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Zhuang J, Zhang N, Wang J, Jiang Y, Zhang H, Chen C. Initial clinical and molecular investigation of 20q13.33 microdeletion with 17q25.3/14q32.31q32.33 microduplication in Chinese pediatric patients. Mol Genet Genomic Med 2024; 12:e2429. [PMID: 38553934 PMCID: PMC10980884 DOI: 10.1002/mgg3.2429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 03/01/2024] [Accepted: 03/19/2024] [Indexed: 04/02/2024] Open
Abstract
BACKGROUND Limited research has been conducted regarding the elucidation of genotype-phenotype correlations within the 20q13.33 region. The genotype-phenotype association of 20q13.33 microdeletion remains inadequately understood. In the present study, two novel cases of 20q13.33 microdeletion were introduced, with the objective of enhancing understanding of the genotype-phenotype relationship. METHODS Two unrelated patients with various abnormal clinical phenotypes from Fujian province Southeast China were enrolled in the present study. Karyotype analysis and chromosomal microarray analysis (CMA) were performed to investigate chromosomal abnormalities and copy number variants. RESULTS The results of high-resolution G-banding karyotype analysis elicited a 46,XY,der(20)add(20)(q13.3) in Patient 1. This patient exhibited various clinical manifestations, such as global developmental delay, intellectual disability, seizures, and other congenital diseases. Subsequently, a 1.0-Mb deletion was identified in the 20q13.33 region alongside a 5.2-Mb duplication in the 14q32.31q32.33 region. In Patient 2, CMA results revealed a 1.8-Mb deletion in the 20q13.33 region with a 4.8-Mb duplication of 17q25.3. The patient exhibited additional abnormal clinical features, including micropenis, congenital heart disease, and a distinctive crying pattern characterized by a crooked mouth. CONCLUSION In the present study, for the first time, an investigation was conducted into two novel cases of 20q13.33 microdeletion with microduplications in the 17q25.3 and 14q32.31q32.33 regions in the Chinese population. The presence of micropenis may be attributed to the 20q13.33 microdeletion, potentially expanding the phenotypic spectrum associated with this deletion.
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Affiliation(s)
- Jianlong Zhuang
- Prenatal Diagnosis Center, Quanzhou Women's and Children's HospitalQuanzhouChina
| | - Na Zhang
- Prenatal Diagnosis Center, Quanzhou Women's and Children's HospitalQuanzhouChina
| | - Junyu Wang
- Prenatal Diagnosis Center, Quanzhou Women's and Children's HospitalQuanzhouChina
| | - Yuying Jiang
- Prenatal Diagnosis Center, Quanzhou Women's and Children's HospitalQuanzhouChina
| | - Hegan Zhang
- Department of GynecologyQuanzhou Women's and Children's HospitalQuanzhouChina
| | - Chunnuan Chen
- Department of NeurologyThe Second Affiliated Hospital of Fujian Medical UniversityQuanzhouChina
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Rittenhouse NL, Dowen JM. Cohesin regulation and roles in chromosome structure and function. Curr Opin Genet Dev 2024; 85:102159. [PMID: 38382406 PMCID: PMC10947815 DOI: 10.1016/j.gde.2024.102159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 01/22/2024] [Accepted: 01/27/2024] [Indexed: 02/23/2024]
Abstract
Chromosome structure regulates DNA-templated processes such as transcription of genes. Dynamic changes to chromosome structure occur during development and in disease contexts. The cohesin complex is a molecular motor that regulates chromosome structure by generating DNA loops that bring two distal genomic sites into close spatial proximity. There are many open questions regarding the formation and dissolution of DNA loops, as well as the role(s) of DNA loops in regulating transcription of the interphase genome. This review focuses on recent discoveries that provide molecular insights into the role of cohesin and chromosome structure in gene transcription during development and disease.
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Affiliation(s)
- Natalie L Rittenhouse
- Curriculum in Genetics & Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jill M Dowen
- Department of Biophysics & Biochemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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AlGethami HJ, Breitbart S, Warsi NM, Fasano A, Ibrahim GM, Gorodetsky C. Severe Pediatric Dystonia Responding to Deep Brain Stimulation in 22q11.2 Microduplication Syndrome: Rare Clinical Presentation. Mov Disord Clin Pract 2024; 11:309-311. [PMID: 38196101 PMCID: PMC10928346 DOI: 10.1002/mdc3.13955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 10/22/2023] [Accepted: 11/29/2023] [Indexed: 01/11/2024] Open
Affiliation(s)
- Hanin Jaber AlGethami
- Division of NeurologyThe Hospital for Sick ChildrenTorontoOntarioCanada
- Department of PediatricsUniversity of TorontoTorontoOntarioCanada
| | - Sara Breitbart
- Division of NeurosurgeryThe Hospital for Sick ChildrenTorontoOntarioCanada
| | - Nebras M. Warsi
- Division of NeurosurgeryThe Hospital for Sick ChildrenTorontoOntarioCanada
- Department of SurgeryUniversity of TorontoTorontoOntarioCanada
| | - Alfonso Fasano
- Division of NeurologyThe Hospital for Sick ChildrenTorontoOntarioCanada
- Edmond J. Safra Program in Parkinson's Disease, Morton and Gloria Shulman Movement Disorders Clinic, Toronto Western Hospital, UHNTorontoOntarioCanada
- Division of NeurologyUniversity of TorontoTorontoOntarioCanada
- Krembil Brain InstituteTorontoOntarioCanada
- CenteR for Advancing Neurotechnological Innovation to Application (CRANIA)TorontoOntarioCanada
| | - George M. Ibrahim
- Division of NeurosurgeryThe Hospital for Sick ChildrenTorontoOntarioCanada
- Department of SurgeryUniversity of TorontoTorontoOntarioCanada
- Institute of Biomedical Engineering, University of TorontoTorontoOntarioCanada
| | - Carolina Gorodetsky
- Division of NeurologyThe Hospital for Sick ChildrenTorontoOntarioCanada
- Department of PediatricsUniversity of TorontoTorontoOntarioCanada
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Xing T, Zhao Y, Wang L, Geng W, Liu W, Zhou J, Huang C, Wang W, Chu X, Liu B, Chen K, Zheng H, Li L. Fine-scale mapping of chromosome 9q22.33 identifies candidate causal variant in ovarian cancer. PeerJ 2024; 12:e16918. [PMID: 38371376 PMCID: PMC10874173 DOI: 10.7717/peerj.16918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 01/18/2024] [Indexed: 02/20/2024] Open
Abstract
Ovarian cancer is a complex polygenic disease in which genetic factors play a significant role in disease etiology. A genome-wide association study (GWAS) identified a novel variant on chromosome 9q22.33 as a susceptibility locus for epithelial ovarian cancer (EOC) in the Han Chinese population. However, the underlying mechanism of this genomic region remained unknown. In this study, we conducted a fine-mapping analysis of 130 kb regions, including 1,039 variants in 200 healthy women. Ten variants were selected to evaluate the association with EOC risk in 1,099 EOC cases and 1,591 controls. We identified two variants that were significantly associated with ovarian cancer risk (rs7027650, P = 1.91 × 10-7; rs1889268, P = 3.71 × 10-2). Expression quantitative trait locus (eQTL) analysis found that rs7027650 was significantly correlated with COL15A1 gene expression (P = 0.009). The Luciferase reporter gene assay confirmed that rs7027650 could interact with the promoter region of COL15A1, reducing its activity. An electrophoretic mobility shift assay (EMSA) showed the allele-specific binding capacity of rs7027650. These findings revealed that rs7027650 could be a potential causal variant at 9q22.33 region and may regulate the expression level of COL15A1. This study offered insight into the molecular mechanism behind a potential causal variant that affects the risk of ovarian cancer.
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Affiliation(s)
- Tongyu Xing
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology, Key Laboratory of Prevention and Control of Human Major Diseases, Ministry of Education, Tianjin’s Clinical Research Center for Cancer, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Yanrui Zhao
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology, Key Laboratory of Prevention and Control of Human Major Diseases, Ministry of Education, Tianjin’s Clinical Research Center for Cancer, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Lili Wang
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology, Key Laboratory of Prevention and Control of Human Major Diseases, Ministry of Education, Tianjin’s Clinical Research Center for Cancer, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Wei Geng
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology, Key Laboratory of Prevention and Control of Human Major Diseases, Ministry of Education, Tianjin’s Clinical Research Center for Cancer, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Wei Liu
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology, Key Laboratory of Prevention and Control of Human Major Diseases, Ministry of Education, Tianjin’s Clinical Research Center for Cancer, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Jingjing Zhou
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology, Key Laboratory of Prevention and Control of Human Major Diseases, Ministry of Education, Tianjin’s Clinical Research Center for Cancer, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Caiyun Huang
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology, Key Laboratory of Prevention and Control of Human Major Diseases, Ministry of Education, Tianjin’s Clinical Research Center for Cancer, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Wei Wang
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology, Key Laboratory of Prevention and Control of Human Major Diseases, Ministry of Education, Tianjin’s Clinical Research Center for Cancer, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Xinlei Chu
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology, Key Laboratory of Prevention and Control of Human Major Diseases, Ministry of Education, Tianjin’s Clinical Research Center for Cancer, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Ben Liu
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology, Key Laboratory of Prevention and Control of Human Major Diseases, Ministry of Education, Tianjin’s Clinical Research Center for Cancer, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Kexin Chen
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology, Key Laboratory of Prevention and Control of Human Major Diseases, Ministry of Education, Tianjin’s Clinical Research Center for Cancer, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Hong Zheng
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology, Key Laboratory of Prevention and Control of Human Major Diseases, Ministry of Education, Tianjin’s Clinical Research Center for Cancer, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Lian Li
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology, Key Laboratory of Prevention and Control of Human Major Diseases, Ministry of Education, Tianjin’s Clinical Research Center for Cancer, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
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Geng K, Merino LG, Veiga RG, Sommerauer C, Epperlein J, Brinkman EK, Kutter C. Intrinsic deletion at 10q23.31, including the PTEN gene locus, is aggravated upon CRISPR-Cas9-mediated genome engineering in HAP1 cells mimicking cancer profiles. Life Sci Alliance 2024; 7:e202302128. [PMID: 37984988 PMCID: PMC10662290 DOI: 10.26508/lsa.202302128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 11/06/2023] [Accepted: 11/07/2023] [Indexed: 11/22/2023] Open
Abstract
The CRISPR-Cas9 system is a powerful tool for studying gene functions and holds potential for disease treatment. However, precise genome editing requires thorough assessments to minimize unintended on- and off-target effects. Here, we report an unexpected 283-kb deletion on Chromosome 10 (10q23.31) in chronic myelogenous leukemia-derived HAP1 cells, which are frequently used in CRISPR screens. The deleted region encodes regulatory genes, including PAPSS2, ATAD1, KLLN, and PTEN We found that this deletion was not a direct consequence of CRISPR-Cas9 off-targeting but rather occurred frequently during the generation of CRISPR-Cas9-modified cells. The deletion was associated with global changes in histone acetylation and gene expression, affecting fundamental cellular processes such as cell cycle and DNA replication. We detected this deletion in cancer patient genomes. As in HAP1 cells, the deletion contributed to similar gene expression patterns among cancer patients despite interindividual differences. Our findings suggest that the unintended deletion of 10q23.31 can confound CRISPR-Cas9 studies and underscore the importance to assess unintended genomic changes in CRISPR-Cas9-modified cells, which could impact cancer research.
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Affiliation(s)
- Keyi Geng
- https://ror.org/056d84691 Department of Microbiology, Tumor, and Cell Biology, Science for Life Laboratory, Karolinska Institute, Solna, Sweden
| | - Lara G Merino
- https://ror.org/056d84691 Department of Microbiology, Tumor, and Cell Biology, Science for Life Laboratory, Karolinska Institute, Solna, Sweden
| | - Raül G Veiga
- https://ror.org/056d84691 Department of Microbiology, Tumor, and Cell Biology, Science for Life Laboratory, Karolinska Institute, Solna, Sweden
| | - Christian Sommerauer
- https://ror.org/056d84691 Department of Microbiology, Tumor, and Cell Biology, Science for Life Laboratory, Karolinska Institute, Solna, Sweden
| | - Janine Epperlein
- https://ror.org/056d84691 Department of Microbiology, Tumor, and Cell Biology, Science for Life Laboratory, Karolinska Institute, Solna, Sweden
| | - Eva K Brinkman
- https://ror.org/056d84691 Department of Microbiology, Tumor, and Cell Biology, Science for Life Laboratory, Karolinska Institute, Solna, Sweden
| | - Claudia Kutter
- https://ror.org/056d84691 Department of Microbiology, Tumor, and Cell Biology, Science for Life Laboratory, Karolinska Institute, Solna, Sweden
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Liu T, Qiu QT, Hua KJ, Ma BG. Chromosome structure modeling tools and their evaluation in bacteria. Brief Bioinform 2024; 25:bbae044. [PMID: 38385874 PMCID: PMC10883143 DOI: 10.1093/bib/bbae044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 12/31/2023] [Accepted: 01/22/2024] [Indexed: 02/23/2024] Open
Abstract
The three-dimensional (3D) structure of bacterial chromosomes is crucial for understanding chromosome function. With the growing availability of high-throughput chromosome conformation capture (3C/Hi-C) data, the 3D structure reconstruction algorithms have become powerful tools to study bacterial chromosome structure and function. It is highly desired to have a recommendation on the chromosome structure reconstruction tools to facilitate the prokaryotic 3D genomics. In this work, we review existing chromosome 3D structure reconstruction algorithms and classify them based on their underlying computational models into two categories: constraint-based modeling and thermodynamics-based modeling. We briefly compare these algorithms utilizing 3C/Hi-C datasets and fluorescence microscopy data obtained from Escherichia coli and Caulobacter crescentus, as well as simulated datasets. We discuss current challenges in the 3D reconstruction algorithms for bacterial chromosomes, primarily focusing on software usability. Finally, we briefly prospect future research directions for bacterial chromosome structure reconstruction algorithms.
