151
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Yu N, Nützmann HW, MacDonald JT, Moore B, Field B, Berriri S, Trick M, Rosser SJ, Kumar SV, Freemont PS, Osbourn A. Delineation of metabolic gene clusters in plant genomes by chromatin signatures. Nucleic Acids Res 2016; 44:2255-65. [PMID: 26895889 PMCID: PMC4797310 DOI: 10.1093/nar/gkw100] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2015] [Revised: 01/20/2016] [Accepted: 02/09/2016] [Indexed: 12/26/2022] Open
Abstract
Plants are a tremendous source of diverse chemicals, including many natural product-derived drugs. It has recently become apparent that the genes for the biosynthesis of numerous different types of plant natural products are organized as metabolic gene clusters, thereby unveiling a highly unusual form of plant genome architecture and offering novel avenues for discovery and exploitation of plant specialized metabolism. Here we show that these clustered pathways are characterized by distinct chromatin signatures of histone 3 lysine trimethylation (H3K27me3) and histone 2 variant H2A.Z, associated with cluster repression and activation, respectively, and represent discrete windows of co-regulation in the genome. We further demonstrate that knowledge of these chromatin signatures along with chromatin mutants can be used to mine genomes for cluster discovery. The roles of H3K27me3 and H2A.Z in repression and activation of single genes in plants are well known. However, our discovery of highly localized operon-like co-regulated regions of chromatin modification is unprecedented in plants. Our findings raise intriguing parallels with groups of physically linked multi-gene complexes in animals and with clustered pathways for specialized metabolism in filamentous fungi.
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Affiliation(s)
- Nan Yu
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | | | - James T MacDonald
- Centre for Synthetic Biology and Innovation, Imperial College, South Kensington Campus, London, SW7 2AZ, UK
| | - Ben Moore
- Centre for Synthetic Biology and Innovation, Imperial College, South Kensington Campus, London, SW7 2AZ, UK
| | - Ben Field
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Souha Berriri
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Martin Trick
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Susan J Rosser
- School of Biological Sciences, University of Edinburgh, King's Building, Edinburgh, EH9 3JR, UK
| | - S Vinod Kumar
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Paul S Freemont
- Centre for Synthetic Biology and Innovation, Imperial College, South Kensington Campus, London, SW7 2AZ, UK
| | - Anne Osbourn
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
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152
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Raviram R, Rocha PP, Müller CL, Miraldi ER, Badri S, Fu Y, Swanzey E, Proudhon C, Snetkova V, Bonneau R, Skok JA. 4C-ker: A Method to Reproducibly Identify Genome-Wide Interactions Captured by 4C-Seq Experiments. PLoS Comput Biol 2016; 12:e1004780. [PMID: 26938081 PMCID: PMC4777514 DOI: 10.1371/journal.pcbi.1004780] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 01/29/2016] [Indexed: 01/17/2023] Open
Abstract
4C-Seq has proven to be a powerful technique to identify genome-wide interactions with a single locus of interest (or "bait") that can be important for gene regulation. However, analysis of 4C-Seq data is complicated by the many biases inherent to the technique. An important consideration when dealing with 4C-Seq data is the differences in resolution of signal across the genome that result from differences in 3D distance separation from the bait. This leads to the highest signal in the region immediately surrounding the bait and increasingly lower signals in far-cis and trans. Another important aspect of 4C-Seq experiments is the resolution, which is greatly influenced by the choice of restriction enzyme and the frequency at which it can cut the genome. Thus, it is important that a 4C-Seq analysis method is flexible enough to analyze data generated using different enzymes and to identify interactions across the entire genome. Current methods for 4C-Seq analysis only identify interactions in regions near the bait or in regions located in far-cis and trans, but no method comprehensively analyzes 4C signals of different length scales. In addition, some methods also fail in experiments where chromatin fragments are generated using frequent cutter restriction enzymes. Here, we describe 4C-ker, a Hidden-Markov Model based pipeline that identifies regions throughout the genome that interact with the 4C bait locus. In addition, we incorporate methods for the identification of differential interactions in multiple 4C-seq datasets collected from different genotypes or experimental conditions. Adaptive window sizes are used to correct for differences in signal coverage in near-bait regions, far-cis and trans chromosomes. Using several datasets, we demonstrate that 4C-ker outperforms all existing 4C-Seq pipelines in its ability to reproducibly identify interaction domains at all genomic ranges with different resolution enzymes.
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Affiliation(s)
- Ramya Raviram
- Department of Pathology, New York University School of Medicine, New York, New York, United States of America.,Department of Biology, New York University, New York, New York, United States of America
| | - Pedro P Rocha
- Department of Pathology, New York University School of Medicine, New York, New York, United States of America
| | - Christian L Müller
- Department of Biology, New York University, New York, New York, United States of America.,Department of Computer Science, Courant Institute of Mathematical Sciences, New York, New York, United States of America.,Simons Center for Data Analysis, New York, New York, United States of America
| | - Emily R Miraldi
- Department of Biology, New York University, New York, New York, United States of America.,Department of Computer Science, Courant Institute of Mathematical Sciences, New York, New York, United States of America.,Simons Center for Data Analysis, New York, New York, United States of America
| | - Sana Badri
- Department of Pathology, New York University School of Medicine, New York, New York, United States of America
| | - Yi Fu
- Department of Pathology, New York University School of Medicine, New York, New York, United States of America.,Department of Biology, New York University, New York, New York, United States of America
| | - Emily Swanzey
- Skirball Institute, New York University School of Medicine, New York, New York, United States of America
| | - Charlotte Proudhon
- Department of Pathology, New York University School of Medicine, New York, New York, United States of America
| | - Valentina Snetkova
- Department of Pathology, New York University School of Medicine, New York, New York, United States of America
| | - Richard Bonneau
- Department of Biology, New York University, New York, New York, United States of America.,Department of Computer Science, Courant Institute of Mathematical Sciences, New York, New York, United States of America.,Simons Center for Data Analysis, New York, New York, United States of America
| | - Jane A Skok
- Department of Pathology, New York University School of Medicine, New York, New York, United States of America
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153
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Solovei I, Thanisch K, Feodorova Y. How to rule the nucleus: divide et impera. Curr Opin Cell Biol 2016; 40:47-59. [PMID: 26938331 DOI: 10.1016/j.ceb.2016.02.014] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 02/04/2016] [Accepted: 02/14/2016] [Indexed: 01/14/2023]
Abstract
Genome-wide molecular studies have provided new insights into the organization of nuclear chromatin by revealing the presence of chromatin domains of differing transcriptional activity, frequency of cis-interactions, proximity to scaffolding structures and replication timing. These studies have not only brought our understanding of genome function to a new level, but also offered functional insight for many phenomena observed in microscopic studies. In this review, we discuss the major principles of nuclear organization based on the spatial segregation of euchromatin and heterochromatin, as well as the dynamic genome rearrangements occurring during cell differentiation and development. We hope to unite the existing molecular and microscopic data on genome organization to get a holistic view of the nucleus, and propose a model, in which repeat repertoire together with scaffolding structures blueprint the functional nuclear architecture.
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Affiliation(s)
- Irina Solovei
- Department of Biology II, Ludwig Maximilians University Munich, Grosshadernerstrasse 2, Planegg-Martinsried 82152, Germany.
| | - Katharina Thanisch
- Department of Biology II, Ludwig Maximilians University Munich, Grosshadernerstrasse 2, Planegg-Martinsried 82152, Germany
| | - Yana Feodorova
- Department of Biology II, Ludwig Maximilians University Munich, Grosshadernerstrasse 2, Planegg-Martinsried 82152, Germany; Department of Medical Biology, Medical University-Plovdiv, Boulevard Vasil Aprilov 15A, Plovdiv 4000, Bulgaria
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154
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Acemel RD, Tena JJ, Irastorza-Azcarate I, Marlétaz F, Gómez-Marín C, de la Calle-Mustienes E, Bertrand S, Diaz SG, Aldea D, Aury JM, Mangenot S, Holland PWH, Devos DP, Maeso I, Escrivá H, Gómez-Skarmeta JL. A single three-dimensional chromatin compartment in amphioxus indicates a stepwise evolution of vertebrate Hox bimodal regulation. Nat Genet 2016; 48:336-41. [PMID: 26829752 DOI: 10.1038/ng.3497] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 12/30/2015] [Indexed: 12/19/2022]
Abstract
The HoxA and HoxD gene clusters of jawed vertebrates are organized into bipartite three-dimensional chromatin structures that separate long-range regulatory inputs coming from the anterior and posterior Hox-neighboring regions. This architecture is instrumental in allowing vertebrate Hox genes to pattern disparate parts of the body, including limbs. Almost nothing is known about how these three-dimensional topologies originated. Here we perform extensive 4C-seq profiling of the Hox cluster in embryos of amphioxus, an invertebrate chordate. We find that, in contrast to the architecture in vertebrates, the amphioxus Hox cluster is organized into a single chromatin interaction domain that includes long-range contacts mostly from the anterior side, bringing distant cis-regulatory elements into contact with Hox genes. We infer that the vertebrate Hox bipartite regulatory system is an evolutionary novelty generated by combining ancient long-range regulatory contacts from DNA in the anterior Hox neighborhood with new regulatory inputs from the posterior side.
