooperative enhancer activation.
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Affiliation(s)
- Sreejith J Nair
- Howard Hughes Medical Institute, Department and School of Medicine, University of California, San Diego, La Jolla, CA, USA.
| | - Lu Yang
- Howard Hughes Medical Institute, Department and School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Dario Meluzzi
- Howard Hughes Medical Institute, Department and School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Soohwan Oh
- Howard Hughes Medical Institute, Department and School of Medicine, University of California, San Diego, La Jolla, CA, USA
- Biological Sciences Graduate Program, University of California, San Diego, La Jolla, CA, USA
| | - Feng Yang
- Howard Hughes Medical Institute, Department and School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Meyer J Friedman
- Howard Hughes Medical Institute, Department and School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Susan Wang
- Howard Hughes Medical Institute, Department and School of Medicine, University of California, San Diego, La Jolla, CA, USA
- Cellular and Molecular Medicine Graduate Program, University of California, San Diego, La Jolla, CA, USA
| | - Tom Suter
- Howard Hughes Medical Institute, Department and School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | | | - Amir Gamliel
- Howard Hughes Medical Institute, Department and School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Qi Ma
- Howard Hughes Medical Institute, Department and School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Jie Zhang
- Howard Hughes Medical Institute, Department and School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Yiren Hu
- Howard Hughes Medical Institute, Department and School of Medicine, University of California, San Diego, La Jolla, CA, USA
- Biological Sciences Graduate Program, University of California, San Diego, La Jolla, CA, USA
| | - Yuliang Tan
- Howard Hughes Medical Institute, Department and School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Kenneth A Ohgi
- Howard Hughes Medical Institute, Department and School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Ranveer Singh Jayani
- Howard Hughes Medical Institute, Department and School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Priya R Banerjee
- Department of Physics, University at Buffalo-SUNY, Buffalo, NY, USA
| | - Aneel K Aggarwal
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Michael G Rosenfeld
- Howard Hughes Medical Institute, Department and School of Medicine, University of California, San Diego, La Jolla, CA, USA.
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31
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Dhaliwal A, Pelka S, Gray DS, Moghe PV. Engineering Lineage Potency and Plasticity of Stem Cells using Epigenetic Molecules. Sci Rep 2018; 8:16289. [PMID: 30389989 PMCID: PMC6215020 DOI: 10.1038/s41598-018-34511-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 10/11/2018] [Indexed: 12/17/2022] Open
Abstract
Stem cells are considered as a multipotent regenerative source for diseased and dysfunctional tissues. Despite the promise of stem cells, the inherent capacity of stem cells to convert to tissue-specific lineages can present a major challenge to the use of stem cells for regenerative medicine. We hypothesized that epigenetic regulating molecules can modulate the stem cell’s developmental program, and thus potentially overcome the limited lineage differentiation that human stem cells exhibit based on the source and processing of stem cells. In this study, we screened a library of 84 small molecule pharmacological agents indicated in nucleosomal modification and identified a sub-set of specific molecules that influenced osteogenesis in human mesenchymal stem cells (hMSCs) while maintaining cell viability in-vitro. Pre-treatment with five candidate hits, Gemcitabine, Decitabine, I-CBP112, Chidamide, and SIRT1/2 inhibitor IV, maximally enhanced osteogenesis in-vitro. In contrast, five distinct molecules, 4-Iodo-SAHA, Scriptaid, AGK2, CI-amidine and Delphidine Chloride maximally inhibited osteogenesis. We then tested the role of these molecules on hMSCs derived from aged human donors and report that small epigenetic molecules, namely Gemcitabine and Chidamide, can significantly promote osteogenic differentiation by 5.9- and 2.3-fold, respectively. Taken together, this study demonstrates new applications of identified small molecule drugs for sensitively regulating the lineage plasticity fates of bone-marrow derived mesenchymal stem cells through modulating the epigenetic profile of the cells.
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Affiliation(s)
- Anandika Dhaliwal
- Department of Biomedical Engineering, Rutgers University, Piscataway, NJ, United States
| | - Sandra Pelka
- Department of Biomedical Engineering, Rutgers University, Piscataway, NJ, United States
| | - David S Gray
- Department of Biomedical Engineering, Rutgers University, Piscataway, NJ, United States
| | - Prabhas V Moghe
- Department of Biomedical Engineering, Rutgers University, Piscataway, NJ, United States. .,Department of Chemical and Biochemical Engineering, Rutgers University, Piscataway, NJ, United States.