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Affiliation(s)
- Tong Liu
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Qin-Tian Qiu
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Kang-Jian Hua
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Bin-Guang Ma
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
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Riviello FN, Daponte A, Ponzi E, Ficarella R, Orsini P, Bucci R, Ventura M, Antonacci F, Catacchio CR, Gentile M. A Rare Case of Concurrent 2q34q36 Duplication and 2q37 Deletion in a Neonate with Syndromic Features. Genes (Basel) 2023; 14:2194. [PMID: 38137016 PMCID: PMC10742419 DOI: 10.3390/genes14122194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 12/02/2023] [Accepted: 12/07/2023] [Indexed: 12/24/2023] Open
Abstract
Large-scale genomic structural variations can have significant clinical implications, depending on the specific altered genomic region. Briefly, 2q37 microdeletion syndrome is a prevalent subtelomeric deletion disorder characterized by variable-sized deletions. Affected patients exhibit a wide range of clinical manifestations, including short stature, facial dysmorphism, and features of autism spectrum disorder, among others. Conversely, isolated duplications of proximal chromosome 2q are rare and lack a distinct phenotype. In this report, we provide an extensive molecular analysis of a 15-day-old newborn referred for syndromic features. Our analysis reveals an 8.5 Mb microdeletion at 2q37.1, which extends to the telomere, in conjunction with an 8.6 Mb interstitial microduplication at 2q34q36.1. Our findings underscore the prominence of 2q37 terminal deletions as commonly reported genomic anomalies. We compare our patient's phenotype with previously reported cases in the literature to contribute to a more refined classification of 2q37 microdeletion syndrome and assess the potential impact of 2q34q36.1 microduplication. We also investigate multiple hypotheses to clarify the genetic mechanisms responsible for the observed genomic rearrangement.
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Affiliation(s)
- Francesco Nicola Riviello
- U.O.C. Laboratorio di Genetica Medica, PO Di Venere—ASL Bari, 70012 Bari, Italy; (F.N.R.); (E.P.); (R.F.); (P.O.); (R.B.)
| | - Alessia Daponte
- Dipartimento di Bioscienze, Biotecnologie e Ambiente, Università degli Studi di Bari “Aldo Moro”, 70125 Bari, Italy; (A.D.); (M.V.); (F.A.)
| | - Emanuela Ponzi
- U.O.C. Laboratorio di Genetica Medica, PO Di Venere—ASL Bari, 70012 Bari, Italy; (F.N.R.); (E.P.); (R.F.); (P.O.); (R.B.)
| | - Romina Ficarella
- U.O.C. Laboratorio di Genetica Medica, PO Di Venere—ASL Bari, 70012 Bari, Italy; (F.N.R.); (E.P.); (R.F.); (P.O.); (R.B.)
| | - Paola Orsini
- U.O.C. Laboratorio di Genetica Medica, PO Di Venere—ASL Bari, 70012 Bari, Italy; (F.N.R.); (E.P.); (R.F.); (P.O.); (R.B.)
| | - Roberta Bucci
- U.O.C. Laboratorio di Genetica Medica, PO Di Venere—ASL Bari, 70012 Bari, Italy; (F.N.R.); (E.P.); (R.F.); (P.O.); (R.B.)
| | - Mario Ventura
- Dipartimento di Bioscienze, Biotecnologie e Ambiente, Università degli Studi di Bari “Aldo Moro”, 70125 Bari, Italy; (A.D.); (M.V.); (F.A.)
| | - Francesca Antonacci
- Dipartimento di Bioscienze, Biotecnologie e Ambiente, Università degli Studi di Bari “Aldo Moro”, 70125 Bari, Italy; (A.D.); (M.V.); (F.A.)
| | - Claudia Rita Catacchio
- Dipartimento di Bioscienze, Biotecnologie e Ambiente, Università degli Studi di Bari “Aldo Moro”, 70125 Bari, Italy; (A.D.); (M.V.); (F.A.)
| | - Mattia Gentile
- U.O.C. Laboratorio di Genetica Medica, PO Di Venere—ASL Bari, 70012 Bari, Italy; (F.N.R.); (E.P.); (R.F.); (P.O.); (R.B.)
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Wang X, Gu WC, Li J, Ma BG. EVRC: reconstruction of chromosome 3D structure models using error-vector resultant algorithm with clustering coefficient. Bioinformatics 2023; 39:btad638. [PMID: 37847746 DOI: 10.1093/bioinformatics/btad638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 09/28/2023] [Accepted: 10/16/2023] [Indexed: 10/19/2023]
Abstract
MOTIVATION Reconstruction of 3D structure models is of great importance for the study of chromosome function. Software tools for this task are highly needed. RESULTS We present a novel reconstruction algorithm, called EVRC, which utilizes co-clustering coefficients and error-vector resultant for chromosome 3D structure reconstruction. As an update of our previous EVR algorithm, EVRC now can deal with both single and multiple chromosomes in structure modeling. To evaluate the effectiveness and accuracy of the EVRC algorithm, we applied it to simulation datasets and real Hi-C datasets. The results show that the reconstructed structures have high similarity to the original/real structures, indicating the effectiveness and robustness of the EVRC algorithm. Furthermore, we applied the algorithm to the 3D conformation reconstruction of the wild-type and mutant Arabidopsis thaliana chromosomes and demonstrated the differences in structural characteristics between different chromosomes. We also accurately showed the conformational change in the centromere region of the mutant compared with the wild-type of Arabidopsis chromosome 1. Our EVRC algorithm is a valuable software tool for the field of chromatin structure reconstruction, and holds great promise for advancing our understanding on the chromosome functions. AVAILABILITY AND IMPLEMENTATION The software is available at https://github.com/mbglab/EVRC.
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Affiliation(s)
- Xiao Wang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Wei-Cheng Gu
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Jie Li
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Bin-Guang Ma
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
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Pląskowska K, Zakrzewska-Czerwińska J. Chromosome structure and DNA replication dynamics during the life cycle of the predatory bacterium Bdellovibrio bacteriovorus. FEMS Microbiol Rev 2023; 47:fuad057. [PMID: 37791401 DOI: 10.1093/femsre/fuad057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 09/27/2023] [Accepted: 10/02/2023] [Indexed: 10/05/2023] Open
Abstract
Bdellovibrio bacteriovorus, an obligate predatory Gram-negative bacterium that proliferates inside and kills other Gram-negative bacteria, was discovered more than 60 years ago. However, we have only recently begun to understand the detailed cell biology of this proficient bacterial killer. Bdellovibrio bacteriovorus exhibits a peculiar life cycle and bimodal proliferation, and thus represents an attractive model for studying novel aspects of bacterial cell biology. The life cycle of B. bacteriovorus consists of two phases: a free-living nonreplicative attack phase and an intracellular reproductive phase. During the reproductive phase, B. bacteriovorus grows as an elongated cell and undergoes binary or nonbinary fission, depending on the prey size. In this review, we discuss: (1) how the chromosome structure of B. bacteriovorus is remodeled during its life cycle; (2) how its chromosome replication dynamics depends on the proliferation mode; (3) how the initiation of chromosome replication is controlled during the life cycle, and (4) how chromosome replication is spatiotemporally coordinated with the proliferation program.
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Affiliation(s)
- Karolina Pląskowska
- Department of Molecular Microbiology, Faculty of Biotechnology, University of Wrocław, ul. Joliot-Curie 14A, Wrocław, Poland
| | - Jolanta Zakrzewska-Czerwińska
- Department of Molecular Microbiology, Faculty of Biotechnology, University of Wrocław, ul. Joliot-Curie 14A, Wrocław, Poland
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Zhang Q, Wang Y, Zhou J, Zhou R, Liu A, Meng L, Ji X, Hu P, Xu Z. 11q13.3q13.4 deletion plus 9q21.13q21.33 duplication in an affected girl arising from a familial four-way balanced chromosomal translocation. Mol Genet Genomic Med 2023; 11:e2248. [PMID: 37475652 PMCID: PMC10568374 DOI: 10.1002/mgg3.2248] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 05/23/2023] [Accepted: 07/12/2023] [Indexed: 07/22/2023] Open
Abstract
BACKGROUND We describe a 13-year-old girl with a 11q13.3q13.4 deletion encompassing the SHANK2 gene and a 9q21.13q21.33 duplication. She presented with pre- and postnatal growth retardation, global developmental delay, severe language delay, cardiac abnormalities, and dysmorphisms. Her maternal family members all had histories of reproductive problems. METHODS Maternal family members with histories of reproductive problems were studied using G-banded karyotyping and optical genome mapping (OGM). Long-range PCR (LR-PCR) and Sanger sequencing were used to confirm the precise break point sequences obtained by OGM. RESULTS G-banded karyotyping characterized the cytogenetic results as 46,XX,der(9)?del(9)(q21q22)t(9;14)(q22;q24),der(11)ins(11;?9)(q13;?q21q22),der(14)t(9;14). Using OGM, we determined that asymptomatic female family members with reproductive problems were carriers of a four-way balanced chromosome translocation. Their karyotype results were further refined as 46,XX,der(9)del(9)(q21.13q21.33)t(9;14)(q21.33;q22.31),der(11)del(11)(q13.3q13.4)ins(11;9)(q13.3;q21.33q21.13),der(14)t(9:14)ins(14;11)(q23.1;q13.4q13.3). Thus, we confirmed that the affected girl inherited the maternally derived chromosome 11. Furthermore, using LR-PCR, we showed that three disease-related genes (TMC1, NTRK2, and KIAA0586) were disrupted by the breakpoints. CONCLUSIONS Our case highlights the importance of timely parental origin testing for patients with rare copy number variations, as well as the accurate characterization of balanced chromosomal rearrangements in families with reproductive problems. In addition, our case demonstrates that OGM is a useful clinical application for analyzing complex structural variations within the human genome.
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Affiliation(s)
- Qinxin Zhang
- Department of Prenatal DiagnosisWomen's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care HospitalNanjingChina
| | - Yan Wang
- Department of Prenatal DiagnosisWomen's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care HospitalNanjingChina
| | - Jing Zhou
- Department of Prenatal DiagnosisWomen's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care HospitalNanjingChina
| | - Ran Zhou
- Department of Prenatal DiagnosisWomen's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care HospitalNanjingChina
| | - An Liu
- Department of Prenatal DiagnosisWomen's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care HospitalNanjingChina
| | - Lulu Meng
- Department of Prenatal DiagnosisWomen's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care HospitalNanjingChina
| | - Xiuqing Ji
- Department of Prenatal DiagnosisWomen's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care HospitalNanjingChina
| | - Ping Hu
- Department of Prenatal DiagnosisWomen's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care HospitalNanjingChina
| | - Zhengfeng Xu
- Department of Prenatal DiagnosisWomen's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care HospitalNanjingChina
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Nascimento LPC, Mergener R, Nunes MR, Muniz VF, Catao JR, da Silveira AKB, Dorfman LE, Graziadio C, Zen PRG. 16p11.2 Microduplication Syndrome with Increased Fluid in the Cisterna: Coincidence or Phenotype Extension? Genes (Basel) 2023; 14:1583. [PMID: 37628634 PMCID: PMC10454344 DOI: 10.3390/genes14081583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 07/28/2023] [Accepted: 07/31/2023] [Indexed: 08/27/2023] Open
Abstract
We report the first case of a child with 16p11.2 microduplication syndrome with increased fluid in the cisterna magna seen on magnetic resonance imaging (MRI). This finding may correspond to a Blake's Pouch Cyst (BPC) or a Mega Cisterna Magna (MCM), being impossible to differentiate through image examination. The molecular duplication was diagnosed using chromosomal microarray analysis with single nucleotide polymorphism (SNP). We review the clinical and neuroimaging features in published case reports in order to observe the findings described in the literature so far and present a skull three-dimensional model to contribute to a better understanding. Despite the variable expressivity of the syndrome being well known, there is no case described in the available literature that mentions the association of 16p11.2 microduplication and the presence of BPC or MCM seen in neuroimaging exams. This finding may represent an extension of the phenotype not yet reported or may present itself as a coincidence in a child with various malformations.
