1
|
Basu S, Shukron O, Hall D, Parutto P, Ponjavic A, Shah D, Boucher W, Lando D, Zhang W, Reynolds N, Sober LH, Jartseva A, Ragheb R, Ma X, Cramard J, Floyd R, Balmer J, Drury TA, Carr AR, Needham LM, Aubert A, Communie G, Gor K, Steindel M, Morey L, Blanco E, Bartke T, Di Croce L, Berger I, Schaffitzel C, Lee SF, Stevens TJ, Klenerman D, Hendrich BD, Holcman D, Laue ED. Publisher Correction: Live-cell three-dimensional single-molecule tracking reveals modulation of enhancer dynamics by NuRD. Nat Struct Mol Biol 2024; 31:390. [PMID: 38102414 PMCID: PMC10873192 DOI: 10.1038/s41594-023-01179-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Affiliation(s)
- S Basu
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - O Shukron
- Department of Applied Mathematics and Computational Biology, Ecole Normale Supérieure, Paris, France
| | - D Hall
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK
| | - P Parutto
- Department of Applied Mathematics and Computational Biology, Ecole Normale Supérieure, Paris, France
| | - A Ponjavic
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
- School of Physics and Astronomy, University of Leeds, Leeds, UK
- School of Food Science and Nutrition, University of Leeds, Leeds, UK
| | - D Shah
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - W Boucher
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - D Lando
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - W Zhang
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - N Reynolds
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK
| | - L H Sober
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - A Jartseva
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - R Ragheb
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK
| | - X Ma
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - J Cramard
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK
| | - R Floyd
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - J Balmer
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - T A Drury
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - A R Carr
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - L-M Needham
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - A Aubert
- The European Molecular Biology Laboratory EMBL, Grenoble, France
| | - G Communie
- The European Molecular Biology Laboratory EMBL, Grenoble, France
| | - K Gor
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
- The European Molecular Biology Laboratory, Heidelberg, Germany
| | - M Steindel
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - L Morey
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Sylvester Comprehensive Cancer Center, Department of Human Genetics, University of Miami Miller School of Medicine, Biomedical Research Building, Miami, FL, USA
| | - E Blanco
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - T Bartke
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Functional Epigenetics, Neuherberg, Germany
| | - L Di Croce
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - I Berger
- School of Biochemistry, University of Bristol, Bristol, UK
| | - C Schaffitzel
- School of Biochemistry, University of Bristol, Bristol, UK
| | - S F Lee
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - T J Stevens
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - D Klenerman
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK.
| | - B D Hendrich
- Department of Biochemistry, University of Cambridge, Cambridge, UK.
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK.
| | - D Holcman
- Department of Applied Mathematics and Computational Biology, Ecole Normale Supérieure, Paris, France.
| | - E D Laue
- Department of Biochemistry, University of Cambridge, Cambridge, UK.
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK.
| |
Collapse
|
2
|
Basu S, Shukron O, Hall D, Parutto P, Ponjavic A, Shah D, Boucher W, Lando D, Zhang W, Reynolds N, Sober LH, Jartseva A, Ragheb R, Ma X, Cramard J, Floyd R, Balmer J, Drury TA, Carr AR, Needham LM, Aubert A, Communie G, Gor K, Steindel M, Morey L, Blanco E, Bartke T, Di Croce L, Berger I, Schaffitzel C, Lee SF, Stevens TJ, Klenerman D, Hendrich BD, Holcman D, Laue ED. Live-cell three-dimensional single-molecule tracking reveals modulation of enhancer dynamics by NuRD. Nat Struct Mol Biol 2023; 30:1628-1639. [PMID: 37770717 PMCID: PMC10643137 DOI: 10.1038/s41594-023-01095-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 08/14/2023] [Indexed: 09/30/2023]
Abstract
To understand how the nucleosome remodeling and deacetylase (NuRD) complex regulates enhancers and enhancer-promoter interactions, we have developed an approach to segment and extract key biophysical parameters from live-cell three-dimensional single-molecule trajectories. Unexpectedly, this has revealed that NuRD binds to chromatin for minutes, decompacts chromatin structure and increases enhancer dynamics. We also uncovered a rare fast-diffusing state of enhancers and found that NuRD restricts the time spent in this state. Hi-C and Cut&Run experiments revealed that NuRD modulates enhancer-promoter interactions in active chromatin, allowing them to contact each other over longer distances. Furthermore, NuRD leads to a marked redistribution of CTCF and, in particular, cohesin. We propose that NuRD promotes a decondensed chromatin environment, where enhancers and promoters can contact each other over longer distances, and where the resetting of enhancer-promoter interactions brought about by the fast decondensed chromatin motions is reduced, leading to more stable, long-lived enhancer-promoter relationships.
