151
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Schilit SL, Menon S, Friedrich C, Kammin T, Wilch E, Hanscom C, Jiang S, Kliesch S, Talkowski ME, Tüttelmann F, MacQueen AJ, Morton CC. SYCP2 Translocation-Mediated Dysregulation and Frameshift Variants Cause Human Male Infertility. Am J Hum Genet 2020; 106:41-57. [PMID: 31866047 DOI: 10.1016/j.ajhg.2019.11.013] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Accepted: 11/21/2019] [Indexed: 12/28/2022] Open
Abstract
Unexplained infertility affects 2%-3% of reproductive-aged couples. One approach to identifying genes involved in infertility is to study subjects with this clinical phenotype and a de novo balanced chromosomal aberration (BCA). While BCAs may reduce fertility by production of unbalanced gametes, a chromosomal rearrangement may also disrupt or dysregulate genes important in fertility. One such subject, DGAP230, has severe oligozoospermia and 46,XY,t(20;22)(q13.3;q11.2). We identified exclusive overexpression of SYCP2 from the der(20) allele that is hypothesized to result from enhancer adoption. Modeling the dysregulation in budding yeast resulted in disrupted structural integrity of the synaptonemal complex, a common cause of defective spermatogenesis in mammals. Exome sequencing of infertile males revealed three heterozygous SYCP2 frameshift variants in additional subjects with cryptozoospermia and azoospermia. In sum, this investigation illustrates the power of precision cytogenetics for annotation of the infertile genome, suggests that these mechanisms should be considered as an alternative etiology to that of segregation of unbalanced gametes in infertile men harboring a BCA, and provides evidence of SYCP2-mediated male infertility in humans.
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152
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Yao S, Dong SS, Ding JM, Rong Y, Zhang YJ, Chen H, Chen JB, Chen YX, Yan H, Dai Z, Guo Y. Sex-specific SNP-SNP interaction analyses within topologically associated domains reveals ANGPT1 as a novel tumor suppressor gene for lung cancer. Genes Chromosomes Cancer 2020; 59:13-22. [PMID: 31385379 DOI: 10.1002/gcc.22793] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 07/16/2019] [Accepted: 07/22/2019] [Indexed: 01/24/2023] Open
Abstract
Genetic interaction has been recognized to be an important cause of the missing heritability. The topologically associating domain (TAD) is a self-interacting genomic region, and the DNA sequences within a TAD physically interact with each other more frequently. Sex differences influence cancer susceptibility at the genetic level. Here, we performed both regular and sex-specific genetic interaction analyses within TAD to identify susceptibility genes for lung cancer in 5204 lung cancer patients and 7389 controls. We found that one SNP pair, rs4262299-rs1654701, was associated with lung cancer in women after multiple testing corrections (combined P = 8.52 × 10-9 ). Single-SNP analyses did not detect significant association signals for these two SNPs. Both identified SNPs are located in the intron region of ANGPT1. We further found that 5% of nonsmall cell lung cancer patients have an alteration in ANGPT1, indicated the potential role of ANGPT1 in the neoplastic progression in lung cancer. The expression of ANGPT1 was significantly down-regulated in patients in lung squamous cell carcinoma and lung adenocarcinoma. We checked the interaction effect on the ANGPT1 expression and lung cancer and found that the minor allele "G" of rs1654701 increased ANGPT1 gene expression and decreased lung cancer risk with the increased dosage of "A" of rs4262299, which consistent with the tumor suppressor function of ANGPT1. Survival analyses found that the high expression of ANGPT1 was individually associated with a higher survival probability in lung cancer patients. In summary, our results suggest that ANGPT1 may be a novel tumor suppressor gene for lung cancer.
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Affiliation(s)
- Shi Yao
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
| | - Shan-Shan Dong
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
| | - Jing-Miao Ding
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
| | - Yu Rong
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
| | - Yu-Jie Zhang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
| | - Hao Chen
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
| | - Jia-Bin Chen
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
| | - Yi-Xiao Chen
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
| | - Han Yan
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
| | - Zhijun Dai
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Shaanxi, P. R. China
| | - Yan Guo
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
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153
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Gaynor KU, Grigorieva IV, Mirczuk SM, Piret SE, Kooblall KG, Stevenson M, Rizzoti K, Bowl MR, Nesbit MA, Christie PT, Fraser WD, Hough T, Whyte MP, Lovell-Badge R, Thakker RV. Studies of mice deleted for Sox3 and uc482: relevance to X-linked hypoparathyroidism. Endocr Connect 2020; 9:EC-19-0478.R1. [PMID: 31961795 PMCID: PMC7040864 DOI: 10.1530/ec-19-0478] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 01/20/2020] [Indexed: 12/18/2022]
Abstract
Hypoparathyroidism is genetically heterogeneous and characterized by low plasma calcium and parathyroid hormone (PTH) concentrations. X-linked hypoparathyroidism (XLHPT) in two American families, is associated with interstitial deletion-insertions involving deletions of chromosome Xq27.1 downstream of SOX3 and insertions of predominantly non-coding DNA from chromosome 2p25.3. These could result in loss, gain, or movement of regulatory elements, which include ultraconserved element uc482, that could alter SOX3 expression,. To investigate this, we analysed SOX3 expression in EBV-transformed lymphoblastoid cells from 3 affected males, 3 unaffected males, and 4 carrier females from one XLHPT family. SOX3 expression was similar in all individuals, indicating that the spatiotemporal effect of the interstitial deletion-insertion on SOX3 expression postulated to occur in developing parathyroids did not manifest in lymphoblastoids. Expression of SNTG2, which is duplicated and inserted into the X chromosome, and ATP11C, which is moved telomerically, were also similarly expressed in all individuals. Investigation of male hemizygous (Sox3-/Y and uc482-/Y) and female heterozygous (Sox3+/- and uc482+/-) knock-out mice, together with wild-type littermates (male Sox3+/Y and uc482+/Y, and female Sox3+/+ and uc482+/+), revealed Sox3-/Y, Sox3+/-, uc482-/Y, and uc482+/- mice to have normal plasma biochemistry, compared to their respective wild-type littermates. When challenged with a low calcium diet, all mice had hypocalcaemia, and elevated plasma PTH concentrations and alkaline phosphatase activities, and Sox3-/Y, Sox3+/-, uc482-/Y, and uc482+/- mice had similar plasma biochemistry, compared to wild-type littermates. Thus, these results indicate that absence of Sox3 or uc482 does not cause hypoparathyroidism, and that XLHPT likely reflects a more complex mechanism.
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Affiliation(s)
- Katherine U Gaynor
- Academic Endocrine Unit, Radcliffe Department of Medicine, University of Oxford, Oxford Centre for Diabetes, Endocrinology and Metabolism, Churchill Hospital, Oxford, UK
| | - Irina V Grigorieva
- Academic Endocrine Unit, Radcliffe Department of Medicine, University of Oxford, Oxford Centre for Diabetes, Endocrinology and Metabolism, Churchill Hospital, Oxford, UK
| | - Samantha M Mirczuk
- Academic Endocrine Unit, Radcliffe Department of Medicine, University of Oxford, Oxford Centre for Diabetes, Endocrinology and Metabolism, Churchill Hospital, Oxford, UK
| | - Sian E Piret
- Academic Endocrine Unit, Radcliffe Department of Medicine, University of Oxford, Oxford Centre for Diabetes, Endocrinology and Metabolism, Churchill Hospital, Oxford, UK
| | - Kreepa G Kooblall
- Academic Endocrine Unit, Radcliffe Department of Medicine, University of Oxford, Oxford Centre for Diabetes, Endocrinology and Metabolism, Churchill Hospital, Oxford, UK
| | - Mark Stevenson
- Academic Endocrine Unit, Radcliffe Department of Medicine, University of Oxford, Oxford Centre for Diabetes, Endocrinology and Metabolism, Churchill Hospital, Oxford, UK
| | | | - Michael R Bowl
- Academic Endocrine Unit, Radcliffe Department of Medicine, University of Oxford, Oxford Centre for Diabetes, Endocrinology and Metabolism, Churchill Hospital, Oxford, UK
| | - M Andrew Nesbit
- Academic Endocrine Unit, Radcliffe Department of Medicine, University of Oxford, Oxford Centre for Diabetes, Endocrinology and Metabolism, Churchill Hospital, Oxford, UK
| | - Paul T Christie
- Academic Endocrine Unit, Radcliffe Department of Medicine, University of Oxford, Oxford Centre for Diabetes, Endocrinology and Metabolism, Churchill Hospital, Oxford, UK
| | - William D Fraser
- Norwich Medical School, Faculty of Medicine and Health Sciences, University of East Anglia, Norwich, UK
| | - Tertius Hough
- MRC Mammalian Genetics Unit, MRC Harwell Institute, Harwell Science and Innovation Campus, Oxfordshire, UK
| | - Michael P Whyte
- Washington University in St Louis School of Medicine, Center for Metabolic Bone Disease and Molecular Research, St Louis, Missouri, USA
| | | | - Rajesh V Thakker
- Academic Endocrine Unit, Radcliffe Department of Medicine, University of Oxford, Oxford Centre for Diabetes, Endocrinology and Metabolism, Churchill Hospital, Oxford, UK
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154
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Gan W, Luo J, Li YZ, Guo JL, Zhu M, Li ML. A computational method to predict topologically associating domain boundaries combining histone Marks and sequence information. BMC Genomics 2019; 20:980. [PMID: 31881832 PMCID: PMC6933632 DOI: 10.1186/s12864-019-6303-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Background The three-dimensional (3D) structure of chromatins plays significant roles during cell differentiation and development. Hi-C and other 3C-based technologies allow us to look deep into the chromatin architectures. Many studies have suggested that topologically associating domains (TAD), as the structure and functional unit, are conserved across different organs. However, our understanding about the underlying mechanism of the TAD boundary formation is still limited. Results We developed a computational method, TAD–Lactuca, to infer this structure by taking the contextual information of the epigenetic modification signals and the primary DNA sequence information on the genome. TAD–Lactuca is found stable in the case of multi-resolutions and different datasets. It could achieve high accuracy and even outperforms the state-of-art methods when the sequence patterns were incorporated. Moreover, several transcript factor binding motifs, besides the well-known CCCTC-binding factor (CTCF) motif, were found significantly enriched on the boundaries. Conclusions We provided a low cost, effective method to predict TAD boundaries. Above results suggested the incorporation of sequence features could significantly improve the performance. The sequence motif enrichment analysis indicates several gene regulation motifs around the boundaries, which is consistent with TADs may serve as the functional units of gene regulation and implies the sequence patterns would be important in chromatin folding.
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Affiliation(s)
- Wei Gan
- College of Computer Science, Sichuan University, Chengdu, 610064, People's Republic of China
| | - Juan Luo
- College of Chemistry, Sichuan University, Chengdu, 610064, People's Republic of China
| | - Yi Zhou Li
- College of Cybersecurity, Sichuan University, Chengdu, 610064, People's Republic of China
| | - Jia Li Guo
- College of Chemistry, Sichuan University, Chengdu, 610064, People's Republic of China
| | - Min Zhu
- College of Computer Science, Sichuan University, Chengdu, 610064, People's Republic of China.
| | - Meng Long Li
- College of Chemistry, Sichuan University, Chengdu, 610064, People's Republic of China.
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155
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Barajas-Mora EM, Feeney AJ. Enhancers as regulators of antigen receptor loci three-dimensional chromatin structure. Transcription 2019; 11:37-51. [PMID: 31829768 DOI: 10.1080/21541264.2019.1699383] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Enhancers are defined as regulatory elements that control transcription in a cell-type and developmental stage-specific manner. They achieve this by physically interacting with their cognate gene promoters. Significantly, these interactions can occur through long genomic distances since enhancers may not be near their cognate promoters. The optimal coordination of enhancer-regulated transcription is essential for the function and identity of the cell. Although great efforts to fully understand the principles of this type of regulation are ongoing, other potential functions of the long-range chromatin interactions (LRCIs) involving enhancers are largely unexplored. We recently uncovered a new role for enhancer elements in determining the three-dimensional (3D) structure of the immunoglobulin kappa (Igκ) light chain receptor locus suggesting a structural function for these DNA elements. This enhancer-mediated locus configuration shapes the resulting Igκ repertoire. We also propose a role for enhancers as critical components of sub-topologically associating domain (subTAD) formation and nuclear spatial localization.