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Affiliation(s)
- Lívia Polisseni Cotta Nascimento
- Graduate Program in Pathology, Federal University of Health Sciences of Porto Alegre (UFCSPA), Porto Alegre 90050-170, RS, Brazil; (L.P.C.N.); (R.M.); (V.F.M.)
- Medical Residency Committee, Federal University of Health Sciences of Porto Alegre (UFCSPA)/Brotherhood of the Santa Casa de Misericórdia of Porto Alegre (ISCMPA), Porto Alegre 90050-170, RS, Brazil;
| | - Rafaella Mergener
- Graduate Program in Pathology, Federal University of Health Sciences of Porto Alegre (UFCSPA), Porto Alegre 90050-170, RS, Brazil; (L.P.C.N.); (R.M.); (V.F.M.)
| | - Marcela Rodrigues Nunes
- Medical Residency Committee, Federal University of Health Sciences of Porto Alegre (UFCSPA)/Brotherhood of the Santa Casa de Misericórdia of Porto Alegre (ISCMPA), Porto Alegre 90050-170, RS, Brazil;
| | - Victória Feitosa Muniz
- Graduate Program in Pathology, Federal University of Health Sciences of Porto Alegre (UFCSPA), Porto Alegre 90050-170, RS, Brazil; (L.P.C.N.); (R.M.); (V.F.M.)
| | - Juliana Rossi Catao
- Medicine Course, Federal University of Health Sciences of Porto Alegre (UFCSPA), Porto Alegre 90050-170, RS, Brazil;
| | - Ana Kalise Böttcher da Silveira
- Undergraduate Program in Biomedical Science, Federal University of Health Sciences of Porto Alegre (UFCSPA), Porto Alegre 90050-170, RS, Brazil;
| | - Luiza Emy Dorfman
- Health School, University of Vale do Rio dos Sinos (Unisinos), São Leopoldo 93022-750, RS, Brazil;
| | - Carla Graziadio
- Department of Clinical Medicine, Federal University of Health Sciences of Porto Alegre (UFCSPA)/Brotherhood of the Santa Casa de Misericórdia of Porto Alegre (ISCMPA), Porto Alegre 90050-170, RS, Brazil;
| | - Paulo Ricardo Gazzola Zen
- Graduate Program in Pathology, Federal University of Health Sciences of Porto Alegre (UFCSPA), Porto Alegre 90050-170, RS, Brazil; (L.P.C.N.); (R.M.); (V.F.M.)
- Department of Clinical Medicine, Federal University of Health Sciences of Porto Alegre (UFCSPA)/Brotherhood of the Santa Casa de Misericórdia of Porto Alegre (ISCMPA), Porto Alegre 90050-170, RS, Brazil;
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12
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Wang Y, Guo Z, Cheng J. Single-cell Hi-C data enhancement with deep residual and generative adversarial networks. Bioinformatics 2023; 39:btad458. [PMID: 37498561 PMCID: PMC10403428 DOI: 10.1093/bioinformatics/btad458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 07/19/2023] [Accepted: 07/25/2023] [Indexed: 07/28/2023] Open
Abstract
MOTIVATION The spatial genome organization of a eukaryotic cell is important for its function. The development of single-cell technologies for probing the 3D genome conformation, especially single-cell chromosome conformation capture techniques, has enabled us to understand genome function better than before. However, due to extreme sparsity and high noise associated with single-cell Hi-C data, it is still difficult to study genome structure and function using the HiC-data of one single cell. RESULTS In this work, we developed a deep learning method ScHiCEDRN based on deep residual networks and generative adversarial networks for the imputation and enhancement of Hi-C data of a single cell. In terms of both image evaluation and Hi-C reproducibility metrics, ScHiCEDRN outperforms the four deep learning methods (DeepHiC, HiCPlus, HiCSR, and Loopenhance) on enhancing the raw single-cell Hi-C data of human and Drosophila. The experiments also show that it can generate single-cell Hi-C data more suitable for identifying topologically associating domain boundaries and reconstructing 3D chromosome structures than the existing methods. Moreover, ScHiCEDRN's performance generalizes well across different single cells and cell types, and it can be applied to improving population Hi-C data. AVAILABILITY AND IMPLEMENTATION The source code of ScHiCEDRN is available at the GitHub repository: https://github.com/BioinfoMachineLearning/ScHiCEDRN.
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Affiliation(s)
- Yanli Wang
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO 65211, United States
- NextGen Precision Health Institute, University of Missouri, Columbia, MO 65211, United States
| | - Zhiye Guo
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO 65211, United States
- NextGen Precision Health Institute, University of Missouri, Columbia, MO 65211, United States
| | - Jianlin Cheng
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO 65211, United States
- NextGen Precision Health Institute, University of Missouri, Columbia, MO 65211, United States
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13
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Linders CC, van Eeghen AM, Zinkstok JR, van den Boogaard MJ, Boot E. Intellectual and Behavioral Phenotypes of Smith-Magenis Syndrome: Comparisons between Individuals with a 17p11.2 Deletion and Pathogenic RAI1 Variant. Genes (Basel) 2023; 14:1514. [PMID: 37628566 PMCID: PMC10453904 DOI: 10.3390/genes14081514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 07/22/2023] [Accepted: 07/23/2023] [Indexed: 08/27/2023] Open
Abstract
AIM Smith-Magenis syndrome (SMS) is a rare genetic neurodevelopmental disorder caused by a 17p11.2 deletion or pathogenic variant in the RAI1 gene. SMS is associated with developmental delay, intellectual disability (ID), and major sleep and behavioral disturbances. To explore how genetic variants may affect intellectual functioning and behavior, we compared intellectual and behavioral phenotypes between individuals with a 17p11.2 deletion and pathogenic RAI1 variant. METHOD We reviewed available clinical records from individuals (aged 0-45 years) with SMS, ascertained through a Dutch multidisciplinary SMS specialty clinic. RESULTS We included a total of 66 individuals (n = 47, 71.2% with a 17p11.2 deletion and n = 19, 28.8% with a pathogenic RAI1 variant) for whom data were available on intellectual functioning, severity of ID (n = 53), and behavioral problems assessed with the Child Behavior Checklist (CBCL, n = 39). Median full-scale IQ scores were lower (56.0 vs. 73.5, p = 0.001) and the proportion of individuals with more severe ID was higher (p = 0.01) in the 17p11.2 deletion group. Median total CBCL 6-18 scores (73.5 vs. 66.0, p = 0.02) and scores on the sub-scales somatic complaints (68.0 vs. 57.0, p = 0.001), withdrawn/depressed behavior (69.5 vs. 55.0, p = 0.02), and internalizing behavior (66.0 vs. 55.0, p = 0.002) were higher in the RAI1 group. CONCLUSION The results of this study suggest that 17p11.2 deletions are associated with a lower level of intellectual functioning and less internalizing of problems compared to pathogenic RAI1 variants. The findings of this study may contribute to personalized-management strategies in individuals with SMS.
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Affiliation(s)
- Cathelijne C. Linders
- Advisium, ’s Heeren Loo, 3818 LA Amersfoort, The Netherlands
- Department of Genetics, University Medical Centre Utrecht, 3584 CX Utrecht, The Netherlands
| | - Agnies M. van Eeghen
- Advisium, ’s Heeren Loo, 3818 LA Amersfoort, The Netherlands
- Department of Pediatrics, Emma Children’s Hospital, Amsterdam, University Medical Center, 1105 AZ Amsterdam, The Netherlands
| | - Janneke R. Zinkstok
- Department of Psychiatry, Radboud University Medical Centre, 6500 HB Nijmegen, The Netherlands
- Karakter Child and Adolescent Psychiatry, 6501 BB Nijmegen, The Netherlands
- Department of Psychiatry and Brain Center, University Medical Center Utrecht, 3584 CG Utrecht, The Netherlands
| | | | - Erik Boot
- Advisium, ’s Heeren Loo, 3818 LA Amersfoort, The Netherlands
- The Dalglish Family 22q Clinic, University Health Network, Toronto, ON M5G 2C4, Canada
- Department of Psychiatry & Neuropsychology, Maastricht University, 6200 AB Maastricht, The Netherlands
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14
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Deng L, Zhao Z, Liu L, Zhong Z, Xie W, Zhou F, Xu W, Zhang Y, Deng Z, Sun Y. Dissection of 3D chromosome organization in Streptomyces coelicolor A3(2) leads to biosynthetic gene cluster overexpression. Proc Natl Acad Sci U S A 2023; 120:e2222045120. [PMID: 36877856 PMCID: PMC10242723 DOI: 10.1073/pnas.2222045120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 02/08/2023] [Indexed: 03/08/2023] Open
Abstract
The soil-dwelling filamentous bacteria, Streptomyces, is widely known for its ability to produce numerous bioactive natural products. Despite many efforts toward their overproduction and reconstitution, our limited understanding of the relationship between the host's chromosome three dimension (3D) structure and the yield of the natural products escaped notice. Here, we report the 3D chromosome organization and its dynamics of the model strain, Streptomyces coelicolor, during the different growth phases. The chromosome undergoes a dramatic global structural change from primary to secondary metabolism, while some biosynthetic gene clusters (BGCs) form special local structures when highly expressed. Strikingly, transcription levels of endogenous genes are found to be highly correlated to the local chromosomal interaction frequency as defined by the value of the frequently interacting regions (FIREs). Following the criterion, an exogenous single reporter gene and even complex BGC can achieve a higher expression after being integrated into the chosen loci, which may represent a unique strategy to activate or enhance the production of natural products based on the local chromosomal 3D organization.
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Affiliation(s)
- Liang Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), Wuhan University, Wuhan430071, China
| | - Zhihu Zhao
- Department of Protein Engineering, Beijing Institute of Biotechnology, Beijing100071, China
| | - Lin Liu
- Epigenetic Division, Wuhan Frasergen Bioinformatics Co., Ltd., Wuhan430075, China
| | - Zhiyu Zhong
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), Wuhan University, Wuhan430071, China
| | - Wenxinyu Xie
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), Wuhan University, Wuhan430071, China
| | - Fan Zhou
- Epigenetic Division, Wuhan Frasergen Bioinformatics Co., Ltd., Wuhan430075, China
| | - Wei Xu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), Wuhan University, Wuhan430071, China
| | - Yubo Zhang
- Animal Functional Genomics Group, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen518120, China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), Wuhan University, Wuhan430071, China
| | - Yuhui Sun
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), Wuhan University, Wuhan430071, China
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15
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Sarasua SM, DeLuca JM, Rogers C, Phelan K, Rennert L, Powder KE, Weisensee K, Boccuto L. Head Size in Phelan-McDermid Syndrome: A Literature Review and Pooled Analysis of 198 Patients Identifies Candidate Genes on 22q13. Genes (Basel) 2023; 14:540. [PMID: 36980813 PMCID: PMC10048319 DOI: 10.3390/genes14030540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 02/11/2023] [Accepted: 02/12/2023] [Indexed: 02/24/2023] Open
Abstract
Phelan-McDermid syndrome (PMS) is a multisystem disorder that is associated with deletions of the 22q13 genomic region or pathogenic variants in the SHANK3 gene. Notable features include developmental issues, absent or delayed speech, neonatal hypotonia, seizures, autism or autistic traits, gastrointestinal problems, renal abnormalities, dolichocephaly, and both macro- and microcephaly. Assessment of the genetic factors that are responsible for abnormal head size in PMS has been hampered by small sample sizes as well as a lack of attention to these features. Therefore, this study was conducted to investigate the relationship between head size and genes on chromosome 22q13. A review of the literature was conducted to identify published cases of 22q13 deletions with information on head size to conduct a pooled association analysis. Across 56 studies, we identified 198 cases of PMS with defined deletion sizes and head size information. A total of 33 subjects (17%) had macrocephaly, 26 (13%) had microcephaly, and 139 (70%) were normocephalic. Individuals with macrocephaly had significantly larger genomic deletions than those with microcephaly or normocephaly (p < 0.0001). A genomic region on 22q13.31 was found to be significantly associated with macrocephaly with CELSR1, GRAMD4, and TBCD122 suggested as candidate genes. Investigation of these genes will aid the understanding of head and brain development.