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32
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Chen Y, Zhang Y, Wang Y, Zhang L, Brinkman EK, Adam SA, Goldman R, van Steensel B, Ma J, Belmont AS. Mapping 3D genome organization relative to nuclear compartments using TSA-Seq as a cytological ruler. J Cell Biol 2018; 217:4025-4048. [PMID: 30154186 PMCID: PMC6219710 DOI: 10.1083/jcb.201807108] [Citation(s) in RCA: 213] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Revised: 08/05/2018] [Accepted: 08/07/2018] [Indexed: 02/03/2023] Open
Abstract
Chen et al. present TSA-Seq, a new mapping method that measures cytological distances relative to spatially distinct nuclear subcompartments. From novel nuclear organization maps of human cells, they identify transcription hot zones of high gene density that are near nuclear speckles and enriched in highly expressed genes, housekeeping genes, and genes with low transcriptional pausing. While nuclear compartmentalization is an essential feature of three-dimensional genome organization, no genomic method exists for measuring chromosome distances to defined nuclear structures. In this study, we describe TSA-Seq, a new mapping method capable of providing a “cytological ruler” for estimating mean chromosomal distances from nuclear speckles genome-wide and for predicting several Mbp chromosome trajectories between nuclear compartments without sophisticated computational modeling. Ensemble-averaged results in K562 cells reveal a clear nuclear lamina to speckle axis correlated with a striking spatial gradient in genome activity. This gradient represents a convolution of multiple spatially separated nuclear domains including two types of transcription “hot zones.” Transcription hot zones protruding furthest into the nuclear interior and positioning deterministically very close to nuclear speckles have higher numbers of total genes, the most highly expressed genes, housekeeping genes, genes with low transcriptional pausing, and super-enhancers. Our results demonstrate the capability of TSA-Seq for genome-wide mapping of nuclear structure and suggest a new model for spatial organization of transcription and gene expression.
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Affiliation(s)
- Yu Chen
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL
| | - Yang Zhang
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL.,Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA
| | - Yuchuan Wang
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA
| | - Liguo Zhang
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL
| | - Eva K Brinkman
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Stephen A Adam
- Department of Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Robert Goldman
- Department of Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Bas van Steensel
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Jian Ma
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA
| | - Andrew S Belmont
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL .,Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL
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33
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Maass PG, Weise A, Rittscher K, Lichtenwald J, Barutcu AR, Liehr T, Aydin A, Wefeld-Neuenfeld Y, Pölsler L, Tinschert S, Rinn JL, Luft FC, Bähring S. Reorganization of inter-chromosomal interactions in the 2q37-deletion syndrome. EMBO J 2018; 37:e96257. [PMID: 29921581 PMCID: PMC6068439 DOI: 10.15252/embj.201696257] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 04/24/2018] [Accepted: 05/14/2018] [Indexed: 12/27/2022] Open
Abstract
Chromosomes occupy distinct interphase territories in the three-dimensional nucleus. However, how these chromosome territories are arranged relative to one another is poorly understood. Here, we investigated the inter-chromosomal interactions between chromosomes 2q, 12, and 17 in human mesenchymal stem cells (MSCs) and MSC-derived cell types by DNA-FISH We compared our findings in normal karyotypes with a three-generation family harboring a 2q37-deletion syndrome, featuring a heterozygous partial deletion of histone deacetylase 4 (HDAC4) on chr2q37. In normal karyotypes, we detected stable, recurring arrangements and interactions between the three chromosomal territories with a tissue-specific interaction bias at certain loci. These inter-chromosomal interactions were confirmed by Hi-C. Interestingly, the disease-related HDAC4 deletion resulted in displaced inter-chromosomal arrangements and altered interactions between the deletion-affected chromosome 2 and chromosome 12 and/or 17 in 2q37-deletion syndrome patients. Our findings provide evidence for a direct link between a structural chromosomal aberration and altered interphase architecture that results in a nuclear configuration, supporting a possible molecular pathogenesis.
