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Hill SL, Rogan PK, Wang YX, Knoll JHM. Differentially accessible, single copy sequences form contiguous domains along metaphase chromosomes that are conserved among multiple tissues. Mol Cytogenet 2021; 14:49. [PMID: 34670606 PMCID: PMC8527651 DOI: 10.1186/s13039-021-00567-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 09/08/2021] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND During mitosis, chromatin engages in a dynamic cycle of condensation and decondensation. Condensation into distinct units to ensure high fidelity segregation is followed by rapid and reproducible decondensation to produce functional daughter cells. Factors contributing to the reproducibility of chromatin structure between cell generations are not well understood. We investigated local metaphase chromosome condensation along mitotic chromosomes within genomic intervals showing differential accessibility (DA) between homologs. DA was originally identified using short sequence-defined single copy (sc) DNA probes of < 5 kb in length by fluorescence in situ hybridization (scFISH) in peripheral lymphocytes. These structural differences between metaphase homologs are non-random, stable, and heritable epigenetic marks which have led to the proposed function of DA as a marker of chromatin memory. Here, we characterize the organization of DA intervals into chromosomal domains by identifying multiple DA loci in close proximity to each other and examine the conservation of DA between tissues. RESULTS We evaluated multiple adjacent scFISH probes at 6 different DA loci from chromosomal regions 2p23, 3p24, 12p12, 15q22, 15q24 and 20q13 within peripheral blood T-lymphocytes. DA was organized within domains that extend beyond the defined boundaries of individual scFISH probes. Based on hybridizations of 2 to 4 scFISH probes per domain, domains ranged in length from 16.0 kb to 129.6 kb. Transcriptionally inert chromosomal DA regions in T-lymphocytes also demonstrated conservation of DA in bone marrow and fibroblast cells. CONCLUSIONS We identified novel chromosomal regions with allelic differences in metaphase chromosome accessibility and demonstrated that these accessibility differences appear to be aggregated into contiguous domains extending beyond individual scFISH probes. These domains are encompassed by previously established topologically associated domain (TAD) boundaries. DA appears to be a conserved feature of human metaphase chromosomes across different stages of lymphocyte differentiation and germ cell origin, consistent with its proposed role in maintenance of intergenerational cellular chromosome memory.
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Affiliation(s)
- Seana L Hill
- Department of Pathology & Laboratory Medicine, Schulich School of Medicine & Dentistry, University of Western Ontario, London, Canada
| | - Peter K Rogan
- Departments of Biochemistry and Oncology, Schulich School of Medicine & Dentistry, University of Western Ontario, London, Canada
- Cytognomix Inc., London, ON, Canada
| | - Yi Xuan Wang
- Department of Pathology & Laboratory Medicine, Schulich School of Medicine & Dentistry, University of Western Ontario, London, Canada
| | - Joan H M Knoll
- Department of Pathology & Laboratory Medicine, Schulich School of Medicine & Dentistry, University of Western Ontario, London, Canada.
- Cytognomix Inc., London, ON, Canada.
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Mostovoy Y, Yilmaz F, Chow SK, Chu C, Lin C, Geiger EA, Meeks NJL, Chatfield KC, Coughlin CR, Surti U, Kwok PY, Shaikh TH. Genomic regions associated with microdeletion/microduplication syndromes exhibit extreme diversity of structural variation. Genetics 2021; 217:6066166. [PMID: 33724415 DOI: 10.1093/genetics/iyaa038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Accepted: 12/18/2020] [Indexed: 11/12/2022] Open
Abstract
Segmental duplications (SDs) are a class of long, repetitive DNA elements whose paralogs share a high level of sequence similarity with each other. SDs mediate chromosomal rearrangements that lead to structural variation in the general population as well as genomic disorders associated with multiple congenital anomalies, including the 7q11.23 (Williams-Beuren Syndrome, WBS), 15q13.3, and 16p12.2 microdeletion syndromes. Population-level characterization of SDs has generally been lacking because most techniques used for analyzing these complex regions are both labor and cost intensive. In this study, we have used a high-throughput technique to genotype complex structural variation with a single molecule, long-range optical mapping approach. We characterized SDs and identified novel structural variants (SVs) at 7q11.23, 15q13.3, and 16p12.2 using optical mapping data from 154 phenotypically normal individuals from 26 populations comprising five super-populations. We detected several novel SVs for each locus, some of which had significantly different prevalence between populations. Additionally, we localized the microdeletion breakpoints to specific paralogous duplicons located within complex SDs in two patients with WBS, one patient with 15q13.3, and one patient with 16p12.2 microdeletion syndromes. The population-level data presented here highlights the extreme diversity of large and complex SVs within SD-containing regions. The approach we outline will greatly facilitate the investigation of the role of inter-SD structural variation as a driver of chromosomal rearrangements and genomic disorders.