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Affiliation(s)
- Sara M. Sarasua
- Healthcare Genetics and Genomics Program, Clemson University School of Nursing, Clemson, SC 29634, USA
| | - Jane M. DeLuca
- Healthcare Genetics and Genomics Program, Clemson University School of Nursing, Clemson, SC 29634, USA
| | | | - Katy Phelan
- Florida Cancer Specialists & Research Institute, Fort Myers, FL 33908, USA
| | - Lior Rennert
- Department of Public Health Sciences, Clemson University, Clemson, SC 29634, USA
| | - Kara E. Powder
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA
| | - Katherine Weisensee
- Department of Sociology, Anthropology and Criminal Justice, Clemson University, Clemson, SC 29634, USA
| | - Luigi Boccuto
- Healthcare Genetics and Genomics Program, Clemson University School of Nursing, Clemson, SC 29634, USA
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16
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Beklemisheva VR, Lemskaya NA, Prokopov DY, Perelman PL, Romanenko SA, Proskuryakova AA, Serdyukova NA, Utkin YA, Nie W, Ferguson-Smith MA, Yang F, Graphodatsky AS. Maps of Constitutive-Heterochromatin Distribution for Four Martes Species (Mustelidae, Carnivora, Mammalia) Show the Formative Role of Macrosatellite Repeats in Interspecific Variation of Chromosome Structure. Genes (Basel) 2023; 14:489. [PMID: 36833416 PMCID: PMC9957230 DOI: 10.3390/genes14020489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/08/2023] [Accepted: 02/09/2023] [Indexed: 02/17/2023] Open
Abstract
Constitutive-heterochromatin placement in the genome affects chromosome structure by occupying centromeric areas and forming large blocks. To investigate the basis for heterochromatin variation in the genome, we chose a group of species with a conserved euchromatin part: the genus Martes [stone marten (M. foina, 2n = 38), sable (M. zibellina, 2n = 38), pine marten (M. martes, 2n = 38), and yellow-throated marten (M. flavigula, 2n = 40)]. We mined the stone marten genome for the most abundant tandem repeats and selected the top 11 macrosatellite repetitive sequences. Fluorescent in situ hybridization revealed distributions of the tandemly repeated sequences (macrosatellites, telomeric repeats, and ribosomal DNA). We next characterized the AT/GC content of constitutive heterochromatin by CDAG (Chromomycin A3-DAPI-after G-banding). The euchromatin conservatism was shown by comparative chromosome painting with stone marten probes in newly built maps of the sable and pine marten. Thus, for the four Martes species, we mapped three different types of tandemly repeated sequences critical for chromosome structure. Most macrosatellites are shared by the four species with individual patterns of amplification. Some macrosatellites are specific to a species, autosomes, or the X chromosome. The variation of core macrosatellites and their prevalence in a genome are responsible for the species-specific variation of the heterochromatic blocks.
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Affiliation(s)
- Violetta R. Beklemisheva
- Department of Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Natalya A. Lemskaya
- Department of Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Dmitry Yu. Prokopov
- Department of Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Polina L. Perelman
- Department of Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Svetlana A. Romanenko
- Department of Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Anastasia A. Proskuryakova
- Department of Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Natalya A. Serdyukova
- Department of Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Yaroslav A. Utkin
- Department of Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Wenhui Nie
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Malcolm A. Ferguson-Smith
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK
| | - Fentang Yang
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo 255049, China
| | - Alexander S. Graphodatsky
- Department of Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
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17
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Wang Y, Zhou H, Fu F, Cheng K, Yu Q, Huang R, Lei T, Yang X, Li D, Liao C. Prenatal Diagnosis of Chromosome 16p11.2 Microdeletion. Genes (Basel) 2022; 13:genes13122315. [PMID: 36553582 PMCID: PMC9778018 DOI: 10.3390/genes13122315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 11/27/2022] [Accepted: 12/06/2022] [Indexed: 12/13/2022] Open
Abstract
(1) Objective: To investigate the prenatal diagnosis and genetic counseling for 16p11.2 microdeletion syndrome and to evaluate its pregnancy outcome. (2) Methods: This study included 4968 pregnant women who selected invasive prenatal diagnoses from 1 January 2017 to 1 August 2022. These 4698 pregnancies underwent chromosomal microarray analysis (CMA), data on 81 fetuses diagnosed with 16p11.2 microdeletion syndrome based on prenatal ultrasound features and genetic test results were recorded, and their pregnancy outcome was evaluated. (3) Results: 1.63% of fetuses (81/4968) were diagnosed with 16p11.2 microdeletion syndrome. Among these, there were skeletal malformations in 48.15% of the 81 fetuses, cardiovascular malformations in 30.86%, central nervous system malformations (CNS) in 11.11%, digestive system structural abnormalities in 6.17%, and isolated ultrasonography markers in 3.70%. (4) Conclusions: 16p11.2 microdeletion syndrome can display various systemic ultrasound abnormalities in the perinatal period but vertebral malformations are the most common. Our study is the first to report that TBX1 and CJA5 are associated with 16p11.2 microdeletion syndrome, expanding the disease spectrum of 16p11.2 microdeletion syndrome. In our study, the ventricular septal defect is the main feature of cardiac structural abnormalities caused by 16p11.2 microdeletion syndrome. In addition, our study highlights the use of CMA in 16p11.2 microdeletion syndrome, analyzed their genetic results, and evaluated the follow-up prognosis, which can be useful for prenatal diagnosis and genetic counseling.
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Affiliation(s)
- You Wang
- The First School of Clinical Medicine, Southern Medical University, Guangzhou 510515, China
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 510620, China
| | - Hang Zhou
- The First School of Clinical Medicine, Southern Medical University, Guangzhou 510515, China
| | - Fang Fu
- The First School of Clinical Medicine, Southern Medical University, Guangzhou 510515, China
| | - Ken Cheng
- The First School of Clinical Medicine, Southern Medical University, Guangzhou 510515, China
- School of Medicine, South China University of Technology, Guangzhou 510641, China
| | - Qiuxia Yu
- The First School of Clinical Medicine, Southern Medical University, Guangzhou 510515, China
| | - Ruibin Huang
- The First School of Clinical Medicine, Southern Medical University, Guangzhou 510515, China
| | - Tingying Lei
- The First School of Clinical Medicine, Southern Medical University, Guangzhou 510515, China
| | - Xin Yang
- The First School of Clinical Medicine, Southern Medical University, Guangzhou 510515, China
| | - Dongzhi Li
- The First School of Clinical Medicine, Southern Medical University, Guangzhou 510515, China
| | - Can Liao
- The First School of Clinical Medicine, Southern Medical University, Guangzhou 510515, China
- Correspondence: ; Tel.: +86-(020)-38076346
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18
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Bertini V, Milone R, Cristofani P, Cambi F, Bosetti C, Barbieri F, Bertelloni S, Cioni G, Valetto A, Battini R. Enhancing DLG2 Implications in Neuropsychiatric Disorders: Analysis of a Cohort of Eight Patients with 11q14.1 Imbalances. Genes (Basel) 2022; 13:genes13050859. [PMID: 35627244 PMCID: PMC9140951 DOI: 10.3390/genes13050859] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/10/2022] [Accepted: 05/10/2022] [Indexed: 11/20/2022] Open
Abstract
Neurodevelopmental disorders (NDDs) are considered synaptopathies, as they are due to anomalies in neuronal connectivity during development. DLG2 is a gene involved insynaptic function; the phenotypic effect of itsalterations in NDDs has been underestimated since few cases have been thoroughly described.We report on eight patients with 11q14.1 imbalances involving DLG2, underlining its potential effects on clinical presentation and its contribution to NDD comorbidity by accurate neuropsychiatric data collection. DLG2 is a very large gene in 11q14.1, extending over 2.172 Mb, with alternative splicing that gives rise to numerous isoforms differentially expressed in brain tissues. A thorough bioinformatic analysis of the altered transcripts was conducted for each patient. The different expression profiles of the isoforms of this gene and their influence on the excitatory–inhibitory balance in crucial brain structures could contribute to the phenotypic variability related to DLG2 alterations. Further studies on patients would be helpful to enrich clinical and neurodevelopmental findings and elucidate the molecular mechanisms subtended to NDDs.
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Affiliation(s)
- Veronica Bertini
- Cytogenetic Unit, Department of Laboratory Medicine, Azienda Ospedaliero-Univeristaria Pisana, Via Roma 57, 56100 Pisa, Italy; (V.B.); (F.C.)
| | - Roberta Milone
- Department of Developmental Neuroscience, IRCCS Fondazione Stella Maris, 56125 Pisa, Italy; (R.M.); (P.C.); (C.B.); (G.C.); (R.B.)
| | - Paola Cristofani
- Department of Developmental Neuroscience, IRCCS Fondazione Stella Maris, 56125 Pisa, Italy; (R.M.); (P.C.); (C.B.); (G.C.); (R.B.)
| | - Francesca Cambi
- Cytogenetic Unit, Department of Laboratory Medicine, Azienda Ospedaliero-Univeristaria Pisana, Via Roma 57, 56100 Pisa, Italy; (V.B.); (F.C.)
| | - Chiara Bosetti
- Department of Developmental Neuroscience, IRCCS Fondazione Stella Maris, 56125 Pisa, Italy; (R.M.); (P.C.); (C.B.); (G.C.); (R.B.)
| | - Filippo Barbieri
- Mental Health Department, ASL Toscana Nordovest, 56100 Pisa, Italy;
| | - Silvano Bertelloni
- Pediatric Endocrinology, Department of Obstetrics, Gynecology and Pediatrics, Azienda Ospedaliero-Universitaria Pisana, Via Roma 57, 56100 Pisa, Italy;
| | - Giovanni Cioni
- Department of Developmental Neuroscience, IRCCS Fondazione Stella Maris, 56125 Pisa, Italy; (R.M.); (P.C.); (C.B.); (G.C.); (R.B.)
- Department of Clinical and Experimental Medicine, University of Pisa, 56100 Pisa, Italy
| | - Angelo Valetto
- Cytogenetic Unit, Department of Laboratory Medicine, Azienda Ospedaliero-Univeristaria Pisana, Via Roma 57, 56100 Pisa, Italy; (V.B.); (F.C.)
- Correspondence:
| | - Roberta Battini
- Department of Developmental Neuroscience, IRCCS Fondazione Stella Maris, 56125 Pisa, Italy; (R.M.); (P.C.); (C.B.); (G.C.); (R.B.)
- Department of Clinical and Experimental Medicine, University of Pisa, 56100 Pisa, Italy
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19
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Papathanasiou S, Markoulaki S, Blaine LJ, Leibowitz ML, Zhang CZ, Jaenisch R, Pellman D. Whole chromosome loss and genomic instability in mouse embryos after CRISPR-Cas9 genome editing. Nat Commun 2021; 12:5855. [PMID: 34615869 PMCID: PMC8494802 DOI: 10.1038/s41467-021-26097-y] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 09/13/2021] [Indexed: 12/26/2022] Open
Abstract
Karyotype alterations have emerged as on-target complications from CRISPR-Cas9 genome editing. However, the events that lead to these karyotypic changes in embryos after Cas9-treatment remain unknown. Here, using imaging and single-cell genome sequencing of 8-cell stage embryos, we track both spontaneous and Cas9-induced karyotype aberrations through the first three divisions of embryonic development. We observe the generation of abnormal structures of the nucleus that arise as a consequence of errors in mitosis, including micronuclei and chromosome bridges, and determine their contribution to common karyotype aberrations including whole chromosome loss that has been recently reported after editing in embryos. Together, these data demonstrate that Cas9-mediated germline genome editing can lead to unwanted on-target side effects, including major chromosome structural alterations that can be propagated over several divisions of embryonic development.
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Affiliation(s)
- Stamatis Papathanasiou
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Logan J Blaine
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Mitchell L Leibowitz
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Cheng-Zhong Zhang
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Rudolf Jaenisch
- Whitehead Institute, Cambridge, MA, USA.
- Massachusetts Institute of Technology, Department of Biology, Cambridge, MA, USA.
| | - David Pellman
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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20
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Miga KH, Sullivan BA. Expanding studies of chromosome structure and function in the era of T2T genomics. Hum Mol Genet 2021; 30:R198-R205. [PMID: 34302168 PMCID: PMC8631062 DOI: 10.1093/hmg/ddab214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 07/16/2021] [Accepted: 07/20/2021] [Indexed: 11/13/2022] Open
Abstract
The recent accomplishment of a truly complete human genome has afforded a new view of chromosome structure and function that was limited 30 years ago. Here, we discuss the expansion of knowledge from the early cytological studies of the genome to the current high-resolution genomic, epigenetic and functional maps that have been achieved by recent technology and computational advances. These studies have revealed unexpected complexities of genome organization and function and uncovered new views of fundamental chromosomal elements. Comprehensive genomic maps will enable accurate diagnosis of human diseases caused by altered chromosome structure and function, facilitate development of chromosome-based therapies and shape the future of preventative medicine and healthcare.