Collapse
Affiliation(s)
- S Basu
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - O Shukron
- Department of Applied Mathematics and Computational Biology, Ecole Normale Supérieure, Paris, France
| | - D Hall
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK
| | - P Parutto
- Department of Applied Mathematics and Computational Biology, Ecole Normale Supérieure, Paris, France
| | - A Ponjavic
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
- School of Physics and Astronomy, University of Leeds, Leeds, UK
- School of Food Science and Nutrition, University of Leeds, Leeds, UK
| | - D Shah
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - W Boucher
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - D Lando
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - W Zhang
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - N Reynolds
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK
| | - L H Sober
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - A Jartseva
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - R Ragheb
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK
| | - X Ma
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - J Cramard
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK
| | - R Floyd
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - J Balmer
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - T A Drury
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - A R Carr
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - L-M Needham
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - A Aubert
- The European Molecular Biology Laboratory EMBL, Grenoble, France
| | - G Communie
- The European Molecular Biology Laboratory EMBL, Grenoble, France
| | - K Gor
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
- The European Molecular Biology Laboratory, Heidelberg, Germany
| | - M Steindel
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - L Morey
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Sylvester Comprehensive Cancer Center, Department of Human Genetics, University of Miami Miller School of Medicine, Biomedical Research Building, Miami, FL, USA
| | - E Blanco
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - T Bartke
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Functional Epigenetics, Neuherberg, Germany
| | - L Di Croce
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - I Berger
- School of Biochemistry, University of Bristol, Bristol, UK
| | - C Schaffitzel
- School of Biochemistry, University of Bristol, Bristol, UK
| | - S F Lee
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - T J Stevens
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - D Klenerman
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK.
| | - B D Hendrich
- Department of Biochemistry, University of Cambridge, Cambridge, UK.
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK.
| | - D Holcman
- Department of Applied Mathematics and Computational Biology, Ecole Normale Supérieure, Paris, France.
| | - E D Laue
- Department of Biochemistry, University of Cambridge, Cambridge, UK.
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK.
| |
Collapse
|
3
|
|
4
|
Plenge RM, Hendrich BD, Schwartz C, Arena JF, Naumova A, Sapienza C, Winter RM, Willard HF. A promoter mutation in the XIST gene in two unrelated families with skewed X-chromosome inactivation. Nat Genet 1997; 17:353-6. [PMID: 9354806 DOI: 10.1038/ng1197-353] [Citation(s) in RCA: 197] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
X-chromosome inactivation is the process by which a cell recognizes the presence of two copies of an X chromosome early in the development of XX embryos and chooses one to be active and one to be inactive. Although it is commonly believed that the initiation of X inactivation is random, with an equal probability (50:50) that either X chromosome will be the inactive X in a given cell, significant variation in the proportion of cells with either X inactive is observed both in mice heterozygous for alleles at the Xce locus and among normal human females in the population. Families in which multiple females demonstrate extremely skewed inactivation patterns that are otherwise quite rare in the general population are thought to reflect possible genetic influences on the X-inactivation process. Here we report a rare cytosine to guanine mutation in the XIST minimal promoter that underlies both epigenetic and functional differences between the two X chromosomes in nine females from two unrelated families. All females demonstrate preferential inactivation of the X chromosome carrying the mutation, suggesting that there is an association between alterations in the regulation of XIST expression and X-chromosome inactivation.
Collapse
Affiliation(s)
- R M Plenge
- Department of Genetics, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | | | | | | | | | | | | | | |
Collapse
|
5
|
Hendrich BD, Plenge RM, Willard HF. Identification and characterization of the human XIST gene promoter: implications for models of X chromosome inactivation. Nucleic Acids Res 1997; 25:2661-71. [PMID: 9185579 PMCID: PMC146792 DOI: 10.1093/nar/25.13.2661] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The XIST gene in both humans and mice is expressed exclusively from the inactive X chromosome and is required for X chromosome inactivation to occur early in development. In order to understand transcriptional regulation of the XIST gene, we have identified and characterized the human XIST promoter and two repeated DNA elements that modulate promoter activity. As determined by reporter gene constructs, the XIST minimal promoter is constitutively active at high levels in human male and female cell lines and in transgenic mice. We demonstrate that this promoter activity is dependent in vitro upon binding of the common transcription factors SP1, YY1 and TBP. We further identify two cis -acting repeated DNA sequences that influence reporter gene activity. First, DNA fragments containing a set of highly conserved repeats located within the 5'-end of XIST stimulate reporter activity 3-fold in transiently transfected cell lines. Second, a 450 bp alternating purine-pyrimidine repeat located 25 kb upstream of the XIST promoter partially suppresses promoter activity by approximately 70% in transient transfection assays. These results indicate that the XIST promoter is constitutively active and that critical steps in the X inactivation process must involve silencing of XIST on the active X chromosome by factors that interact with and/or recognize sequences located outside the minimal promoter.