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Affiliation(s)
- E Mauricio Barajas-Mora
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.,Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Ann J Feeney
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
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156
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Muro EM, Ibn-Salem J, Andrade-Navarro MA. The distributions of protein coding genes within chromatin domains in relation to human disease. Epigenetics Chromatin 2019; 12:72. [PMID: 31805995 PMCID: PMC6894242 DOI: 10.1186/s13072-019-0317-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 11/19/2019] [Indexed: 12/02/2022] Open
Abstract
Background Our understanding of the nuclear chromatin structure has increased hugely during the last years mainly as a consequence of the advances in chromatin conformation capture methods like Hi-C. The unprecedented resolution of genome-wide interaction maps shows functional consequences that extend the initial thought of an efficient DNA packaging mechanism: gene regulation, DNA repair, chromosomal translocations and evolutionary rearrangements seem to be only the peak of the iceberg. One key concept emerging from this research is the topologically associating domains (TADs) whose functional role in gene regulation and their association with disease is not fully untangled. Results We report that the lower the number of protein coding genes inside TADs, the higher the tendency of those genes to be associated with disease (p-value = 4 × \documentclass[12pt]{minimal}
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\begin{document}$$10^{-54}$$\end{document}10-54). Moreover, housekeeping genes are less associated with disease than other genes. Accordingly, they are depleted in TADs containing less than three protein coding genes (p-value = 3.9 × \documentclass[12pt]{minimal}
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\begin{document}$$10^{-34}$$\end{document}10-34). We observed that TADs with higher ratios of enhancers versus genes contained higher numbers of disease-associated genes. We interpret these results as an indication that sharing enhancers among genes reduces their involvement in disease. Larger TADs would have more chances to accommodate many genes and select for enhancer sharing along evolution. Conclusions Genes associated with human disease do not distribute randomly over the TADs. Our observations suggest general rules that confer functional stability to TADs, adding more evidence to the role of TADs as regulatory units.
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Affiliation(s)
- Enrique M Muro
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg University of Mainz, Hans-Dieter-Hüsch-Weg 15, 55128, Mainz, Germany.
| | - Jonas Ibn-Salem
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg University of Mainz, Hans-Dieter-Hüsch-Weg 15, 55128, Mainz, Germany
| | - Miguel A Andrade-Navarro
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg University of Mainz, Hans-Dieter-Hüsch-Weg 15, 55128, Mainz, Germany
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157
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Identification of novel genes associated with longevity in Drosophila melanogaster - a computational approach. Aging (Albany NY) 2019; 11:11244-11267. [PMID: 31794428 PMCID: PMC6932890 DOI: 10.18632/aging.102527] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 11/18/2019] [Indexed: 12/13/2022]
Abstract
Despite a growing number of studies on longevity in Drosophila, genetic factors influencing lifespan are still poorly understood. In this paper we propose a conceptually new approach for the identification of novel longevity-associated genes and potential target genes for SNPs in non-coding regions by utilizing the knowledge of co-location of various loci, governed by the three-dimensional architecture of the Drosophila genome. Firstly, we created networks between genes/genomic regions harboring SNPs deemed to be significant in two longevity GWAS summary statistics datasets using intra- and inter-chromosomal interaction frequencies (Hi-C data) as a measure of co-location. These networks were further extended to include regions strongly interacting with previously selected regions. Using various network measures, literature search and additional bioinformatics resources, we investigated the plausibility of genes found to have genuine association with longevity. Several of the newly identified genes were common between the two GWAS datasets and these possessed human orthologs. We also found that the proportion of non-coding SNPs in borders between topologically associated domains is significantly higher than expected by chance. Assuming co-location, we investigated potential target genes for non-coding SNPs. This approach therefore offers a stepping stone to identification of novel genes and SNP targets linked to human longevity.
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158
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Neurobiological functions of transcriptional enhancers. Nat Neurosci 2019; 23:5-14. [PMID: 31740812 DOI: 10.1038/s41593-019-0538-5] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 10/16/2019] [Indexed: 02/08/2023]
Abstract
Transcriptional enhancers are regulatory DNA elements that underlie the specificity and dynamic patterns of gene expression. Over the past decade, large-scale functional genomics projects have driven transformative progress in our understanding of enhancers. These data have relevance for identifying mechanisms of gene regulation in the CNS, elucidating the function of non-coding regulatory sequences in neurobiology and linking sequence variation within enhancers to genetic risk for neurological and psychiatric disorders. However, the sheer volume and complexity of genomic data presents a challenge to interpreting enhancer function in normal and pathogenic neurobiological processes. Here, to advance the application of genome-scale enhancer data, we offer a primer on current models of enhancer function in the CNS, we review how enhancers regulate gene expression across the neuronal lifespan, and we suggest how emerging findings regarding the role of non-coding sequence variation offer opportunities for understanding brain disorders and developing new technologies for neuroscience.
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159
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McCole RB, Erceg J, Saylor W, Wu CT. Ultraconserved Elements Occupy Specific Arenas of Three-Dimensional Mammalian Genome Organization. Cell Rep 2019; 24:479-488. [PMID: 29996107 DOI: 10.1016/j.celrep.2018.06.031] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 05/09/2018] [Accepted: 06/07/2018] [Indexed: 12/23/2022] Open
Abstract
This study explores the relationship between three-dimensional genome organization and ultraconserved elements (UCEs), an enigmatic set of DNA elements that are perfectly conserved between the reference genomes of distantly related species. Examining both human and mouse genomes, we interrogate the relationship of UCEs to three features of chromosome organization derived from Hi-C studies. We find that UCEs are enriched within contact domains and, further, that the subset of UCEs within domains shared across diverse cell types are linked to kidney-related and neuronal processes. In boundaries, UCEs are generally depleted, with those that do overlap boundaries being overrepresented in exonic UCEs. Regarding loop anchors, UCEs are neither overrepresented nor underrepresented, but those present in loop anchors are enriched for splice sites. Finally, as the relationships between UCEs and human Hi-C features are conserved in mouse, our findings suggest that UCEs contribute to interspecies conservation of genome organization and, thus, genome stability.
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Affiliation(s)
- Ruth B McCole
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Jelena Erceg
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Wren Saylor
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Chao-Ting Wu
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
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160
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Razin SV, Ulianov SV, Gavrilov AA. 3D Genomics. Mol Biol 2019; 53:802-812. [DOI: 10.1134/s0026893319060153] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 06/01/2019] [Accepted: 06/03/2019] [Indexed: 08/30/2023]
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161
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Ghavi-Helm Y. Functional Consequences of Chromosomal Rearrangements on Gene Expression: Not So Deleterious After All? J Mol Biol 2019; 432:665-675. [PMID: 31626801 DOI: 10.1016/j.jmb.2019.09.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 09/04/2019] [Accepted: 09/12/2019] [Indexed: 12/14/2022]
Abstract
Chromosomes are folded and organized into topologically associating domains (TADs) which provide a framework for the interaction of enhancers with the promoter of their target gene(s). Structural rearrangements observed during evolution or in disease contexts suggest that changes in genome organization strongly affect gene expression and can have drastic phenotypic effects. In this review, I will discuss how recent genomic engineering experiments reveal a more contrasted picture, suggesting that TADs are important but not always essential for gene expression regulation.
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Affiliation(s)
- Yad Ghavi-Helm
- Institut de Génomique Fonctionnelle de Lyon, Univ Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, 46 Allée D'Italie, F-69364 Lyon, France.
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162
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Hanna MD, Moretti PN, P de Oliveira C, A Rosa MT, R Versiani B, de Oliveira SF, Pic-Taylor A, F Mazzeu J. Defining the Critical Region for Intellectual Disability and Brain Malformations in 6q27 Microdeletions. Mol Syndromol 2019; 10:202-208. [PMID: 31602192 DOI: 10.1159/000501008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/07/2019] [Indexed: 11/19/2022] Open
Abstract
Terminal microdeletions of the long arm of chromosome 6 are associated with a phenotype that includes multiple brain malformations, intellectual disability, and epilepsy. A 1.7-Mb region has been proposed to contain a gene responsible for the brain anomalies. Here, we present the case of a 12-year-old girl with multiple brain alterations and moderate intellectual disability with a 18-kb deletion in chromosome 6q27, which is smaller than the microdeletions previously described by microarray analysis. We refined the smallest region of overlap possibly associated with the phenotype of brain malformations and intellectual disability to a segment of 325 kb, comprising the DLL1, PSMB1, TBP, and PDCD2 genes since these genes were structurally and/or functionally lost in the smaller deletions described to date. We hypothesize that DLL1 is responsible for brain malformations and possibly interacts with other adjacent genes. The TBP gene encodes a transcription factor which is potentially related to cognitive development. TBP is linked to PSMB1 and PDCD2 in a conserved manner among mammals, suggesting a potential interaction between these genes. In conclusion, the 6q27 microdeletion is a complex syndrome with variable expressivity of brain malformations and intellectual disability phenotypes which are possibly triggered by the 4 genes described and adjacent genes susceptible to gene regulation changes.
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Affiliation(s)
- Marcela D Hanna
- Programa de Pós-Graduação em Ciências da Saúde, Faculdade de Ciências da Saúde, Universidade de Brasília, Brasília, Brazil.,Departamento de Genética e Morfologia, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, Brazil
| | | | | | - Maria T A Rosa
- Secretaria de Estado de Saúde do Distrito Federal, Brasília, Brazil
| | - Beatriz R Versiani
- Hospital Universitário de Brasília, Universidade de Brasília, Brasília, Brazil
| | - Silviene F de Oliveira
- Programa de Pós-Graduação em Ciências da Saúde, Faculdade de Ciências da Saúde, Universidade de Brasília, Brasília, Brazil.,Departamento de Genética e Morfologia, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, Brazil
| | - Aline Pic-Taylor
- Programa de Pós-Graduação em Ciências da Saúde, Faculdade de Ciências da Saúde, Universidade de Brasília, Brasília, Brazil.,Departamento de Genética e Morfologia, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, Brazil
| | - Juliana F Mazzeu
- Programa de Pós-Graduação em Ciências da Saúde, Faculdade de Ciências da Saúde, Universidade de Brasília, Brasília, Brazil.,Faculdade de Medicina, Universidade de Brasília, Brasília, Brazil
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163
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Cheutin T, Cavalli G. The multiscale effects of polycomb mechanisms on 3D chromatin folding. Crit Rev Biochem Mol Biol 2019; 54:399-417. [PMID: 31698957 DOI: 10.1080/10409238.2019.1679082] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 10/08/2019] [Accepted: 10/08/2019] [Indexed: 12/30/2022]
Abstract
Polycomb group (PcG) proteins silence master regulatory genes required to properly confer cell identity during the development of both Drosophila and mammals. They may act through chromatin compaction and higher-order folding of chromatin inside the cell nucleus. During the last decade, analysis on interphase chromosome architecture discovered self-interacting regions named topologically associated domains (TADs). TADs result from the 3D chromatin folding of a succession of transcribed and repressed epigenomic domains and from loop extrusion mediated by cohesin/CTCF in mammals. Polycomb silenced chromatin constitutes one type of repressed epigenomic domains which form compacted nano-compartments inside cell nuclei. Recruitment of canonical PcG proteins on chromatin relies on initial binding to discrete elements and further spreading into large chromatin domains covered with H3K27me3. Some of these discrete elements have a bivalent nature both in mammals and Drosophila and are dynamically regulated during development. Loops can occur between them, suggesting that their interaction plays both functional and structural roles. Formation of large chromatin domains covered by H3K27me3 seems crucial for PcG silencing and PcG proteins might exert their function through compaction of these domains in both mammals and flies, rather than by directly controlling the nucleosomal accessibility of discrete regulatory elements. In addition, PcG chromatin domains interact over long genomic distances, shaping a higher-order chromatin network. Therefore, PcG silencing might rely on multiscale chromatin folding to maintain cell identity during differentiation.
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Affiliation(s)
- Thierry Cheutin
- Institute of Human Genetics, CNRS and the University of Montpellier, Montpellier, France
| | - Giacomo Cavalli
- Institute of Human Genetics, CNRS and the University of Montpellier, Montpellier, France
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164
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Sauerwald N, Singhal A, Kingsford C. Analysis of the structural variability of topologically associated domains as revealed by Hi-C. NAR Genom Bioinform 2019; 2. [PMID: 31687663 PMCID: PMC6824515 DOI: 10.1093/nargab/lqz008] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Three-dimensional chromosome structure plays an integral role in gene expression and regulation, replication timing, and other cellular processes. Topologically associated domains (TADs), building blocks of chromosome structure, are genomic regions with higher contact frequencies within the region than outside the region. A central question is the degree to which TADs are conserved or vary between conditions. We analyze 137 Hi-C samples from 9 studies under 3 measures to quantify the effects of various sources of biological and experimental variation. We observe significant variation in TAD sets between both non-replicate and replicate samples, and provide initial evidence that this variability does not come from genetic sequence differences. The effects of experimental protocol differences are also measured, demonstrating that samples can have protocol-specific structural changes, but that TADs are generally robust to lab-specific differences. This study represents a systematic quantification of key factors influencing comparisons of chromosome structure, suggesting significant variability and the potential for cell-type-specific structural features, which has previously not been systematically explored. The lack of observed influence of heredity and genetic differences on chromosome structure suggests that factors other than the genetic sequence are driving this structure, which plays an important role in human disease and cellular functioning.