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Affiliation(s)
- Karen H Miga
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Beth A Sullivan
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
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21
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Lioy VS, Lorenzi JN, Najah S, Poinsignon T, Leh H, Saulnier C, Aigle B, Lautru S, Thibessard A, Lespinet O, Leblond P, Jaszczyszyn Y, Gorrichon K, Varoquaux N, Junier I, Boccard F, Pernodet JL, Bury-Moné S. Dynamics of the compartmentalized Streptomyces chromosome during metabolic differentiation. Nat Commun 2021; 12:5221. [PMID: 34471117 PMCID: PMC8410849 DOI: 10.1038/s41467-021-25462-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 07/21/2021] [Indexed: 02/07/2023] Open
Abstract
Bacteria of the genus Streptomyces are prolific producers of specialized metabolites, including antibiotics. The linear chromosome includes a central region harboring core genes, as well as extremities enriched in specialized metabolite biosynthetic gene clusters. Here, we show that chromosome structure in Streptomyces ambofaciens correlates with genetic compartmentalization during exponential phase. Conserved, large and highly transcribed genes form boundaries that segment the central part of the chromosome into domains, whereas the terminal ends tend to be transcriptionally quiescent compartments with different structural features. The onset of metabolic differentiation is accompanied by a rearrangement of chromosome architecture, from a rather 'open' to a 'closed' conformation, in which highly expressed specialized metabolite biosynthetic genes form new boundaries. Thus, our results indicate that the linear chromosome of S. ambofaciens is partitioned into structurally distinct entities, suggesting a link between chromosome folding, gene expression and genome evolution.
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Affiliation(s)
- Virginia S Lioy
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France.
| | - Jean-Noël Lorenzi
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Soumaya Najah
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Thibault Poinsignon
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Hervé Leh
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Corinne Saulnier
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | | | - Sylvie Lautru
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | | | - Olivier Lespinet
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | | | - Yan Jaszczyszyn
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Kevin Gorrichon
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Nelle Varoquaux
- Université Grenoble Alpes, CNRS, Grenoble INP, TIMC-IMAG, Grenoble, France
| | - Ivan Junier
- Université Grenoble Alpes, CNRS, Grenoble INP, TIMC-IMAG, Grenoble, France
| | - Frédéric Boccard
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Jean-Luc Pernodet
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Stéphanie Bury-Moné
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France.
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22
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Guo MS, Kawamura R, Littlehale ML, Marko JF, Laub MT. High-resolution, genome-wide mapping of positive supercoiling in chromosomes. eLife 2021; 10:e67236. [PMID: 34279217 PMCID: PMC8360656 DOI: 10.7554/elife.67236] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 07/16/2021] [Indexed: 12/15/2022] Open
Abstract
Supercoiling impacts DNA replication, transcription, protein binding to DNA, and the three-dimensional organization of chromosomes. However, there are currently no methods to directly interrogate or map positive supercoils, so their distribution in genomes remains unknown. Here, we describe a method, GapR-seq, based on the chromatin immunoprecipitation of GapR, a bacterial protein that preferentially recognizes overtwisted DNA, for generating high-resolution maps of positive supercoiling. Applying this method to Escherichia coli and Saccharomyces cerevisiae, we find that positive supercoiling is widespread, associated with transcription, and particularly enriched between convergently oriented genes, consistent with the 'twin-domain' model of supercoiling. In yeast, we also find positive supercoils associated with centromeres, cohesin-binding sites, autonomously replicating sites, and the borders of R-loops (DNA-RNA hybrids). Our results suggest that GapR-seq is a powerful approach, likely applicable in any organism, to investigate aspects of chromosome structure and organization not accessible by Hi-C or other existing methods.
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Affiliation(s)
- Monica S Guo
- Department of Biology, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Ryo Kawamura
- Department of Molecular Biosciences, Northwestern UniversityEvanstonUnited States
| | - Megan L Littlehale
- Department of Biology, Massachusetts Institute of TechnologyCambridgeUnited States
| | - John F Marko
- Department of Molecular Biosciences, Northwestern UniversityEvanstonUnited States
- Department of Physics and Astronomy, Northwestern UniversityEvanstonUnited States
| | - Michael T Laub
- Department of Biology, Massachusetts Institute of TechnologyCambridgeUnited States
- Howard Hughes Medical Institute, Massachusetts Institute of TechnologyCambridgeUnited States
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24
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Abstract
The past decade has increased our understanding of how genome topology controls RAG endonuclease-mediated assembly of lymphocyte AgR genes. New technologies have illuminated how the large IgH, Igκ, TCRα/δ, and TCRβ loci fold into compact structures that place their numerous V gene segments in similar three-dimensional proximity to their distal recombination center composed of RAG-bound (D)J gene segments. Many studies have shown that CTCF and cohesin protein-mediated chromosome looping have fundamental roles in lymphocyte lineage- and developmental stage-specific locus compaction as well as broad usage of V segments. CTCF/cohesin-dependent loops have also been shown to direct and restrict RAG activity within chromosome domains. We summarize recent work in elucidating molecular mechanisms that govern three-dimensional chromosome organization and in investigating how these dynamic mechanisms control V(D)J recombination. We also introduce remaining questions for how CTCF/cohesin-dependent and -independent genome architectural mechanisms might regulate compaction and recombination of AgR loci.
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Affiliation(s)
- Brittney M Allyn
- Immunology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104; and
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Kyutae D Lee
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Craig H Bassing
- Immunology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104; and
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
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25
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Kim C, Kim J, Kim S, Cook DE, Evans KS, Andersen EC, Lee J. Long-read sequencing reveals intra-species tolerance of substantial structural variations and new subtelomere formation in C. elegans. Genome Res 2019; 29:1023-1035. [PMID: 31123081 PMCID: PMC6581047 DOI: 10.1101/gr.246082.118] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 04/22/2019] [Indexed: 12/05/2022]
Abstract
Long-read sequencing technologies have contributed greatly to comparative genomics among species and can also be applied to study genomics within a species. In this study, to determine how substantial genomic changes are generated and tolerated within a species, we sequenced a C. elegans strain, CB4856, which is one of the most genetically divergent strains compared to the N2 reference strain. For this comparison, we used the Pacific Biosciences (PacBio) RSII platform (80×, N50 read length 11.8 kb) and generated de novo genome assembly to the level of pseudochromosomes containing 76 contigs (N50 contig = 2.8 Mb). We identified structural variations that affected as many as 2694 genes, most of which are at chromosome arms. Subtelomeric regions contained the most extensive genomic rearrangements, which even created new subtelomeres in some cases. The subtelomere structure of Chromosome VR implies that ancestral telomere damage was repaired by alternative lengthening of telomeres even in the presence of a functional telomerase gene and that a new subtelomere was formed by break-induced replication. Our study demonstrates that substantial genomic changes including structural variations and new subtelomeres can be tolerated within a species, and that these changes may accumulate genetic diversity within a species.
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Affiliation(s)
- Chuna Kim
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Korea 08826
- Department of Biological Sciences, Seoul National University, Seoul, Korea 08826
| | - Jun Kim
- Department of Biological Sciences, Seoul National University, Seoul, Korea 08826
- Research Institute of Basic Sciences, Seoul National University, Seoul, Korea 08826
| | - Sunghyun Kim
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Korea 08826
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, California 90089, USA
| | - Daniel E Cook
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, USA
| | - Kathryn S Evans
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, USA
| | - Erik C Andersen
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, USA
| | - Junho Lee
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Korea 08826
- Department of Biological Sciences, Seoul National University, Seoul, Korea 08826
- Research Institute of Basic Sciences, Seoul National University, Seoul, Korea 08826
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26
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Abstract
The canonical model of RB-mediated tumour suppression developed over the past 30 years is based on the regulation of E2F transcription factors to restrict cell cycle progression. Several additional functions have been proposed for RB, on the basis of which a non-canonical RB pathway can be described. Mechanistically, the non-canonical RB pathway promotes histone modification and regulates chromosome structure in a manner distinct from cell cycle regulation. These functions have implications for chemotherapy response and resistance to targeted anticancer agents. This Opinion offers a framework to guide future studies of RB in basic and clinical research.
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Affiliation(s)
- Frederick A Dick
- London Regional Cancer Program, Children's Health Research Institute, Western University, London, Ontario, Canada.
- London Regional Cancer Program, Department of Biochemistry, Western University, London, Ontario, Canada.
| | - David W Goodrich
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Julien Sage
- Departments of Pediatrics and Genetics, Stanford University, Stanford, CA, USA
| | - Nicholas J Dyson
- Massachusetts General Hospital Cancer Center, Laboratory of Molecular Oncology, Harvard Medical School, Charlestown, MA, USA
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27
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Wojciechowski M, Różycki B, Huy PDQ, Li MS, Bayer EA, Cieplak M. Dual binding in cohesin-dockerin complexes: the energy landscape and the role of short, terminal segments of the dockerin module. Sci Rep 2018; 8:5051. [PMID: 29568013 PMCID: PMC5864761 DOI: 10.1038/s41598-018-23380-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 03/05/2018] [Indexed: 01/09/2023] Open
Abstract
The assembly of the polysaccharide degradating cellulosome machinery is mediated by tight binding between cohesin and dockerin domains. We have used an empirical model known as FoldX as well as molecular mechanics methods to determine the free energy of binding between a cohesin and a dockerin from Clostridium thermocellum in two possible modes that differ by an approximately 180° rotation. Our studies suggest that the full-length wild-type complex exhibits dual binding at room temperature, i.e., the two modes of binding have comparable probabilities at equilibrium. The ability to bind in the two modes persists at elevated temperatures. However, single-point mutations or truncations of terminal segments in the dockerin result in shifting the equilibrium towards one of the binding modes. Our molecular dynamics simulations of mechanical stretching of the full-length wild-type cohesin-dockerin complex indicate that each mode of binding leads to two kinds of stretching pathways, which may be mistakenly taken as evidence of dual binding.
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Affiliation(s)
- Michał Wojciechowski
- Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, PL-02668, Warsaw, Poland
| | - Bartosz Różycki
- Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, PL-02668, Warsaw, Poland
| | - Pham Dinh Quoc Huy
- Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, PL-02668, Warsaw, Poland
- Institute for Computational Sciences and Technology, SBI building, Quang Trung Software city, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City, Vietnam
| | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, PL-02668, Warsaw, Poland
| | - Edward A Bayer
- Department of Biomolecular Sciences, The Weizmann Institute of Science, 234 Herzl Street, Rehovot, 7610001, Israel
| | - Marek Cieplak
- Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, PL-02668, Warsaw, Poland.
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28
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Yang S, Qin X, Cheng C, Li Z, Lou Q, Li J, Chen J. Organization and evolution of four differentially amplified tandem repeats in the Cucumis hystrix genome. Planta 2017; 246:749-761. [PMID: 28668977 DOI: 10.1007/s00425-017-2716-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 05/29/2017] [Indexed: 05/18/2023]
Abstract
Three subtelomeric satellites and one interstitial 5S rDNA were characterized in Cucumis hystrix, and the pericentromeric signals of two C. hystrix subtelomeric satellites along C. sativus chromosomes supported the hypothesis of chromosome fusion in Cucumis. Tandem repeats are chromosome structural fractions consisting of highly repetitive sequences organized in large tandem arrays in most eukaryotes. Differentiation of tandem repeats directly affects the chromosome structure, which contributes to species formation and evolution. Cucumis hystrix (2n = 2x = 24) is the only wild Cucumis species grouped into the same subgenus with C. sativus (2n = 2x = 14), hence its phylogenetic position confers a vital role for C. hystrix to understand the chromosome evolution in Cucumis. However, our knowledge of C. hystrix tandem repeats is insufficient for a detailed understanding of the chromosome evolution in Cucumis. Based on de novo tandem repeat characterization using bioinformatics and in situ hybridization (ISH), we identified and characterized four differentially amplified tandem repeats, Cucumis hystrix satellite 1-3 (CuhySat1-CuhySat3) located at the subtelomeric regions of all chromosomes, and Cucumis hystrix 5S (Cuhy5S) located at the interstitial regions of one single chromosome pair. Comparative ISH mapping using CuhySat1-3 and Cuhy5S revealed high homology of tandem repeats between C. hystrix and C. sativus. Intriguingly, we found signal distribution variations of CuhySat2 and CuhySat3 on C. sativus chromosomes. In comparison to their subtelomeric signal distribution on C. hystrix chromosomes, CuhySat3 showed a pericentromeric signal distribution and CuhySat2 showed both subtelomeric and pericentromeric signal distributions on C. sativus chromosomes. This detailed characterization of four C. hystrix tandem repeats significantly widens our knowledge of the C. hystrix chromosome structure, and the observed signal distribution variations will be helpful for understanding the chromosome evolution of Cucumis.
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Affiliation(s)
- Shuqiong Yang
- State Key Lab of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaodong Qin
- State Key Lab of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Chunyan Cheng
- State Key Lab of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ziang Li
- State Key Lab of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qunfeng Lou
- State Key Lab of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ji Li
- State Key Lab of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jinfeng Chen
- State Key Lab of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
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29
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Kuznetsova MA, Chaban IA, Sheval EV. Visualization of chromosome condensation in plants with large chromosomes. BMC Plant Biol 2017; 17:153. [PMID: 28899358 PMCID: PMC5596468 DOI: 10.1186/s12870-017-1102-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 09/07/2017] [Indexed: 05/13/2023]
Abstract
BACKGROUND Most data concerning chromosome organization have been acquired from studies of a small number of model organisms, the majority of which are mammals. In plants with large genomes, the chromosomes are significantly larger than the animal chromosomes that have been studied to date, and it is possible that chromosome condensation in such plants was modified during evolution. Here, we analyzed chromosome condensation and decondensation processes in order to find structural mechanisms that allowed for an increase in chromosome size. RESULTS We found that anaphase and telophase chromosomes of plants with large chromosomes (average 2C DNA content exceeded 0.8 pg per chromosome) contained chromatin-free cavities in their axial regions in contrast to well-characterized animal chromosomes, which have high chromatin density in the axial regions. Similar to animal chromosomes, two intermediates of chromatin folding were visible inside condensing (during prophase) and decondensing (during telophase) chromosomes of Nigella damascena: approximately 150 nm chromonemata and approximately 300 nm fibers. The spatial folding of the latter fibers occurs in a fundamentally different way than in animal chromosomes, which leads to the formation of chromosomes with axial chromatin-free cavities. CONCLUSION Different compaction topology, but not the number of compaction levels, allowed for the evolution of increased chromosome size in plants.