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Affiliation(s)
- Philipp G Maass
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Experimental and Clinical Research Center (ECRC), a joint cooperation between the Charité Medical Faculty and the Max Delbrück Center for Molecular Medicine (MDC), Berlin, Germany
- Max Delbrück Center for Molecular Medicine (MDC), Berlin, Germany
| | - Anja Weise
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Katharina Rittscher
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Julia Lichtenwald
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - A Rasim Barutcu
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Thomas Liehr
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Atakan Aydin
- Experimental and Clinical Research Center (ECRC), a joint cooperation between the Charité Medical Faculty and the Max Delbrück Center for Molecular Medicine (MDC), Berlin, Germany
- Max Delbrück Center for Molecular Medicine (MDC), Berlin, Germany
| | | | - Laura Pölsler
- Zentrum Medizinische Genetik, Medizinische Universität, Innsbruck, Austria
| | - Sigrid Tinschert
- Zentrum Medizinische Genetik, Medizinische Universität, Innsbruck, Austria
| | - John L Rinn
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Department of Biochemistry, BioFrontiers, University of Colorado, Boulder, CO, USA
| | - Friedrich C Luft
- Experimental and Clinical Research Center (ECRC), a joint cooperation between the Charité Medical Faculty and the Max Delbrück Center for Molecular Medicine (MDC), Berlin, Germany
- Max Delbrück Center for Molecular Medicine (MDC), Berlin, Germany
- Department of Medicine, Division of Clinical Pharmacology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Sylvia Bähring
- Experimental and Clinical Research Center (ECRC), a joint cooperation between the Charité Medical Faculty and the Max Delbrück Center for Molecular Medicine (MDC), Berlin, Germany
- Max Delbrück Center for Molecular Medicine (MDC), Berlin, Germany
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34
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Quinodoz SA, Ollikainen N, Tabak B, Palla A, Schmidt JM, Detmar E, Lai MM, Shishkin AA, Bhat P, Takei Y, Trinh V, Aznauryan E, Russell P, Cheng C, Jovanovic M, Chow A, Cai L, McDonel P, Garber M, Guttman M. Higher-Order Inter-chromosomal Hubs Shape 3D Genome Organization in the Nucleus. Cell 2018; 174:744-757.e24. [PMID: 29887377 PMCID: PMC6548320 DOI: 10.1016/j.cell.2018.05.024] [Citation(s) in RCA: 524] [Impact Index Per Article: 87.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 03/18/2018] [Accepted: 05/10/2018] [Indexed: 11/22/2022]
Abstract
Eukaryotic genomes are packaged into a 3-dimensional structure in the nucleus. Current methods for studying genome-wide structure are based on proximity ligation. However, this approach can fail to detect known structures, such as interactions with nuclear bodies, because these DNA regions can be too far apart to directly ligate. Accordingly, our overall understanding of genome organization remains incomplete. Here, we develop split-pool recognition of interactions by tag extension (SPRITE), a method that enables genome-wide detection of higher-order interactions within the nucleus. Using SPRITE, we recapitulate known structures identified by proximity ligation and identify additional interactions occurring across larger distances, including two hubs of inter-chromosomal interactions that are arranged around the nucleolus and nuclear speckles. We show that a substantial fraction of the genome exhibits preferential organization relative to these nuclear bodies. Our results generate a global model whereby nuclear bodies act as inter-chromosomal hubs that shape the overall packaging of DNA in the nucleus.
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Affiliation(s)
- Sofia A Quinodoz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Noah Ollikainen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Barbara Tabak
- Program in Bioinformatics and Integrative Biology and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Ali Palla
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Jan Marten Schmidt
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Elizabeth Detmar
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Mason M Lai
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Alexander A Shishkin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Prashant Bhat
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yodai Takei
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Vickie Trinh
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Erik Aznauryan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Pamela Russell
- Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora, CO 80045, USA
| | - Christine Cheng
- Department of Biology, Boston University, Boston, MA 02215, USA
| | - Marko Jovanovic
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Amy Chow
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Long Cai
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Patrick McDonel
- Program in Bioinformatics and Integrative Biology and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Manuel Garber
- Program in Bioinformatics and Integrative Biology and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Mitchell Guttman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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35
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Abstract
Imaging (fluorescence in situ hybridization [FISH]) and genome-wide chromosome conformation capture (Hi-C) are two major approaches to the study of higher-order genome organization in the nucleus. Intra-chromosomal and inter-chromosomal interactions (referred to as non-homologous chromosomal contacts [NHCCs]) have been observed by several FISH-based studies, but locus-specific NHCCs have not been detected by Hi-C. Due to crosslinking, neither of these approaches assesses spatiotemporal properties. Toward resolving the discrepancies between imaging and Hi-C, we sought to understand the spatiotemporal properties of NHCCs in living cells by CRISPR/Cas9 live-cell imaging (CLING). In mammalian cells, we find that NHCCs are stable and occur as frequently as intra-chromosomal interactions, but NHCCs occur at farther spatial distance that could explain their lack of detection in Hi-C. By revealing the spatiotemporal properties in living cells, our study provides fundamental insights into the biology of NHCCs.
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Affiliation(s)
- Philipp G Maass
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - A Rasim Barutcu
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Catherine L Weiner
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - John L Rinn
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA.