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Affiliation(s)
- Rafael D Acemel
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Seville, Spain
| | - Juan J Tena
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Seville, Spain
| | - Ibai Irastorza-Azcarate
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Seville, Spain
| | | | - Carlos Gómez-Marín
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Seville, Spain
| | - Elisa de la Calle-Mustienes
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Seville, Spain
| | - Stéphanie Bertrand
- Université Pierre et Marie Curie Université Paris 6, CNRS, UMR 7232, Biologie Integrative des Organismes Marins (BIOM), Observatoire Océanologique de Banyuls-sur-Mer, Banyuls-sur-Mer, France
| | - Sergio G Diaz
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Seville, Spain
| | - Daniel Aldea
- Université Pierre et Marie Curie Université Paris 6, CNRS, UMR 7232, Biologie Integrative des Organismes Marins (BIOM), Observatoire Océanologique de Banyuls-sur-Mer, Banyuls-sur-Mer, France
| | - Jean-Marc Aury
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France
| | - Sophie Mangenot
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France
| | | | - Damien P Devos
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Seville, Spain
| | - Ignacio Maeso
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Seville, Spain
| | - Hector Escrivá
- Université Pierre et Marie Curie Université Paris 6, CNRS, UMR 7232, Biologie Integrative des Organismes Marins (BIOM), Observatoire Océanologique de Banyuls-sur-Mer, Banyuls-sur-Mer, France
| | - José Luis Gómez-Skarmeta
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Seville, Spain
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155
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Visualizing the HoxD Gene Cluster at the Nanoscale Level. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2016; 80:9-16. [PMID: 26767994 DOI: 10.1101/sqb.2015.80.027177] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Transcription of HoxD cluster genes in limbs is coordinated by two topologically associating domains (TADs), neighboring the cluster and containing various enhancers. Here, we use a combination of microscopy approaches and chromosome conformation capture to assess the structural changes occurring in this global architecture in various functional states. We observed that despite their spatial juxtaposition, the TADs are consistently kept as distinct three-dimensional units. Hox genes located at their boundary can show significant spatial segregation over long distances, suggesting that physical elongation of the HoxD cluster occurs. The use of superresolution imaging (STORM [stochastic optical reconstruction microscopy]) revealed that the gene cluster can be in an either compact or elongated shape. The latter configuration is observed in transcriptionally active tissue and in embryonic stem cells, consistent with chromosome conformation capture results. Such morphological changes at HoxD in developing digits seem to be associated with its position at the boundary between two TADs and support the idea that chromatin dynamics is important in the establishment of transcriptional activity.
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156
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Barutcu AR, Fritz AJ, Zaidi SK, van Wijnen AJ, Lian JB, Stein JL, Nickerson JA, Imbalzano AN, Stein GS. C-ing the Genome: A Compendium of Chromosome Conformation Capture Methods to Study Higher-Order Chromatin Organization. J Cell Physiol 2016. [DOI: 10.1002/jcp.25062 order by 1-- -] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Affiliation(s)
- A. Rasim Barutcu
- Department of Cell and Developmental Biology; University of Massachusetts Medical School; Worcester Massachusetts
| | - Andrew J. Fritz
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
| | - Sayyed K. Zaidi
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
| | - André J. van Wijnen
- Departments of Orthopedic Surgery and Biochemistry & Molecular Biology; Mayo Clinic; Rochester Massachusetts
| | - Jane B. Lian
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
| | - Janet L. Stein
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
| | - Jeffrey A. Nickerson
- Department of Cell and Developmental Biology; University of Massachusetts Medical School; Worcester Massachusetts
| | - Anthony N. Imbalzano
- Department of Cell and Developmental Biology; University of Massachusetts Medical School; Worcester Massachusetts
| | - Gary S. Stein
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
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157
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Barutcu AR, Fritz AJ, Zaidi SK, van Wijnen AJ, Lian JB, Stein JL, Nickerson JA, Imbalzano AN, Stein GS. C-ing the Genome: A Compendium of Chromosome Conformation Capture Methods to Study Higher-Order Chromatin Organization. J Cell Physiol 2016. [DOI: 10.1002/jcp.25062 order by 8029-- awyx] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Affiliation(s)
- A. Rasim Barutcu
- Department of Cell and Developmental Biology; University of Massachusetts Medical School; Worcester Massachusetts
| | - Andrew J. Fritz
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
| | - Sayyed K. Zaidi
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
| | - André J. van Wijnen
- Departments of Orthopedic Surgery and Biochemistry & Molecular Biology; Mayo Clinic; Rochester Massachusetts
| | - Jane B. Lian
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
| | - Janet L. Stein
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
| | - Jeffrey A. Nickerson
- Department of Cell and Developmental Biology; University of Massachusetts Medical School; Worcester Massachusetts
| | - Anthony N. Imbalzano
- Department of Cell and Developmental Biology; University of Massachusetts Medical School; Worcester Massachusetts
| | - Gary S. Stein
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
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158
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Barutcu AR, Fritz AJ, Zaidi SK, van Wijnen AJ, Lian JB, Stein JL, Nickerson JA, Imbalzano AN, Stein GS. C-ing the Genome: A Compendium of Chromosome Conformation Capture Methods to Study Higher-Order Chromatin Organization. J Cell Physiol 2016. [DOI: 10.1002/jcp.25062 and 1880=1880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Affiliation(s)
- A. Rasim Barutcu
- Department of Cell and Developmental Biology; University of Massachusetts Medical School; Worcester Massachusetts
| | - Andrew J. Fritz
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
| | - Sayyed K. Zaidi
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
| | - André J. van Wijnen
- Departments of Orthopedic Surgery and Biochemistry & Molecular Biology; Mayo Clinic; Rochester Massachusetts
| | - Jane B. Lian
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
| | - Janet L. Stein
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
| | - Jeffrey A. Nickerson
- Department of Cell and Developmental Biology; University of Massachusetts Medical School; Worcester Massachusetts
| | - Anthony N. Imbalzano
- Department of Cell and Developmental Biology; University of Massachusetts Medical School; Worcester Massachusetts
| | - Gary S. Stein
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
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159
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Barutcu AR, Fritz AJ, Zaidi SK, van Wijnen AJ, Lian JB, Stein JL, Nickerson JA, Imbalzano AN, Stein GS. C-ing the Genome: A Compendium of Chromosome Conformation Capture Methods to Study Higher-Order Chromatin Organization. J Cell Physiol 2016. [DOI: 10.1002/jcp.25062 order by 1-- gadu] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Affiliation(s)
- A. Rasim Barutcu
- Department of Cell and Developmental Biology; University of Massachusetts Medical School; Worcester Massachusetts
| | - Andrew J. Fritz
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
| | - Sayyed K. Zaidi
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
| | - André J. van Wijnen
- Departments of Orthopedic Surgery and Biochemistry & Molecular Biology; Mayo Clinic; Rochester Massachusetts
| | - Jane B. Lian
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
| | - Janet L. Stein
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
| | - Jeffrey A. Nickerson
- Department of Cell and Developmental Biology; University of Massachusetts Medical School; Worcester Massachusetts
| | - Anthony N. Imbalzano
- Department of Cell and Developmental Biology; University of Massachusetts Medical School; Worcester Massachusetts
| | - Gary S. Stein
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
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160
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Barutcu AR, Fritz AJ, Zaidi SK, van Wijnen AJ, Lian JB, Stein JL, Nickerson JA, Imbalzano AN, Stein GS. C-ing the Genome: A Compendium of Chromosome Conformation Capture Methods to Study Higher-Order Chromatin Organization. J Cell Physiol 2016. [DOI: 10.1002/jcp.25062 order by 8029-- -] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Affiliation(s)
- A. Rasim Barutcu
- Department of Cell and Developmental Biology; University of Massachusetts Medical School; Worcester Massachusetts
| | - Andrew J. Fritz
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
| | - Sayyed K. Zaidi
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
| | - André J. van Wijnen
- Departments of Orthopedic Surgery and Biochemistry & Molecular Biology; Mayo Clinic; Rochester Massachusetts
| | - Jane B. Lian
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
| | - Janet L. Stein
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
| | - Jeffrey A. Nickerson
- Department of Cell and Developmental Biology; University of Massachusetts Medical School; Worcester Massachusetts
| | - Anthony N. Imbalzano
- Department of Cell and Developmental Biology; University of Massachusetts Medical School; Worcester Massachusetts
| | - Gary S. Stein
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
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161
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Matelot M, Noordermeer D. Determination of High-Resolution 3D Chromatin Organization Using Circular Chromosome Conformation Capture (4C-seq). Methods Mol Biol 2016; 1480:223-41. [PMID: 27659989 DOI: 10.1007/978-1-4939-6380-5_20] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
3D chromatin organization is essential for many aspects of transcriptional regulation. Circular Chromosome Conformation Capture followed by Illumina sequencing (4C-seq) is among the most powerful techniques to determine 3D chromatin organization. 4C-seq, like other modifications of the original 3C technique, uses the principle of "proximity ligation" to identify and quantify ten thousands of genomic interactions at a kilobase scale in a single experiment for predefined loci in the genome.In this chapter we focus on the experimental steps in the 4C-seq protocol, providing detailed descriptions on the preparation of cells, the construction of the circularized 3C library and the generation of the Illumina high throughput sequencing library. This protocol is particularly suited for the use of mammalian tissue samples, but can be used with minimal changes on circulating cells and cell lines from other sources as well. In the final section of this chapter, we provide a brief overview of data analysis approaches, accompanied by links to publicly available analysis tools.
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Affiliation(s)
- Mélody Matelot
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris Sud, University Paris-Saclay, 1 Avenue de la terrasse, 91198, Gif sur Yvette, France
| | - Daan Noordermeer
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris Sud, University Paris-Saclay, 1 Avenue de la terrasse, 91198, Gif sur Yvette, France.