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Affiliation(s)
- Maria A Kuznetsova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992, Moscow, Russia
| | - Inna A Chaban
- All-Russian Research Institute of Agricultural Biotechnology, Timiryazevskaja 42, 127550, Moscow, Russia
| | - Eugene V Sheval
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992, Moscow, Russia.
- LIA 1066 LFR2O French-Russian Joint Cancer Research Laboratory, 94805, Villejuif, France.
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30
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Schalbetter SA, Goloborodko A, Fudenberg G, Belton JM, Miles C, Yu M, Dekker J, Mirny L, Baxter J. SMC complexes differentially compact mitotic chromosomes according to genomic context. Nat Cell Biol 2017; 19:1071-1080. [PMID: 28825700 PMCID: PMC5640152 DOI: 10.1038/ncb3594] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 07/19/2017] [Indexed: 12/26/2022]
Abstract
Structural maintenance of chromosomes (SMC) protein complexes are key determinants of chromosome conformation. Using Hi-C and polymer modelling, we study how cohesin and condensin, two deeply conserved SMC complexes, organize chromosomes in the budding yeast Saccharomyces cerevisiae. The canonical role of cohesin is to co-align sister chromatids, while condensin generally compacts mitotic chromosomes. We find strikingly different roles for the two complexes in budding yeast mitosis. First, cohesin is responsible for compacting mitotic chromosome arms, independently of sister chromatid cohesion. Polymer simulations demonstrate that this role can be fully accounted for through cis-looping of chromatin. Second, condensin is generally dispensable for compaction along chromosome arms. Instead, it plays a targeted role compacting the rDNA proximal regions and promoting resolution of peri-centromeric regions. Our results argue that the conserved mechanism of SMC complexes is to form chromatin loops and that distinct SMC-dependent looping activities are selectively deployed to appropriately compact chromosomes.
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MESH Headings
- Adenosine Triphosphatases/genetics
- Adenosine Triphosphatases/metabolism
- Cell Cycle Proteins/genetics
- Cell Cycle Proteins/metabolism
- Chromatin/chemistry
- Chromatin/genetics
- Chromatin/metabolism
- Chromatin Assembly and Disassembly
- Chromosomal Proteins, Non-Histone/genetics
- Chromosomal Proteins, Non-Histone/metabolism
- Chromosome Structures
- Chromosomes, Fungal/chemistry
- Chromosomes, Fungal/genetics
- Chromosomes, Fungal/metabolism
- Computer Simulation
- DNA, Fungal/chemistry
- DNA, Fungal/genetics
- DNA, Fungal/metabolism
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- DNA, Ribosomal/metabolism
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/metabolism
- Mitosis
- Models, Genetic
- Models, Molecular
- Multiprotein Complexes/genetics
- Multiprotein Complexes/metabolism
- Nucleic Acid Conformation
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/growth & development
- Saccharomyces cerevisiae/metabolism
- Saccharomyces cerevisiae Proteins/genetics
- Saccharomyces cerevisiae Proteins/metabolism
- Structure-Activity Relationship
- Cohesins
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Affiliation(s)
| | - Anton Goloborodko
- Institute for Medical Engineering and Sciences, Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Geoffrey Fudenberg
- Institute for Medical Engineering and Sciences, Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Jon-Matthew Belton
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Catrina Miles
- Genome Damage and Stability Centre, Science Park Road, University of Sussex, Falmer, Brighton BN1 9RQ, UK
| | - Miao Yu
- Genome Damage and Stability Centre, Science Park Road, University of Sussex, Falmer, Brighton BN1 9RQ, UK
| | - Job Dekker
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Leonid Mirny
- Institute for Medical Engineering and Sciences, Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Jonathan Baxter
- Genome Damage and Stability Centre, Science Park Road, University of Sussex, Falmer, Brighton BN1 9RQ, UK
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31
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Valenzuela CY. Selective intra-dinucleotide interactions and periodicities of bases separated by K sites: a new vision and tool for phylogeny analyses. Biol Res 2017; 50:3. [PMID: 28193284 PMCID: PMC5307875 DOI: 10.1186/s40659-017-0112-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 02/06/2017] [Indexed: 11/06/2022] Open
Abstract
Direct tests of the random or non-random distribution of nucleotides on genomes have been devised to test the hypothesis of neutral, nearly-neutral or selective evolution. These tests are based on the direct base distribution and are independent of the functional (coding or non-coding) or structural (repeated or unique sequences) properties of the DNA. The first approach described the longitudinal distribution of bases in tandem repeats under the Bose-Einstein statistics. A huge deviation from randomness was found. A second approach was the study of the base distribution within dinucleotides whose bases were separated by 0, 1, 2… K nucleotides. Again an enormous difference from the random distribution was found with significances out of tables and programs. These test values were periodical and included the 16 dinucleotides. For example a high "positive" (more observed than expected dinucleotides) value, found in dinucleotides whose bases were separated by (3K + 2) sites, was preceded by two smaller "negative" (less observed than expected dinucleotides) values, whose bases were separated by (3K) or (3K + 1) sites. We examined mtDNAs, prokaryote genomes and some eukaryote chromosomes and found that the significant non-random interactions and periodicities were present up to 1000 or more sites of base separation and in human chromosome 21 until separations of more than 10 millions sites. Each nucleotide has its own significant value of its distance to neutrality; this yields 16 hierarchical significances. A three dimensional table with the number of sites of separation between the bases and the 16 significances (the third dimension is the dinucleotide, individual or taxon involved) gives directly an evolutionary state of the analyzed genome that can be used to obtain phylogenies. An example is provided.
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Affiliation(s)
- Carlos Y Valenzuela
- Programa de Genética Humana, Instituto de Ciencias Biomédicas (ICBM), Facultad de Medicina, Universidad de Chile, Independencia 1027, Casilla 70061, Independencia, Chile.
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Yoon SW, Lee MS, Xaver M, Zhang L, Hong SG, Kong YJ, Cho HR, Kleckner N, Kim KP. Meiotic prophase roles of Rec8 in crossover recombination and chromosome structure. Nucleic Acids Res 2016; 44:9296-9314. [PMID: 27484478 PMCID: PMC5100558 DOI: 10.1093/nar/gkw682] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2015] [Accepted: 07/22/2016] [Indexed: 12/02/2022] Open
Abstract
Rec8 is a prominent component of the meiotic prophase chromosome axis that mediates sister chromatid cohesion, homologous recombination and chromosome synapsis. Here, we explore the prophase roles of Rec8. (i) During the meiotic divisions, Rec8 phosphorylation mediates its separase-mediated cleavage. We show here that such cleavage plays no detectable role for chromosomal events of prophase. (ii) We have analyzed in detail three rec8 phospho-mutants, with 6, 24 or 29 alanine substitutions. A distinct ‘separation of function’ phenotype is revealed. In the mutants, axis formation and recombination initiation are normal, as is non-crossover recombination; in contrast, crossover (CO)-related events are defective. Moreover, the severities of these defects increase coordinately with the number of substitution mutations, consistent with the possibility that global phosphorylation of Rec8 is important for these effects. (iii) We have analyzed the roles of three kinases that phosphorylate Rec8 during prophase. Timed inhibition of Dbf4-dependent Cdc7 kinase confers defects concordant with rec8 phospho-mutant phenotypes. Inhibition of Hrr25 or Cdc5/polo-like kinase does not. Our results suggest that Rec8's prophase function, independently of cohesin cleavage, contributes to CO-specific events in conjunction with the maintenance of homolog bias at the leptotene/zygotene transition of meiotic prophase.
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Affiliation(s)
- Sang-Wook Yoon
- Department of Life Science, Chung-Ang University, Seoul 156-756, Korea
| | - Min-Su Lee
- Department of Life Science, Chung-Ang University, Seoul 156-756, Korea
| | - Martin Xaver
- Max Perutz Laboratories, Chromosome Biology, University of Vienna, Vienna Biocenter, Vienna 1030, Austria
| | - Liangran Zhang
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Soo-Gil Hong
- Department of Life Science, Chung-Ang University, Seoul 156-756, Korea
| | - Yoon-Ju Kong
- Department of Life Science, Chung-Ang University, Seoul 156-756, Korea
| | - Hong-Rae Cho
- Department of Life Science, Chung-Ang University, Seoul 156-756, Korea
| | - Nancy Kleckner
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Keun P Kim
- Department of Life Science, Chung-Ang University, Seoul 156-756, Korea
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Abstract
Erwin Schrödinger's 1944 publication What is Life? is a classic of twentieth century science writing. In his book, Schrödinger discussed the chromosome fibre as the seat of heredity and variation thanks to a hypothetical aperiodic structure - a suggestion that famously spurred on a generation of scientists in their pursuit of the gene as a physico-chemical entity. While historical attention has been given to physicists who were inspired by the book, little has been written about its biologist readers. This paper examines the case of the English evolutionary botanist and cytologist Irène Manton, who took an interest in What is Life? for its relevance to her own research in chromosome structure as a clue to plant phylogeny. Drawing on recently discovered correspondence between Manton and Schrödinger, the paper reconstructs Manton 's path to the book (including the role of the chemist-philosopher Michael Polanyi) and her response to it by way of throwing new light on a pivotal moment in the history of the debate on chromosome structure.
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Affiliation(s)
- Nicola Williams
- School of Philosophy, Religion and History of Science, University of Leeds, Leeds, LS2 9JT, UK.
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Maiato H. Miguel Mota (1922-2016)-the kinetochore engine(er). Chromosome Res 2016; 24:281-3. [PMID: 27106904 DOI: 10.1007/s10577-016-9523-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2016] [Accepted: 04/11/2016] [Indexed: 11/25/2022]
Affiliation(s)
- Helder Maiato
- Chromosome Instability & Dynamics Lab., IBMC - Instituto de Biologia Molecular e Celular, i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.
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Crawley O, Barroso C, Testori S, Ferrandiz N, Silva N, Castellano-Pozo M, Jaso-Tamame AL, Martinez-Perez E. Cohesin-interacting protein WAPL-1 regulates meiotic chromosome structure and cohesion by antagonizing specific cohesin complexes. eLife 2016; 5:e10851. [PMID: 26841696 PMCID: PMC4758955 DOI: 10.7554/elife.10851] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 12/23/2015] [Indexed: 12/21/2022] Open
Abstract
Wapl induces cohesin dissociation from DNA throughout the mitotic cell cycle, modulating sister chromatid cohesion and higher-order chromatin structure. Cohesin complexes containing meiosis-specific kleisin subunits govern most aspects of meiotic chromosome function, but whether Wapl regulates these complexes remains unknown. We show that during C. elegans oogenesis WAPL-1 antagonizes binding of cohesin containing COH-3/4 kleisins, but not REC-8, demonstrating that sensitivity to WAPL-1 is dictated by kleisin identity. By restricting the amount of chromosome-associated COH-3/4 cohesin, WAPL-1 controls chromosome structure throughout meiotic prophase. In the absence of REC-8, WAPL-1 inhibits COH-3/4-mediated cohesion, which requires crossover-fated events formed during meiotic recombination. Thus, WAPL-1 promotes functional specialization of meiotic cohesin: WAPL-1-sensitive COH-3/4 complexes modulate higher-order chromosome structure, while WAPL-1-refractory REC-8 complexes provide stable cohesion. Surprisingly, a WAPL-1-independent mechanism removes cohesin before metaphase I. Our studies provide insight into how meiosis-specific cohesin complexes are regulated to ensure formation of euploid gametes.