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Affiliation(s)
- Natalie Sauerwald
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Akshat Singhal
- Department of Computer Science, Stony Brook University, Stony Brook, NY 11790, USA
| | - Carl Kingsford
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA 15213, USA
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165
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Zhang Y, Li T, Preissl S, Amaral ML, Grinstein JD, Farah EN, Destici E, Qiu Y, Hu R, Lee AY, Chee S, Ma K, Ye Z, Zhu Q, Huang H, Fang R, Yu L, Izpisua Belmonte JC, Wu J, Evans SM, Chi NC, Ren B. Transcriptionally active HERV-H retrotransposons demarcate topologically associating domains in human pluripotent stem cells. Nat Genet 2019; 51:1380-1388. [PMID: 31427791 PMCID: PMC6722002 DOI: 10.1038/s41588-019-0479-7] [Citation(s) in RCA: 189] [Impact Index Per Article: 37.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 07/09/2019] [Indexed: 12/24/2022]
Abstract
Chromatin architecture has been implicated in cell type-specific gene regulatory programs, yet how chromatin remodels during development remains to be fully elucidated. Here, by interrogating chromatin reorganization during human pluripotent stem cell (hPSC) differentiation, we discover a role for the primate-specific endogenous retrotransposon human endogenous retrovirus subfamily H (HERV-H) in creating topologically associating domains (TADs) in hPSCs. Deleting these HERV-H elements eliminates their corresponding TAD boundaries and reduces the transcription of upstream genes, while de novo insertion of HERV-H elements can introduce new TAD boundaries. The ability of HERV-H to create TAD boundaries depends on high transcription, as transcriptional repression of HERV-H elements prevents the formation of boundaries. This ability is not limited to hPSCs, as these actively transcribed HERV-H elements and their corresponding TAD boundaries also appear in pluripotent stem cells from other hominids but not in more distantly related species lacking HERV-H elements. Overall, our results provide direct evidence for retrotransposons in actively shaping cell type- and species-specific chromatin architecture.
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Affiliation(s)
- Yanxiao Zhang
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Ting Li
- Department of Medicine, Division of Cardiology, University of California San Diego, La Jolla, CA, USA
| | - Sebastian Preissl
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
- Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Maria Luisa Amaral
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Jonathan D Grinstein
- Department of Medicine, Division of Cardiology, University of California San Diego, La Jolla, CA, USA
| | - Elie N Farah
- Department of Medicine, Division of Cardiology, University of California San Diego, La Jolla, CA, USA
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Eugin Destici
- Department of Medicine, Division of Cardiology, University of California San Diego, La Jolla, CA, USA
| | - Yunjiang Qiu
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Rong Hu
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Ah Young Lee
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Sora Chee
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Kaiyue Ma
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Zhen Ye
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Quan Zhu
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Hui Huang
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Rongxin Fang
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Leqian Yu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | | | - Jun Wu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Sylvia M Evans
- Department of Medicine, Division of Cardiology, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Neil C Chi
- Department of Medicine, Division of Cardiology, University of California San Diego, La Jolla, CA, USA.
- Institute of Genomic Medicine, School of Medicine, University of California San Diego, La Jolla, CA, USA.
| | - Bing Ren
- Ludwig Institute for Cancer Research, La Jolla, CA, USA.
- Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
- Institute of Genomic Medicine, School of Medicine, University of California San Diego, La Jolla, CA, USA.
- Moores Cancer Center, School of Medicine, University of California San Diego, La Jolla, CA, USA.
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166
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Potuijt JWP, Galjaard RJH, van der Spek PJ, van Nieuwenhoven CA, Ahituv N, Oberg KC, Hovius SER. A multidisciplinary review of triphalangeal thumb. J Hand Surg Eur Vol 2019; 44:59-68. [PMID: 30318985 PMCID: PMC6297887 DOI: 10.1177/1753193418803521] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Despite being a rare congenital limb anomaly, triphalangeal thumb is a subject of research in various scientific fields, providing new insights in clinical research and evolutionary biology. The findings of triphalangeal thumb can be predictive for other congenital anomalies as part of an underlying syndrome. Furthermore, triphalangeal thumb is still being used as a model in molecular genetics to study gene regulation by long-range regulatory elements. We present a review that summarizes a number of scientifically relevant topics that involve the triphalangeal thumb phenotype. Future initiatives involving multidisciplinary teams collaborating in the field of triphalangeal thumb research can lead to a better understanding of the pathogenesis and molecular mechanisms of this condition as well as other congenital upper limb anomalies.
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Affiliation(s)
- Jacob W. P. Potuijt
- Department of Plastic and Reconstructive Surgery and Hand Surgery, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands,Jacob W. P. Potuijt, Department of Plastic, Reconstructive and Hand Surgery, Erasmus MC, University Medical Center Rotterdam, Ee-1589 Postbus 2040, 3015 GE Rotterdam, The Netherlands.
| | - Robert-Jan H. Galjaard
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Peter J. van der Spek
- Department of Bioinformatics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands,Department of Pathology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Christianne A. van Nieuwenhoven
- Department of Plastic and Reconstructive Surgery and Hand Surgery, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, SF, USA,Institute for Human Genetics, University of California San Francisco, SF, USA
| | - Kerby C. Oberg
- Department of Pathology and Human Anatomy, Loma Linda University, Loma Linda, USA
| | - Steven E. R. Hovius
- Department of Plastic and Reconstructive Surgery and Hand Surgery, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
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167
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Sauerwald N, Kingsford C. Quantifying the similarity of topological domains across normal and cancer human cell types. Bioinformatics 2019; 34:i475-i483. [PMID: 29949963 PMCID: PMC6022623 DOI: 10.1093/bioinformatics/bty265] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Motivation Three-dimensional chromosome structure has been increasingly shown to influence various levels of cellular and genomic functions. Through Hi-C data, which maps contact frequency on chromosomes, it has been found that structural elements termed topologically associating domains (TADs) are involved in many regulatory mechanisms. However, we have little understanding of the level of similarity or variability of chromosome structure across cell types and disease states. In this study, we present a method to quantify resemblance and identify structurally similar regions between any two sets of TADs. Results We present an analysis of 23 human Hi-C samples representing various tissue types in normal and cancer cell lines. We quantify global and chromosome-level structural similarity, and compare the relative similarity between cancer and non-cancer cells. We find that cancer cells show higher structural variability around commonly mutated pan-cancer genes than normal cells at these same locations. Availability and implementation Software for the methods and analysis can be found at https://github.com/Kingsford-Group/localtadsim
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Affiliation(s)
- Natalie Sauerwald
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Carl Kingsford
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA
- To whom correspondence should be addressed.
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168
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Poot M. Mutations in Mediator Complex Genes CDK8, MED12, MED13, and MEDL13 Mediate Overlapping Developmental Syndromes. Mol Syndromol 2019; 10:239-242. [PMID: 32021594 DOI: 10.1159/000502346] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/22/2019] [Indexed: 12/18/2022] Open
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169
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Abstract
DNA is packaged into chromosomes, which are further organized into domains: Regions of the genome which are more likely to self-interact. Domains have been observed in species ranging from bacteria to humans and are thought to play an important role in gene regulation. Yet the mechanisms of domain formation are not fully understood. Here we use computer simulations to investigate domain formation in yeast. Our model reproduces the experimentally observed domains using only nucleosome positioning information as an input, implying that (unlike in higher eukaryotes) domain boundary locations are largely determined at this level. Our results reveal how irregular nucleosome spacing impacts the 3D chromosome organization, pointing to a direct link between nucleosome positioning and genome regulation at the large scale. We use molecular dynamics simulations based on publicly available micrococcal nuclease sequencing data for nucleosome positions to predict the 3D structure of chromatin in the yeast genome. Our main aim is to shed light on the mechanism underlying the formation of chromosomal interaction domains, chromosome regions of around 0.5 to 10 kbp which show enriched self-interactions, which were experimentally observed in recent MicroC experiments (importantly these are at a different length scale from the 100- to 1,000-kbp–sized domains observed in higher eukaryotes). We show that the sole input of nucleosome positioning data is already sufficient to determine the patterns of chromatin interactions and domain boundaries seen experimentally to a high degree of accuracy. Since the nucleosome spacing so strongly affects the larger-scale domain structure, we next examine the genome-wide linker-length distribution in more detail, finding that it is highly irregular and varies in different genomic regions such as gene bodies, promoters, and active and inactive genes. Finally we use our simple simulation model to characterize in more detail how irregular nucleosome spacing may affect local chromatin structure.
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170
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Genetic Variation in Long-Range Enhancers. Curr Top Behav Neurosci 2019; 42:35-50. [PMID: 31396896 DOI: 10.1007/7854_2019_110] [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: 03/17/2023]
Abstract
Cis-regulatory elements (CREs), including insulators, promoters, and enhancers, play critical roles in the establishment and maintenance of normal cellular function. Within each cell, the 3D structure of chromatin is arranged in specific patterns to expose the CREs required for optimal spatiotemporal regulation of gene expression. CREs can act over large distances along the linear genome, facilitated by looping of the intervening chromatin to allow direct interaction between distal regulatory elements and their target genes. A number of pathologies are associated with dysregulation of CRE function, including developmental disorders, cancers, and neuropsychiatric disease. A majority of known neuropsychiatric disease risk loci are noncoding, and increasing evidence suggests that they contribute to disease through disruption of CREs. As such, rather than directly altering the amino acid content of proteins, these variants are instead thought to affect where, when, and to what extent a given gene is expressed. The distances over which CREs can operate often render their target genes difficult to identify. Furthermore, as many risk loci contain multiple variants in high linkage disequilibrium, identification of the causative single nucleotide polymorphism(s) therein is not straightforward. Thus, deciphering the genetic etiology of complex neuropsychiatric disorders presents a significant challenge.
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171
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Yauy K, Schneider A, Ng BL, Gaillard JB, Sati S, Coubes C, Wells C, Tournaire M, Guignard T, Bouret P, Geneviève D, Puechberty J, Pellestor F, Gatinois V. Disruption of chromatin organisation causes MEF2C gene overexpression in intellectual disability: a case report. BMC Med Genomics 2019; 12:116. [PMID: 31375103 PMCID: PMC6679470 DOI: 10.1186/s12920-019-0558-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 07/15/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Balanced structural variants are mostly described in disease with gene disruption or subtle rearrangement at breakpoints. CASE PRESENTATION Here we report a patient with mild intellectual deficiency who carries a de novo balanced translocation t(3;5). Breakpoints were fully explored by microarray, Array Painting and Sanger sequencing. No gene disruption was found but the chromosome 5 breakpoint was localized 228-kb upstream of the MEF2C gene. The predicted Topologically Associated Domains analysis shows that it contains only the MEF2C gene and a long non-coding RNA LINC01226. RNA studies looking for MEF2C gene expression revealed an overexpression of MEF2C in the lymphoblastoid cell line of the patient. CONCLUSIONS Pathogenicity of MEF2C overexpression is still unclear as only four patients with mild intellectual deficiency carrying 5q14.3 microduplications containing MEF2C are described in the literature. The microduplications in these individuals also contain other genes expressed in the brain. The patient presented the same phenotype as 5q14.3 microduplication patients. We report the first case of a balanced translocation leading to an overexpression of MEF2C similar to a functional duplication.
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Affiliation(s)
- Kevin Yauy
- Unité de Génétique Chromosomique, Département de Génétique Médicale, Maladies Rares et Médecine Personnalisée, Hôpital Arnaud de Villeneuve, CHU de Montpellier, Montpellier, France
| | - Anouck Schneider
- Unité de Génétique Chromosomique, Département de Génétique Médicale, Maladies Rares et Médecine Personnalisée, Hôpital Arnaud de Villeneuve, CHU de Montpellier, Montpellier, France
| | - Bee Ling Ng
- Cytometry Core Facility, The Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Jean-Baptiste Gaillard
- Unité de Génétique Chromosomique, Département de Génétique Médicale, Maladies Rares et Médecine Personnalisée, Hôpital Arnaud de Villeneuve, CHU de Montpellier, Montpellier, France
| | - Satish Sati
- Chromatin and Cell Biology Group, CNRS-Institute of Human Genetics, Montpellier, France
| | - Christine Coubes
- Service de Génétique Clinique, Département de Génétique Médicale, Maladies Rares et Médecine Personnalisée, Centre de Référence Anomalies du Développement et Syndromes Malformatifs, Hôpital Arnaud de Villeneuve, CHU de Montpellier, Montpellier, France
| | - Constance Wells
- Service de Génétique Clinique, Département de Génétique Médicale, Maladies Rares et Médecine Personnalisée, Centre de Référence Anomalies du Développement et Syndromes Malformatifs, Hôpital Arnaud de Villeneuve, CHU de Montpellier, Montpellier, France
| | - Magali Tournaire
- Unité de Génétique Chromosomique, Département de Génétique Médicale, Maladies Rares et Médecine Personnalisée, Hôpital Arnaud de Villeneuve, CHU de Montpellier, Montpellier, France
| | - Thomas Guignard
- Unité de Génétique Chromosomique, Département de Génétique Médicale, Maladies Rares et Médecine Personnalisée, Hôpital Arnaud de Villeneuve, CHU de Montpellier, Montpellier, France
| | - Pauline Bouret
- Unité de Génétique Chromosomique, Département de Génétique Médicale, Maladies Rares et Médecine Personnalisée, Hôpital Arnaud de Villeneuve, CHU de Montpellier, Montpellier, France
| | - David Geneviève
- Service de Génétique Clinique, Département de Génétique Médicale, Maladies Rares et Médecine Personnalisée, Centre de Référence Anomalies du Développement et Syndromes Malformatifs, Hôpital Arnaud de Villeneuve, CHU de Montpellier, Montpellier, France
| | - Jacques Puechberty
- Service de Génétique Clinique, Département de Génétique Médicale, Maladies Rares et Médecine Personnalisée, Centre de Référence Anomalies du Développement et Syndromes Malformatifs, Hôpital Arnaud de Villeneuve, CHU de Montpellier, Montpellier, France
| | - Franck Pellestor
- Unité de Génétique Chromosomique, Département de Génétique Médicale, Maladies Rares et Médecine Personnalisée, Hôpital Arnaud de Villeneuve, CHU de Montpellier, Montpellier, France
| | - Vincent Gatinois
- Unité de Génétique Chromosomique, Département de Génétique Médicale, Maladies Rares et Médecine Personnalisée, Hôpital Arnaud de Villeneuve, CHU de Montpellier, Montpellier, France.
