Transcriptional Dysregulation in NIPBL and Cohesin Mutant Human Cells
Cohesin regulates sister chromatid cohesion during the mitotic cell cycle with Nipped-B-Like (NIPBL) facilitating its loading and unloading. In addition to this canonical role, cohesin has also been demonstrated to play a critical role in regulation of gene expression in nondividing cells. Heterozyg...
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| Published in | PLoS biology Vol. 7; no. 5; p. e1000119 |
|---|---|
| Main Authors | , , , , , , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
United States
Public Library of Science
26.05.2009
Public Library of Science (PLoS) |
| Subjects | |
| Online Access | Get full text |
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| Abstract | Cohesin regulates sister chromatid cohesion during the mitotic cell cycle with Nipped-B-Like (NIPBL) facilitating its loading and unloading. In addition to this canonical role, cohesin has also been demonstrated to play a critical role in regulation of gene expression in nondividing cells. Heterozygous mutations in the cohesin regulator NIPBL or cohesin structural components SMC1A and SMC3 result in the multisystem developmental disorder Cornelia de Lange Syndrome (CdLS). Genome-wide assessment of transcription in 16 mutant cell lines from severely affected CdLS probands has identified a unique profile of dysregulated gene expression that was validated in an additional 101 samples and correlates with phenotypic severity. This profile could serve as a diagnostic and classification tool. Cohesin binding analysis demonstrates a preference for intergenic regions suggesting a cis-regulatory function mimicking that of a boundary/insulator interacting protein. However, the binding sites are enriched within the promoter regions of the dysregulated genes and are significantly decreased in CdLS proband, indicating an alternative role of cohesin as a transcription factor. |
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| AbstractList | Genome-wide studies using cells from patients with Cornelia de Lange Syndrome reveal a role for cohesin in regulating gene expression in human cells.
Cohesin regulates sister chromatid cohesion during the mitotic cell cycle with Nipped-B-Like (NIPBL) facilitating its loading and unloading. In addition to this canonical role, cohesin has also been demonstrated to play a critical role in regulation of gene expression in nondividing cells. Heterozygous mutations in the cohesin regulator
NIPBL
or cohesin structural components
SMC1A
and
SMC3
result in the multisystem developmental disorder Cornelia de Lange Syndrome (CdLS). Genome-wide assessment of transcription in 16 mutant cell lines from severely affected CdLS probands has identified a unique profile of dysregulated gene expression that was validated in an additional 101 samples and correlates with phenotypic severity. This profile could serve as a diagnostic and classification tool. Cohesin binding analysis demonstrates a preference for intergenic regions suggesting a
cis
-regulatory function mimicking that of a boundary/insulator interacting protein. However, the binding sites are enriched within the promoter regions of the dysregulated genes and are significantly decreased in CdLS proband, indicating an alternative role of cohesin as a transcription factor.
Appropriate segregation of chromosomes to daughter cells depends upon proper cohesion of sister chromatids during mitosis. The multiprotein cohesin complex and its regulators are key factors in this process. Intriguingly, recent work has shown that the cohesin complex also has other cellular roles, including a role in regulating gene expression. Additionally, mutations in cohesin structural and regulatory components have been linked to human multisystem developmental disorders such as Cornelia de Lange Syndrome (CdLS), but the role cohesin is playing in the pathogenesis of this disorder is unknown. To define the role that cohesin plays in regulating gene expression in human cells, we analyzed gene expression and genome-wide cohesin binding patterns in cells from normal subjects and from CdLS probands with mutations in the cohesin regulator
NIPBL
or in the cohesin structural component
SMC1A