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Affiliation(s)
- Oliver Crawley
- Meiosis group, MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Consuelo Barroso
- Meiosis group, MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Sarah Testori
- Meiosis group, MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Nuria Ferrandiz
- Meiosis group, MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Nicola Silva
- Meiosis group, MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Maikel Castellano-Pozo
- Meiosis group, MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Angel Luis Jaso-Tamame
- Meiosis group, MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Enrique Martinez-Perez
- Meiosis group, MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College London, London, United Kingdom
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Abstract
This article describes how empirical discoveries in the 1930s-1950s regarding population variation for chromosomal inversions affected Theodosius Dobzhansky and Richard Goldschmidt. A significant fraction of the empirical work I discuss was done by Dobzhansky and his coworkers; Goldschmidt was an astute interpreter, with strong and unusual commitments. I argue that both belong to a mechanistic tradition in genetics, concerned with the effects of chromosomal organization and systems on the inheritance patterns of species. Their different trajectories illustrate how scientists' commitments affect how they interpret new evidence and adjust to it. Dobzhansky was moved to revised views about selection, while Goldschmidt moved his attention to different genetic phenomena. However different, there are significant connections between the two that enrich our understanding of their views. I focus on two: the role of developmental considerations in Dobzhansky's thought and the role of neutrality and drift in Goldschmidt's evolutionary account. Dobzhansky's struggle with chromosomal variation is not solely about competing schools of thought within the selectionist camp, as insightfully articulated by John Beatty, but also a story of competition between selectionist thinking and developmental perspectives. In contraposition, Goldschmidt emphasized the role of low penetrance mutations that spread neutrally and pointed out that drift could result from developmental canalization. This account adds to the dominant story about Goldschmidt's resistance to the splitting of development from genetics, as told by Garland Allen and Michael Dietrich. The story I tell illustrates how developmental thinking and genetic thinking conflicted and influenced researchers with different convictions about the significance of chromosomal organization.
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Affiliation(s)
- Ehud Lamm
- The Cohn Institute for the History and Philosophy of Sciences and Ideas, Tel Aviv University, 69978, Tel Aviv, Israel.
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Rajkumari K, John KJ, Yadav SR, Bhat KV, Shamurailatpam A, Rao SR. CYTOGENETICAL TREATISE OF INDIAN REPRESENTATIVE SPECIES OF CUCUMIS. A KARYOTYPIC APPROACH. Tsitol Genet 2015; 49:50-60. [PMID: 26841494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Karyomorphological studies have been carried out in nine species and five varieties of the genus Cucumis representing Indian gene pool. The present investigations reveal the occurrence of two somatic chromosome numbers 2n = 14, 24 in the genus. C. ritchiei and C. indicus the two new species, were found to be having somatic chromosome numbers of 2n = 24 and 2n = 20 respectively. The wild species viz. C. hystrix, C. setosus, C. prophetarum, C. dipsaceus, C. indicus have very less number of median-centromeric chromosomes, high asymmetry indices, while melon groups have intermediate number of median -centromeric chromosomes. C. sativus, C. callosus, C. ritchiei show lesser number median-cen-tromeric chromosomes and very less asymmetry indices. The importance of karyotypic variation with respect to speciation within the genus Cucumis have been discussed.
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Yu D, Li S, Jiang N. [Infantile spasm associated with 5q14.3 microdeletion syndrome: clinical and genetic characterization of a core family]. Zhonghua Er Ke Za Zhi 2015; 53:140-142. [PMID: 25876691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
OBJECTIVE To characterize the clinical feature of a child with infantile spasm, karyotype and molecular cytogenetic analyses were performed to investigate the cause of disease and choose a suitable prenatal diagnostic method for the couple with the child. METHOD Routine G-banding was performed to analyze the karyotype of the patient and her parents, and molecular karyotyping was performed using SNP array. Confirmation and segregation studies were performed by fluorescence in situ hybridization (FISH). RESULT The patient presented with severe psychomotor retardation, epilepsy, muscular hypotonia, stereotypic behavior and facial phenotype characterized by bulging forehead, cupid-bow upper lip, large ears with prominent lobes and pronounced occipital protuberance. Subdural collection of fluid was shown in cranial CT scan, and frequent interictal epileptiform discharges and hypsarrhythmia was shown in EEG monitoring. Routine G-banding revealed a normal female karyotype. A 2.03 Mb deletion in 5q14.3 including MEF2C gene was revealed using SNP array, and the patient's molecular karyotype was arr 5q14.3 (87 538 430-89 565 757) ×1. FISH with locus-specific probe RP11-293L20 from the deleted region on metaphase preparations of the patient and her parents confirmed the de novo occurrence of the deletion. CONCLUSION The microdeletion of 5q14.3 was the cause of infantile spasm in the patient. FISH confirmed the de novo occurrence of the microdeletion. SNP array should be chosen as prenatal diagnostic method for the couple with the child.
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Affiliation(s)
- Dongyi Yu
- Department of Genetics, Qingdao Maternal and Children's Hospital, Qingdao 266034, China.
| | - Shuo Li
- Department of Genetics, Qingdao Maternal and Children's Hospital, Qingdao 266034, China
| | - Nan Jiang
- Department of Genetics, Qingdao Maternal and Children's Hospital, Qingdao 266034, China
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Abstract
Chromatin structure can affect the organization and maintenance of chromosomes. Recent discoveries in several filamentous fungi suggest mechanisms for the clustering and co-regulation of secondary metabolite genes or pathogenicity islands. An extreme case of this may be fungal 'accessory', 'conditionally dispensable', or 'supernumerary' chromosomes that often confer beneficial traits. Fungal supernumerary chromosomes may be derived by similar mechanisms as animal or plant B chromosomes, and we thus propose that this term should be reconsidered to capture the wide variety of fungal accessory chromosomes. In some fungi, both the 'ends' of chromosomes and these 'odd B chromosomes are enriched with a silencing histone modification, H3 lysine 27 trimethylation (H3K27me3), suggesting parallel mechanisms in evolving subtelomeric or B-chromosomal pathogenicity islands and secondary metabolite clusters (SMCs).
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Affiliation(s)
- Jonathan M Galazka
- Department of Biochemistry and Biophysics, Center of Genome Research and Biocomputing, Oregon State University, Corvallis, OR 97331, United States
| | - Michael Freitag
- Department of Biochemistry and Biophysics, Center of Genome Research and Biocomputing, Oregon State University, Corvallis, OR 97331, United States.
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Abstract
The study of chromosomal organization and segregation in a handful of bacteria has revealed surprising variety in the mechanisms mediating such fundamental processes. In this study, we further emphasized this diversity by revealing an original organization of the Pseudomonas aeruginosa chromosome. We analyzed the localization of 20 chromosomal markers and several components of the replication machinery in this important opportunistic γ-proteobacteria pathogen. This technique allowed us to show that the 6.3 Mb unique circular chromosome of P. aeruginosa is globally oriented from the old pole of the cell to the division plane/new pole along the oriC-dif axis. The replication machinery is positioned at mid-cell, and the chromosomal loci from oriC to dif are moved sequentially to mid-cell prior to replication. The two chromosomal copies are subsequently segregated at their final subcellular destination in the two halves of the cell. We identified two regions in which markers localize at similar positions, suggesting a bias in the distribution of chromosomal regions in the cell. The first region encompasses 1.4 Mb surrounding oriC, where loci are positioned around the 0.2/0.8 relative cell length upon segregation. The second region contains at least 800 kb surrounding dif, where loci show an extensive colocalization step following replication. We also showed that disrupting the ParABS system is very detrimental in P. aeruginosa. Possible mechanisms responsible for the coordinated chromosomal segregation process and for the presence of large distinctive regions are discussed. The processes of chromosomal disposition, replication, and segregation in bacteria have been characterized only in a handful of species, yet there is remarkable diversity in the ways such fundamental processes are managed. In this study, we analyzed the subcellular chromosomal organization of Pseudomonas aeruginosa, an important bacterial pathogen belonging to a large bacterial group involved in plant and human diseases. Most bacterial genomes are circular molecules, and DNA replication proceeds bidirectionally from a single origin to the opposite Ter region, where the replication forks meet. Analysis by fluorescence microscopy of 20 chromosomal markers and components of the replication machinery revealed that the 6.3 Mb chromosome is globally oriented from the old pole of the cell to the division plane/new pole along the oriC-Ter axis. The replication machinery is positioned at mid-cell, and chromosomal loci from oriC to Ter are moved sequentially to mid-cell prior to replication. The two sister chromosomes are subsequently segregated at their final subcellular destination in the two halves of the cell. This study also identified two large regions in which several chromosomal loci show a biased localization pattern, suggesting that processes responsible for long-range chromosomal organization might exist in P. aeruginosa.
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Affiliation(s)
- Isabelle Vallet-Gely
- CNRS, Centre de Génétique Moléculaire, UPR3404, Gif-sur-Yvette, France
- Université Paris-Sud, Orsay, France
- * E-mail: (IV-G); (FB)
| | - Frédéric Boccard
- CNRS, Centre de Génétique Moléculaire, UPR3404, Gif-sur-Yvette, France
- Université Paris-Sud, Orsay, France
- * E-mail: (IV-G); (FB)
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Aragon L, Martinez-Perez E, Merkenschlager M. Condensin, cohesin and the control of chromatin states. Curr Opin Genet Dev 2013; 23:204-11. [PMID: 23312842 DOI: 10.1016/j.gde.2012.11.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Accepted: 11/08/2012] [Indexed: 10/27/2022]
Abstract
Cohesin and condensin complexes are essential for defining the topology of chromosomes through the cell cycle. Here we look at the emerging role of these complexes in regulating chromatin structure and gene expression and reflect on how these activities could be linked with chromosome topology.
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Affiliation(s)
- Luis Aragon
- Cell Cycle Group, MRC Clinical Sciences Centre, Imperial College London, Du Cane Road, London W12 0NN, UK.
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Noble WS, Blau CA, Dekker J, Duan ZJ, Mao Y. The structure and function of chromatin and chromosomes. Pac Symp Biocomput 2012:434-440. [PMID: 22174298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
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Yang XY, Zhang Y, Sun XP, Cui YG, Qian XQ, Mao YD, Liu JY. [Sperm chromatin structure assay predicts the outcome of intrauterine insemination]. Zhonghua Nan Ke Xue 2011; 17:977-983. [PMID: 22141266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
OBJECTIVE Sperm chromatin structure assay (SCSA), as a clinically practical technique for the analysis of DNA damage, is rarely reported in China. This study focuses on the correlation of DNA damage with the pregnancy rate of intrauterine insemination (IUI). METHODS We performed semen analysis for 482 couples undergoing IUI, calculated the DNA fragmentation index (DFI) by SCSA, and observed the relationship between DFI and the pregnancy rate of IUI. RESULTS Clinical pregnancy was achieved in 5 (5.26%) of the 95 cases with DFI > 25%, and in 59 (15.25%) of the 387 cases with DFI < or = 25%. Those with sperm DFI >25% had significantly lower rates of biochemical pregnancy and clinical pregnancy than those with DFI < or = 25% (OR: 0.37, 95% CI: 0.14 - 0.96 and OR: 0.38, 95% CI: 0.16 - 0.97). No significant differences were found in the DFI of 54 cases between the first and the second cycle ([15.05 +/- 7.98]% vs [17.25 +/- 12.18]%, P > 0.05). Sperm DFI was significantly negatively correlated with sperm concentration, sperm motility and total progressively motile sperm count (P < 0.01). CONCLUSION The pregnancy rate of IUI is significantly lower in couples with DFI >25% than in those with DFI < or = 25%. Sperm DFI obtained from SCSA is partly correlated with sperm concentration and motility, and it is a robust predictor of the IUI outcome.
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Affiliation(s)
- Xiao-yu Yang
- Center of Reproductive Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, China
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Abstract
To understand how chromosome shapes are determined by actions of condensins and cohesin, we devised a series of protocols in which their levels are precisely changed in Xenopus egg extracts. When the relative ratio of condensin I to II is forced to be smaller, embryonic chromosomes become shorter and thicker, being reminiscent of somatic chromosomes. Further depletion of condensin II unveils its contribution to axial shortening of chromosomes. Cohesin helps juxtapose sister chromatid arms by collaborating with condensin I and counteracting condensin II. Thus, chromosome shaping is achieved by an exquisite balance among condensin I and II and cohesin.
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Affiliation(s)
- Keishi Shintomi
- Chromosome Dynamics Laboratory, RIKEN Advanced Science Institute, Saitama 351-0198, Japan
| | - Tatsuya Hirano
- Chromosome Dynamics Laboratory, RIKEN Advanced Science Institute, Saitama 351-0198, Japan
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Mun JH, Kwon SJ, Seol YJ, Kim JA, Jin M, Kim JS, Lim MH, Lee SI, Hong JK, Park TH, Lee SC, Kim BJ, Seo MS, Baek S, Lee MJ, Shin JY, Hahn JH, Hwang YJ, Lim KB, Park JY, Lee J, Yang TJ, Yu HJ, Choi IY, Choi BS, Choi SR, Ramchiary N, Lim YP, Fraser F, Drou N, Soumpourou E, Trick M, Bancroft I, Sharpe AG, Parkin IAP, Batley J, Edwards D, Park BS. Sequence and structure of Brassica rapa chromosome A3. Genome Biol 2010; 11:R94. [PMID: 20875114 PMCID: PMC2965386 DOI: 10.1186/gb-2010-11-9-r94] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2010] [Revised: 09/07/2010] [Accepted: 09/27/2010] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND The species Brassica rapa includes important vegetable and oil crops. It also serves as an excellent model system to study polyploidy-related genome evolution because of its paleohexaploid ancestry and its close evolutionary relationships with Arabidopsis thaliana and other Brassica species with larger genomes. Therefore, its genome sequence will be used to accelerate both basic research on genome evolution and applied research across the cultivated Brassica species. RESULTS We have determined and analyzed the sequence of B. rapa chromosome A3. We obtained 31.9 Mb of sequences, organized into nine contigs, which incorporated 348 overlapping BAC clones. Annotation revealed 7,058 protein-coding genes, with an average gene density of 4.6 kb per gene. Analysis of chromosome collinearity with the A. thaliana genome identified conserved synteny blocks encompassing the whole of the B. rapa chromosome A3 and sections of four A. thaliana chromosomes. The frequency of tandem duplication of genes differed between the conserved genome segments in B. rapa and A. thaliana, indicating differential rates of occurrence/retention of such duplicate copies of genes. Analysis of 'ancestral karyotype' genome building blocks enabled the development of a hypothetical model for the derivation of the B. rapa chromosome A3. CONCLUSIONS We report the near-complete chromosome sequence from a dicotyledonous crop species. This provides an example of the complexity of genome evolution following polyploidy. The high degree of contiguity afforded by the clone-by-clone approach provides a benchmark for the performance of whole genome shotgun approaches presently being applied in B. rapa and other species with complex genomes.