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172
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Computational Processing and Quality Control of Hi-C, Capture Hi-C and Capture-C Data. Genes (Basel) 2019; 10:genes10070548. [PMID: 31323892 PMCID: PMC6678864 DOI: 10.3390/genes10070548] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 07/06/2019] [Accepted: 07/14/2019] [Indexed: 01/08/2023] Open
Abstract
Hi-C, capture Hi-C (CHC) and Capture-C have contributed greatly to our present understanding of the three-dimensional organization of genomes in the context of transcriptional regulation by characterizing the roles of topological associated domains, enhancer promoter loops and other three-dimensional genomic interactions. The analysis is based on counts of chimeric read pairs that map to interacting regions of the genome. However, the processing and quality control presents a number of unique challenges. We review here the experimental and computational foundations and explain how the characteristics of restriction digests, sonication fragments and read pairs can be exploited to distinguish technical artefacts from valid read pairs originating from true chromatin interactions.
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173
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Abstract
Structural and quantitative chromosomal rearrangements, collectively referred to as structural variation (SV), contribute to a large extent to the genetic diversity of the human genome and thus are of high relevance for cancer genetics, rare diseases and evolutionary genetics. Recent studies have shown that SVs can not only affect gene dosage but also modulate basic mechanisms of gene regulation. SVs can alter the copy number of regulatory elements or modify the 3D genome by disrupting higher-order chromatin organization such as topologically associating domains. As a result of these position effects, SVs can influence the expression of genes distant from the SV breakpoints, thereby causing disease. The impact of SVs on the 3D genome and on gene expression regulation has to be considered when interpreting the pathogenic potential of these variant types.
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Affiliation(s)
- Malte Spielmann
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Darío G Lupiáñez
- Epigenetics and Sex Development Group, Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Berlin-Buch, Germany
| | - Stefan Mundlos
- Max Planck Institute for Molecular Genetics, RG Development & Disease, Berlin, Germany. .,Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, Berlin, Germany.
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174
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Hu H, Kahrizi K, Musante L, Fattahi Z, Herwig R, Hosseini M, Oppitz C, Abedini SS, Suckow V, Larti F, Beheshtian M, Lipkowitz B, Akhtarkhavari T, Mehvari S, Otto S, Mohseni M, Arzhangi S, Jamali P, Mojahedi F, Taghdiri M, Papari E, Soltani Banavandi MJ, Akbari S, Tonekaboni SH, Dehghani H, Ebrahimpour MR, Bader I, Davarnia B, Cohen M, Khodaei H, Albrecht B, Azimi S, Zirn B, Bastami M, Wieczorek D, Bahrami G, Keleman K, Vahid LN, Tzschach A, Gärtner J, Gillessen-Kaesbach G, Varaghchi JR, Timmermann B, Pourfatemi F, Jankhah A, Chen W, Nikuei P, Kalscheuer VM, Oladnabi M, Wienker TF, Ropers HH, Najmabadi H. Genetics of intellectual disability in consanguineous families. Mol Psychiatry 2019; 24:1027-1039. [PMID: 29302074 DOI: 10.1038/s41380-017-0012-2] [Citation(s) in RCA: 119] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 10/19/2017] [Accepted: 10/30/2017] [Indexed: 01/17/2023]
Abstract
Autosomal recessive (AR) gene defects are the leading genetic cause of intellectual disability (ID) in countries with frequent parental consanguinity, which account for about 1/7th of the world population. Yet, compared to autosomal dominant de novo mutations, which are the predominant cause of ID in Western countries, the identification of AR-ID genes has lagged behind. Here, we report on whole exome and whole genome sequencing in 404 consanguineous predominantly Iranian families with two or more affected offspring. In 219 of these, we found likely causative variants, involving 77 known and 77 novel AR-ID (candidate) genes, 21 X-linked genes, as well as 9 genes previously implicated in diseases other than ID. This study, the largest of its kind published to date, illustrates that high-throughput DNA sequencing in consanguineous families is a superior strategy for elucidating the thousands of hitherto unknown gene defects underlying AR-ID, and it sheds light on their prevalence.
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Affiliation(s)
- Hao Hu
- Max-Planck-Institute for Molecular Genetics, 14195, Berlin, Germany.,Guangzhou Women and Children's Medical Center, 510623, Guangzhou, China
| | - Kimia Kahrizi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Luciana Musante
- Max-Planck-Institute for Molecular Genetics, 14195, Berlin, Germany
| | - Zohreh Fattahi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Ralf Herwig
- Max-Planck-Institute for Molecular Genetics, 14195, Berlin, Germany
| | - Masoumeh Hosseini
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Cornelia Oppitz
- IMP-Research Institute of Molecular Pathology, 1030, Vienna, Austria
| | - Seyedeh Sedigheh Abedini
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Vanessa Suckow
- Max-Planck-Institute for Molecular Genetics, 14195, Berlin, Germany
| | - Farzaneh Larti
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Maryam Beheshtian
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | | | - Tara Akhtarkhavari
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Sepideh Mehvari
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Sabine Otto
- Max-Planck-Institute for Molecular Genetics, 14195, Berlin, Germany
| | - Marzieh Mohseni
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Sanaz Arzhangi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Payman Jamali
- Shahrood Genetic Counseling Center, Welfare Office, Semnan, 36156, Iran
| | - Faezeh Mojahedi
- Mashhad Medical Genetic Counseling Center, Mashhad, 91767, Iran
| | - Maryam Taghdiri
- Shiraz Genetic Counseling Center, Welfare Office, Shiraz, Iran
| | - Elaheh Papari
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | | | - Saeide Akbari
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Seyed Hassan Tonekaboni
- Pediatric Neurology Research Center, Mofid Children's Hospital, Shahid Beheshti University of Medical Sciences, Tehran, 15468, Iran
| | - Hossein Dehghani
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Mohammad Reza Ebrahimpour
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Ingrid Bader
- Kinderzentrum München, Technische Universität München, 81377, München, Germany
| | - Behzad Davarnia
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Monika Cohen
- Children's Center Munich, 81377, Munich, Germany
| | - Hossein Khodaei
- Meybod Genetics Research Center, Welfare Organization, Yazd, 89651, Iran
| | - Beate Albrecht
- Institute of Human Genetics, University Hospital Essen, 45122, Essen, Germany
| | - Sarah Azimi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Birgit Zirn
- Genetikum Counseling Center, 70173, Stuttgart, Germany
| | - Milad Bastami
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Dagmar Wieczorek
- Institute of Human Genetics and Anthropology, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany
| | - Gholamreza Bahrami
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Krystyna Keleman
- IMP-Research Institute of Molecular Pathology, 1030, Vienna, Austria.,Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA, 20147, USA
| | - Leila Nouri Vahid
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Andreas Tzschach
- Max-Planck-Institute for Molecular Genetics, 14195, Berlin, Germany.,Institute of Clinical Genetics, Technische Universität Dresden, Dresden, Germany
| | - Jutta Gärtner
- University Medical Center, Georg August University Göttingen, 37075, Göttingen, Germany
| | | | | | - Bernd Timmermann
- Max-Planck-Institute for Molecular Genetics, 14195, Berlin, Germany
| | | | - Aria Jankhah
- Shiraz Genetic Counseling Center, Shiraz, 71346, Iran
| | - Wei Chen
- Berlin Institute for Medical Systems Biology, Max Delbrueck Center for Molecular Medicine, 13125, Berlin, Germany
| | - Pooneh Nikuei
- Molecular Medicine Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | | | - Morteza Oladnabi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Thomas F Wienker
- Max-Planck-Institute for Molecular Genetics, 14195, Berlin, Germany
| | - Hans-Hilger Ropers
- Max-Planck-Institute for Molecular Genetics, 14195, Berlin, Germany. .,Institute of Human Genetics, University Medicine, Mainz, Germany.
| | - Hossein Najmabadi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran. .,Kariminejad - Najmabadi Pathology & Genetics Centre, Tehran, 14667-13713, Iran.
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175
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Nowacka-Woszuk J, Szczerbal I, Stachowiak M, Szydlowski M, Nizanski W, Dzimira S, Maslak A, Payan-Carreira R, Wydooghe E, Nowak T, Switonski M. Association between polymorphisms in the SOX9 region and canine disorder of sex development (78,XX; SRY-negative) revisited in a multibreed case-control study. PLoS One 2019; 14:e0218565. [PMID: 31220175 PMCID: PMC6586338 DOI: 10.1371/journal.pone.0218565] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 06/03/2019] [Indexed: 12/04/2022] Open
Abstract
Testicular or ovotesticular disorders of sex development (DSD) in individuals with female karyotype (XX) lacking the SRY gene has been observed in several mammalian species, including dogs. A genetic background for this abnormality has been extensively sought, and the region harboring the SOX9 gene has often been considered key in canine DSD. Three types of polymorphism have been studied in this region to date: a) copy number variation (CNV) in a region about 400 kb upstream of SOX9, named CNVR1; b) duplication of SOX9; and c) insertion of a single G-nucleotide (rs852549625) approximately 2.2 Mb upstream of SOX9. The aim of this study was thus to comprehensively analyze these polymorphisms in a large multibreed case-control cohort containing 45 XX DSD dogs, representing 23 breeds. The control set contained 57 fertile females. Droplet digital PCR (ddPCR) was used to study CNVR1 and the duplication of SOX9. Fluorescent in situ hybridization (FISH) was used to visualize copy numbers on a cellular level. The Sanger sequencing approach was performed to analyze the region harboring the G-insertion. We confirmed that CNVR1 is highly polymorphic and that copy numbers varied between 0 and 7 in the case and control cohorts. Interestingly, the number of copies was significantly higher (P = 0.038) in XX DSD dogs (mean = 2.7) than in the control females (mean = 2.0) but not in all studied breeds. Duplication of the SOX9 gene was noted only in a single XX DSD dog (an American Bully), which had three copies of SOX9. Distribution of the G-nucleotide insertion was similar in the XX DSD (frequency 0.20) and control (frequency 0.14) cohorts. Concluding, our study showed that CNVR1, located upstream of SOX9, is associated with the XX DSD phenotype, though in a breed-specific manner. Duplication of the SOX9 gene is a rare cause of this disorder in dogs. Moreover, we did not observe any association of G-insertion with the DSD phenotype. We assume that the genetic background of XX DSD can be different in certain breeds.