Collapse
Affiliation(s)
- B D Hendrich
- Department of Genetics and Center for Human Genetics, Case Western Reserve University School of Medicine, Cleveland, OH 44106-4955, USA
| | | | | |
Collapse
|
6
|
Abstract
Epigenetic gene regulation refers to different states of phenotypic expression caused by differential effects of chromosome or chromatin packaging rather than by differences in DNA sequence. Examples of epigenetic regulation can be found in organisms as diverse as the yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe, the fruit fly Drosophila melanogaster, the nematode Caenorhabditis elegans, and mammals. Three major types of epigenetic regulation are considered in this review: dosage compensation, imprinting and position effect variegation. While the specific details and mechanisms of each is quite different, they all involve either local or extensive alterations in chromatin structure. A number of genes implicated in epigenetic regulation have been isolated and their products identified as proteins or RNA molecules involved at various levels in DNA, chromatin or chromosome binding. While in general our understanding of mammalian epigenetic phenomena is not as advanced as that in model systems, the detailed molecular and genetic understanding of processes responsible for conditional gene silencing in invertebrate systems provides strong models for consideration of such effects in human and mouse genetics.
Collapse
Affiliation(s)
- B D Hendrich
- Department of Genetics, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | | |
Collapse
|
7
|
Abstract
The human XIST gene, a candidate for a role in X chromosome inactivation, has recently been cloned and sequenced, yielding a 17 kb cDNA with no apparent significant, conserved open reading frame. In addition, the XIST transcript has been localized within the nucleus to the Barr body by RNA in situ hybridization. This subnuclear localization and lack of any significant protein-coding potential suggest that XIST may act as a functional RNA within the nucleus. In the absence of a conserved open reading frame, we have turned to evolutionary studies as a first step toward elucidating a function for XIST in the process of X inactivation. While probes for XIST detect homologues in numerous eutherians, sequence comparisons require significant gapping and reveal identity levels intermediate between those seen for coding and non-coding regions in other genes. Further, sequence comparison of the most likely candidate open reading frame among several primate species reveals sequence changes not normally associated with protein-coding regions. Other features of XIST are conserved in different species, however, including the position of a major transcription start site and active X chromosome-specific DNA methylation patterns at the gene's 5' end. Finally, a possible molecular basis for differing propensity toward X inactivation between Xce alleles in mouse is investigated by comparing the sequence of the Xist conserved 5' repeats in mouse strains carrying different Xce alleles.
Collapse
Affiliation(s)
- B D Hendrich
- Department of Genetics, Case Western Reserve University School of Medicine, Cleveland, OH 44106-4955
| | | | | |
Collapse
|
8
|
Brown CJ, Hendrich BD, Rupert JL, Lafrenière RG, Xing Y, Lawrence J, Willard HF. The human XIST gene: analysis of a 17 kb inactive X-specific RNA that contains conserved repeats and is highly localized within the nucleus. Cell 1992; 71:527-42. [PMID: 1423611 DOI: 10.1016/0092-8674(92)90520-m] [Citation(s) in RCA: 906] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
X chromosome inactivation in mammalian females results in the cis-limited transcriptional inactivity of most of the genes on one X chromosome. The XIST gene is unique among X-linked genes in being expressed exclusively from the inactive X chromosome. Human XIST cDNAs containing at least eight exons and totaling 17 kb have been isolated and sequenced within the region on the X chromosome known to contain the X inactivation center. The XIST gene includes several tandem repeats, the most 5' of which are evolutionarily conserved. The gene does not contain any significant conserved ORFs and thus does not appear to encode a protein, suggesting that XIST may function as a structural RNA within the nucleus. Consistent with this, fluorescence in situ hybridization experiments demonstrate localization of XIST RNA within the nucleus to a position indistinguishable from the X inactivation-associated Barr body.
Collapse
Affiliation(s)
- C J Brown
- Department of Genetics, Stanford University, California 94305
| | | | | | | | | | | | | |
Collapse
|