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36
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Maass PG, Barutcu AR, Shechner DM, Weiner CL, Melé M, Rinn JL. Spatiotemporal allele organization by allele-specific CRISPR live-cell imaging (SNP-CLING). Nat Struct Mol Biol 2018; 25:176-184. [PMID: 29343869 PMCID: PMC5805655 DOI: 10.1038/s41594-017-0015-3] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 11/30/2017] [Indexed: 12/23/2022]
Abstract
Imaging and chromatin capture techniques have shed important insights into our understanding of nuclear organization. A limitation of these techniques is the inability to resolve allele-specific spatiotemporal properties of genomic loci in living cells. Here, we describe an allele-specific CRISPR live-cell DNA imaging technique (SNP-CLING) to provide the first comprehensive insights into allelic positioning across space and time in mouse embryonic stem cells and fibroblasts. In 3D-imaging, we studied alleles on different chromosomes in relation to one another and relative to nuclear substructures such as the nucleolus. We find that alleles maintain similar positions relative to each other and the nucleolus, however loci occupy different unique positions. To monitor spatiotemporal dynamics by SNP-CLING, we performed 4D-imaging, determining that alleles are either stably positioned, or fluctuating during cell state transitions, such as apoptosis. SNP-CLING is a universally applicable technique that enables dissecting allele-specific spatiotemporal genome organization in live cells.
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Affiliation(s)
- Philipp G Maass
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.
| | - A Rasim Barutcu
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - David M Shechner
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA.,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA.,Department of Pharmacology, The University of Washington, Seattle, WA, USA
| | - Catherine L Weiner
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA.,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Marta Melé
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - John L Rinn
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA. .,Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA. .,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA. .,Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA. .,Department of Biochemistry, University of Colorado, BioFrontiers, Boulder, CO, USA.
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37
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Benvegnù S, Mateo MI, Palomer E, Jurado-Arjona J, Dotti CG. Aging Triggers Cytoplasmic Depletion and Nuclear Translocation of the E3 Ligase Mahogunin: A Function for Ubiquitin in Neuronal Survival. Mol Cell 2017; 66:358-372.e7. [DOI: 10.1016/j.molcel.2017.04.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 12/19/2016] [Accepted: 04/05/2017] [Indexed: 12/20/2022]
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38
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Complex multi-enhancer contacts captured by Genome Architecture Mapping (GAM). Nature 2017; 543:519-524. [PMID: 28273065 PMCID: PMC5366070 DOI: 10.1038/nature21411] [Citation(s) in RCA: 425] [Impact Index Per Article: 60.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2015] [Accepted: 01/18/2017] [Indexed: 12/22/2022]
Abstract
The organization of the genome in the nucleus and the interactions of genes with their regulatory elements are key features of transcriptional control and their disruption can cause disease. We developed a novel genome-wide method, Genome Architecture Mapping (GAM), for measuring chromatin contacts, and other features of three-dimensional chromatin topology, based on sequencing DNA from a large collection of thin nuclear sections. We apply GAM to mouse embryonic stem cells and identify an enrichment for specific interactions between active genes and enhancers across very large genomic distances, using a mathematical model ‘SLICE’ (Statistical Inference of Co-segregation). GAM also reveals an abundance of three-way contacts genome-wide, especially between regions that are highly transcribed or contain super-enhancers, highlighting a previously inaccessible complexity in genome architecture and a major role for gene-expression specific contacts in organizing the genome in mammalian nuclei.