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Affiliation(s)
- Joanna Nowacka-Woszuk
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Poznan, Poland
| | - Izabela Szczerbal
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Poznan, Poland
| | - Monika Stachowiak
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Poznan, Poland
| | - Maciej Szydlowski
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Poznan, Poland
| | - Wojciech Nizanski
- Department of Reproduction and Clinic of Farm Animals, Wroclaw University of Environmental and Life Sciences, Wroclaw, Poland
| | - Stanislaw Dzimira
- Department of Pathology, Wroclaw University of Environmental and Life Sciences, Wroclaw, Poland
| | | | - Rita Payan-Carreira
- CECAV, Centro de Ciência Animal e Veterinária, Universidade de Trás-os-Montes e Alto Douro, Quinta de Prados, Vila Real, Portugal
| | - Eline Wydooghe
- Department of Reproduction, Obstetrics, and Herd Health, Clinic of Small Animal Reproduction, Ghent University, Merelbeke, Belgium
| | - Tomasz Nowak
- Department of Animal Reproduction, Poznan University of Life Sciences, Poznan, Poland
| | - Marek Switonski
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Poznan, Poland
- * E-mail:
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176
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Collas P, Liyakat Ali TM, Brunet A, Germier T. Finding Friends in the Crowd: Three-Dimensional Cliques of Topological Genomic Domains. Front Genet 2019; 10:602. [PMID: 31275364 PMCID: PMC6593077 DOI: 10.3389/fgene.2019.00602] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 06/05/2019] [Indexed: 12/31/2022] Open
Abstract
The mammalian genome is intricately folded in a three-dimensional topology believed to be important for the orchestration of gene expression regulating development, differentiation and tissue homeostasis. Important features of spatial genome conformation in the nucleus are promoter-enhancer contacts regulating gene expression within topologically-associated domains (TADs), short- and long-range interactions between TADs and associations of chromatin with nucleoli and nuclear speckles. In addition, anchoring of chromosomes to the nuclear lamina via lamina-associated domains (LADs) at the nuclear periphery is a key regulator of the radial distribution of chromatin. To what extent TADs and LADs act in concert as genomic organizers to shape the three-dimensional topology of chromatin has long remained unknown. A new study addressing this key question provides evidence of (i) preferred long-range associations between TADs forming TAD “cliques” which organize large heterochromatin domains, and (ii) stabilization of TAD cliques by LADs at the nuclear periphery after induction of terminal differentiation. Here, we review these findings, address the issue of whether TAD cliques exist in single cells and discuss the extent of cell-to-cell heterogeneity in higher-order chromatin conformation. The recent observations provide a first appreciation of changes in 4-dimensional higher-order genome topologies during differentiation.
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Affiliation(s)
- Philippe Collas
- Department of Molecular Medicine, Faculty of Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway.,Department of Immunology and Transfusion Medicine, Oslo University Hospital, Oslo, Norway
| | - Tharvesh M Liyakat Ali
- Department of Molecular Medicine, Faculty of Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Annaël Brunet
- Department of Molecular Medicine, Faculty of Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Thomas Germier
- Department of Molecular Medicine, Faculty of Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
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177
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Zheng H, Xie W. The role of 3D genome organization in development and cell differentiation. Nat Rev Mol Cell Biol 2019; 20:535-550. [DOI: 10.1038/s41580-019-0132-4] [Citation(s) in RCA: 282] [Impact Index Per Article: 56.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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178
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Xu J, Liu Y. A guide to visualizing the spatial epigenome with super-resolution microscopy. FEBS J 2019; 286:3095-3109. [PMID: 31127980 DOI: 10.1111/febs.14938] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 03/24/2019] [Accepted: 05/23/2019] [Indexed: 12/28/2022]
Abstract
Genomic DNA in eukaryotic cells is tightly compacted with histone proteins into nucleosomes, which are further packaged into the higher-order chromatin structure. The physical structuring of chromatin is highly dynamic and regulated by a large number of epigenetic modifications in response to various environmental exposures, both in normal development and pathological processes such as aging and cancer. Higher-order chromatin structure has been indirectly inferred by conventional bulk biochemical assays on cell populations, which do not allow direct visualization of the spatial information of epigenomics (referred to as spatial epigenomics). With recent advances in super-resolution microscopy, the higher-order chromatin structure can now be visualized in vivo at an unprecedent resolution. This opens up new opportunities to study physical compaction of 3D chromatin structure in single cells, maintaining a well-preserved spatial context of tissue microenvironment. This review discusses the recent application of super-resolution fluorescence microscopy to investigate the higher-order chromatin structure of different epigenomic states. We also envision the synergistic integration of super-resolution microscopy and high-throughput genomic technologies for the analysis of spatial epigenomics to fully understand the genome function in normal biological processes and diseases.
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Affiliation(s)
- Jianquan Xu
- Biomedical Optical Imaging Laboratory, Departments of Medicine and Bioengineering, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yang Liu
- Biomedical Optical Imaging Laboratory, Departments of Medicine and Bioengineering, University of Pittsburgh, Pittsburgh, PA, USA
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179
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Lai X, Stigliani A, Vachon G, Carles C, Smaczniak C, Zubieta C, Kaufmann K, Parcy F. Building Transcription Factor Binding Site Models to Understand Gene Regulation in Plants. MOLECULAR PLANT 2019; 12:743-763. [PMID: 30447332 DOI: 10.1016/j.molp.2018.10.010] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 09/20/2018] [Accepted: 10/30/2018] [Indexed: 06/09/2023]
Abstract
Transcription factors (TFs) are key cellular components that control gene expression. They recognize specific DNA sequences, the TF binding sites (TFBSs), and thus are targeted to specific regions of the genome where they can recruit transcriptional co-factors and/or chromatin regulators to fine-tune spatiotemporal gene regulation. Therefore, the identification of TFBSs in genomic sequences and their subsequent quantitative modeling is of crucial importance for understanding and predicting gene expression. Here, we review how TFBSs can be determined experimentally, how the TFBS models can be constructed in silico, and how they can be optimized by taking into account features such as position interdependence within TFBSs, DNA shape, and/or by introducing state-of-the-art computational algorithms such as deep learning methods. In addition, we discuss the integration of context variables into the TFBS modeling, including nucleosome positioning, chromatin states, methylation patterns, 3D genome architectures, and TF cooperative binding, in order to better predict TF binding under cellular contexts. Finally, we explore the possibilities of combining the optimized TFBS model with technological advances, such as targeted TFBS perturbation by CRISPR, to better understand gene regulation, evolution, and plant diversity.
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Affiliation(s)
- Xuelei Lai
- CNRS, Univ. Grenoble Alpes, CEA, INRA, BIG-LPCV, 38000 Grenoble, France.
| | - Arnaud Stigliani
- CNRS, Univ. Grenoble Alpes, CEA, INRA, BIG-LPCV, 38000 Grenoble, France
| | - Gilles Vachon
- CNRS, Univ. Grenoble Alpes, CEA, INRA, BIG-LPCV, 38000 Grenoble, France
| | - Cristel Carles
- CNRS, Univ. Grenoble Alpes, CEA, INRA, BIG-LPCV, 38000 Grenoble, France
| | - Cezary Smaczniak
- Department for Plant Cell and Molecular Biology, Institute for Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Chloe Zubieta
- CNRS, Univ. Grenoble Alpes, CEA, INRA, BIG-LPCV, 38000 Grenoble, France
| | - Kerstin Kaufmann
- Department for Plant Cell and Molecular Biology, Institute for Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - François Parcy
- CNRS, Univ. Grenoble Alpes, CEA, INRA, BIG-LPCV, 38000 Grenoble, France.
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180
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Krumm A, Duan Z. Understanding the 3D genome: Emerging impacts on human disease. Semin Cell Dev Biol 2019; 90:62-77. [PMID: 29990539 PMCID: PMC6329682 DOI: 10.1016/j.semcdb.2018.07.004] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 07/03/2018] [Indexed: 12/13/2022]
Abstract
Recent burst of new technologies that allow for quantitatively delineating chromatin structure has greatly expanded our understanding of how the genome is organized in the three-dimensional (3D) space of the nucleus. It is now clear that the hierarchical organization of the eukaryotic genome critically impacts nuclear activities such as transcription, replication, as well as cellular and developmental events such as cell cycle, cell fate decision and embryonic development. In this review, we discuss new insights into how the structural features of the 3D genome hierarchy are established and maintained, how this hierarchy undergoes dynamic rearrangement during normal development and how its perturbation will lead to human disease, highlighting the accumulating evidence that links the diverse 3D genome architecture components to a multitude of human diseases and the emerging mechanisms by which 3D genome derangement causes disease phenotypes.
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Affiliation(s)
- Anton Krumm
- Department of Microbiology, University of Washington, USA.
| | - Zhijun Duan
- Institute for Stem Cell and Regenerative Medicine, University of Washington, USA; Division of Hematology, Department of Medicine, University of Washington, USA.
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181
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Cortesi A, Pesant M, Sinha S, Marasca F, Sala E, Gregoretti F, Antonelli L, Oliva G, Chiereghin C, Soldà G, Bodega B. 4q-D4Z4 chromatin architecture regulates the transcription of muscle atrophic genes in facioscapulohumeral muscular dystrophy. Genome Res 2019; 29:883-895. [PMID: 31097473 PMCID: PMC6581056 DOI: 10.1101/gr.233288.117] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 05/13/2019] [Indexed: 12/11/2022]
Abstract
Despite increasing insights in genome structure organization, the role of DNA repetitive elements, accounting for more than two thirds of the human genome, remains elusive. Facioscapulohumeral muscular dystrophy (FSHD) is associated with deletion of D4Z4 repeat array below 11 units at 4q35.2. It is known that the deletion alters chromatin structure in cis, leading to gene up-regulation. Here we show a genome-wide role of 4q-D4Z4 array in modulating gene expression via 3D nuclear contacts. We have developed an integrated strategy of 4q-D4Z4-specific 4C-seq and chromatin segmentation analyses, showing that 4q-D4Z4 3D interactome and chromatin states of interacting genes are impaired in FSHD1 condition; in particular, genes that have lost the 4q-D4Z4 interaction and with a more active chromatin state are enriched for muscle atrophy transcriptional signature. Expression level of these genes is restored by the interaction with an ectopic 4q-D4Z4 array, suggesting that the repeat directly modulates the transcription of contacted targets. Of note, the up-regulation of atrophic genes is a common feature of several FSHD1 and FSHD2 patients, indicating that we have identified a core set of deregulated genes involved in FSHD pathophysiology.
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Affiliation(s)
- Alice Cortesi
- Istituto Nazionale di Genetica Molecolare "Romeo ed Enrica Invernizzi" (INGM), 20122, Milan, Italy
| | - Matthieu Pesant
- Istituto Nazionale di Genetica Molecolare "Romeo ed Enrica Invernizzi" (INGM), 20122, Milan, Italy
| | - Shruti Sinha
- Istituto Nazionale di Genetica Molecolare "Romeo ed Enrica Invernizzi" (INGM), 20122, Milan, Italy
| | - Federica Marasca
- Istituto Nazionale di Genetica Molecolare "Romeo ed Enrica Invernizzi" (INGM), 20122, Milan, Italy
| | - Eleonora Sala
- Istituto Nazionale di Genetica Molecolare "Romeo ed Enrica Invernizzi" (INGM), 20122, Milan, Italy
| | - Francesco Gregoretti
- CNR Institute for High Performance Computing and Networking (ICAR), 8013, Naples, Italy
| | - Laura Antonelli
- CNR Institute for High Performance Computing and Networking (ICAR), 8013, Naples, Italy
| | - Gennaro Oliva
- CNR Institute for High Performance Computing and Networking (ICAR), 8013, Naples, Italy
| | - Chiara Chiereghin
- Department of Biomedical Sciences, Humanitas University, 20090, Pieve Emanuele, Milan, Italy
- Humanitas Clinical and Research Center, 20089, Rozzano, Milan, Italy
| | - Giulia Soldà
- Department of Biomedical Sciences, Humanitas University, 20090, Pieve Emanuele, Milan, Italy
- Humanitas Clinical and Research Center, 20089, Rozzano, Milan, Italy
| | - Beatrice Bodega
- Istituto Nazionale di Genetica Molecolare "Romeo ed Enrica Invernizzi" (INGM), 20122, Milan, Italy
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182
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Mota-Gómez I, Lupiáñez DG. A (3D-Nuclear) Space Odyssey: Making Sense of Hi-C Maps. Genes (Basel) 2019; 10:E415. [PMID: 31146487 PMCID: PMC6627722 DOI: 10.3390/genes10060415] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 05/26/2019] [Accepted: 05/28/2019] [Indexed: 01/26/2023] Open
Abstract
Three-dimensional (3D)-chromatin organization is critical for proper enhancer-promoter communication and, therefore, for a precise execution of the transcriptional programs governing cellular processes. The emergence of Chromosome Conformation Capture (3C) methods, in particular Hi-C, has allowed the investigation of chromatin interactions on a genome-wide scale, revealing the existence of overlapping molecular mechanisms that we are just starting to decipher. Therefore, disentangling Hi-C signal into these individual components is essential to provide meaningful biological data interpretation. Here, we discuss emerging views on the molecular forces shaping the genome in 3D, with a focus on their respective contributions and interdependence. We discuss Hi-C data at both population and single-cell levels, thus providing criteria to interpret genomic function in the 3D-nuclear space.
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Affiliation(s)
- Irene Mota-Gómez
- Epigenetics and Sex Development Group, Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Berlin 10115, Germany.
| | - Darío G Lupiáñez
- Epigenetics and Sex Development Group, Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Berlin 10115, Germany.