. We found a strikingly conserved pattern of gene dysregulation in these different cell lines that correlates with disease severity and a significant correlation between gene dysregulation and cohesin binding around misexpressed genes. The observed pattern of binding and misexpression is consistent with cohesin having a putative role as a boundary/insulator interacting protein or transcription factor, the activity of which is disrupted in CdLS probands. Cohesin regulates sister chromatid cohesion during the mitotic cell cycle with Nipped-B-Like (NIPBL) facilitating its loading and unloading. In addition to this canonical role, cohesin has also been demonstrated to play a critical role in regulation of gene expression in nondividing cells. Heterozygous mutations in the cohesin regulator NIPBL or cohesin structural components SMC1A and SMC3 result in the multisystem developmental disorder Cornelia de Lange Syndrome (CdLS). Genome-wide assessment of transcription in 16 mutant cell lines from severely affected CdLS probands has identified a unique profile of dysregulated gene expression that was validated in an additional 101 samples and correlates with phenotypic severity. This profile could serve as a diagnostic and classification tool. Cohesin binding analysis demonstrates a preference for intergenic regions suggesting a cis-regulatory function mimicking that of a boundary/insulator interacting protein. However, the binding sites are enriched within the promoter regions of the dysregulated genes and are significantly decreased in CdLS proband, indicating an alternative role of cohesin as a transcription factor. Cohesin regulates sister chromatid cohesion during the mitotic cell cycle with Nipped-B-Like (NIPBL) facilitating its loading and unloading. In addition to this canonical role, cohesin has also been demonstrated to play a critical role in regulation of gene expression in nondividing cells. Heterozygous mutations in the cohesin regulator NIPBL or cohesin structural components SMC1A and SMC3 result in the multisystem developmental disorder Cornelia de Lange Syndrome (CdLS). Genome-wide assessment of transcription in 16 mutant cell lines from severely affected CdLS probands has identified a unique profile of dysregulated gene expression that was validated in an additional 101 samples and correlates with phenotypic severity. This profile could serve as a diagnostic and classification tool. Cohesin binding analysis demonstrates a preference for intergenic regions suggesting a cis-regulatory function mimicking that of a boundary/insulator interacting protein. However, the binding sites are enriched within the promoter regions of the dysregulated genes and are significantly decreased in CdLS proband, indicating an alternative role of cohesin as a transcription factor. Cohesin regulates sister chromatid cohesion during the mitotic cell cycle with Nipped-B-Like (NIPBL) facilitating its loading and unloading. In addition to this canonical role, cohesin has also been demonstrated to play a critical role in regulation of gene expression in nondividing cells. Heterozygous mutations in the cohesin regulator NIPBL or cohesin structural components SMC1A and SMC3 result in the multisystem developmental disorder Cornelia de Lange Syndrome (CdLS). Genome-wide assessment of transcription in 16 mutant cell lines from severely affected CdLS probands has identified a unique profile of dysregulated gene expression that was validated in an additional 101 samples and correlates with phenotypic severity. This profile could serve as a diagnostic and classification tool. Cohesin binding analysis demonstrates a preference for intergenic regions suggesting a cis-regulatory function mimicking that of a boundary/insulator interacting protein. However, the binding sites are enriched within the promoter regions of the dysregulated genes and are significantly decreased in CdLS proband, indicating an alternative role of cohesin as a transcription factor.Cohesin regulates sister chromatid cohesion during the mitotic cell cycle with Nipped-B-Like (NIPBL) facilitating its loading and unloading. In addition to this canonical role, cohesin has also been demonstrated to play a critical role in regulation of gene expression in nondividing cells. Heterozygous mutations in the cohesin regulator NIPBL or cohesin structural components SMC1A and SMC3 result in the multisystem developmental disorder Cornelia de Lange Syndrome (CdLS). Genome-wide assessment of transcription in 16 mutant cell lines from severely affected CdLS probands has identified a unique profile of dysregulated gene expression that was validated in an additional 101 samples and correlates with phenotypic severity. This profile could serve as a diagnostic and classification tool. Cohesin binding analysis demonstrates a preference for intergenic regions suggesting a cis-regulatory function mimicking that of a boundary/insulator interacting protein. However, the binding sites are enriched within the promoter regions of the dysregulated genes and are significantly decreased in CdLS proband, indicating an alternative role of cohesin as a transcription factor. Genome-wide studies using cells from patients with