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162
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Barutcu AR, Fritz AJ, Zaidi SK, van Wijnen AJ, Lian JB, Stein JL, Nickerson JA, Imbalzano AN, Stein GS. C-ing the Genome: A Compendium of Chromosome Conformation Capture Methods to Study Higher-Order Chromatin Organization. J Cell Physiol 2016. [DOI: 10.1002/jcp.25062 order by 8029-- #] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Affiliation(s)
- A. Rasim Barutcu
- Department of Cell and Developmental Biology; University of Massachusetts Medical School; Worcester Massachusetts
| | - Andrew J. Fritz
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
| | - Sayyed K. Zaidi
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
| | - André J. van Wijnen
- Departments of Orthopedic Surgery and Biochemistry & Molecular Biology; Mayo Clinic; Rochester Massachusetts
| | - Jane B. Lian
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
| | - Janet L. Stein
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
| | - Jeffrey A. Nickerson
- Department of Cell and Developmental Biology; University of Massachusetts Medical School; Worcester Massachusetts
| | - Anthony N. Imbalzano
- Department of Cell and Developmental Biology; University of Massachusetts Medical School; Worcester Massachusetts
| | - Gary S. Stein
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
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163
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Barutcu AR, Fritz AJ, Zaidi SK, van Wijnen AJ, Lian JB, Stein JL, Nickerson JA, Imbalzano AN, Stein GS. C-ing the Genome: A Compendium of Chromosome Conformation Capture Methods to Study Higher-Order Chromatin Organization. J Cell Physiol 2016. [DOI: 10.1002/jcp.25062 order by 1-- #] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Affiliation(s)
- A. Rasim Barutcu
- Department of Cell and Developmental Biology; University of Massachusetts Medical School; Worcester Massachusetts
| | - Andrew J. Fritz
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
| | - Sayyed K. Zaidi
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
| | - André J. van Wijnen
- Departments of Orthopedic Surgery and Biochemistry & Molecular Biology; Mayo Clinic; Rochester Massachusetts
| | - Jane B. Lian
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
| | - Janet L. Stein
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
| | - Jeffrey A. Nickerson
- Department of Cell and Developmental Biology; University of Massachusetts Medical School; Worcester Massachusetts
| | - Anthony N. Imbalzano
- Department of Cell and Developmental Biology; University of Massachusetts Medical School; Worcester Massachusetts
| | - Gary S. Stein
- Department of Biochemistry; University of Vermont College of Medicine; Burlington Vermont
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164
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Davies JO, Telenius JM, McGowan S, Roberts NA, Taylor S, Higgs DR, Hughes JR. Multiplexed analysis of chromosome conformation at vastly improved sensitivity. Nat Methods 2016; 13:74-80. [PMID: 26595209 PMCID: PMC4724891 DOI: 10.1038/nmeth.3664] [Citation(s) in RCA: 176] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 10/26/2015] [Indexed: 12/27/2022]
Abstract
Methods for analyzing chromosome conformation in mammalian cells are either low resolution or low throughput and are technically challenging. In next-generation (NG) Capture-C, we have redesigned the Capture-C method to achieve unprecedented levels of sensitivity and reproducibility. NG Capture-C can be used to analyze many genetic loci and samples simultaneously. High-resolution data can be produced with as few as 100,000 cells, and single-nucleotide polymorphisms can be used to generate allele-specific tracks. The method is straightforward to perform and should greatly facilitate the investigation of many questions related to gene regulation as well as the functional dissection of traits examined in genome-wide association studies.
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Affiliation(s)
- James O.J. Davies
- Medical Research Council, Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford, UK
| | - Jelena M. Telenius
- Medical Research Council, Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford, UK
| | - Simon McGowan
- Computational Biology Research Group, Weatherall Institute of Molecular Medicine, Oxford University, Oxford, UK
| | - Nigel A. Roberts
- Medical Research Council, Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford, UK
| | - Stephen Taylor
- Computational Biology Research Group, Weatherall Institute of Molecular Medicine, Oxford University, Oxford, UK
| | - Douglas R. Higgs
- Medical Research Council, Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford, UK
| | - Jim R. Hughes
- Medical Research Council, Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford, UK
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165
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Barutcu AR, Fritz AJ, Zaidi SK, vanWijnen AJ, Lian JB, Stein JL, Nickerson JA, Imbalzano AN, Stein GS. C-ing the Genome: A Compendium of Chromosome Conformation Capture Methods to Study Higher-Order Chromatin Organization. J Cell Physiol 2016; 231:31-5. [PMID: 26059817 PMCID: PMC4586368 DOI: 10.1002/jcp.25062] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 06/02/2015] [Indexed: 12/16/2022]
Abstract
Three-dimensional organization of the chromatin has important roles in transcription, replication, DNA repair, and pathologic events such as translocations. There are two fundamental ways to study higher-order chromatin organization: microscopic and molecular approaches. In this review, we briefly introduce the molecular approaches, focusing on chromosome conformation capture or "3C" technology and its derivatives, which can be used to probe chromatin folding at resolutions beyond that provided by microscopy techniques. We further discuss the different types of data generated by the 3C-based methods and how they can be used to answer distinct biological questions.
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Affiliation(s)
- A. Rasim Barutcu
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA
| | - Andrew J. Fritz
- Department of Biochemistry, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT 05405, USA
| | - Sayyed K. Zaidi
- Department of Biochemistry, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT 05405, USA
| | - André J. vanWijnen
- Departments of Orthopedic Surgery and Biochemistry & Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Jane B. Lian
- Department of Biochemistry, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT 05405, USA
| | - Janet L. Stein
- Department of Biochemistry, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT 05405, USA
| | - Jeffrey A. Nickerson
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA
| | - Anthony N. Imbalzano
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA
| | - Gary S. Stein
- Department of Biochemistry, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT 05405, USA
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166
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Subdivision of the lateral plate mesoderm and specification of the forelimb and hindlimb forming domains. Semin Cell Dev Biol 2016; 49:102-8. [DOI: 10.1016/j.semcdb.2015.11.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 11/17/2015] [Accepted: 11/21/2015] [Indexed: 11/15/2022]
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167
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Verdin H, Fernández-Miñán A, Benito-Sanz S, Janssens S, Callewaert B, De Waele K, De Schepper J, François I, Menten B, Heath KE, Gómez-Skarmeta JL, De Baere E. Profiling of conserved non-coding elements upstream of SHOX and functional characterisation of the SHOX cis-regulatory landscape. Sci Rep 2015; 5:17667. [PMID: 26631348 PMCID: PMC4668379 DOI: 10.1038/srep17667] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 11/02/2015] [Indexed: 02/07/2023] Open
Abstract
Genetic defects such as copy number variations (CNVs) in non-coding regions containing conserved non-coding elements (CNEs) outside the transcription unit of their target gene, can underlie genetic disease. An example of this is the short stature homeobox (SHOX) gene, regulated by seven CNEs located downstream and upstream of SHOX, with proven enhancer capacity in chicken limbs. CNVs of the downstream CNEs have been reported in many idiopathic short stature (ISS) cases, however, only recently have a few CNVs of the upstream enhancers been identified. Here, we set out to provide insight into: (i) the cis-regulatory role of these upstream CNEs in human cells, (ii) the prevalence of upstream CNVs in ISS, and (iii) the chromatin architecture of the SHOX cis-regulatory landscape in chicken and human cells. Firstly, luciferase assays in human U2OS cells, and 4C-seq both in chicken limb buds and human U2OS cells, demonstrated cis-regulatory enhancer capacities of the upstream CNEs. Secondly, CNVs of these upstream CNEs were found in three of 501 ISS patients. Finally, our 4C-seq interaction map of the SHOX region reveals a cis-regulatory domain spanning more than 1 Mb and harbouring putative new cis-regulatory elements.
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Affiliation(s)
- Hannah Verdin
- Center for Medical Genetics Ghent, Ghent University, Ghent, Belgium
| | - Ana Fernández-Miñán
- Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas and Universidad Pablo de Olavide, Sevilla, Spain
| | - Sara Benito-Sanz
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, Universidad Autónoma de Madrid, IdiPAZ, Madrid, Spain.,Centro de Investigación Biomédica en Enfermedades Raras (CIBERER), Instituto Carlos III, Madrid, Spain
| | - Sandra Janssens
- Center for Medical Genetics Ghent, Ghent University, Ghent, Belgium
| | - Bert Callewaert
- Center for Medical Genetics Ghent, Ghent University, Ghent, Belgium
| | | | - Jean De Schepper
- Department of Pediatrics, Ghent University Hospital, Ghent, Belgium
| | - Inge François
- Department of Pediatric Endocrinology, University Hospitals Leuven, Leuven, Belgium
| | - Björn Menten
- Center for Medical Genetics Ghent, Ghent University, Ghent, Belgium
| | - Karen E Heath
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, Universidad Autónoma de Madrid, IdiPAZ, Madrid, Spain.,Centro de Investigación Biomédica en Enfermedades Raras (CIBERER), Instituto Carlos III, Madrid, Spain
| | - José Luis Gómez-Skarmeta
- Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas and Universidad Pablo de Olavide, Sevilla, Spain
| | - Elfride De Baere
- Center for Medical Genetics Ghent, Ghent University, Ghent, Belgium
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168
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Aranda S, Mas G, Di Croce L. Regulation of gene transcription by Polycomb proteins. SCIENCE ADVANCES 2015; 1:e1500737. [PMID: 26665172 PMCID: PMC4672759 DOI: 10.1126/sciadv.1500737] [Citation(s) in RCA: 237] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2015] [Accepted: 09/17/2015] [Indexed: 05/14/2023]
Abstract
The Polycomb group (PcG) of proteins defines a subset of factors that physically associate and function to maintain the positional identity of cells from the embryo to adult stages. PcG has long been considered a paradigmatic model for epigenetic maintenance of gene transcription programs. Despite intensive research efforts to unveil the molecular mechanisms of action of PcG proteins, several fundamental questions remain unresolved: How many different PcG complexes exist in mammalian cells? How are PcG complexes targeted to specific loci? How does PcG regulate transcription? In this review, we discuss the diversity of PcG complexes in mammalian cells, examine newly identified modes of recruitment to chromatin, and highlight the latest insights into the molecular mechanisms underlying the function of PcGs in transcription regulation and three-dimensional chromatin conformation.