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183
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The bipartite TAD organization of the X-inactivation center ensures opposing developmental regulation of Tsix and Xist. Nat Genet 2019; 51:1024-1034. [PMID: 31133748 PMCID: PMC6551226 DOI: 10.1038/s41588-019-0412-0] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Accepted: 04/04/2019] [Indexed: 01/08/2023]
Abstract
The mouse X-inactivation center (Xic) locus represents a powerful model for understanding the links between genome architecture and gene regulation, with the non-coding genes Xist and Tsix showing opposite developmental expression patterns while being organized as an overlapping sense/antisense unit. The Xic is organized into two topologically associating domains (TADs) but the role of this architecture in orchestrating cis-regulatory information remains elusive. To explore this, we generated genomic inversions that swap the Xist/Tsix transcriptional unit and place their promoters in each other’s TAD. We found that this led to a switch in their expression dynamics: Xist became precociously and ectopically up-regulated, both in male and female pluripotent cells, while Tsix expression aberrantly persisted during differentiation. The topological partitioning of the Xic is thus critical to ensure proper developmental timing of X inactivation. Our study illustrates how the genomic architecture of cis-regulatory landscapes can affect the regulation of mammalian developmental processes.
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184
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Lauer S, Gresham D. An evolving view of copy number variants. Curr Genet 2019; 65:1287-1295. [PMID: 31076843 DOI: 10.1007/s00294-019-00980-0] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 04/17/2019] [Accepted: 04/20/2019] [Indexed: 01/08/2023]
Abstract
Copy number variants (CNVs) are regions of the genome that vary in integer copy number. CNVs, which comprise both amplifications and deletions of DNA sequence, have been identified across all domains of life, from bacteria and archaea to plants and animals. CNVs are an important source of genetic diversity, and can drive rapid adaptive evolution and progression of heritable and somatic human diseases, such as cancer. However, despite their evolutionary importance and clinical relevance, CNVs remain understudied compared to single-nucleotide variants (SNVs). This is a consequence of the inherent difficulties in detecting CNVs at low-to-intermediate frequencies in heterogeneous populations of cells. Here, we discuss molecular methods used to detect CNVs, the limitations associated with using these techniques, and the application of new and emerging technologies that present solutions to these challenges. The goal of this short review and perspective is to highlight aspects of CNV biology that are understudied and define avenues for further research that address specific gaps in our knowledge of these complex alleles. We describe our recently developed method for CNV detection in which a fluorescent gene functions as a single-cell CNV reporter and present key findings from our evolution experiments in Saccharomyces cerevisiae. Using a CNV reporter, we found that CNVs are generated at a high rate and undergo selection with predictable dynamics across independently evolving replicate populations. Many CNVs appear to be generated through DNA replication-based processes that are mediated by the presence of short, interrupted, inverted-repeat sequences. Our results have important implications for the role of CNVs in evolutionary processes and the molecular mechanisms that underlie CNV formation. We discuss the possible extension of our method to other applications, including tracking the dynamics of CNVs in models of human tumors.
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Affiliation(s)
- Stephanie Lauer
- Institute for Systems Genetics, New York University Langone Health, New York, NY, USA
| | - David Gresham
- Center for Genomics and System Biology, Department of Biology, New York University, New York, NY, USA.
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185
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Torres-Ruiz R, Benítez-Burraco A, Martínez-Lage M, Rodríguez-Perales S, García-Bellido P. Functional characterization of two enhancers located downstream FOXP2. BMC MEDICAL GENETICS 2019; 20:65. [PMID: 31046704 PMCID: PMC6498672 DOI: 10.1186/s12881-019-0810-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Accepted: 04/17/2019] [Indexed: 01/01/2023]
Abstract
BACKGROUND Mutations in the coding region of FOXP2 are known to cause speech and language impairment. However, it is not clear how dysregulation of the gene contributes to language deficit. Interestingly, microdeletions of the region downstream the gene have been associated with cognitive deficits. METHODS Here, we investigate changes in FOXP2 expression in the SK-N-MC neuroblastoma human cell line after deletion by CRISPR-Cas9 of two enhancers located downstream of the gene. RESULTS Deletion of any of these two functional enhancers downregulates FOXP2, but also upregulates the closest 3' gene MDFIC. Because this effect is not statistically significant in a HEK 293 cell line, derived from the human kidney, both enhancers might confer a tissue specific regulation to both genes. We have also found that the deletion of any of these enhancers downregulates six well-known FOXP2 target genes in the SK-N-MC cell line. CONCLUSIONS We expect these findings contribute to a deeper understanding of how FOXP2 and MDFIC are regulated to pace neuronal development supporting cognition, speech and language.
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Affiliation(s)
- Raúl Torres-Ruiz
- Molecular Cytogenetics Group, Centro Nacional Investigaciones Oncológicas (CNIO), Madrid, Spain
| | - Antonio Benítez-Burraco
- Department of Spanish, Linguistics, and Theory of Literature (Linguistics), University of Seville, Seville, Spain.
| | - Marta Martínez-Lage
- Molecular Cytogenetics Group, Centro Nacional Investigaciones Oncológicas (CNIO), Madrid, Spain
| | | | - Paloma García-Bellido
- Faculty of Modern Languages, University of Oxford, Oxford, UK.,Faculty of Linguistics, Philology and Phonetics, University of Oxford, Oxford, UK
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186
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Pellestor F, Gatinois V. Chromoanasynthesis: another way for the formation of complex chromosomal abnormalities in human reproduction. Hum Reprod 2019; 33:1381-1387. [PMID: 30325427 DOI: 10.1093/humrep/dey231] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Indexed: 12/24/2022] Open
Abstract
Chromoanasynthesis has been described as a novel cause of massive constitutional chromosomal rearrangements. Based on DNA replication machinery defects, chromoanasynthesis is characterized by the presence of chromosomal duplications and triplications locally clustered on one single chromosome, or a few chromosomes, associated with various other types of structural rearrangements. Two distinct mechanisms have been described for the formation of these chaotic genomic disorders, i.e. the fork stalling and template switching and the microhomology-mediated break-induced replication. Micronucleus-based processes have been evidenced as a causative mechanism, thus, highlighting the close connection between segregation errors and structural rearrangements. Accumulating data indicate that chromoanasynthesis is operating in human germline cells and during early embryonic development. The development of new tools for quantifying chromoanasynthesis events should provide further insight into the impact of this catastrophic cellular phenomenon in human reproduction.
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Affiliation(s)
- Franck Pellestor
- Unit of Chromosomal Genetics, Department of Medical Genetics, Arnaud de Villeneuve Hospital, Montpellier CHU, Montpellier, France
| | - Vincent Gatinois
- Unit of Chromosomal Genetics, Department of Medical Genetics, Arnaud de Villeneuve Hospital, Montpellier CHU, Montpellier, France
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187
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Bejjani F, Evanno E, Zibara K, Piechaczyk M, Jariel-Encontre I. The AP-1 transcriptional complex: Local switch or remote command? Biochim Biophys Acta Rev Cancer 2019; 1872:11-23. [PMID: 31034924 DOI: 10.1016/j.bbcan.2019.04.003] [Citation(s) in RCA: 159] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 04/19/2019] [Accepted: 04/22/2019] [Indexed: 12/19/2022]
Abstract
The ubiquitous family of AP-1 dimeric transcription complexes is involved in virtually all cellular and physiological functions. It is paramount for cells to reprogram gene expression in response to cues of many sorts and is involved in many tumorigenic processes. How AP-1 controls gene transcription has largely remained elusive till recently. The advent of the "omics" technologies permitting genome-wide studies of transcription factors has however changed and improved our view of AP-1 mechanistical actions. If these studies confirm that AP-1 can sometimes act as a local transcriptional switch operating in the vicinity of transcription start sites (TSS), they strikingly indicate that AP-1 principally operates as a remote command binding to distal enhancers, placing chromatin architecture dynamics at the heart of its transcriptional actions. They also unveil novel constraints operating on AP-1, as well as novel mechanisms used to regulate gene expression via transcription-pioneering-, chromatin-remodeling- and chromatin accessibility maintenance effects.
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Affiliation(s)
- Fabienne Bejjani
- Equipe Labellisée Ligue Nationale contre le Cancer, Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France; PRASE and Biology Department, Faculty of Sciences - I, Lebanese University, Beirut, Lebanon
| | - Emilie Evanno
- Equipe Labellisée Ligue Nationale contre le Cancer, Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Kazem Zibara
- PRASE and Biology Department, Faculty of Sciences - I, Lebanese University, Beirut, Lebanon
| | - Marc Piechaczyk
- Equipe Labellisée Ligue Nationale contre le Cancer, Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France.
| | - Isabelle Jariel-Encontre
- Equipe Labellisée Ligue Nationale contre le Cancer, Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France.
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188
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Paulsen J, Liyakat Ali TM, Nekrasov M, Delbarre E, Baudement MO, Kurscheid S, Tremethick D, Collas P. Long-range interactions between topologically associating domains shape the four-dimensional genome during differentiation. Nat Genet 2019; 51:835-843. [PMID: 31011212 DOI: 10.1038/s41588-019-0392-0] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Accepted: 03/12/2019] [Indexed: 01/01/2023]
Abstract
Genomic information is selectively used to direct spatial and temporal gene expression during differentiation. Interactions between topologically associating domains (TADs) and between chromatin and the nuclear lamina organize and position chromosomes in the nucleus. However, how these genomic organizers together shape genome architecture is unclear. Here, using a dual-lineage differentiation system, we report long-range TAD-TAD interactions that form constitutive and variable TAD cliques. A differentiation-coupled relationship between TAD cliques and lamina-associated domains suggests that TAD cliques stabilize heterochromatin at the nuclear periphery. We also provide evidence of dynamic TAD cliques during mouse embryonic stem-cell differentiation and somatic cell reprogramming and of inter-TAD associations in single-cell high-resolution chromosome conformation capture (Hi-C) data. TAD cliques represent a level of four-dimensional genome conformation that reinforces the silencing of repressed developmental genes.
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Affiliation(s)
- Jonas Paulsen
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Tharvesh M Liyakat Ali
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Maxim Nekrasov
- Department of Genome Sciences, The John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory, Australia.,Biomolecular Research Facility, The John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Erwan Delbarre
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Marie-Odile Baudement
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Sebastian Kurscheid
- Department of Genome Sciences, The John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - David Tremethick
- Department of Genome Sciences, The John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory, Australia.
| | - Philippe Collas
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway. .,Norwegian Center for Stem Cell Research, Department of Immunology and Transfusion Medicine, Oslo University Hospital, Oslo, Norway.
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189
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Laugsch M, Bartusel M, Rehimi R, Alirzayeva H, Karaolidou A, Crispatzu G, Zentis P, Nikolic M, Bleckwehl T, Kolovos P, van Ijcken WFJ, Šarić T, Koehler K, Frommolt P, Lachlan K, Baptista J, Rada-Iglesias A. Modeling the Pathological Long-Range Regulatory Effects of Human Structural Variation with Patient-Specific hiPSCs. Cell Stem Cell 2019; 24:736-752.e12. [PMID: 30982769 DOI: 10.1016/j.stem.2019.03.004] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 01/03/2019] [Accepted: 03/06/2019] [Indexed: 11/18/2022]
Abstract
The pathological consequences of structural variants disrupting 3D genome organization can be difficult to elucidate in vivo due to differences in gene dosage sensitivity between mice and humans. This is illustrated by branchiooculofacial syndrome (BOFS), a rare congenital disorder caused by heterozygous mutations within TFAP2A, a neural crest regulator for which humans, but not mice, are haploinsufficient. Here, we present a BOFS patient carrying a heterozygous inversion with one breakpoint located within a topologically associating domain (TAD) containing enhancers essential for TFAP2A expression in human neural crest cells (hNCCs). Using patient-specific hiPSCs, we show that, although the inversion shuffles the TFAP2A hNCC enhancers with novel genes within the same TAD, this does not result in enhancer adoption. Instead, the inversion disconnects one TFAP2A allele from its cognate enhancers, leading to monoallelic and haploinsufficient TFAP2A expression in patient hNCCs. Our work illustrates the power of hiPSC differentiation to unveil long-range pathomechanisms.
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Affiliation(s)
- Magdalena Laugsch
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany; Institute of Human Genetics, CMMC, University Hospital Cologne, Cologne, Germany
| | - Michaela Bartusel
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Rizwan Rehimi
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Hafiza Alirzayeva
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Agathi Karaolidou
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Giuliano Crispatzu
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Peter Zentis
- Cluster of Excellence Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Milos Nikolic
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Tore Bleckwehl
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Petros Kolovos
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
| | | | - Tomo Šarić
- Center for Physiology and Pathophysiology, Institute for Neurophysiology, Medical Faculty, University of Cologne, Cologne, Germany
| | - Katrin Koehler
- Department of Pediatrics, University Clinic Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Peter Frommolt
- Cluster of Excellence Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Katherine Lachlan
- Human Genetics & Genomic Medicine, University of Southampton, Southampton General Hospital, Southampton, UK; Clinical Genetics Service, University Hospital Southampton NHS Foundation Trust, Princess Anne Hospital, Southampton, UK
| | - Julia Baptista
- Molecular Genetics Department, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK; Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK.
| | - Alvaro Rada-Iglesias
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany; Cluster of Excellence Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany; Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), University of Cantabria, Cantabria, Spain.