Cornelia de Lange Syndrome reveal a role for cohesin in regulating gene expression in human cells. Cohesin regulates sister chromatid cohesion during the mitotic cell cycle with Nipped-B-Like (NIPBL) facilitating its loading and unloading. In addition to this canonical role, cohesin has also been demonstrated to play a critical role in regulation of gene expression in nondividing cells. Heterozygous mutations in the cohesin regulator NIPBL or cohesin structural components SMC1A and SMC3 result in the multisystem developmental disorder Cornelia de Lange Syndrome (CdLS). Genome-wide assessment of transcription in 16 mutant cell lines from severely affected CdLS probands has identified a unique profile of dysregulated gene expression that was validated in an additional 101 samples and correlates with phenotypic severity. This profile could serve as a diagnostic and classification tool. Cohesin binding analysis demonstrates a preference for intergenic regions suggesting a cis-regulatory function mimicking that of a boundary/insulator interacting protein. However, the binding sites are enriched within the promoter regions of the dysregulated genes and are significantly decreased in CdLS proband, indicating an alternative role of cohesin as a transcription factor. Author Summary Appropriate segregation of chromosomes to daughter cells depends upon proper cohesion of sister chromatids during mitosis. The multiprotein cohesin complex and its regulators are key factors in this process. Intriguingly, recent work has shown that the cohesin complex also has other cellular roles, including a role in regulating gene expression. Additionally, mutations in cohesin structural and regulatory components have been linked to human multisystem developmental disorders such as Cornelia de Lange Syndrome (CdLS), but the role cohesin is playing in the pathogenesis of this disorder is unknown. To define the role that cohesin plays in regulating gene expression in human cells, we analyzed gene expression and genome-wide cohesin binding patterns in cells from normal subjects and from CdLS probands with mutations in the cohesin regulator NIPBL or in the cohesin structural component SMC1A. We found a strikingly conserved pattern of gene dysregulation in these different cell lines that correlates with disease severity and a significant correlation between gene dysregulation and cohesin binding around misexpressed genes. The observed pattern of binding and misexpression is consistent with cohesin having a putative role as a boundary/insulator interacting protein or transcription factor, the activity of which is disrupted in CdLS probands. |
| Audience | Academic |
| Author | Krantz, Ian D. Kaur, Maninder Spinner, Nancy B. Liu, Jinglan Kondoh, Tatsuro Vega, Hugo Zhang, Zhe Clark, Dinah Rappaport, Eric Shirahige, Katsuhiko Itoh, Takehiko Deardorff, Matthew A. Jackson, Laird G. Tandy, Stephany Bando, Masashige |
| AuthorAffiliation | 5 Division of Developmental Disability, Misakaenosono Mutsumi Developmental, Medical, and Welfare Center, Isahaya, Japan 3 Laboratory of Chromosome Structure and Function, Department of Biological Science, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama City, Kanagawa, Japan 7 Instituto de Genética, Universidad Nacional de Colombia, Bogotá, Colombia 1 Division of Human Genetics, Abramson Research Institute, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America MRC Human Genetics Unit, United Kingdom 4 The University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America 6 NAPCORE, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America 8 Department of Obstetrics and Gynecology, Drexel University School of Medicine, Philadelphia, Pennsylvania, United States of America 2 Center for Biomedical Informatics, The Children's Hospital of Philadelphia, |
| AuthorAffiliation_xml | – name: 1 Division of Human Genetics, Abramson Research Institute, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America – name: 3 Laboratory of Chromosome Structure and Function, Department of Biological Science, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama City, Kanagawa, Japan – name: 2 Center for Biomedical Informatics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America – name: MRC Human Genetics Unit, United Kingdom – name: 4 The University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America – name: 5 Division of Developmental Disability, Misakaenosono Mutsumi Developmental, Medical, and Welfare Center, Isahaya, Japan – name: 6 NAPCORE, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America – name: 7 Instituto de Genética, Universidad Nacional de Colombia, Bogotá, Colombia – name: 8 Department of Obstetrics and Gynecology, Drexel University School of Medicine, Philadelphia, Pennsylvania, United States of America |