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Affiliation(s)
- Yulia Mostovoy
- Cardiovascular Research Institute, UCSF School of Medicine, San Francisco, CA 94143, USA
| | - Feyza Yilmaz
- Department of Integrative Biology, University of Colorado Denver, Denver, CO 80204, USA.,Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Stephen K Chow
- Cardiovascular Research Institute, UCSF School of Medicine, San Francisco, CA 94143, USA
| | - Catherine Chu
- Cardiovascular Research Institute, UCSF School of Medicine, San Francisco, CA 94143, USA
| | - Chin Lin
- Cardiovascular Research Institute, UCSF School of Medicine, San Francisco, CA 94143, USA
| | - Elizabeth A Geiger
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Naomi J L Meeks
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Kathryn C Chatfield
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado School of Medicine, Aurora, CO 80045, USA.,Department of Pediatrics, Section of Cardiology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Curtis R Coughlin
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Urvashi Surti
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Pui-Yan Kwok
- Cardiovascular Research Institute, UCSF School of Medicine, San Francisco, CA 94143, USA.,Department of Dermatology, UCSF School of Medicine, San Francisco, CA 94143, USA.,Institute for Human Genetics, UCSF School of Medicine, San Francisco, CA 94143, USA
| | - Tamim H Shaikh
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado School of Medicine, Aurora, CO 80045, USA
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Karger L, Khan WA, Calabio R, Singh R, Xiang B, Babu A, Cohen N, Yang AC, Scott SA. Maternal uniparental disomy of chromosome 15 and concomitant STRC and CATSPER2 deletion-mediated deafness-infertility syndrome. Am J Med Genet A 2017; 173:1436-1439. [PMID: 28317263 DOI: 10.1002/ajmg.a.38154] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 01/03/2017] [Accepted: 01/06/2017] [Indexed: 11/12/2022]
Affiliation(s)
- Lisa Karger
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Wahab A Khan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Rafaela Calabio
- Division of Neonatology, Mount Sinai West, New York, New York
| | - Ram Singh
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Bixia Xiang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Arvind Babu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Ninette Cohen
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Amy C Yang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Stuart A Scott
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
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Parks MM, Lawrence CE, Raphael BJ. Detecting non-allelic homologous recombination from high-throughput sequencing data. Genome Biol 2015; 16:72. [PMID: 25886137 PMCID: PMC4425883 DOI: 10.1186/s13059-015-0633-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 03/16/2015] [Indexed: 12/27/2022] Open
Abstract
Non-allelic homologous recombination (NAHR) is a common mechanism for generating genome rearrangements and is implicated in numerous genetic disorders, but its detection in high-throughput sequencing data poses a serious challenge. We present a probabilistic model of NAHR and demonstrate its ability to find NAHR in low-coverage sequencing data from 44 individuals. We identify NAHR-mediated deletions or duplications in 109 of 324 potential NAHR loci in at least one of the individuals. These calls segregate by ancestry, are more common in closely spaced repeats, often result in duplicated genes or pseudogenes, and affect highly studied genes such as GBA and CYP2E1.
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Affiliation(s)
- Matthew M Parks
- Division of Applied Mathematics, Brown University, Providence, USA.
| | - Charles E Lawrence
- Division of Applied Mathematics, Brown University, Providence, USA. .,Center for Computational Molecular Biology, Brown University, Providence, USA.
| | - Benjamin J Raphael
- Center for Computational Molecular Biology, Brown University, Providence, USA. .,Department of Computer Science, Brown University, Providence, USA.