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39
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Wachsmuth M, Knoch TA, Rippe K. Dynamic properties of independent chromatin domains measured by correlation spectroscopy in living cells. Epigenetics Chromatin 2016; 9:57. [PMID: 28035241 PMCID: PMC5192577 DOI: 10.1186/s13072-016-0093-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 09/12/2016] [Indexed: 01/08/2023] Open
Abstract
Background Genome organization into subchromosomal topologically associating domains (TADs) is linked to cell-type-specific gene expression programs. However, dynamic properties of such domains remain elusive, and it is unclear how domain plasticity modulates genomic accessibility for soluble factors. Results Here, we combine and compare a high-resolution topology analysis of interacting chromatin loci with fluorescence correlation spectroscopy measurements of domain dynamics in single living cells. We identify topologically and dynamically independent chromatin domains of ~1 Mb in size that are best described by a loop-cluster polymer model. Hydrodynamic relaxation times and gyration radii of domains are larger for open (161 ± 15 ms, 297 ± 9 nm) than for dense chromatin (88 ± 7 ms, 243 ± 6 nm) and increase globally upon chromatin hyperacetylation or ATP depletion. Conclusions Based on the domain structure and dynamics measurements, we propose a loop-cluster model for chromatin domains. It suggests that the regulation of chromatin accessibility for soluble factors displays a significantly stronger dependence on factor concentration than search processes within a static network. Electronic supplementary material The online version of this article (doi:10.1186/s13072-016-0093-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Malte Wachsmuth
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Tobias A Knoch
- Biophysical Genomics Group, Department of Cell Biology and Genetics, Erasmus Medical Center, Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands
| | - Karsten Rippe
- Research Group Genome Organization and Function, Deutsches Krebsforschungszentrum (DKFZ) & BioQuant, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
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40
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Dhaliwal A, Brenner M, Wolujewicz P, Zhang Z, Mao Y, Batish M, Kohn J, Moghe PV. Profiling stem cell states in three-dimensional biomaterial niches using high content image informatics. Acta Biomater 2016; 45:98-109. [PMID: 27590870 PMCID: PMC5262522 DOI: 10.1016/j.actbio.2016.08.052] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 08/23/2016] [Accepted: 08/29/2016] [Indexed: 02/06/2023]
Abstract
A predictive framework for the evolution of stem cell biology in 3-D is currently lacking. In this study we propose deep image informatics of the nuclear biology of stem cells to elucidate how 3-D biomaterials steer stem cell lineage phenotypes. The approach is based on high content imaging informatics to capture minute variations in the 3-D spatial organization of splicing factor SC-35 in the nucleoplasm as a marker to classify emergent cell phenotypes of human mesenchymal stem cells (hMSCs). The cells were cultured in varied 3-D culture systems including hydrogels, electrospun mats and salt leached scaffolds. The approach encompasses high resolution 3-D imaging of SC-35 domains and high content image analysis (HCIA) to compute quantitative 3-D nuclear metrics for SC-35 organization in single cells in concert with machine learning approaches to construct a predictive cell-state classification model. Our findings indicate that hMSCs cultured in collagen hydrogels and induced to differentiate into osteogenic or adipogenic lineages could be classified into the three lineages (stem, adipogenic, osteogenic) with ⩾80% precision and sensitivity, within 72h. Using this framework, the augmentation of osteogenesis by scaffold design exerted by porogen leached scaffolds was also profiled within 72h with ∼80% high sensitivity. Furthermore, by employing 3-D SC-35 organizational metrics, differential osteogenesis induced by novel electrospun fibrous polymer mats incorporating decellularized matrix could also be elucidated and predictably modeled at just 3days with high precision. We demonstrate that 3-D SC-35 organizational metrics can be applied to model the stem cell state in 3-D scaffolds. We propose that this methodology can robustly discern minute changes in stem cell states within complex 3-D architectures and map single cell biological readouts that are critical to assessing population level cell heterogeneity. STATEMENT OF SIGNIFICANCE The sustained development and validation of bioactive materials relies on technologies that can sensitively discern cell response dynamics to biomaterials, while capturing cell-to-cell heterogeneity and preserving cellular native phenotypes. In this study, we illustrate the application of a novel high content image informatics platform to classify emergent human mesenchymal stem cell (hMSC) phenotypes in a diverse range of 3-D biomaterial scaffolds with high sensitivity and precision, and track cell responses to varied external stimuli. A major in silico innovation is the proposed image profiling technology based on unique three dimensional textural signatures of a mechanoreporter protein within the nuclei of stem cells cultured in 3-D scaffolds. This technology will accelerate the pace of high-fidelity biomaterial screening.
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Affiliation(s)
- Anandika Dhaliwal
- Department of Biomedical Engineering, Rutgers University, Piscataway, NJ, United States
| | - Matthew Brenner
- Department of Biomedical Engineering, Rutgers University, Piscataway, NJ, United States
| | - Paul Wolujewicz
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers University, Newark, NJ, United States
| | - Zheng Zhang
- Department of Chemistry and Chemical Biology, New Jersey Center for Biomaterials, Rutgers University, Piscataway, NJ, United States
| | - Yong Mao
- Department of Chemistry and Chemical Biology, New Jersey Center for Biomaterials, Rutgers University, Piscataway, NJ, United States
| | - Mona Batish
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers University, Newark, NJ, United States
| | - Joachim Kohn
- Department of Chemistry and Chemical Biology, New Jersey Center for Biomaterials, Rutgers University, Piscataway, NJ, United States
| | - Prabhas V Moghe
- Department of Biomedical Engineering, Rutgers University, Piscataway, NJ, United States; Department of Chemical and Biochemical Engineering, Rutgers University, Piscataway, NJ, United States.