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Affiliation(s)
- Sergi Aranda
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona 08002, Spain
| | - Gloria Mas
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona 08002, Spain
| | - Luciano Di Croce
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona 08002, Spain
- Institucio Catalana de Recerca i Estudis Avançats, Pg Lluis Companys 23, Barcelona 08010, Spain
- Corresponding author. E-mail:
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169
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Liu GY, Zhao GN, Chen XF, Hao DL, Zhao X, Lv X, Liu DP. The long noncoding RNA Gm15055 represses Hoxa gene expression by recruiting PRC2 to the gene cluster. Nucleic Acids Res 2015; 44:2613-27. [PMID: 26615201 PMCID: PMC4824075 DOI: 10.1093/nar/gkv1315] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 11/11/2015] [Indexed: 11/17/2022] Open
Abstract
The Hox genes encode transcription factors that determine embryonic pattern formation. In embryonic stem cells, the Hox genes are silenced by PRC2. Recent studies have reported a role for long noncoding RNAs in PRC2 recruitment in vertebrates. However, little is known about how PRC2 is recruited to the Hox genes in ESCs. Here, we used stable knockdown and knockout strategies to characterize the function of the long noncoding RNA Gm15055 in the regulation of Hoxa genes in mouse ESCs. We found that Gm15055 is highly expressed in mESCs and its expression is maintained by OCT4. Gm15055 represses Hoxa gene expression by recruiting PRC2 to the cluster and maintaining the H3K27me3 modification on Hoxa promoters. A chromosome conformation capture assay revealed the close physical association of the Gm15055 locus to multiple sites at the Hoxa gene cluster in mESCs, which may facilitate the in cis targeting of Gm15055 RNA to the Hoxa genes. Furthermore, an OCT4-responsive positive cis-regulatory element is found in the Gm15055 gene locus, which potentially regulates both Gm15055 itself and the Hoxa gene activation. This study suggests how PRC2 is recruited to the Hoxa locus in mESCs, and implies an elaborate mechanism for Hoxa gene regulation in mESCs.
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Affiliation(s)
- Guo-You Liu
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, P.R. China
| | - Guang-Nian Zhao
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, P.R. China
| | - Xiao-Feng Chen
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, P.R. China
| | - De-Long Hao
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, P.R. China
| | - Xiang Zhao
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, P.R. China
| | - Xiang Lv
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, P.R. China
| | - De-Pei Liu
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, P.R. China
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170
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Remeseiro S, Hörnblad A, Spitz F. Gene regulation during development in the light of topologically associating domains. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2015; 5:169-85. [PMID: 26558551 DOI: 10.1002/wdev.218] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 08/31/2015] [Accepted: 09/15/2015] [Indexed: 01/20/2023]
Abstract
During embryonic development, complex transcriptional programs govern the precision of gene expression. Many key developmental genes are regulated via cis-regulatory elements that are located far away in the linear genome. How sequences located hundreds of kilobases away from a promoter can influence its activity has been the subject of numerous speculations, which all underline the importance of the 3D-organization of the genome. The recent advent of chromosome conformation capture techniques has put into focus the subdivision of the genome into topologically associating domains (TADs). TADs may influence regulatory activities on multiple levels. The relative invariance of TAD limits across cell types suggests that they may form fixed structural domains that could facilitate and/or confine long-range regulatory interactions. However, most recent studies suggest that interactions within TADs are more variable and dynamic than initially described. Hence, different models are emerging regarding how TADs shape the complex 3D conformations, and thereafter influence the networks of cis-interactions that govern gene expression during development. For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Silvia Remeseiro
- Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Andreas Hörnblad
- Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - François Spitz
- Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
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171
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Nanoscale spatial organization of the HoxD gene cluster in distinct transcriptional states. Proc Natl Acad Sci U S A 2015; 112:13964-9. [PMID: 26504220 DOI: 10.1073/pnas.1517972112] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Chromatin condensation plays an important role in the regulation of gene expression. Recently, it was shown that the transcriptional activation of Hoxd genes during vertebrate digit development involves modifications in 3D interactions within and around the HoxD gene cluster. This reorganization follows a global transition from one set of regulatory contacts to another, between two topologically associating domains (TADs) located on either side of the HoxD locus. Here, we use 3D DNA FISH to assess the spatial organization of chromatin at and around the HoxD gene cluster and report that although the two TADs are tightly associated, they appear as spatially distinct units. We measured the relative position of genes within the cluster and found that they segregate over long distances, suggesting that a physical elongation of the HoxD cluster can occur. We analyzed this possibility by super-resolution imaging (STORM) and found that tissues with distinct transcriptional activity exhibit differing degrees of elongation. We also observed that the morphological change of the HoxD cluster in developing digits is associated with its position at the boundary between the two TADs. Such variations in the fine-scale architecture of the gene cluster suggest causal links among its spatial configuration, transcriptional activation, and the flanking chromatin context.
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172
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Yao L, Berman BP, Farnham PJ. Demystifying the secret mission of enhancers: linking distal regulatory elements to target genes. Crit Rev Biochem Mol Biol 2015; 50:550-73. [PMID: 26446758 PMCID: PMC4666684 DOI: 10.3109/10409238.2015.1087961] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Enhancers are short regulatory sequences bound by sequence-specific transcription factors and play a major role in the spatiotemporal specificity of gene expression patterns in development and disease. While it is now possible to identify enhancer regions genomewide in both cultured cells and primary tissues using epigenomic approaches, it has been more challenging to develop methods to understand the function of individual enhancers because enhancers are located far from the gene(s) that they regulate. However, it is essential to identify target genes of enhancers not only so that we can understand the role of enhancers in disease but also because this information will assist in the development of future therapeutic options. After reviewing models of enhancer function, we discuss recent methods for identifying target genes of enhancers. First, we describe chromatin structure-based approaches for directly mapping interactions between enhancers and promoters. Second, we describe the use of correlation-based approaches to link enhancer state with the activity of nearby promoters and/or gene expression. Third, we describe how to test the function of specific enhancers experimentally by perturbing enhancer–target relationships using high-throughput reporter assays and genome editing. Finally, we conclude by discussing as yet unanswered questions concerning how enhancers function, how target genes can be identified, and how to distinguish direct from indirect changes in gene expression mediated by individual enhancers.
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Affiliation(s)
- Lijing Yao
- a Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California , Los Angeles , CA , USA and
| | - Benjamin P Berman
- b Department of Biomedical Sciences , Bioinformatics and Computational Biology Research Center, Cedars-Sinai Medical Center , Los Angeles , CA , USA
| | - Peggy J Farnham
- a Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California , Los Angeles , CA , USA and
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173
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Schoenfelder S, Sugar R, Dimond A, Javierre BM, Armstrong H, Mifsud B, Dimitrova E, Matheson L, Tavares-Cadete F, Furlan-Magaril M, Segonds-Pichon A, Jurkowski W, Wingett SW, Tabbada K, Andrews S, Herman B, LeProust E, Osborne CS, Koseki H, Fraser P, Luscombe NM, Elderkin S. Polycomb repressive complex PRC1 spatially constrains the mouse embryonic stem cell genome. Nat Genet 2015; 47:1179-1186. [PMID: 26323060 PMCID: PMC4847639 DOI: 10.1038/ng.3393] [Citation(s) in RCA: 265] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 08/05/2015] [Indexed: 02/08/2023]
Abstract
The Polycomb repressive complexes PRC1 and PRC2 maintain embryonic stem cell (ESC) pluripotency by silencing lineage-specifying developmental regulator genes. Emerging evidence suggests that Polycomb complexes act through controlling spatial genome organization. We show that PRC1 functions as a master regulator of mouse ESC genome architecture by organizing genes in three-dimensional interaction networks. The strongest spatial network is composed of the four Hox gene clusters and early developmental transcription factor genes, the majority of which contact poised enhancers. Removal of Polycomb repression leads to disruption of promoter-promoter contacts in the Hox gene network. In contrast, promoter-enhancer contacts are maintained in the absence of Polycomb repression, with accompanying widespread acquisition of active chromatin signatures at network enhancers and pronounced transcriptional upregulation of network genes. Thus, PRC1 physically constrains developmental transcription factor genes and their enhancers in a silenced but poised spatial network. We propose that the selective release of genes from this spatial network underlies cell fate specification during early embryonic development.
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Affiliation(s)
| | - Robert Sugar
- EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Andrew Dimond
- Nuclear Dynamics Programme, The Babraham Institute, Cambridge, UK
| | | | - Harry Armstrong
- Nuclear Dynamics Programme, The Babraham Institute, Cambridge, UK
| | - Borbala Mifsud
- Cancer Research UK London Research Institute, London, UK
- Department of Genetics, Evolution & Environment, University College London, London, UK
| | - Emilia Dimitrova
- Nuclear Dynamics Programme, The Babraham Institute, Cambridge, UK
- Department of Biochemistry, Oxford University, Oxford, UK
| | - Louise Matheson
- Nuclear Dynamics Programme, The Babraham Institute, Cambridge, UK
| | - Filipe Tavares-Cadete
- Cancer Research UK London Research Institute, London, UK
- present address: Okinawa Institute for Science and Technology Graduate University, Okinawa, Japan
| | | | | | - Wiktor Jurkowski
- Nuclear Dynamics Programme, The Babraham Institute, Cambridge, UK
| | - Steven W Wingett
- Nuclear Dynamics Programme, The Babraham Institute, Cambridge, UK
- Bioinformatics, The Babraham Institute, Cambridge, UK
| | - Kristina Tabbada
- Nuclear Dynamics Programme, The Babraham Institute, Cambridge, UK
| | - Simon Andrews
- Bioinformatics, The Babraham Institute, Cambridge, UK
| | - Bram Herman
- Agilent Technologies Inc., Santa Clara, California, USA
| | | | | | - Haruhiko Koseki
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Peter Fraser
- Nuclear Dynamics Programme, The Babraham Institute, Cambridge, UK
| | - Nicholas M Luscombe
- EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
- Cancer Research UK London Research Institute, London, UK
- Department of Genetics, Evolution & Environment, University College London, London, UK
- Okinawa Institute for Science and Technology Graduate University, Okinawa, Japan
| | - Sarah Elderkin
- Nuclear Dynamics Programme, The Babraham Institute, Cambridge, UK
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174
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Hayward AG, Joshi P, Skromne I. Spatiotemporal analysis of zebrafishhoxgene regulation by Cdx4. Dev Dyn 2015; 244:1564-73. [DOI: 10.1002/dvdy.24343] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 08/07/2015] [Accepted: 08/24/2015] [Indexed: 12/16/2022] Open
Affiliation(s)
| | - Piyush Joshi
- Department of Biology; University of Miami; Coral Gables Florida
| | - Isaac Skromne
- Department of Biology; University of Miami; Coral Gables Florida
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175
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Millau JF, Gaudreau L. Detection of Short-Range DNA Interactions in Mammalian Cells Using High-Resolution Circular Chromosome Conformation Capture Coupled to Deep Sequencing. Methods Mol Biol 2015; 1334:245-59. [PMID: 26404155 DOI: 10.1007/978-1-4939-2877-4_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
DNA interactions shape the genome to physically and functionally connect regulatory elements to their target genes. Studying these interactions is crucial to understanding the molecular mechanisms that regulate gene expression. In this chapter, we present a protocol for high-resolution circular chromosome conformation capture coupled to deep sequencing. This methodology allows to investigate short-range DNA interactions (<100 kbp) and to obtain high-resolution DNA interaction maps of loci. It is a powerful tool to explore how regulatory elements and genes are connected together.