| Author_xml | – sequence: 1 givenname: Jinglan surname: Liu fullname: Liu, Jinglan – sequence: 2 givenname: Zhe surname: Zhang fullname: Zhang, Zhe – sequence: 3 givenname: Masashige surname: Bando fullname: Bando, Masashige – sequence: 4 givenname: Takehiko surname: Itoh fullname: Itoh, Takehiko – sequence: 5 givenname: Matthew A. surname: Deardorff fullname: Deardorff, Matthew A. – sequence: 6 givenname: Dinah surname: Clark fullname: Clark, Dinah – sequence: 7 givenname: Maninder surname: Kaur fullname: Kaur, Maninder – sequence: 8 givenname: Stephany surname: Tandy fullname: Tandy, Stephany – sequence: 9 givenname: Tatsuro surname: Kondoh fullname: Kondoh, Tatsuro – sequence: 10 givenname: Eric surname: Rappaport fullname: Rappaport, Eric – sequence: 11 givenname: Nancy B. surname: Spinner fullname: Spinner, Nancy B. – sequence: 12 givenname: Hugo surname: Vega fullname: Vega, Hugo – sequence: 13 givenname: Laird G. surname: Jackson fullname: Jackson, Laird G. – sequence: 14 givenname: Katsuhiko surname: Shirahige fullname: Shirahige, Katsuhiko – sequence: 15 givenname: Ian D. surname: Krantz fullname: Krantz, Ian D. |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/19468298$$D View this record in MEDLINE/PubMed |
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| ContentType | Journal Article |
| Copyright | COPYRIGHT 2009 Public Library of Science Liu et al. 2009 2009 Liu et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: Liu J, Zhang Z, Bando M, Itoh T, Deardorff MA, et al. (2009) Transcriptional Dysregulation in NIPBL and Cohesin Mutant Human Cells. PLoS Biol 7(5): e1000119. doi:10.1371/journal.pbio.1000119 |
| Copyright_xml | – notice: COPYRIGHT 2009 Public Library of Science – notice: Liu et al. 2009 – notice: 2009 Liu et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: Liu J, Zhang Z, Bando M, Itoh T, Deardorff MA, et al. (2009) Transcriptional Dysregulation in NIPBL and Cohesin Mutant Human Cells. PLoS Biol 7(5): e1000119. doi:10.1371/journal.pbio.1000119 |
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| Keywords | Proteins Promoter Regions, Genetic Chromatin Immunoprecipitation Oligonucleotide Array Sequence Analysis Chromosomal Proteins, Non-Histone Gene Expression Regulation Polymerase Chain Reaction Databases, Genetic De Lange Syndrome Cell Cycle Proteins Chondroitin Sulfate Proteoglycans |
| Language | English |
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| Notes | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 The author(s) have made the following declarations about their contributions: Conceived and designed the experiments: KS IDK. Performed the experiments: JL MB TI. Analyzed the data: JL ZZ MB. Contributed reagents/materials/analysis tools: MAD DC MK ST TK ER NBS HV LGJ. Wrote the paper: JL ZZ IDK. Figure preparation: ZZ JL KS IDK. |
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| Snippet | Cohesin regulates sister chromatid cohesion during the mitotic cell cycle with Nipped-B-Like (NIPBL) facilitating its loading and unloading. In addition to... Genome-wide studies using cells from patients with Cornelia de Lange Syndrome reveal a role for cohesin in regulating gene expression in human cells. Cohesin... Genome-wide studies using cells from patients with Cornelia de Lange Syndrome reveal a role for cohesin in regulating gene expression in human cells. Cohesin... Cohesin regulates sister chromatid cohesion during the mitotic cell cycle with Nipped-B-Like (NIPBL) facilitating its loading and unloading. In addition to... |
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| SubjectTerms | Analysis Binding sites Cell Biology/Gene Expression Cell cycle Cell Cycle Proteins - genetics Chondroitin Sulfate Proteoglycans - genetics Chromatin Immunoprecipitation Chromosomal Proteins, Non-Histone - genetics Databases, Genetic De Lange Syndrome - genetics Developmental Biology/Developmental Molecular Mechanisms Developmental Biology/Molecular Development Gene Expression Regulation Genetic transcription Genetics Genetics and Genomics/Chromosome Biology Genetics and Genomics/Epigenetics Genetics and Genomics/Gene Expression Genetics and Genomics/Genetics of Disease Genetics and Genomics/Genomics Genetics and Genomics/Medical Genetics Genomes Human cell culture Oligonucleotide Array Sequence Analysis Pediatrics and Child Health/Child Development Polymerase Chain Reaction Promoter Regions, Genetic - genetics Proteins Proteins - genetics |
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| Title | Transcriptional Dysregulation in NIPBL and Cohesin Mutant Human Cells |
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