1
|
Yu HJ, Byun YH, Park CK. Techniques for assessing telomere length: A methodological review. Comput Struct Biotechnol J 2024; 23:1489-1498. [PMID: 38633384 PMCID: PMC11021795 DOI: 10.1016/j.csbj.2024.04.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 04/04/2024] [Accepted: 04/05/2024] [Indexed: 04/19/2024] Open
Abstract
Telomeres are located at the ends of chromosomes and have specific sequences with a distinctive structure that safeguards genes. They possess capping structures that protect chromosome ends from fusion events and ensure chromosome stability. Telomeres shorten in length during each cycle of cell division. When this length reaches a certain threshold, it can lead to genomic instability, thus being implicated in various diseases, including cancer and neurodegenerative disorders. The possibility of telomeres serving as a biomarker for aging and age-related disease is being explored, and their significance is still under study. This is because post-mitotic cells, which are mature cells that do not undergo mitosis, do not experience telomere shortening due to age. Instead, other causes, for example, exposure to oxidative stress, can directly damage the telomeres, causing genomic instability. Nonetheless, a general agreement has been established that measuring telomere length offers valuable insights and forms a crucial foundation for analyzing gene expression and epigenetic data. Numerous approaches have been developed to accurately measure telomere lengths. In this review, we summarize various methods and their advantages and limitations for assessing telomere length.
Collapse
Affiliation(s)
- Hyeon Jong Yu
- Department of Neurosurgery, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Yoon Hwan Byun
- Department of Neurosurgery, SMG-SNU Boramae Medical Center, Seoul, Republic of Korea
| | - Chul-Kee Park
- Department of Neurosurgery, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| |
Collapse
|
2
|
Sampaio Moura N, Schledwitz A, Alizadeh M, Kodan A, Njei LP, Raufman JP. Cholinergic Mechanisms in Gastrointestinal Neoplasia. Int J Mol Sci 2024; 25:5316. [PMID: 38791353 PMCID: PMC11120676 DOI: 10.3390/ijms25105316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 05/09/2024] [Accepted: 05/11/2024] [Indexed: 05/26/2024] Open
Abstract
Acetylcholine-activated receptors are divided broadly into two major structurally distinct classes: ligand-gated ion channel nicotinic and G-protein-coupled muscarinic receptors. Each class encompasses several structurally related receptor subtypes with distinct patterns of tissue expression and post-receptor signal transduction mechanisms. The activation of both nicotinic and muscarinic cholinergic receptors has been associated with the induction and progression of gastrointestinal neoplasia. Herein, after briefly reviewing the classification of acetylcholine-activated receptors and the role that nicotinic and muscarinic cholinergic signaling plays in normal digestive function, we consider the mechanics of acetylcholine synthesis and release by neuronal and non-neuronal cells in the gastrointestinal microenvironment, and current methodology and challenges in measuring serum and tissue acetylcholine levels accurately. Then, we critically evaluate the evidence that constitutive and ligand-induced activation of acetylcholine-activated receptors plays a role in promoting gastrointestinal neoplasia. We focus primarily on adenocarcinomas of the stomach, pancreas, and colon, because these cancers are particularly common worldwide and, when diagnosed at an advanced stage, are associated with very high rates of morbidity and mortality. Throughout this comprehensive review, we concentrate on identifying novel ways to leverage these observations for prognostic and therapeutic purposes.
Collapse
Affiliation(s)
- Natalia Sampaio Moura
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Maryland School of Medicine, Baltimore, MD 21201, USA; (N.S.M.); (A.S.); (A.K.)
| | - Alyssa Schledwitz
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Maryland School of Medicine, Baltimore, MD 21201, USA; (N.S.M.); (A.S.); (A.K.)
| | - Madeline Alizadeh
- The Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA;
| | - Asha Kodan
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Maryland School of Medicine, Baltimore, MD 21201, USA; (N.S.M.); (A.S.); (A.K.)
| | - Lea-Pearl Njei
- Department of Biological Science, University of Maryland, Baltimore County, Baltimore, MD 21250, USA;
| | - Jean-Pierre Raufman
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Maryland School of Medicine, Baltimore, MD 21201, USA; (N.S.M.); (A.S.); (A.K.)