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Affiliation(s)
- Jeong-Hwan Mun
- Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, 150 Suin-ro, Gwonseon-gu, Suwon 441-707, Korea
| | - Soo-Jin Kwon
- Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, 150 Suin-ro, Gwonseon-gu, Suwon 441-707, Korea
| | - Young-Joo Seol
- Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, 150 Suin-ro, Gwonseon-gu, Suwon 441-707, Korea
| | - Jin A Kim
- Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, 150 Suin-ro, Gwonseon-gu, Suwon 441-707, Korea
| | - Mina Jin
- Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, 150 Suin-ro, Gwonseon-gu, Suwon 441-707, Korea
| | - Jung Sun Kim
- Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, 150 Suin-ro, Gwonseon-gu, Suwon 441-707, Korea
| | - Myung-Ho Lim
- Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, 150 Suin-ro, Gwonseon-gu, Suwon 441-707, Korea
| | - Soo-In Lee
- Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, 150 Suin-ro, Gwonseon-gu, Suwon 441-707, Korea
| | - Joon Ki Hong
- Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, 150 Suin-ro, Gwonseon-gu, Suwon 441-707, Korea
| | - Tae-Ho Park
- Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, 150 Suin-ro, Gwonseon-gu, Suwon 441-707, Korea
| | - Sang-Choon Lee
- Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, 150 Suin-ro, Gwonseon-gu, Suwon 441-707, Korea
| | - Beom-Jin Kim
- Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, 150 Suin-ro, Gwonseon-gu, Suwon 441-707, Korea
| | - Mi-Suk Seo
- Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, 150 Suin-ro, Gwonseon-gu, Suwon 441-707, Korea
| | - Seunghoon Baek
- Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, 150 Suin-ro, Gwonseon-gu, Suwon 441-707, Korea
| | - Min-Jee Lee
- Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, 150 Suin-ro, Gwonseon-gu, Suwon 441-707, Korea
| | - Ja Young Shin
- Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, 150 Suin-ro, Gwonseon-gu, Suwon 441-707, Korea
| | - Jang-Ho Hahn
- Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, 150 Suin-ro, Gwonseon-gu, Suwon 441-707, Korea
| | - Yoon-Jung Hwang
- Department of Horticulture, College of Agriculture and Life Science, Kyungpook National University, 1370 Sangyeok-dong, Buk-gu, Daegu 702-701, Korea
| | - Ki-Byung Lim
- Department of Horticulture, College of Agriculture and Life Science, Kyungpook National University, 1370 Sangyeok-dong, Buk-gu, Daegu 702-701, Korea
| | - Jee Young Park
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, 599 Gwanak-ro, Gwanak-gu, Seoul 151-921, Korea
| | - Jonghoon Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, 599 Gwanak-ro, Gwanak-gu, Seoul 151-921, Korea
| | - Tae-Jin Yang
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, 599 Gwanak-ro, Gwanak-gu, Seoul 151-921, Korea
| | - Hee-Ju Yu
- Department of Life Sciences, The Catholic University of Korea, 43-1 Yeokgok 2-dong, Wonmi-gu, Bucheon 420-743, Korea
| | - Ik-Young Choi
- National Instrumentation Center for Environmental Management, Seoul National University, 599 Gwanak-ro, Gwanak-gu, Seoul 151-921, Korea
| | - Beom-Soon Choi
- National Instrumentation Center for Environmental Management, Seoul National University, 599 Gwanak-ro, Gwanak-gu, Seoul 151-921, Korea
| | - Su Ryun Choi
- Department of Horticulture, Chungnam National University, 220 Kung-dong, Yusong-gu, Daejon 305-764, Korea
| | - Nirala Ramchiary
- Department of Horticulture, Chungnam National University, 220 Kung-dong, Yusong-gu, Daejon 305-764, Korea
| | - Yong Pyo Lim
- Department of Horticulture, Chungnam National University, 220 Kung-dong, Yusong-gu, Daejon 305-764, Korea
| | | | - Nizar Drou
- John Innes Centre, Colney, Norwich NR4 7UH, UK
| | | | | | | | - Andrew G Sharpe
- NRC Plant Biotechnology Institute, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
| | - Isobel AP Parkin
- Agriculture and Agri-Food Canada, Saskatoon Research Centre, Saskatoon, SK S7N OX2, Canada
| | - Jacqueline Batley
- ARC Centre of Excellence for Integrative Legume Research and School of Land, Crop and Food Sciences, University of Queensland, Brisbane, QLD 4067, Australia
| | - Dave Edwards
- Australian Centre for Plant Functional Genomics and School of Land Crop and Food Sciences, University of Queensland, Brisbane, QLD 4067, Australia
| | - Beom-Seok Park
- Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, 150 Suin-ro, Gwonseon-gu, Suwon 441-707, Korea
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Matsuda A, Shao L, Boulanger J, Kervrann C, Carlton PM, Kner P, Agard D, Sedat JW. Condensed mitotic chromosome structure at nanometer resolution using PALM and EGFP- histones. PLoS One 2010; 5:e12768. [PMID: 20856676 PMCID: PMC2939896 DOI: 10.1371/journal.pone.0012768] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2010] [Accepted: 08/19/2010] [Indexed: 11/18/2022] Open
Abstract
Photoactivated localization microscopy (PALM) and related fluorescent biological imaging methods are capable of providing very high spatial resolutions (up to 20 nm). Two major demands limit its widespread use on biological samples: requirements for photoactivatable/photoconvertible fluorescent molecules, which are sometimes difficult to incorporate, and high background signals from autofluorescence or fluorophores in adjacent focal planes in three-dimensional imaging which reduces PALM resolution significantly. We present here a high-resolution PALM method utilizing conventional EGFP as the photoconvertible fluorophore, improved algorithms to deal with high levels of biological background noise, and apply this to imaging higher order chromatin structure. We found that the emission wavelength of EGFP is efficiently converted from green to red when exposed to blue light in the presence of reduced riboflavin. The photon yield of red-converted EGFP using riboflavin is comparable to other bright photoconvertible fluorescent proteins that allow <20 nm resolution. We further found that image pre-processing using a combination of denoising and deconvolution of the raw PALM images substantially improved the spatial resolution of the reconstruction from noisy images. Performing PALM on Drosophila mitotic chromosomes labeled with H2AvD-EGFP, a histone H2A variant, revealed filamentous components of ∼70 nm. This is the first observation of fine chromatin filaments specific for one histone variant at a resolution approximating that of conventional electron microscope images (10-30 nm). As demonstrated by modeling and experiments on a challenging specimen, the techniques described here facilitate super-resolution fluorescent imaging with common biological samples.
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Affiliation(s)
- Atsushi Matsuda
- Department of Biochemistry and Biophysics, The Keck Center for Advanced Microscopy, University of California San Francisco, San Francisco, California, United States of America
| | - Lin Shao
- Department of Biochemistry and Biophysics, The Keck Center for Advanced Microscopy, University of California San Francisco, San Francisco, California, United States of America
| | | | - Charles Kervrann
- INRIA Rennes Bretagne Atlantique, Campus Universitaire de Beaulieu, Rennes, France
| | - Peter M. Carlton
- Department of Biochemistry and Biophysics, The Keck Center for Advanced Microscopy, University of California San Francisco, San Francisco, California, United States of America
| | - Peter Kner
- Department of Biochemistry and Biophysics, The Keck Center for Advanced Microscopy, University of California San Francisco, San Francisco, California, United States of America
| | - David Agard
- Howard Hughes Medical Institute and Department of Biochemistry and Biophysics, The Keck Center for Advanced Microscopy, University of California San Francisco, San Francisco, California, United States of America
| | - John W. Sedat
- Department of Biochemistry and Biophysics, The Keck Center for Advanced Microscopy, University of California San Francisco, San Francisco, California, United States of America
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Abstract
DNA topoisomerases are enzymes that disentangle the topological problems that arise in double-stranded DNA. Many of these can be solved by the generation of either single or double strand breaks. However, where there is a clear requirement to alter DNA topology by introducing transient double strand breaks, only DNA topoisomerase II (TOP2) can carry out this reaction. Extensive biochemical and structural studies have provided detailed models of how TOP2 alters DNA structure, and recent molecular studies have greatly expanded knowledge of the biological contexts in which TOP2 functions, such as DNA replication, transcription and chromosome segregation -- processes that are essential for preventing tumorigenesis.
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Affiliation(s)
- John L Nitiss
- Molecular Pharmacology Department, St Jude Children's Research Hospital, Memphis, TN 38105, USA.
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Victoria B, Ahmed A, Zuerner RL, Ahmed N, Bulach DM, Quinteiro J, Hartskeerl RA. Conservation of the S10-spc-alpha locus within otherwise highly plastic genomes provides phylogenetic insight into the genus Leptospira. PLoS One 2008; 3:e2752. [PMID: 18648538 PMCID: PMC2481283 DOI: 10.1371/journal.pone.0002752] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2008] [Accepted: 06/24/2008] [Indexed: 11/21/2022] Open
Abstract
S10-spc-α is a 17.5 kb cluster of 32 genes encoding ribosomal proteins. This locus has an unusual composition and organization in Leptospira interrogans. We demonstrate the highly conserved nature of this region among diverse Leptospira and show its utility as a phylogenetically informative region. Comparative analyses were performed by PCR using primer sets covering the whole locus. Correctly sized fragments were obtained by PCR from all L. interrogans strains tested for each primer set indicating that this locus is well conserved in this species. Few differences were detected in amplification profiles between different pathogenic species, indicating that the S10-spc-α locus is conserved among pathogenic Leptospira. In contrast, PCR analysis of this locus using DNA from saprophytic Leptospira species and species with an intermediate pathogenic capacity generated varied results. Sequence alignment of the S10-spc-α locus from two pathogenic species, L. interrogans and L. borgpetersenii, with the corresponding locus from the saprophyte L. biflexa serovar Patoc showed that genetic organization of this locus is well conserved within Leptospira. Multilocus sequence typing (MLST) of four conserved regions resulted in the construction of well-defined phylogenetic trees that help resolve questions about the interrelationships of pathogenic Leptospira. Based on the results of secY sequence analysis, we found that reliable species identification of pathogenic Leptospira is possible by comparative analysis of a 245 bp region commonly used as a target for diagnostic PCR for leptospirosis. Comparative analysis of Leptospira strains revealed that strain H6 previously classified as L. inadai actually belongs to the pathogenic species L. interrogans and that L. meyeri strain ICF phylogenetically co-localized with the pathogenic clusters. These findings demonstrate that the S10-spc-α locus is highly conserved throughout the genus and may be more useful in comparing evolution of the genus than loci studied previously.
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Affiliation(s)
- Berta Victoria
- Department of Biochemistry and Molecular Biology, Faculty of Biology, University of Santiago de Compostela, Galicia, Spain
| | - Ahmed Ahmed
- WHO/FAO/OIE and National Collaborating Centre for Reference and Research on Leptospirosis, Department of Biomedical Research, Royal Tropical Institute (KIT), Amsterdam, The Netherlands
| | - Richard L. Zuerner
- Bacterial Diseases of Livestock Research Unit, National Animal Disease Center, Agricultural Research Service, U.S. Department of Agriculture, Ames, Iowa, United States of America
| | - Niyaz Ahmed
- Pathogen Evolution Laboratory, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Dieter M. Bulach
- Australian Research Council Centre of Excellence in Structural and Functional Microbial Genomics, Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Javier Quinteiro
- Department of Biochemistry and Molecular Biology, Faculty of Biology, University of Santiago de Compostela, Galicia, Spain
| | - Rudy A. Hartskeerl
- WHO/FAO/OIE and National Collaborating Centre for Reference and Research on Leptospirosis, Department of Biomedical Research, Royal Tropical Institute (KIT), Amsterdam, The Netherlands
- * E-mail:
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