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Affiliation(s)
- Jean-François Millau
- Département de Biologie, Faculté des Sciences, Université de Sherbrooke, 2500 Boulevard de L'Université, Sherbrooke, QC, Canada, J1K 2R1.
| | - Luc Gaudreau
- Département de Biologie, Faculté des Sciences, Université de Sherbrooke, 2500 Boulevard de L'Université, Sherbrooke, QC, Canada, J1K 2R1
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176
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Wang X, Xu M, Zhao G, Liu G, Hao D, Lv X, Liu D. Exploring CTCF and cohesin related chromatin architecture at HOXA gene cluster in primary human fibroblasts. SCIENCE CHINA. LIFE SCIENCES 2015; 58:860-6. [PMID: 26376810 DOI: 10.1007/s11427-015-4913-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 07/02/2015] [Indexed: 01/06/2023]
Abstract
Spatial expression patterns of homeobox (HOX) genes delineate positional identity of primary fibroblasts from different topographic sites. The molecular mechanism underlying the establishing or maintaining of HOX gene expression pattern remains an attractive developmental issue to be addressed. Our previous work suggested a critical role of CTCF/cohesin-mediated higher- order chromatin structure in RA-induced HOXA activation in human teratocarcinoma NT2/D1 cells. This study investigated the recruitment of CTCF and cohesin, and the higher-order chromatin structure of the HOXA locus in fetal lung and adult foreskin fibroblasts, which display complementary HOXA gene expression patterns. Chromatin contacts between the CTCF-binding sites were observed with lower frequency in human foreskin fibroblasts. This observation is consistent with the lower level of cohesin recruitment and 5' HOXA gene expression in the same cells. We also showed that CTCF-binding site A56 (CBSA56) related chromatin structures exhibit the most notable changes in between the two types of cell, and hence may stand for one of the key CTCF-binding sites for cell-type specific chromatin structure organization. Together, these results imply that CTCF/cohesin coordinates HOXA cluster higher-order chromatin structure and expression during development, and provide insight into the relationship between cell-type specific chromatin organization and the spatial collinearity.
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Affiliation(s)
- Xing Wang
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Miao Xu
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - GuangNian Zhao
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - GuoYou Liu
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - DeLong Hao
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Xiang Lv
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China.
| | - DePei Liu
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China.
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177
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Srivastava S, Dhawan J, Mishra RK. Epigenetic mechanisms and boundaries in the regulation of mammalian Hox clusters. Mech Dev 2015; 138 Pt 2:160-169. [PMID: 26254900 DOI: 10.1016/j.mod.2015.07.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 07/29/2015] [Accepted: 07/30/2015] [Indexed: 01/07/2023]
Abstract
Hox gene expression imparts segment identity to body structures along the anterior-posterior axis and is tightly governed by higher order chromatin mechanisms. Chromatin regulatory features of the homeotic complex are best defined in Drosophila melanogaster, where multiple cis-regulatory elements have been identified that ensure collinear Hox gene expression patterns in accordance with their genomic organization. Recent studies focused on delineating the epigenetic features of the vertebrate Hox clusters have helped reveal their dynamic chromatin organization and its impact on gene expression. Enrichment for the 'activating' H3K4me3 and 'repressive' H3K27me3 histone modifications is a particularly strong read-out for transcriptional status and correlates well with the evidence for chromatin loop domain structures and stage specific topological changes at these loci. However, it is not clear how such distinct domains are imposed and regulated independent of each other. Comparative analysis of the chromatin structure and organization of the homeotic gene clusters in fly and mammals is increasingly revealing the functional conservation of chromatin mediated mechanisms. Here we discuss the case for interspersed boundary elements existing within mammalian Hox clusters along with their possible roles and mechanisms of action. Recent studies suggest a role for factors other than the well characterized vertebrate boundary factor CTCF, such as the GAGA binding factor (GAF), in maintaining chromatin domains at the Hox loci. We also present data demonstrating how such regulatory elements may be involved in organizing higher order structure and demarcating active domains of gene expression at the mammalian Hox clusters.
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Affiliation(s)
- Surabhi Srivastava
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500007, India.
| | - Jyotsna Dhawan
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500007, India
| | - Rakesh K Mishra
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500007, India
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178
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Raviram R, Rocha PP, Bonneau R, Skok JA. Interpreting 4C-Seq data: how far can we go? Epigenomics 2015; 6:455-7. [PMID: 25431936 DOI: 10.2217/epi.14.47] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Affiliation(s)
- Ramya Raviram
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
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179
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One, Two, Three: Polycomb Proteins Hit All Dimensions of Gene Regulation. Genes (Basel) 2015; 6:520-42. [PMID: 26184319 PMCID: PMC4584315 DOI: 10.3390/genes6030520] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 06/30/2015] [Indexed: 12/16/2022] Open
Abstract
Polycomb group (PcG) proteins contribute to the formation and maintenance of a specific repressive chromatin state that prevents the expression of genes in a particular space and time. Polycomb repressive complexes (PRCs) consist of several PcG proteins with specific regulatory or catalytic properties. PRCs are recruited to thousands of target genes, and various recruitment factors, including DNA-binding proteins and non-coding RNAs, are involved in the targeting. PcG proteins contribute to a multitude of biological processes by altering chromatin features at different scales. PcG proteins mediate both biochemical modifications of histone tails and biophysical modifications (e.g., chromatin fiber compaction and three-dimensional (3D) chromatin conformation). Here, we review the role of PcG proteins in nuclear architecture, describing their impact on the structure of the chromatin fiber, on chromatin interactions, and on the spatial organization of the genome in nuclei. Although little is known about the role of plant PcG proteins in nuclear organization, much is known in the animal field, and we highlight similarities and differences in the roles of PcG proteins in 3D gene regulation in plants and animals.
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180
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Mozgova I, Köhler C, Hennig L. Keeping the gate closed: functions of the polycomb repressive complex PRC2 in development. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 83:121-32. [PMID: 25762111 DOI: 10.1111/tpj.12828] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 03/09/2015] [Accepted: 03/10/2015] [Indexed: 05/08/2023]
Abstract
Plant ontogeny relies on the correct timing and sequence of transitions between individual developmental phases. These are specified by gene expression patterns that are established by the balanced action of activators and repressors. Polycomb repressive complexes (PRCs) represent an evolutionarily conserved system of epigenetic gene repression that governs the establishment and maintenance of cell, tissue and organ identity, contributing to the correct execution of the developmental programs. PRC2 is a four-subunit histone methyltransferase complex that catalyzes trimethylation of lysine 27 on histone H3 (H3K27me3), which contributes to the change of chromatin structure and long-lasting gene repression. Here, we review the composition and molecular function of the different known PRC2 complexes in plants, and focus on the role of PRC2 in mediating the establishment of different developmental phases and transitions between them.
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Affiliation(s)
- Iva Mozgova
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-75007, Uppsala, Sweden
| | - Claudia Köhler
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-75007, Uppsala, Sweden
| | - Lars Hennig
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-75007, Uppsala, Sweden
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181
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Genome-wide binding and mechanistic analyses of Smchd1-mediated epigenetic regulation. Proc Natl Acad Sci U S A 2015; 112:E3535-44. [PMID: 26091879 DOI: 10.1073/pnas.1504232112] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Structural maintenance of chromosomes flexible hinge domain containing 1 (Smchd1) is an epigenetic repressor with described roles in X inactivation and genomic imprinting, but Smchd1 is also critically involved in the pathogenesis of facioscapulohumeral dystrophy. The underlying molecular mechanism by which Smchd1 functions in these instances remains unknown. Our genome-wide transcriptional and epigenetic analyses show that Smchd1 binds cis-regulatory elements, many of which coincide with CCCTC-binding factor (Ctcf) binding sites, for example, the clustered protocadherin (Pcdh) genes, where we show Smchd1 and Ctcf act in opposing ways. We provide biochemical and biophysical evidence that Smchd1-chromatin interactions are established through the homodimeric hinge domain of Smchd1 and, intriguingly, that the hinge domain also has the capacity to bind DNA and RNA. Our results suggest Smchd1 imparts epigenetic regulation via physical association with chromatin, which may antagonize Ctcf-facilitated chromatin interactions, resulting in coordinated transcriptional control.