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Khan WA, Rogan PK, Knoll JHM. Localized, non-random differences in chromatin accessibility between homologous metaphase chromosomes. Mol Cytogenet 2014; 7:70. [PMID: 25520753 PMCID: PMC4269072 DOI: 10.1186/s13039-014-0070-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 10/06/2014] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Condensation differences along the lengths of homologous, mitotic metaphase chromosomes are well known. This study reports molecular cytogenetic data showing quantifiable localized differences in condensation between homologs that are related to differences in accessibility (DA) of associated DNA probe targets. Reproducible DA was observed for ~10% of locus-specific, short (1.5-5 kb) single copy DNA probes used in fluorescence in situ hybridization. RESULTS Fourteen probes (from chromosomes 1, 5, 9, 11, 15, 17, 22) targeting genic and intergenic regions were developed and hybridized to cells from 10 individuals with cytogenetically-distinguishable homologs. Differences in hybridization between homologs were non-random for 8 genomic regions (RGS7, CACNA1B, GABRA5, SNRPN, HERC2, PMP22:IVS3, ADORA2B:IVS1, ACR) and were not unique to known imprinted domains or specific chromosomes. DNA probes within CCNB1, C9orf66, ADORA2B:Promoter-Ex1, PMP22:IVS4-Ex 5, and intergenic region 1p36.3 showed no DA (equivalent accessibility), while OPCML showed unbiased DA. To pinpoint probe locations, we performed 3D-structured illumination microscopy (3D-SIM). This showed that genomic regions with DA had 3.3-fold greater volumetric, integrated probe intensities and broad distributions of probe depths along axial and lateral axes of the 2 homologs, compared to a low copy probe target (NOMO1) with equivalent accessibility. Genomic regions with equivalent accessibility were also enriched for epigenetic marks of open interphase chromatin (DNase I HS, H3K27Ac, H3K4me1) to a greater extent than regions with DA. CONCLUSIONS This study provides evidence that DA is non-random and reproducible; it is locus specific, but not unique to known imprinted regions or specific chromosomes. Non-random DA was also shown to be heritable within a 2 generation family. DNA probe volume and depth measurements of hybridized metaphase chromosomes further show locus-specific chromatin accessibility differences by super-resolution 3D-SIM. Based on these data and the analysis of interphase epigenetic marks of genomic intervals with DA, we conclude that there are localized differences in compaction of homologs during mitotic metaphase and that these differences may arise during or preceding metaphase chromosome compaction. Our results suggest new directions for locus-specific structural analysis of metaphase chromosomes, motivated by the potential relationship of these findings to underlying epigenetic changes established during interphase.
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Affiliation(s)
- Wahab A Khan
- />Department of Pathology and Laboratory Medicine, University of Western Ontario, London, ON N6A 5C1 Canada
- />Cytognomix, Inc, London, ON N6G 4X8 Canada
| | - Peter K Rogan
- />Departments of Biochemistry and Computer Science, University of Western Ontario, London, ON N6A 5C1 Canada
- />Cytognomix, Inc, London, ON N6G 4X8 Canada
| | - Joan HM Knoll
- />Department of Pathology and Laboratory Medicine, University of Western Ontario, London, ON N6A 5C1 Canada
- />Cytognomix, Inc, London, ON N6G 4X8 Canada
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Dorman SN, Shirley BC, Knoll JHM, Rogan PK. Expanding probe repertoire and improving reproducibility in human genomic hybridization. Nucleic Acids Res 2013; 41:e81. [PMID: 23376933 PMCID: PMC3627568 DOI: 10.1093/nar/gkt048] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Revised: 12/21/2012] [Accepted: 01/11/2013] [Indexed: 12/12/2022] Open
Abstract
Diagnostic DNA hybridization relies on probes composed of single copy (sc) genomic sequences. Sc sequences in probe design ensure high specificity and avoid cross-hybridization to other regions of the genome, which could lead to ambiguous results that are difficult to interpret. We examine how the distribution and composition of repetitive sequences in the genome affects sc probe performance. A divide and conquer algorithm was implemented to design sc probes. With this approach, sc probes can include divergent repetitive elements, which hybridize to unique genomic targets under higher stringency experimental conditions. Genome-wide custom probe sets were created for fluorescent in situ hybridization (FISH) and microarray genomic hybridization. The scFISH probes were developed for detection of copy number changes within small tumour suppressor genes and oncogenes. The microarrays demonstrated increased reproducibility by eliminating cross-hybridization to repetitive sequences adjacent to probe targets. The genome-wide microarrays exhibited lower median coefficients of variation (17.8%) for two HapMap family trios. The coefficients of variations of commercial probes within 300 nt of a repetitive element were 48.3% higher than the nearest custom probe. Furthermore, the custom microarray called a chromosome 15q11.2q13 deletion more consistently. This method for sc probe design increases probe coverage for FISH and lowers variability in genomic microarrays.