- Veterans Affairs Maryland Healthcare System, Baltimore, MD 21201, USA
- Marlene and Stewart Greenebaum Cancer Center, University of Maryland Medical Center, Baltimore, MD 21201, USA
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| |
Collapse
|
3
|
Singh M, Raseley K, Perez AM, MacKenzie D, Kosiyatrakul ST, Desai S, Batista N, Guru N, Loomba KK, Abid HZ, Wang Y, Udo-Bellner L, Stout RF, Schildkraut CL, Xiao M, Zhang D. Elucidation of the molecular mechanism of the breakage-fusion-bridge (BFB) cycle using a CRISPR-dCas9 cellular model. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.03.587951. [PMID: 38617299 PMCID: PMC11014597 DOI: 10.1101/2024.04.03.587951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Chromosome instability (CIN) is frequently observed in many tumors. The breakage-fusion-bridge (BFB) cycle has been proposed to be one of the main drivers of CIN during tumorigenesis and tumor evolution. However, the detailed mechanisms for the individual steps of the BFB cycle warrants further investigation. Here, we demonstrated that a nuclease-dead Cas9 (dCas9) coupled with a telomere-specific single-guide RNA (sgTelo) can be used to model the BFB cycle. First, we showed that targeting dCas9 to telomeres using sgTelo impeded DNA replication at telomeres and induced a pronounced increase of replication stress and DNA damage. Using Single-Molecule Telomere Assay via Optical Mapping (SMTA-OM), we investigated the genome-wide features of telomeres in the dCas9/sgTelo cells and observed a dramatic increase of chromosome end fusions, including fusion/ITS+ and fusion/ITS-.Consistently, we also observed an increase in the formation of dicentric chromosomes, anaphase bridges, and intercellular telomeric chromosome bridges (ITCBs). Utilizing the dCas9/sgTelo system, we uncovered many novel molecular and structural features of the ITCB and demonstrated that multiple DNA repair pathways are implicated in the formation of ITCBs. Our studies shed new light on the molecular mechanisms of the BFB cycle, which will advance our understanding of tumorigenesis, tumor evolution, and drug resistance.
Collapse
|
4
|
Uppuluri L, Shi CH, Varapula D, Young E, Ehrlich RL, Wang Y, Piazza D, Mell JC, Yip KY, Xiao M. A long-read sequencing strategy with overlapping linkers on adjacent fragments (OLAF-Seq) for targeted resequencing and enrichment. Sci Rep 2024; 14:5583. [PMID: 38448490 PMCID: PMC10917763 DOI: 10.1038/s41598-024-56402-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 03/06/2024] [Indexed: 03/08/2024] Open
Abstract
In this report, we present OLAF-Seq, a novel strategy to construct a long-read sequencing library such that adjacent fragments are linked with end-terminal duplications. We use the CRISPR-Cas9 nickase enzyme and a pool of multiple sgRNAs to perform non-random fragmentation of targeted long DNA molecules (> 300kb) into smaller library-sized fragments (about 20 kbp) in a manner so as to retain physical linkage information (up to 1000 bp) between adjacent fragments. DNA molecules targeted for fragmentation are preferentially ligated with adaptors for sequencing, so this method can enrich targeted regions while taking advantage of the long-read sequencing platforms. This enables the sequencing of target regions with significantly lower total coverage, and the genome sequence within linker regions provides information for assembly and phasing. We demonstrated the validity and efficacy of the method first using phage and then by sequencing a panel of 100 full-length cancer-related genes (including both exons and introns) in the human genome. When the designed linkers contained heterozygous genetic variants, long haplotypes could be established. This sequencing strategy can be readily applied in both PacBio and Oxford Nanopore platforms for both long and short genes with an easy protocol. This economically viable approach is useful for targeted enrichment of hundreds of target genomic regions and where long no-gap contigs need deep sequencing.
Collapse
Affiliation(s)
- Lahari Uppuluri
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, 19104, USA
| | - Christina Huan Shi
- Cancer Genome and Epigenetics Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, 92037, USA
| | - Dharma Varapula
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, 19104, USA
| | - Eleanor Young
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, 19104, USA
| | - Rachel L Ehrlich
- Department of Microbiology and Immunology, College of Medicine, Drexel University, Philadelphia, PA, 19104, USA
- Center for Genomic Sciences, Institute of Molecular Medicine and Infectious Disease, Drexel University, Philadelphia, PA, 19104, USA
| | - Yilin Wang
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, 19104, USA
| | - Danielle Piazza
- Department of Microbiology and Immunology, College of Medicine, Drexel University, Philadelphia, PA, 19104, USA
- Center for Genomic Sciences, Institute of Molecular Medicine and Infectious Disease, Drexel University, Philadelphia, PA, 19104, USA
| | - Joshua Chang Mell
- Department of Microbiology and Immunology, College of Medicine, Drexel University, Philadelphia, PA, 19104, USA
- Center for Genomic Sciences, Institute of Molecular Medicine and Infectious Disease, Drexel University, Philadelphia, PA, 19104, USA
| | - Kevin Y Yip
- Cancer Genome and Epigenetics Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, 92037, USA
| | - Ming Xiao
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, 19104, USA.
- Center for Genomic Sciences, Institute of Molecular Medicine and Infectious Disease, Drexel University, Philadelphia, PA, 19104, USA.