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182
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Sjöstedt E, Fagerberg L, Hallström BM, Häggmark A, Mitsios N, Nilsson P, Pontén F, Hökfelt T, Uhlén M, Mulder J. Defining the Human Brain Proteome Using Transcriptomics and Antibody-Based Profiling with a Focus on the Cerebral Cortex. PLoS One 2015; 10:e0130028. [PMID: 26076492 PMCID: PMC4468152 DOI: 10.1371/journal.pone.0130028] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 05/15/2015] [Indexed: 01/25/2023] Open
Abstract
The mammalian brain is a complex organ composed of many specialized cells, harboring sets of both common, widely distributed, as well as specialized and discretely localized proteins. Here we focus on the human brain, utilizing transcriptomics and public available Human Protein Atlas (HPA) data to analyze brain-enriched (frontal cortex) polyadenylated messenger RNA and long non-coding RNA and generate a genome-wide draft of global and cellular expression patterns of the brain. Based on transcriptomics analysis of altogether 27 tissues, we have estimated that approximately 3% (n=571) of all protein coding genes and 13% (n=87) of the long non-coding genes expressed in the human brain are enriched, having at least five times higher expression levels in brain as compared to any of the other analyzed peripheral tissues. Based on gene ontology analysis and detailed annotation using antibody-based tissue micro array analysis of the corresponding proteins, we found the majority of brain-enriched protein coding genes to be expressed in astrocytes, oligodendrocytes or in neurons with molecular properties linked to synaptic transmission and brain development. Detailed analysis of the transcripts and the genetic landscape of brain-enriched coding and non-coding genes revealed brain-enriched splice variants. Several clusters of neighboring brain-enriched genes were also identified, suggesting regulation of gene expression on the chromatin level. This multi-angle approach uncovered the brain-enriched transcriptome and linked genes to cell types and functions, providing novel insights into the molecular foundation of this highly specialized organ.
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Affiliation(s)
- Evelina Sjöstedt
- Science for Life Laboratory, School of Biotechnology, KTH-Royal Institute of Technology, Stockholm, Sweden; Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Linn Fagerberg
- Science for Life Laboratory, School of Biotechnology, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Björn M Hallström
- Science for Life Laboratory, School of Biotechnology, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Anna Häggmark
- Science for Life Laboratory, School of Biotechnology, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Nicholas Mitsios
- Science for Life Laboratory, Department of Neuroscience, Karolinska Institute, Stockholm, Sweden
| | - Peter Nilsson
- Science for Life Laboratory, School of Biotechnology, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Fredrik Pontén
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Tomas Hökfelt
- Science for Life Laboratory, Department of Neuroscience, Karolinska Institute, Stockholm, Sweden
| | - Mathias Uhlén
- Science for Life Laboratory, School of Biotechnology, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Jan Mulder
- Science for Life Laboratory, Department of Neuroscience, Karolinska Institute, Stockholm, Sweden
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183
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Evolutionary comparison reveals that diverging CTCF sites are signatures of ancestral topological associating domains borders. Proc Natl Acad Sci U S A 2015; 112:7542-7. [PMID: 26034287 DOI: 10.1073/pnas.1505463112] [Citation(s) in RCA: 116] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Increasing evidence in the last years indicates that the vast amount of regulatory information contained in mammalian genomes is organized in precise 3D chromatin structures. However, the impact of this spatial chromatin organization on gene expression and its degree of evolutionary conservation is still poorly understood. The Six homeobox genes are essential developmental regulators organized in gene clusters conserved during evolution. Here, we reveal that the Six clusters share a deeply evolutionarily conserved 3D chromatin organization that predates the Cambrian explosion. This chromatin architecture generates two largely independent regulatory landscapes (RLs) contained in two adjacent topological associating domains (TADs). By disrupting the conserved TAD border in one of the zebrafish Six clusters, we demonstrate that this border is critical for preventing competition between promoters and enhancers located in separated RLs, thereby generating different expression patterns in genes located in close genomic proximity. Moreover, evolutionary comparison of Six-associated TAD borders reveals the presence of CCCTC-binding factor (CTCF) sites with diverging orientations in all studied deuterostomes. Genome-wide examination of mammalian HiC data reveals that this conserved CTCF configuration is a general signature of TAD borders, underscoring that common organizational principles underlie TAD compartmentalization in deuterostome evolution.
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184
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Sexton T, Cavalli G. The role of chromosome domains in shaping the functional genome. Cell 2015; 160:1049-59. [PMID: 25768903 DOI: 10.1016/j.cell.2015.02.040] [Citation(s) in RCA: 271] [Impact Index Per Article: 30.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Indexed: 10/23/2022]
Abstract
The genome must be highly compacted to fit within eukaryotic nuclei but must be accessible to the transcriptional machinery to allow appropriate expression of genes in different cell types and throughout developmental pathways. A growing body of work has shown that the genome, analogously to proteins, forms an ordered, hierarchical structure that closely correlates and may even be causally linked with regulation of functions such as transcription. This review describes our current understanding of how these functional genomic "secondary and tertiary structures" form a blueprint for global nuclear architecture and the potential they hold for understanding and manipulating genomic regulation.
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Affiliation(s)
- Tom Sexton
- Institute of Genetics and Molecular and Cellular Biology (IGBMC), 1 rue Laurent Fries, 67404 Illkirch, France.
| | - Giacomo Cavalli
- Institute of Human Genetics (IGH), 141 rue de la Cardonille, 34396 Montpellier, France.
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185
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Sheikh BN, Downer NL, Kueh AJ, Thomas T, Voss AK. Excessive versus physiologically relevant levels of retinoic acid in embryonic stem cell differentiation. Stem Cells 2015; 32:1451-8. [PMID: 25099890 DOI: 10.1002/stem.1604] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Revised: 10/28/2013] [Accepted: 11/03/2013] [Indexed: 01/01/2023]
Abstract
Over the past two decades, embryonic stem cells (ESCs) have been established as a valuable system to study the complex molecular events that underlie the collinear activation of Hox genes during development. When ESCs are induced to differentiate in response to retinoic acid (RA), Hox genes are transcriptionally activated in their chromosomal order, with the most 3' Hox genes activated first, sequentially followed by more 5' Hox genes. In contrast to the low levels of RA detected during gastrulation (∼33 nM), a time when Hox genes are induced during embryonic development, high levels of RA are used to study Hox gene activation in ESCs in vitro (1-10 µM). This compelled us to compare RA-induced ESC differentiation in vitro with Hox gene activation in vivo. In this study, we show that treatment of ESCs for 2 days with RA best mimics activation of Hox genes during embryonic development. Furthermore, we show that defects in Hox gene expression known to occur in embryos lacking the histone acetyltransferase MOZ (also called MYST3 or KAT6A) were masked in Moz-deficient ESCs when excessive RA (0.5-5 µM) was used. The role of MOZ in Hox gene activation was only evident when ESCs were differentiated at low concentrations of RA, namely 20 nM, which is similar to RA levels in vivo. Our results demonstrate that using RA at physiologically relevant levels to study the activation of Hox genes, more accurately reflects the molecular events during the early phase of Hox gene activation in vivo.
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Affiliation(s)
- Bilal N Sheikh
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia; Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
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186
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Razin SV, Borunova VV, Iarovaia OV, Vassetzky YS. Nuclear matrix and structural and functional compartmentalization of the eucaryotic cell nucleus. BIOCHEMISTRY (MOSCOW) 2015; 79:608-18. [PMID: 25108324 DOI: 10.1134/s0006297914070037] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Becoming popular at the end of the 20th century, the concept of the nuclear matrix implies the existence of a nuclear skeleton that organizes functional elements in the cell nucleus. This review presents a critical analysis of the results obtained in the study of nuclear matrix in the light of current views on the organization of the cell nucleus. Numerous studies of nuclear matrix have failed to provide evidence of the existence of such a structure. Moreover, the existence of a filamentous structure that supports the nuclear compartmentalization appears to be unnecessary, since this function is performed by the folded genome itself.
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Affiliation(s)
- S V Razin
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia.
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187
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MOZ and BMI1 play opposing roles during Hox gene activation in ES cells and in body segment identity specification in vivo. Proc Natl Acad Sci U S A 2015; 112:5437-42. [PMID: 25922517 DOI: 10.1073/pnas.1422872112] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Hox genes underlie the specification of body segment identity in the anterior-posterior axis. They are activated during gastrulation and undergo a dynamic shift from a transcriptionally repressed to an active chromatin state in a sequence that reflects their chromosomal location. Nevertheless, the precise role of chromatin modifying complexes during the initial activation phase remains unclear. In the current study, we examined the role of chromatin regulators during Hox gene activation. Using embryonic stem cell lines lacking the transcriptional activator MOZ and the polycomb-family repressor BMI1, we showed that MOZ and BMI1, respectively, promoted and repressed Hox genes during the shift from the transcriptionally repressed to the active state. Strikingly however, MOZ but not BMI1 was required to regulate Hox mRNA levels after the initial activation phase. To determine the interaction of MOZ and BMI1 in vivo, we interrogated their role in regulating Hox genes and body segment identity using Moz;Bmi1 double deficient mice. We found that the homeotic transformations and shifts in Hox gene expression boundaries observed in single Moz and Bmi1 mutant mice were rescued to a wild type identity in Moz;Bmi1 double knockout animals. Together, our findings establish that MOZ and BMI1 play opposing roles during the onset of Hox gene expression in the ES cell model and during body segment identity specification in vivo. We propose that chromatin-modifying complexes have a previously unappreciated role during the initiation phase of Hox gene expression, which is critical for the correct specification of body segment identity.
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188
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Vieux-Rochas M, Fabre PJ, Leleu M, Duboule D, Noordermeer D. Clustering of mammalian Hox genes with other H3K27me3 targets within an active nuclear domain. Proc Natl Acad Sci U S A 2015; 112:4672-7. [PMID: 25825760 PMCID: PMC4403207 DOI: 10.1073/pnas.1504783112] [Citation(s) in RCA: 109] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Embryogenesis requires the precise activation and repression of many transcriptional regulators. The Polycomb group proteins and the associated H3K27me3 histone mark are essential to maintain the inactive state of many of these genes. Mammalian Hox genes are targets of Polycomb proteins and form local 3D clusters centered on the H3K27me3 mark. More distal contacts have also been described, yet their selectivity, dynamics, and relation to other layers of chromatin organization remained elusive. We report that repressed Hox genes form mutual intra- and interchromosomal interactions with other genes located in strong domains labeled by H3K27me3. These interactions occur in a central and active nuclear environment that consists of the HiC compartment A, away from peripheral lamina-associated domains. Interactions are independent of nearby H3K27me3-marked loci and determined by chromosomal distance and cell-type-specific scaling factors, thus inducing a moderate reorganization during embryogenesis. These results provide a simplified view of nuclear organization whereby Polycomb proteins may have evolved to repress genes located in gene-dense regions whose position is restricted to central, active, nuclear environments.