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41
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The host protein CLUH participates in the subnuclear transport of influenza virus ribonucleoprotein complexes. Nat Microbiol 2016; 1:16062. [DOI: 10.1038/nmicrobiol.2016.62] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 03/31/2016] [Indexed: 11/08/2022]
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42
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Vaquerizas JM, Akhtar A, Luscombe NM. Large-scale nuclear architecture and transcriptional control. Subcell Biochem 2016; 52:279-95. [PMID: 21557088 DOI: 10.1007/978-90-481-9069-0_13] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Transcriptional regulation is one the most basic mechanisms for controlling gene expression. Over the past few years, much research has been devoted to understanding the interplay between transcription factors, histone modifications and associated enzymes required to achieve this control. However, it is becoming increasingly apparent that the three-dimensional conformation of chromatin in the interphase nucleus also plays a critical role in regulating transcription. Chromatin localisation in the nucleus is highly organised, and early studies described strong interactions between chromatin and sub-nuclear components. Single-gene studies have shed light on how chromosomal architecture affects gene expression. Lately, this has been complemented by whole-genome studies that have determined the global chromatin conformation of living cells in interphase. These studies have greatly expanded our understanding of nuclear architecture and its interplay with different physiological processes. Despite these advances, however, most of the mechanisms used to impose the three-dimensional chromatin structure remain unknown. Here, we summarise the different levels of chromatin organisation in the nucleus and discuss current efforts into characterising the mechanisms that govern it.
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43
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Brackley CA, Brown JM, Waithe D, Babbs C, Davies J, Hughes JR, Buckle VJ, Marenduzzo D. Predicting the three-dimensional folding of cis-regulatory regions in mammalian genomes using bioinformatic data and polymer models. Genome Biol 2016; 17:59. [PMID: 27036497 PMCID: PMC4815170 DOI: 10.1186/s13059-016-0909-0] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 02/23/2016] [Indexed: 12/20/2022] Open
Abstract
The three-dimensional (3D) organization of chromosomes can be probed using methods like Capture-C. However, it is unclear how such population-level data relate to the organization within a single cell, and the mechanisms leading to the observed interactions are still largely obscure. We present a polymer modeling scheme based on the assumption that chromosome architecture is maintained by protein bridges, which form chromatin loops. To test the model, we perform FISH experiments and compare with Capture-C data. Starting merely from the locations of protein binding sites, our model accurately predicts the experimentally observed chromatin interactions, revealing a population of 3D conformations.
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Affiliation(s)
- Chris A. Brackley
- />SUPA, School of Physics and Astronomy, University of Edinburgh, Mayfield Road, Edinburgh, EH9 3JZ UK
| | - Jill M. Brown
- />MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford, OX3 9DS UK
| | - Dominic Waithe
- />Wolfson Imaging Centre Oxford, Weatherall Institute of Molecular Medicine, Oxford University, Oxford, OX3 9DS UK
| | - Christian Babbs
- />MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford, OX3 9DS UK
| | - James Davies
- />MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford, OX3 9DS UK
| | - Jim R. Hughes
- />MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford, OX3 9DS UK
| | - Veronica J. Buckle
- />MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford, OX3 9DS UK
| | - Davide Marenduzzo
- />SUPA, School of Physics and Astronomy, University of Edinburgh, Mayfield Road, Edinburgh, EH9 3JZ UK
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44
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Zhang Q, Kota KP, Alam SG, Nickerson JA, Dickinson RB, Lele TP. Coordinated Dynamics of RNA Splicing Speckles in the Nucleus. J Cell Physiol 2015; 231:1269-75. [PMID: 26496460 DOI: 10.1002/jcp.25224] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 10/21/2015] [Indexed: 12/28/2022]
Abstract
Despite being densely packed with chromatin, nuclear bodies and a nucleoskeletal network, the nucleus is a remarkably dynamic organelle. Chromatin loops form and relax, RNA transcripts and transcription factors move diffusively, and nuclear bodies move. We show here that RNA splicing speckled domains (splicing speckles) fluctuate in constrained nuclear volumes and remodel their shapes. Small speckles move in a directed way toward larger speckles with which they fuse. This directed movement is reduced upon decreasing cellular ATP levels or inhibiting RNA polymerase II activity. The random movement of speckles is reduced upon decreasing cellular ATP levels, moderately reduced after inhibition of SWI/SNF chromatin remodeling and modestly increased upon inhibiting RNA polymerase II activity. To define the paths through which speckles can translocate in the nucleus, we generated a pressure gradient to create flows in the nucleus. In response to the pressure gradient, speckles moved along curvilinear paths in the nucleus. Collectively, our results demonstrate a new type of ATP-dependent motion in the nucleus. We present a model where recycling splicing factors return as part of small sub-speckles from distal sites of RNA processing to larger splicing speckles by a directed ATP-driven mechanism through interchromatin spaces.