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Affiliation(s)
- Stephanie N. Dorman
- Department of Biochemistry, University of Western Ontario, London, Ontario N6A 3K7, Canada, Department of Computer Science, University of Western Ontario, London, Ontario N6A 3K7, Canada and Department of Pathology, University of Western Ontario, London, Ontario N6A 3K7, Canada
| | - Ben C. Shirley
- Department of Biochemistry, University of Western Ontario, London, Ontario N6A 3K7, Canada, Department of Computer Science, University of Western Ontario, London, Ontario N6A 3K7, Canada and Department of Pathology, University of Western Ontario, London, Ontario N6A 3K7, Canada
| | - Joan H. M. Knoll
- Department of Biochemistry, University of Western Ontario, London, Ontario N6A 3K7, Canada, Department of Computer Science, University of Western Ontario, London, Ontario N6A 3K7, Canada and Department of Pathology, University of Western Ontario, London, Ontario N6A 3K7, Canada
| | - Peter K. Rogan
- Department of Biochemistry, University of Western Ontario, London, Ontario N6A 3K7, Canada, Department of Computer Science, University of Western Ontario, London, Ontario N6A 3K7, Canada and Department of Pathology, University of Western Ontario, London, Ontario N6A 3K7, Canada
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Khan WA, Chisholm R, Tadayyon S, Subasinghe A, Norton P, Samarabandu J, Johnston LJ, Knoll JH, Rogan PK. Relating centromeric topography in fixed human chromosomes to α-satellite DNA and CENP-B distribution. Cytogenet Genome Res 2013; 139:234-42. [PMID: 23548580 DOI: 10.1159/000348744] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/12/2012] [Indexed: 11/19/2022] Open
Abstract
Despite extensive analyses on the centromere and its associated proteins, detailed studies of centromeric DNA structure have provided limited information about its topography in condensed chromatin. We have developed a method with correlative fluorescence light microscopy and atomic force microscopy that investigates the physical and structural organization of α-satellite DNA sequences in the context of its associated protein, CENP-B, on human metaphase chromosome topography. Comparison of centromeric DNA and protein distribution patterns in fixed homologous chromosomes indicates that CENP-B and α-satellite DNA are distributed distinctly from one another and relative to observed centromeric ridge topography. Our approach facilitates correlated studies of multiple chromatin components comprising higher-order structures of human metaphase chromosomes.
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Affiliation(s)
- W A Khan
- Department of Pathology, Schulich School of Medicine and Dentistry, London, Ont, Canada
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Park NI, Rogan PK, Tarnowski HE, Knoll JH. Structural and genic characterization of stable genomic regions in breast cancer: relevance to chemotherapy. Mol Oncol 2012; 6:347-59. [PMID: 22342187 PMCID: PMC5528331 DOI: 10.1016/j.molonc.2012.01.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2011] [Revised: 11/28/2011] [Accepted: 01/02/2012] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Cancer genomes accumulate frequent and diverse chromosomal abnormalities as well as gene mutations but must maintain the ability to survive in vivo. We hypothesize that genetic selection acts to maintain tumour survival by preserving copy number of specific genes and genomic regions. Genomic regions and genes that remain unaltered in copy number and expression, respectively, may be essential for maintaining tumour survival. METHODS We analyzed copy number data of 243 previously reported breast tumours and computationally derived stable copy number regions. To identify genes in stable copy number regions with nominal changes in expression, datasets for tumour and normal samples were compared. Results were replicated by analysis of a series of independent copy number, expression and genomic sequencing studies. A subset of stable regions, including stable paralogous regions, were confirmed by quantitative PCR and fluorescence in situ hybridization (FISH) in 5 breast cancer cell lines. We deduced a comprehensive set of dually stable genes (i.e. maintaining nominal copy number and expression) which were categorized according to pathway and ontology assignments. The stability of genes encoding therapeutic drug targets was also assessed. RESULTS AND CONCLUSION Tumour genome analysis revealed 766 unstable (amplified and/or deleted) and 812 stable contiguous genomic regions. Replication analysis of an independent set of 171 breast tumours confirmed copy number stability of 1.3 Gb of the genome. We found that 5804 of these genes were dually stable. The composition of this gene set remained essentially unchanged (<2% reduction) after accounting for commonly mutated breast cancer genes found by sequencing and differential expression. The stable breast cancer genome is enriched for cellular metabolism, regulation of gene expression, DNA packaging (chromatin and nucleosome assembly), and regulation of apoptosis functions. Stable genes participating in multiple essential pathways were consistently found to be targets of chemotherapies. Preservation of stable, essential genes may be related to the effectiveness of certain chemotherapeutic agents that act on multiple gene products in this set.
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Affiliation(s)
- Nicole I. Park
- Department of Pathology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, Canada
| | - Peter K. Rogan
- Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, Canada
- Department of Computer Science, University of Western Ontario, London, ON, Canada
| | - Heather E. Tarnowski
- Department of Pathology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, Canada
| | - Joan H.M. Knoll
- Department of Pathology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, Canada
- Molecular Pathology, Laboratory Medicine Program, London Health Sciences Centre, ON, Canada
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