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190
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Szabo Q, Bantignies F, Cavalli G. Principles of genome folding into topologically associating domains. SCIENCE ADVANCES 2019; 5:eaaw1668. [PMID: 30989119 PMCID: PMC6457944 DOI: 10.1126/sciadv.aaw1668] [Citation(s) in RCA: 327] [Impact Index Per Article: 65.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 02/20/2019] [Indexed: 05/12/2023]
Abstract
This review discusses the features of TADs across species, and their role in chromosome organization, genome function, and evolution.
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Affiliation(s)
- Quentin Szabo
- Institute of Human Genetics, CNRS and University of Montpellier, Montpellier, France
| | - Frédéric Bantignies
- Institute of Human Genetics, CNRS and University of Montpellier, Montpellier, France
| | - Giacomo Cavalli
- Institute of Human Genetics, CNRS and University of Montpellier, Montpellier, France
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191
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Complex epigenetic regulation of alkaloid biosynthesis and host interaction by heterochromatin protein I in a fungal endophyte-plant symbiosis. Fungal Genet Biol 2019; 125:71-83. [DOI: 10.1016/j.fgb.2019.02.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 01/29/2019] [Accepted: 02/03/2019] [Indexed: 01/10/2023]
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192
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Seselgyte R, Bryant D, Demetriou C, Ishida M, Peskett E, Moreno N, Morrogh D, Sell D, Lees M, Farrall M, Moore GE, Sommerlad B, Pauws E, Stanier P. Disruption of FOXF2 as a Likely Cause of Absent Uvula in an Egyptian Family. J Dent Res 2019; 98:659-665. [PMID: 30917284 DOI: 10.1177/0022034519837245] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
This study investigated the genetic basis of an unusual autosomal dominant phenotype characterized by familial absent uvula, with a short posterior border of the soft palate, abnormal tonsillar pillars, and velopharyngeal insufficiency. Cytogenetic analysis and single-nucleotide polymorphism-based linkage analysis were investigated in a 4-generation family with 8 affected individuals. Whole exome sequencing data were overlaid, and segregation analysis identified a single missense variant, p.Q433P in the FOXF2 transcription factor, that fully segregated with the phenotype. This was found to be in linkage disequilibrium with a small 6p25.3 tandem duplication affecting FOXC1 and GMDS. Notably, the copy number imbalances of this region are commonly associated with pathologies that are not present in this family. Bioinformatic predictions with luciferase reporter studies of the FOXF2 missense variant indicated a negative impact, affecting both protein stability and transcriptional activation. Foxf 2 is expressed in the posterior mouse palate, and knockout animals develop an overt cleft palate. Since mice naturally lack the structural equivalent of the uvula, we demonstrated FOXF2 expression in the developing human uvula. Decipher also records 2 individuals with hypoplastic or bifid uvulae with copy number variants affecting FOXF2. Nevertheless, given cosegregation with the 6p25.3 duplications, we cannot rule out a combined effect of these gains and the missense variant on FOXF2 function, which may account for the rare palate phenotype observed.
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Affiliation(s)
- R Seselgyte
- 1 Genetics and Genomic Medicine, UCL GOS Institute of Child Health, London, UK
| | - D Bryant
- 1 Genetics and Genomic Medicine, UCL GOS Institute of Child Health, London, UK
| | - C Demetriou
- 1 Genetics and Genomic Medicine, UCL GOS Institute of Child Health, London, UK
| | - M Ishida
- 1 Genetics and Genomic Medicine, UCL GOS Institute of Child Health, London, UK
| | - E Peskett
- 1 Genetics and Genomic Medicine, UCL GOS Institute of Child Health, London, UK
| | - N Moreno
- 2 Developmental Biology and Cancer, UCL GOS Institute of Child Health, London, UK
| | - D Morrogh
- 3 NE Thames Regional Genetics Service Laboratory, Great Ormond Street Hospital NHS Trust, London, UK
| | - D Sell
- 4 North Thames Cleft Centre, St Andrew's Centre, Broomfield Hospital, Chelmsford, UK; Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - M Lees
- 4 North Thames Cleft Centre, St Andrew's Centre, Broomfield Hospital, Chelmsford, UK; Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK.,5 Department of Clinical Genetics, Great Ormond Street Hospital NHS Trust, London, UK
| | - M Farrall
- 6 Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - G E Moore
- 1 Genetics and Genomic Medicine, UCL GOS Institute of Child Health, London, UK
| | - B Sommerlad
- 4 North Thames Cleft Centre, St Andrew's Centre, Broomfield Hospital, Chelmsford, UK; Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - E Pauws
- 2 Developmental Biology and Cancer, UCL GOS Institute of Child Health, London, UK
| | - P Stanier
- 1 Genetics and Genomic Medicine, UCL GOS Institute of Child Health, London, UK
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193
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Huynh L, Hormozdiari F. TAD fusion score: discovery and ranking the contribution of deletions to genome structure. Genome Biol 2019; 20:60. [PMID: 30898144 PMCID: PMC6427865 DOI: 10.1186/s13059-019-1666-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 03/01/2019] [Indexed: 11/17/2022] Open
Abstract
Deletions that fuse two adjacent topologically associating domains (TADs) can cause severe developmental disorders. We provide a formal method to quantify deletions based on their potential disruption of the three-dimensional genome structure, denoted as the TAD fusion score. Furthermore, we show that deletions that cause TAD fusion are rare and under negative selection in the general population. Finally, we show that our method correctly gives higher scores to deletions reported to cause various disorders, including developmental disorders and cancer, in comparison to the deletions reported in the 1000 Genomes Project. The TAD fusion score tool is publicly available at https://github.com/HormozdiariLab/TAD-fusion-score .
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Affiliation(s)
| | - Fereydoun Hormozdiari
- Genome Center, UC Davis, Davis, USA.
- UC Davis MIND Institute, Sacramento, USA.
- Department of Biochemistry and Molecular Medicine, UC Davis, Sacramento, USA.
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194
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Fritz AJ, Gillis NE, Gerrard DL, Rodriguez PD, Hong D, Rose JT, Ghule PN, Bolf EL, Gordon JA, Tye CE, Boyd JR, Tracy KM, Nickerson JA, van Wijnen AJ, Imbalzano AN, Heath JL, Frietze SE, Zaidi SK, Carr FE, Lian JB, Stein JL, Stein GS. Higher order genomic organization and epigenetic control maintain cellular identity and prevent breast cancer. Genes Chromosomes Cancer 2019; 58:484-499. [PMID: 30873710 DOI: 10.1002/gcc.22731] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 01/07/2019] [Accepted: 01/07/2019] [Indexed: 12/24/2022] Open
Abstract
Cells establish and sustain structural and functional integrity of the genome to support cellular identity and prevent malignant transformation. In this review, we present a strategic overview of epigenetic regulatory mechanisms including histone modifications and higher order chromatin organization (HCO) that are perturbed in breast cancer onset and progression. Implications for dysfunctions that occur in hormone regulation, cell cycle control, and mitotic bookmarking in breast cancer are considered, with an emphasis on epithelial-to-mesenchymal transition and cancer stem cell activities. The architectural organization of regulatory machinery is addressed within the contexts of translating cancer-compromised genomic organization to advances in breast cancer risk assessment, diagnosis, prognosis, and identification of novel therapeutic targets with high specificity and minimal off target effects.
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Affiliation(s)
- A J Fritz
- Department of Biochemistry, Larner College of Medicine, University of Vermont, Burlington, Vermont.,University of Vermont Cancer Center, Burlington, Vermont
| | - N E Gillis
- University of Vermont Cancer Center, Burlington, Vermont.,Department of Pharmacology, Larner college of Medicine, University of Vermont, Burlington, Vermont
| | - D L Gerrard
- Cellular Molecular Biomedical Sciences Program, University of Vermont, Burlington, Vermont.,Department of Biomedical and Health Sciences, University of Vermont, Burlington, Vermont
| | - P D Rodriguez
- Cellular Molecular Biomedical Sciences Program, University of Vermont, Burlington, Vermont.,Department of Biomedical and Health Sciences, University of Vermont, Burlington, Vermont
| | - D Hong
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts
| | - J T Rose
- Department of Biochemistry, Larner College of Medicine, University of Vermont, Burlington, Vermont.,University of Vermont Cancer Center, Burlington, Vermont
| | - P N Ghule
- Department of Biochemistry, Larner College of Medicine, University of Vermont, Burlington, Vermont.,University of Vermont Cancer Center, Burlington, Vermont
| | - E L Bolf
- University of Vermont Cancer Center, Burlington, Vermont.,Department of Pharmacology, Larner college of Medicine, University of Vermont, Burlington, Vermont
| | - J A Gordon
- Department of Biochemistry, Larner College of Medicine, University of Vermont, Burlington, Vermont.,University of Vermont Cancer Center, Burlington, Vermont
| | - C E Tye
- Department of Biochemistry, Larner College of Medicine, University of Vermont, Burlington, Vermont.,University of Vermont Cancer Center, Burlington, Vermont
| | - J R Boyd
- Department of Biochemistry, Larner College of Medicine, University of Vermont, Burlington, Vermont.,University of Vermont Cancer Center, Burlington, Vermont
| | - K M Tracy
- Department of Biochemistry, Larner College of Medicine, University of Vermont, Burlington, Vermont.,University of Vermont Cancer Center, Burlington, Vermont
| | - J A Nickerson
- Division of Genes and Development of the Department of Pediatrics, University of Massachusetts Medical School, Worcester, Massachusetts
| | - A J van Wijnen
- Orthopedic Surgery and Biochemistry and Molecular Biology, Mayo Clinic Minnesota, Rochester, Minnesota
| | - A N Imbalzano
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts
| | - J L Heath
- Department of Biochemistry, Larner College of Medicine, University of Vermont, Burlington, Vermont.,University of Vermont Cancer Center, Burlington, Vermont.,Department of Pediatrics, Larner College of Medicine, University of Vermont, Burlington, Vermont
| | - S E Frietze
- Cellular Molecular Biomedical Sciences Program, University of Vermont, Burlington, Vermont.,Department of Biomedical and Health Sciences, University of Vermont, Burlington, Vermont
| | - S K Zaidi
- Department of Biochemistry, Larner College of Medicine, University of Vermont, Burlington, Vermont.,University of Vermont Cancer Center, Burlington, Vermont
| | - F E Carr
- Department of Biochemistry, Larner College of Medicine, University of Vermont, Burlington, Vermont.,University of Vermont Cancer Center, Burlington, Vermont.,Department of Pharmacology, Larner college of Medicine, University of Vermont, Burlington, Vermont
| | - J B Lian
- Department of Biochemistry, Larner College of Medicine, University of Vermont, Burlington, Vermont.,University of Vermont Cancer Center, Burlington, Vermont
| | - J L Stein
- Department of Biochemistry, Larner College of Medicine, University of Vermont, Burlington, Vermont.,University of Vermont Cancer Center, Burlington, Vermont
| | - G S Stein
- Department of Biochemistry, Larner College of Medicine, University of Vermont, Burlington, Vermont.,University of Vermont Cancer Center, Burlington, Vermont
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195
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Pellestor F. Chromoanagenesis: cataclysms behind complex chromosomal rearrangements. Mol Cytogenet 2019; 12:6. [PMID: 30805029 PMCID: PMC6371609 DOI: 10.1186/s13039-019-0415-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 01/17/2019] [Indexed: 12/21/2022] Open
Abstract
Background During the last decade, genome sequencing projects in cancer genomes as well as in patients with congenital diseases and healthy individuals have led to the identification of new types of massive chromosomal rearrangements arising during single chaotic cellular events. These unanticipated catastrophic phenomenon are termed chromothripsis, chromoanasynthesis and chromoplexis., and are grouped under the name of “chromoanagenesis”. Results For each process, several specific features have been described, allowing each phenomenon to be distinguished from each other and to understand its mechanism of formation and to better understand its aetiology. Thus, chromothripsis derives from chromosome shattering followed by the random restitching of chromosomal fragments with low copy-number change whereas chromoanasynthesis results from erroneous DNA replication of a chromosome through serial fork stalling and template switching with variable copy-number gains, and chromoplexy refers to the occurrence of multiple inter-and intra-chromosomal translocations and deletions with little or no copy-number alterations in prostate cancer. Cumulating data and experimental models have shown that chromothripsis and chromoanasynthesis may essentially result from lagging chromosome encapsulated in micronuclei or telomere attrition and end-to-end telomere fusion. Conclusion The concept of chromanagenesis has provided new insight into the aetiology of complex structural rearrangements, the connection between defective cell cycle progression and genomic instability, and the complexity of cancer evolution. Increasing reported chromoanagenesis events suggest that these chaotic mechanisms are probably much more frequent than anticipated.