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Affiliation(s)
- Qiao Zhang
- Department of Chemical Engineering, University of Florida, Gainesville, Florida
| | - Krishna P Kota
- Department of Cellular and Tissue Imaging, Perkin Elmer Inc., Waltham, Massachusetts
| | - Samer G Alam
- Department of Chemical Engineering, University of Florida, Gainesville, Florida
| | - Jeffrey A Nickerson
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Richard B Dickinson
- Department of Chemical Engineering, University of Florida, Gainesville, Florida
| | - Tanmay P Lele
- Department of Chemical Engineering, University of Florida, Gainesville, Florida
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45
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Snyers L, Zupkovitz G, Almeder M, Fliesser M, Stoisser A, Weipoltshammer K, Schöfer C. Distinct chromatin signature of histone H3 variant H3.3 in human cells. Nucleus 2015; 5:449-61. [PMID: 25482197 PMCID: PMC4164487 DOI: 10.4161/nucl.36229] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Actively transcribed regions of the genome have been found enriched for the histone H3 variant H3.3. This variant is incorporated into nucleosomes throughout the cell cycle whereas the canonical isoforms are predominately deposited in association with replication. In order to obtain a global picture of the deposition pattern at the single cell level we expressed H3.3 in both normal and malignant human cells and analyzed nuclei using conventional and structured illumination imaging (SIM). We found that the distribution pattern of H3.3 in interphase differs from that of the canonical histone H3 variants and this difference is conveyed to mitotic chromosomes which display a distinct H3.3 banding pattern. Histone H3.3 localization positively correlated with markers for transcriptionally active chromatin and, notably, H3.3 was almost completely absent from the inactive X chromosome. Collectively, our data show that histone variant H3.3 occupies distinct intranuclear chromatin domains and that these genomic loci are associated with gene expression.
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Affiliation(s)
- Luc Snyers
- a Department for Cell and Developmental Biology; Medical Imaging Cluster; Medical University of Vienna; Vienna, Austria
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46
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Wickramasinghe VO, Laskey RA. Control of mammalian gene expression by selective mRNA export. Nat Rev Mol Cell Biol 2015; 16:431-42. [PMID: 26081607 DOI: 10.1038/nrm4010] [Citation(s) in RCA: 144] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Nuclear export of mRNAs is a crucial step in the regulation of gene expression, linking transcription in the nucleus to translation in the cytoplasm. Although important components of the mRNA export machinery are well characterized, such as transcription-export complexes TREX and TREX-2, recent work has shown that, in some instances, mammalian mRNA export can be selective and can regulate crucial biological processes such as DNA repair, gene expression, maintenance of pluripotency, haematopoiesis, proliferation and cell survival. Such findings show that mRNA export is an unexpected, yet potentially important, mechanism for the control of gene expression and of the mammalian transcriptome.
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Affiliation(s)
- Vihandha O Wickramasinghe
- Medical Research Centre (MRC) Cancer Unit, Hutchison/MRC Research Centre, Box 197, Biomedical Campus, Cambridge CB2 0XZ, UK
| | - Ronald A Laskey
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
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47
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Silva AM, Brown JM, Buckle VJ, Wade-Martins R, Lufino MMP. Expanded GAA repeats impair FXN gene expression and reposition the FXN locus to the nuclear lamina in single cells. Hum Mol Genet 2015; 24:3457-71. [PMID: 25814655 PMCID: PMC4498154 DOI: 10.1093/hmg/ddv096] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 03/12/2015] [Indexed: 02/07/2023] Open
Abstract
Abnormally expanded DNA repeats are associated with several neurodegenerative diseases. In Friedreich's ataxia (FRDA), expanded GAA repeats in intron 1 of the frataxin gene (FXN) reduce FXN mRNA levels in averaged cell samples through a poorly understood mechanism. By visualizing FXN expression and nuclear localization in single cells, we show that GAA-expanded repeats decrease the number of FXN mRNA molecules, slow transcription, and increase FXN localization at the nuclear lamina (NL). Restoring histone acetylation reverses NL positioning. Expanded GAA-FXN loci in FRDA patient cells show increased NL localization with increased silencing of alleles and reduced transcription from alleles positioned peripherally. We also demonstrate inefficiencies in transcription initiation and elongation from the expanded GAA-FXN locus at single-cell resolution. We suggest that repressive epigenetic modifications at the expanded GAA-FXN locus may lead to NL relocation, where further repression may occur.