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Affiliation(s)
- Maxence Vieux-Rochas
- School of Life Sciences, Swiss Federal Institute of Technology - Lausanne (EPFL), 1015 Lausanne, Switzerland; and
| | - Pierre J Fabre
- School of Life Sciences, Swiss Federal Institute of Technology - Lausanne (EPFL), 1015 Lausanne, Switzerland; and
| | - Marion Leleu
- School of Life Sciences, Swiss Federal Institute of Technology - Lausanne (EPFL), 1015 Lausanne, Switzerland; and
| | - Denis Duboule
- School of Life Sciences, Swiss Federal Institute of Technology - Lausanne (EPFL), 1015 Lausanne, Switzerland; and Department of Genetics and Evolution, University of Geneva, 1205 Geneva, Switzerland
| | - Daan Noordermeer
- School of Life Sciences, Swiss Federal Institute of Technology - Lausanne (EPFL), 1015 Lausanne, Switzerland; and
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189
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Risca VI, Greenleaf WJ. Unraveling the 3D genome: genomics tools for multiscale exploration. Trends Genet 2015; 31:357-72. [PMID: 25887733 DOI: 10.1016/j.tig.2015.03.010] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 03/16/2015] [Accepted: 03/24/2015] [Indexed: 12/15/2022]
Abstract
A decade of rapid method development has begun to yield exciting insights into the 3D architecture of the metazoan genome and the roles it may play in regulating transcription. Here we review core methods and new tools in the modern genomicist's toolbox at three length scales, ranging from single base pairs to megabase-scale chromosomal domains, and discuss the emerging picture of the 3D genome that these tools have revealed. Blind spots remain, especially at intermediate length scales spanning a few nucleosomes, but thanks in part to new technologies that permit targeted alteration of chromatin states and time-resolved studies, the next decade holds great promise for hypothesis-driven research into the mechanisms that drive genome architecture and transcriptional regulation.
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Affiliation(s)
- Viviana I Risca
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - William J Greenleaf
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
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190
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Abstract
Over the past decade, techniques based on chromosome conformation capture (3C) have accelerated our understanding of eukaryote's nuclear architecture. Coupled to high throughput sequencing and bioinformatics they have unveiled different organizational levels of the genome at an unprecedented scale. Initially performed using large populations of cells, a new variant of these techniques can be applied to single cell. Although it can be shown that chromosome folding varies from one cell to the other, their overall organization into topologically associating domains is conserved between cells of the same population. Interestingly, the predicted chromosome structures reveal that regions engaged in trans-chromosomal interactions are preferentially localized at the surface of the chromosome territory. These results confirm and extend previous observations on individual loci therefore highlighting the power of 3C based techniques.
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Affiliation(s)
- David Umlauf
- Université de Toulouse, université Paul Sabatier, laboratoire de biologie moléculaire des eucaryotes, CNRS, 118 route de Narbonne, 31000 Toulouse, France
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191
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3D genome architecture from populations to single cells. Curr Opin Genet Dev 2015; 31:36-41. [DOI: 10.1016/j.gde.2015.04.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 04/02/2015] [Indexed: 02/03/2023]
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192
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Narendra V, Rocha PP, An D, Raviram R, Skok JA, Mazzoni EO, Reinberg D. CTCF establishes discrete functional chromatin domains at the Hox clusters during differentiation. Science 2015; 347:1017-21. [PMID: 25722416 DOI: 10.1126/science.1262088] [Citation(s) in RCA: 387] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Polycomb and Trithorax group proteins encode the epigenetic memory of cellular positional identity by establishing inheritable domains of repressive and active chromatin within the Hox clusters. Here we demonstrate that the CCCTC-binding factor (CTCF) functions to insulate these adjacent yet antagonistic chromatin domains during embryonic stem cell differentiation into cervical motor neurons. Deletion of CTCF binding sites within the Hox clusters results in the expansion of active chromatin into the repressive domain. CTCF functions as an insulator by organizing Hox clusters into spatially disjoint domains. Ablation of CTCF binding disrupts topological boundaries such that caudal Hox genes leave the repressed domain and become subject to transcriptional activation. Hence, CTCF is required to insulate facultative heterochromatin from impinging euchromatin to produce discrete positional identities.
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Affiliation(s)
- Varun Narendra
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA. Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Pedro P Rocha
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
| | - Disi An
- Department of Biology, New York University, New York, NY 10003, USA
| | - Ramya Raviram
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
| | - Jane A Skok
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
| | - Esteban O Mazzoni
- Department of Biology, New York University, New York, NY 10003, USA.
| | - Danny Reinberg
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA. Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA.
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193
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YAP regulates the expression of Hoxa1 and Hoxc13 in mouse and human oral and skin epithelial tissues. Mol Cell Biol 2015; 35:1449-61. [PMID: 25691658 DOI: 10.1128/mcb.00765-14] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Yes-associated protein (YAP) is a Hippo signaling transcriptional coactivator that plays pivotal roles in stem cell proliferation, organ size control, and tumor development. The downstream targets of YAP have been shown to be highly context dependent. In this study, we used the embryonic mouse tooth germ as a tool to search for the downstream targets of YAP in ectoderm-derived tissues. Yap deficiency in the dental epithelium resulted in a small tooth germ with reduced epithelial cell proliferation. We compared the gene expression profiles of embryonic day 14.5 (E14.5) Yap conditional knockout and YAP transgenic mouse tooth germs using transcriptome sequencing (RNA-Seq) and further confirmed the differentially expressed genes using real-time PCR and in situ hybridization. We found that YAP regulates the expression of Hoxa1 and Hoxc13 in oral and dental epithelial tissues as well as in the epidermis of skin during embryonic and adult stages. Sphere formation assay suggested that Hoxa1 and Hoxc13 are functionally involved in YAP-regulated epithelial progenitor cell proliferation, and chromatin immunoprecipitation (ChIP) assay implies that YAP may regulate Hoxa1 and Hoxc13 expression through TEAD transcription factors. These results provide mechanistic insights into abnormal YAP activities in mice and humans.
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194
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Chromatin-Driven Behavior of Topologically Associating Domains. J Mol Biol 2015; 427:608-25. [DOI: 10.1016/j.jmb.2014.09.013] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 09/17/2014] [Accepted: 09/23/2014] [Indexed: 12/19/2022]
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195
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Kurscheid S, Bady P, Sciuscio D, Samarzija I, Shay T, Vassallo I, Criekinge WV, Daniel RT, van den Bent MJ, Marosi C, Weller M, Mason WP, Domany E, Stupp R, Delorenzi M, Hegi ME. Chromosome 7 gain and DNA hypermethylation at the HOXA10 locus are associated with expression of a stem cell related HOX-signature in glioblastoma. Genome Biol 2015; 16:16. [PMID: 25622821 PMCID: PMC4342872 DOI: 10.1186/s13059-015-0583-7] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 01/08/2015] [Indexed: 11/12/2022] Open
Abstract
Background HOX genes are a family of developmental genes that are expressed neither in the developing forebrain nor in the normal brain. Aberrant expression of a HOX-gene dominated stem-cell signature in glioblastoma has been linked with increased resistance to chemo-radiotherapy and sustained proliferation of glioma initiating cells. Here we describe the epigenetic and genetic alterations and their interactions associated with the expression of this signature in glioblastoma. Results We observe prominent hypermethylation of the HOXA locus 7p15.2 in glioblastoma in contrast to non-tumoral brain. Hypermethylation is associated with a gain of chromosome 7, a hallmark of glioblastoma, and may compensate for tumor-driven enhanced gene dosage as a rescue mechanism by preventing undue gene expression. We identify the CpG island of the HOXA10 alternative promoter that appears to escape hypermethylation in the HOX-high glioblastoma. An additive effect of gene copy gain at 7p15.2 and DNA methylation at key regulatory CpGs in HOXA10 is significantly associated with HOX-signature expression. Additionally, we show concordance between methylation status and presence of active or inactive chromatin marks in glioblastoma-derived spheres that are HOX-high or HOX-low, respectively. Conclusions Based on these findings, we propose co-evolution and interaction between gene copy gain, associated with a gain of chromosome 7, and additional epigenetic alterations as key mechanisms triggering a coordinated, but inappropriate, HOX transcriptional program in glioblastoma. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0583-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sebastian Kurscheid
- Neurosurgery, Lausanne University Hospital, Lausanne, 1011, Switzerland. .,Neuroscience Research Center, Lausanne University Hospital, Lausanne, 1011, Switzerland. .,Bioinformatics Core Facility, Swiss Institute for Bioinformatics, Lausanne, 1005, Switzerland. .,Present address: The John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2601, Australia.
| | - Pierre Bady
- Neurosurgery, Lausanne University Hospital, Lausanne, 1011, Switzerland. .,Neuroscience Research Center, Lausanne University Hospital, Lausanne, 1011, Switzerland. .,Bioinformatics Core Facility, Swiss Institute for Bioinformatics, Lausanne, 1005, Switzerland. .,Department of Education and Research, University of Lausanne, Lausanne, 1011, Switzerland.
| | - Davide Sciuscio
- Neurosurgery, Lausanne University Hospital, Lausanne, 1011, Switzerland. .,Neuroscience Research Center, Lausanne University Hospital, Lausanne, 1011, Switzerland.
| | - Ivana Samarzija
- Neurosurgery, Lausanne University Hospital, Lausanne, 1011, Switzerland. .,Neuroscience Research Center, Lausanne University Hospital, Lausanne, 1011, Switzerland.