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Affiliation(s)
- Franck Pellestor
- Unit of Chromosomal Genetics, Department of Medical Genetics, Arnaud de Villeneuve Hospital, Montpellier CHRU, 371, avenue du Doyen Gaston Giraud, 34295 Montpellier cedex 5, France.,INSERM 1183 Unit «Genome and Stem Cell Plasticity in Development and Aging », Institute of Regenerative Medicine and Biotherapies, St Eloi Hospital, Montpellier, France
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196
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van Meurs JB, Boer CG, Lopez-Delgado L, Riancho JA. Role of Epigenomics in Bone and Cartilage Disease. J Bone Miner Res 2019; 34:215-230. [PMID: 30715766 DOI: 10.1002/jbmr.3662] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Revised: 12/03/2018] [Accepted: 01/02/2019] [Indexed: 12/14/2022]
Abstract
Phenotypic variation in skeletal traits and diseases is the product of genetic and environmental factors. Epigenetic mechanisms include information-containing factors, other than DNA sequence, that cause stable changes in gene expression and are maintained during cell divisions. They represent a link between environmental influences, genome features, and the resulting phenotype. The main epigenetic factors are DNA methylation, posttranslational changes of histones, and higher-order chromatin structure. Sometimes non-coding RNAs, such as microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), are also included in the broad term of epigenetic factors. There is rapidly expanding experimental evidence for a role of epigenetic factors in the differentiation of bone cells and the pathogenesis of skeletal disorders, such as osteoporosis and osteoarthritis. However, different from genetic factors, epigenetic signatures are cell- and tissue-specific and can change with time. Thus, elucidating their role has particular difficulties, especially in human studies. Nevertheless, epigenomewide association studies are beginning to disclose some disease-specific patterns that help to understand skeletal cell biology and may lead to development of new epigenetic-based biomarkers, as well as new drug targets useful for treating diffuse and localized disorders. Here we provide an overview and update of recent advances on the role of epigenomics in bone and cartilage diseases. © 2019 American Society for Bone and Mineral Research.
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Affiliation(s)
| | - Cindy G Boer
- Department of Internal Medicine, Erasmus MC, Rotterdam, The Netherlands
| | - Laura Lopez-Delgado
- Department of Internal Medicine, Hospital U M Valdecilla, University of Cantabria, IDIVAL, Santander, Spain
| | - Jose A Riancho
- Department of Internal Medicine, Hospital U M Valdecilla, University of Cantabria, IDIVAL, Santander, Spain
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197
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Olszewska M, Wiland E, Huleyuk N, Fraczek M, Midro AT, Zastavna D, Kurpisz M. Chromosome (re)positioning in spermatozoa of fathers and sons - carriers of reciprocal chromosome translocation (RCT). BMC Med Genomics 2019; 12:30. [PMID: 30709354 PMCID: PMC6359769 DOI: 10.1186/s12920-018-0470-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 12/28/2018] [Indexed: 01/05/2023] Open
Abstract
Background Non-random chromosome positioning has been observed in the nuclei of several different tissue types, including human spermatozoa. The nuclear arrangement of chromosomes can be altered in men with decreased semen parameters or increased DNA fragmentation and in males with chromosomal numerical or structural aberrations. An aim of this study was to determine whether and how the positioning of nine chromosome centromeres was (re)arranged in the spermatozoa of fathers and sons – carriers of the same reciprocal chromosome translocation (RCT). Methods Fluorescence in situ hybridization (FISH) was applied to analyse the positioning of sperm chromosomes in a group of 13 carriers of 11 RCTs, including two familial RCT cases: t(4;5) and t(7;10), followed by analysis of eight control individuals. Additionally, sperm chromatin integrity was evaluated using TUNEL and Aniline Blue techniques. Results In the analysed familial RCT cases, repositioning of the chromosomes occurred in a similar way when compared to the data generated in healthy controls, even if some differences between father and son were further observed. These differences might have arisen from various statuses of sperm chromatin disintegration. Conclusions Nuclear topology appears as another aspect of epigenetic genomic regulation that may influence DNA functioning. We have re-documented that chromosomal positioning is defined in control males and that a particular RCT is reflected in the individual pattern of chromosomal topology. The present study examining the collected RCT group, including two familial cases, additionally showed that chromosomal factors (karyotype and hyperhaploidy) have superior effects, strongly influencing the chromosomal topology, when confronted with sperm chromatin integrity components (DNA fragmentation or chromatin deprotamination). Electronic supplementary material The online version of this article (10.1186/s12920-018-0470-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Marta Olszewska
- Institute of Human Genetics, Polish Academy of Sciences, Strzeszynska 32, 60-479, Poznan, Poland
| | - Ewa Wiland
- Institute of Human Genetics, Polish Academy of Sciences, Strzeszynska 32, 60-479, Poznan, Poland
| | - Nataliya Huleyuk
- National Academy of Medical Sciences of Ukraine, Institute of Hereditary Pathology, Lysenko Str. 31a, Lviv, 79000, Ukraine
| | - Monika Fraczek
- Institute of Human Genetics, Polish Academy of Sciences, Strzeszynska 32, 60-479, Poznan, Poland
| | - Alina T Midro
- Department of Clinical Genetics, Medical University of Bialystok, Waszyngtona 13, PO Box 22, 15-089, Bialystok, Poland
| | - Danuta Zastavna
- National Academy of Medical Sciences of Ukraine, Institute of Hereditary Pathology, Lysenko Str. 31a, Lviv, 79000, Ukraine.,Department of Biotechnology and Bioinformatics, Faculty of Chemistry, Rzeszow University of Technology, Al. Powstancow Warszawy 6, 35-959, Rzeszow, Poland
| | - Maciej Kurpisz
- Institute of Human Genetics, Polish Academy of Sciences, Strzeszynska 32, 60-479, Poznan, Poland.
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198
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Denisenko E, Guler R, Mhlanga M, Suzuki H, Brombacher F, Schmeier S. Transcriptionally induced enhancers in the macrophage immune response to Mycobacterium tuberculosis infection. BMC Genomics 2019; 20:71. [PMID: 30669987 PMCID: PMC6341744 DOI: 10.1186/s12864-019-5450-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Accepted: 01/11/2019] [Indexed: 12/18/2022] Open
Abstract
Background Tuberculosis is a life-threatening infectious disease caused by Mycobacterium tuberculosis (M.tb). M.tb subverts host immune responses to build a favourable niche and survive inside of host macrophages. Macrophages can control or eliminate the infection, if acquire appropriate functional phenotypes. Transcriptional regulation is a key process that governs the activation and maintenance of these phenotypes. Among the factors orchestrating transcriptional regulation during M.tb infection, transcriptional enhancers still remain unexplored. Results We analysed transcribed enhancers in M.tb-infected mouse bone marrow-derived macrophages. We established a link between known M.tb-responsive transcription factors and transcriptional activation of enhancers and their target genes. Our data suggest that enhancers might drive macrophage response via transcriptional activation of key immune genes, such as Tnf, Tnfrsf1b, Irg1, Hilpda, Ccl3, and Ccl4. We report enhancers acquiring transcription de novo upon infection. Finally, we link highly transcriptionally induced enhancers to activation of genes with previously unappreciated roles in M.tb infection, such as Fbxl3, Tapt1, Edn1, and Hivep1. Conclusions Our findings suggest the importance of macrophage host transcriptional enhancers during M.tb infection. Our study extends current knowledge of the regulation of macrophage responses to M.tb infection and provides a basis for future functional studies on enhancer-gene interactions in this process. Electronic supplementary material The online version of this article (10.1186/s12864-019-5450-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Elena Denisenko
- Massey University, Institute of Natural and Mathematical Sciences, Albany, Auckland, New Zealand
| | - Reto Guler
- Division of Immunology and South African Medical Research Council (SAMRC) Immunology of Infectious Diseases, Faculty of Health Sciences, Institute of Infectious Diseases and Molecular Medicine (IDM), University of Cape Town, Cape Town, South Africa.,International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town Component, Cape Town, South Africa
| | - Musa Mhlanga
- Gene Expression and Biophysics Group, CSIR Synthetic Biology ERA, Pretoria, South Africa.,Division of Chemical Systems and Synthetic Biology, Institute of Infectious Diseases and Molecular Medicine (IDM), University of Cape Town, Cape Town, South Africa.,Gene Expression and Biophysics Unit, Instituto de Medicina Molecular, Faculdade de Medicina Universidade de Lisboa, Lisbon, Portugal
| | - Harukazu Suzuki
- Division of Genomic Technologies, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Japan
| | - Frank Brombacher
- Division of Immunology and South African Medical Research Council (SAMRC) Immunology of Infectious Diseases, Faculty of Health Sciences, Institute of Infectious Diseases and Molecular Medicine (IDM), University of Cape Town, Cape Town, South Africa.,International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town Component, Cape Town, South Africa
| | - Sebastian Schmeier
- Massey University, Institute of Natural and Mathematical Sciences, Albany, Auckland, New Zealand.
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199
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Gurova KV. Chromatin Stability as a Target for Cancer Treatment. Bioessays 2019; 41:e1800141. [PMID: 30566250 PMCID: PMC6522245 DOI: 10.1002/bies.201800141] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 10/29/2018] [Indexed: 12/14/2022]
Abstract
In this essay, I propose that DNA-binding anti-cancer drugs work more via chromatin disruption than DNA damage. Success of long-awaited drugs targeting cancer-specific drivers is limited by the heterogeneity of tumors. Therefore, chemotherapy acting via universal targets (e.g., DNA) is still the mainstream treatment for cancer. Nevertheless, the problem with targeting DNA is insufficient efficacy due to high toxicity. I propose that this problem stems from the presumption that DNA damage is critical for the anti-cancer activity of these drugs. DNA in cells exists as chromatin, and many DNA-targeting drugs alter chromatin structure by destabilizing nucleosomes and inducing histone eviction from chromatin. This effect has been largely ignored because DNA damage is seen as the major reason for anti-cancer activity. I discuss how DNA-binding molecules destabilize chromatin, why this effect is more toxic to tumoral than normal cells, and why cells die as a result of chromatin destabilization.
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Affiliation(s)
- Katerina V Gurova
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, NY, 14263. Tel 1-716-845-4760,
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200
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Troll CJ, Putnam NH, Hartley PD, Rice B, Blanchette M, Siddiqui S, Ganbat JO, Powers MP, Ramakrishnan R, Kunder CA, Bustamante CD, Zehnder JL, Green RE, Costa HA. Structural Variation Detection by Proximity Ligation from Formalin-Fixed, Paraffin-Embedded Tumor Tissue. J Mol Diagn 2018; 21:375-383. [PMID: 30605765 DOI: 10.1016/j.jmoldx.2018.11.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 10/23/2018] [Accepted: 11/17/2018] [Indexed: 12/11/2022] Open
Abstract
The clinical management and therapy of many solid tumor malignancies depends on detection of medically actionable or diagnostically relevant genetic variation. However, a principal challenge for genetic assays from tumors is the fragmented and chemically damaged state of DNA in formalin-fixed, paraffin-embedded (FFPE) samples. From highly fragmented DNA and RNA there is no current technology for generating long-range DNA sequence data as is required to detect genomic structural variation or long-range genotype phasing. We have developed a high-throughput chromosome conformation capture approach for FFPE samples that we call Fix-C, which is similar in concept to Hi-C. Fix-C enables structural variation detection from archival FFPE samples. This method was applied to 15 clinical adenocarcinoma- and sarcoma-positive control specimens spanning a broad range of tumor purities. In this panel, Fix-C analysis achieves a 90% concordance rate with fluorescence in situ hybridization assays, the current clinical gold standard. In addition, novel structural variation undetected by other methods could be identified, and long-range chromatin configuration information recovered from these FFPE samples harboring highly degraded DNA. This powerful approach will enable detailed resolution of global genome rearrangement events during cancer progression from FFPE material and will inform the development of targeted molecular diagnostic assays for patient care.
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Affiliation(s)
- Christopher J Troll
- Division of Research and Development, Dovetail Genomics, LLC, Santa Cruz, California
| | - Nicholas H Putnam
- Division of Research and Development, Dovetail Genomics, LLC, Santa Cruz, California
| | - Paul D Hartley
- Division of Research and Development, Dovetail Genomics, LLC, Santa Cruz, California
| | - Brandon Rice
- Division of Research and Development, Dovetail Genomics, LLC, Santa Cruz, California
| | - Marco Blanchette
- Division of Research and Development, Dovetail Genomics, LLC, Santa Cruz, California
| | - Sameed Siddiqui
- Division of Research and Development, Dovetail Genomics, LLC, Santa Cruz, California
| | - Javkhlan-Ochir Ganbat
- Division of Research and Development, Dovetail Genomics, LLC, Santa Cruz, California
| | - Martin P Powers
- Division of Research and Development, Dovetail Genomics, LLC, Santa Cruz, California
| | - Ramesh Ramakrishnan
- Division of Research and Development, Dovetail Genomics, LLC, Santa Cruz, California
| | - Christian A Kunder
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Carlos D Bustamante
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, California; Department of Genetics, Stanford University School of Medicine, Stanford, California
| | - James L Zehnder
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Richard E Green
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California.
| | - Helio A Costa
- Department of Pathology, Stanford University School of Medicine, Stanford, California; Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, California.
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