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Affiliation(s)
- Ana M Silva
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, UK, Faculdade de Medicina, Universidade de Lisboa, Lisboa 1649-028, Portugal and
| | - Jill M Brown
- Medical Research Council, Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Veronica J Buckle
- Medical Research Council, Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Richard Wade-Martins
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, UK,
| | - Michele M P Lufino
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, UK,
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48
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Derlig K, Giessl A, Brandstätter JH, Enz R, Dahlhaus R. Special characteristics of the transcription and splicing machinery in photoreceptor cells of the mammalian retina. Cell Tissue Res 2015; 362:281-94. [PMID: 26013685 DOI: 10.1007/s00441-015-2204-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 04/23/2015] [Indexed: 01/26/2023]
Abstract
Chromatin organization and the management of transcription and splicing are fundamental to the correct functioning of every cell but, in particular, for highly active cells such as photoreceptors, the sensory neurons of the retina. Rod photoreceptor cells of nocturnal animals have recently been shown to have an inverted chromatin architecture compared with rod photoreceptor cells of diurnal animals. The heterochromatin is concentrated in the center of the nucleus, whereas the genetically active euchromatin is positioned close to the nuclear membrane. This unique chromatin architecture suggests that the transcription and splicing machinery is also subject to specific adaptations in these cells. Recently, we described the protein Simiate, which is enriched in nuclear speckles and seems to be involved in transcription and splicing processes. Here, we examine the distribution of Simiate and nuclear speckles in neurons of mouse retinae. In retinal neurons of the inner nuclear and ganglion cell layer, Simiate is concentrated in a clustered pattern in the nuclear interior, whereas in rod and cone photoreceptor cells, Simiate is present at the nuclear periphery. Further staining with markers for the transcription and splicing machinery has confirmed the localization of nuclear speckle components at the periphery. Comparing the distribution of nuclear speckles in retinae of the nocturnal mouse with the diurnal degu, we found no differences in the arrangement of the transcription and splicing machinery in their photoreceptor cells, thus suggesting that the organization of these machineries is not related to the animal's lifestyle but rather represents a general characteristic of photoreceptor organization and function.
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Affiliation(s)
- Kristin Derlig
- Institute for Biochemistry, Emil-Fischer Center, FAU Erlangen-Nürnberg, Fahrstrasse 17, 91054, Erlangen, Germany
| | - Andreas Giessl
- Department of Biology, Animal Physiology, FAU Erlangen-Nürnberg, 91058, Erlangen, Germany
| | | | - Ralf Enz
- Institute for Biochemistry, Emil-Fischer Center, FAU Erlangen-Nürnberg, Fahrstrasse 17, 91054, Erlangen, Germany
| | - Regina Dahlhaus
- Institute for Biochemistry, Emil-Fischer Center, FAU Erlangen-Nürnberg, Fahrstrasse 17, 91054, Erlangen, Germany.
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49
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Arai T, Kano F, Murata M. Translocation of forkhead box O1 to the nuclear periphery induces histone modifications that regulate transcriptional repression of PCK1 in HepG2 cells. Genes Cells 2015; 20:340-57. [PMID: 25736587 DOI: 10.1111/gtc.12226] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 12/23/2014] [Indexed: 12/25/2022]
Abstract
Forkhead box O1 (FOXO1) is an important target for insulin. It is widely accepted that insulin-induced phosphorylation of FOXO1 by Akt leads to its nuclear exclusion and results in the inhibition of FOXO1-mediated transcription of the gluconeogenic gene phosphoenolpyruvate carboxykinase 1 (PCK1) in hepatocytes. However, many results that contradict this model have accumulated. Here, we provide a new mechanism for insulin-dependent repression of FOXO1-mediated transcription. We showed insulin-induced translocation of endogenous Ser256-phosphorylated FOXO1, which is essential for regulation of FOXO1-mediated transcription, from nuclear speckles to the nuclear periphery. This insulin-dependent translocation of FOXO1 regulated transcriptional repression of PCK1 concomitant with the formation of the FOXO1-euchromatic histone-lysine N-methyltransferase2 (EHMT2) complex and histone modifications of the PCK1 promoter region. Notably, our results suggest that FOXO1 uses nucleoporin 98 kDa NUP98 for this transcriptional regulation. These results provide a new insight into various FOXO1-mediated transcriptional regulation and FOXO1-mediated essential biological pathways.
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Affiliation(s)
- Tamaki Arai
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo, 153-8902, Japan
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50
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Gavrilov AA, Razin SV. Compartmentalization of the cell nucleus and spatial organization of the genome. Mol Biol 2015. [DOI: 10.1134/s0026893315010033] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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