| | - Tal Shay
- Ben-Gurion University of the Negev, Beersheba, Israel.
| | - Irene Vassallo
- Neurosurgery, Lausanne University Hospital, Lausanne, 1011, Switzerland. .,Neuroscience Research Center, Lausanne University Hospital, Lausanne, 1011, Switzerland.
| | - Wim V Criekinge
- Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Ghent, Belgium.
| | - Roy T Daniel
- Neurosurgery, Lausanne University Hospital, Lausanne, 1011, Switzerland.
| | - Martin J van den Bent
- Department of Neurology/Neurooncology, Erasmus MC Cancer Center, Rotterdam, The Netherlands.
| | - Christine Marosi
- Department of Medicine, Medical University Vienna, Vienna, Austria.
| | - Michael Weller
- Department of Neurology, University of Tübingen, Tübingen, Germany. .,Department of Neurology, University Hospital Zurich, Zurich, Switzerland.
| | - Warren P Mason
- Princess Margaret Hospital, University of Toronto, Toronto, Canada.
| | - Eytan Domany
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel.
| | - Roger Stupp
- Neurosurgery, Lausanne University Hospital, Lausanne, 1011, Switzerland. .,Department of Oncology, University Hospital Zurich, Zurich, 8091, Switzerland.
| | - Mauro Delorenzi
- Bioinformatics Core Facility, Swiss Institute for Bioinformatics, Lausanne, 1005, Switzerland. .,Ludwig Center for Cancer Research, University of Lausanne, Lausanne, 1011, Switzerland. .,Department of Oncology, University of Lausanne, Lausanne, 1011, Switzerland.
| | - Monika E Hegi
- Neurosurgery, Lausanne University Hospital, Lausanne, 1011, Switzerland. .,Neuroscience Research Center, Lausanne University Hospital, Lausanne, 1011, Switzerland.
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196
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Spencer DH, Young MA, Lamprecht TL, Helton NM, Fulton R, O'Laughlin M, Fronick C, Magrini V, Demeter RT, Miller CA, Klco JM, Wilson RK, Ley TJ. Epigenomic analysis of the HOX gene loci reveals mechanisms that may control canonical expression patterns in AML and normal hematopoietic cells. Leukemia 2015; 29:1279-89. [PMID: 25600023 DOI: 10.1038/leu.2015.6] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 11/19/2014] [Accepted: 12/16/2014] [Indexed: 01/05/2023]
Abstract
HOX genes are highly expressed in many acute myeloid leukemia (AML) samples, but the patterns of expression and associated regulatory mechanisms are not clearly understood. We analyzed RNA sequencing data from 179 primary AML samples and normal hematopoietic cells to understand the range of expression patterns in normal versus leukemic cells. HOX expression in AML was restricted to specific genes in the HOXA or HOXB loci, and was highly correlated with recurrent cytogenetic abnormalities. However, the majority of samples expressed a canonical set of HOXA and HOXB genes that was nearly identical to the expression signature of normal hematopoietic stem/progenitor cells. Transcriptional profiles at the HOX loci were similar between normal cells and AML samples, and involved bidirectional transcription at the center of each gene cluster. Epigenetic analysis of a subset of AML samples also identified common regions of chromatin accessibility in AML samples and normal CD34(+) cells that displayed differences in methylation depending on HOX expression patterns. These data provide an integrated epigenetic view of the HOX gene loci in primary AML samples, and suggest that HOX expression in most AML samples represents a normal stem cell program that is controlled by epigenetic mechanisms at specific regulatory elements.
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Affiliation(s)
- D H Spencer
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - M A Young
- Department of Pediatrics, Washington University School of Medicine, St Louis, MO, USA
| | - T L Lamprecht
- Department of Internal Medicine, Division of Oncology, Section of Stem Cell Biology, Washington University School of Medicine, St Louis, MO, USA
| | - N M Helton
- Department of Internal Medicine, Division of Oncology, Section of Stem Cell Biology, Washington University School of Medicine, St Louis, MO, USA
| | - R Fulton
- The Genome Institute, Washington University, St Louis, MO, USA
| | - M O'Laughlin
- The Genome Institute, Washington University, St Louis, MO, USA
| | - C Fronick
- The Genome Institute, Washington University, St Louis, MO, USA
| | - V Magrini
- The Genome Institute, Washington University, St Louis, MO, USA
| | - R T Demeter
- The Genome Institute, Washington University, St Louis, MO, USA
| | - C A Miller
- The Genome Institute, Washington University, St Louis, MO, USA
| | - J M Klco
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - R K Wilson
- The Genome Institute, Washington University, St Louis, MO, USA
| | - T J Ley
- 1] Department of Internal Medicine, Division of Oncology, Section of Stem Cell Biology, Washington University School of Medicine, St Louis, MO, USA [2] The Genome Institute, Washington University, St Louis, MO, USA
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197
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Magbanua JP, Runneburger E, Russell S, White R. A variably occupied CTCF binding site in the ultrabithorax gene in the Drosophila bithorax complex. Mol Cell Biol 2015; 35:318-30. [PMID: 25368383 PMCID: PMC4295388 DOI: 10.1128/mcb.01061-14] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Revised: 09/10/2014] [Accepted: 10/25/2014] [Indexed: 11/20/2022] Open
Abstract
Although the majority of genomic binding sites for the insulator protein CCCTC-binding factor (CTCF) are constitutively occupied, a subset show variable occupancy. Such variable sites provide an opportunity to assess context-specific CTCF functions in gene regulation. Here, we have identified a variably occupied CTCF site in the Drosophila Ultrabithorax (Ubx) gene. This site is occupied in tissues where Ubx is active (third thoracic leg imaginal disc) but is not bound in tissues where the Ubx gene is repressed (first thoracic leg imaginal disc). Using chromatin conformation capture, we show that this site preferentially interacts with the Ubx promoter region in the active state. The site lies close to Ubx enhancer elements and is also close to the locations of several gypsy transposon insertions that disrupt Ubx expression, leading to the bx mutant phenotype. gypsy insertions carry the Su(Hw)-dependent gypsy insulator and were found to affect both CTCF binding at the variable site and the chromatin topology. This suggests that insertion of the gypsy insulator in this region interferes with CTCF function and supports a model for the normal function of the variable CTCF site as a chromatin loop facilitator, promoting interaction between Ubx enhancers and the Ubx transcription start site.
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Affiliation(s)
- Jose Paolo Magbanua
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
| | - Estelle Runneburger
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
| | - Steven Russell
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Robert White
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
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198
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Abstract
There is no obvious morphological counterpart of the autopod (wrist/ankle and digits) in living fishes. Comparative molecular data may provide insight into understanding both the homology of elements and the evolutionary developmental mechanisms behind the fin to limb transition. In mouse limbs the autopod is built by a "late" phase of Hoxd and Hoxa gene expression, orchestrated by a set of enhancers located at the 5' end of each cluster. Despite a detailed mechanistic understanding of mouse limb development, interpretation of Hox expression patterns and their regulation in fish has spawned multiple hypotheses as to the origin and function of "autopod" enhancers throughout evolution. Using phylogenetic footprinting, epigenetic profiling, and transgenic reporters, we have identified and functionally characterized hoxD and hoxA enhancers in the genomes of zebrafish and the spotted gar, Lepisosteus oculatus, a fish lacking the whole genome duplication of teleosts. Gar and zebrafish "autopod" enhancers drive expression in the distal portion of developing zebrafish pectoral fins, and respond to the same functional cues as their murine orthologs. Moreover, gar enhancers drive reporter gene expression in both the wrist and digits of mouse embryos in patterns that are nearly indistinguishable from their murine counterparts. These functional genomic data support the hypothesis that the distal radials of bony fish are homologous to the wrist and/or digits of tetrapods.
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199
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Williamson I, Berlivet S, Eskeland R, Boyle S, Illingworth RS, Paquette D, Dostie J, Bickmore WA. Spatial genome organization: contrasting views from chromosome conformation capture and fluorescence in situ hybridization. Genes Dev 2014; 28:2778-91. [PMID: 25512564 PMCID: PMC4265680 DOI: 10.1101/gad.251694.114] [Citation(s) in RCA: 190] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Accepted: 10/30/2014] [Indexed: 01/28/2023]
Abstract
Although important for gene regulation, most studies of genome organization use either fluorescence in situ hybridization (FISH) or chromosome conformation capture (3C) methods. FISH directly visualizes the spatial relationship of sequences but is usually applied to a few loci at a time. The frequency at which sequences are ligated together by formaldehyde cross-linking can be measured genome-wide by 3C methods, with higher frequencies thought to reflect shorter distances. FISH and 3C should therefore give the same views of genome organization, but this has not been tested extensively. We investigated the murine HoxD locus with 3C carbon copy (5C) and FISH in different developmental and activity states and in the presence or absence of epigenetic regulators. We identified situations in which the two data sets are concordant but found other conditions under which chromatin topographies extrapolated from 5C or FISH data are not compatible. We suggest that products captured by 3C do not always reflect spatial proximity, with ligation occurring between sequences located hundreds of nanometers apart, influenced by nuclear environment and chromatin composition. We conclude that results obtained at high resolution with either 3C methods or FISH alone must be interpreted with caution and that views about genome organization should be validated by independent methods.
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Affiliation(s)
- Iain Williamson
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Soizik Berlivet
- Department of Biochemistry, Goodman Cancer Research Center, McGill University, Montréal, Québec H3G1Y6, Canada
| | - Ragnhild Eskeland
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Shelagh Boyle
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Robert S Illingworth
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | | | | | - Wendy A Bickmore
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom;
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200
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Lonfat N, Montavon T, Darbellay F, Gitto S, Duboule D. Convergent evolution of complex regulatory landscapes and pleiotropy at Hox loci. Science 2014; 346:1004-6. [DOI: 10.1126/science.1257493] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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