| |
Collapse
|
5
|
Zhang Z, Rong X, Xie T, Li Z, Song H, Zhen S, Wang H, Wu J, Jaffrey SR, Li X. Fluorogenic CRISPR for genomic DNA imaging. Nat Commun 2024; 15:934. [PMID: 38296979 PMCID: PMC10831063 DOI: 10.1038/s41467-024-45163-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 01/15/2024] [Indexed: 02/02/2024] Open
Abstract
Genomic DNA exhibits high heterogeneity in terms of its dynamic within the nucleus, its structure and functional roles. CRISPR-based imaging approaches can image genomic loci in living cells. However, conventional CRISPR-based tools involve expressing constitutively fluorescent proteins, resulting in high background and nonspecific nucleolar signal. Here, we construct fluorogenic CRISPR (fCRISPR) to overcome these issues. fCRISPR is designed with dCas9, an engineered sgRNA, and a fluorogenic protein. Fluorogenic proteins are degraded unless they are bound to specific RNA hairpins. These hairpins are inserted into sgRNA, resulting in dCas9: sgRNA: fluorogenic protein ternary complexes that enable fluorogenic DNA imaging. With fCRISPR, we image various genomic DNA in different human cells with high signal-to-noise ratio and sensitivity. Furthermore, fCRISPR tracks chromosomes dynamics and length. fCRISPR also allows DNA double-strand breaks (DSBs) and repair to be tracked in real time. Taken together, fCRISPR offers a high-contrast and sensitive platform for imaging genomic loci.
Collapse
Affiliation(s)
- Zhongxuan Zhang
- Beijing Institute of Life Sciences, Chinese Academy of Science, 100101, Beijing, China
- Department of Respiratory and Critical Care Medicine, The Affiliated Hospital of Southwest Medical University, 646000, Luzhou, Sichuan, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China
| | - Xiaoxiao Rong
- Beijing Institute of Life Sciences, Chinese Academy of Science, 100101, Beijing, China
- College of Life Science, Hebei University, Baoding, 071002, Hebei, China
| | - Tianjin Xie
- Beijing Institute of Life Sciences, Chinese Academy of Science, 100101, Beijing, China
- School of Chemistry and Chemical Engineering, Southwest University, Beibei District, 400715, Chongqing, China
| | - Zehao Li
- Beijing Institute of Life Sciences, Chinese Academy of Science, 100101, Beijing, China
- College of Life Science, Hebei University, Baoding, 071002, Hebei, China
| | - Haozhi Song
- Beijing Institute of Life Sciences, Chinese Academy of Science, 100101, Beijing, China
| | - Shujun Zhen
- School of Chemistry and Chemical Engineering, Southwest University, Beibei District, 400715, Chongqing, China
| | - Haifeng Wang
- School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Center for Synthetic and Systems Biology, Tsinghua University, 100084, Beijing, China
| | - Jiahui Wu
- Department of Chemistry, University of Massachusetts, Amherst, MA, 01003, USA
| | - Samie R Jaffrey
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, NY, 10065, USA
| | - Xing Li
- Beijing Institute of Life Sciences, Chinese Academy of Science, 100101, Beijing, China.
- Department of Respiratory and Critical Care Medicine, The Affiliated Hospital of Southwest Medical University, 646000, Luzhou, Sichuan, China.
- University of Chinese Academy of Sciences, 100049, Beijing, China.
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China.
| |
Collapse
|
6
|
Raseley K, Jinwala Z, Zhang D, Xiao M. Single-Molecule Telomere Assay via Optical Mapping (SMTA-OM) Can Potentially Define the ALT Positivity of Cancer. Genes (Basel) 2023; 14:1278. [PMID: 37372458 DOI: 10.3390/genes14061278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 06/05/2023] [Accepted: 06/07/2023] [Indexed: 06/29/2023] Open
Abstract
Telomeres play an essential role in protecting the ends of linear chromosomes and maintaining the integrity of the human genome. One of the key hallmarks of cancers is their replicative immortality. As many as 85-90% of cancers activate the expression of telomerase (TEL+) as the telomere maintenance mechanism (TMM), and 10-15% of cancers utilize the homology-dependent repair (HDR)-based Alternative Lengthening of Telomere (ALT+) pathway. Here, we performed statistical analysis of our previously reported telomere profiling results from Single Molecule Telomere Assay via Optical Mapping (SMTA-OM), which is capable of quantifying individual telomeres from single molecules across all chromosomes. By comparing the telomeric features from SMTA-OM in TEL+ and ALT+ cancer cells, we demonstrated that ALT+ cancer cells display certain unique telomeric profiles, including increased fusions/internal telomere-like sequence (ITS+), fusions/internal telomere-like sequence loss (ITS-), telomere-free ends (TFE), super-long telomeres, and telomere length heterogeneity, compared to TEL+ cancer cells. Therefore, we propose that ALT+ cancer cells can be differentiated from TEL+ cancer cells using the SMTA-OM readouts as biomarkers. In addition, we observed variations in SMTA-OM readouts between different ALT+ cell lines that may potentially be used as biomarkers for discerning subtypes of ALT+ cancer and monitoring the response to cancer therapy.
Collapse
Affiliation(s)
- Kaitlin Raseley
- School of Biomedical Engineering, Drexel University, Philadelphia, PA 19104, USA
| | - Zeal Jinwala
- School of Biomedical Engineering, Drexel University, Philadelphia, PA 19104, USA
| | - Dong Zhang
- Department of Biomedical Sciences, College of Osteopathic Medicine, New York Institute of Technology, Old Westbury, NY 11568, USA
- Center for Cancer Research, New York Institute of Technology, Old Westbury, NY 11568, USA
| | - Ming Xiao
- School of Biomedical Engineering, Drexel University, Philadelphia, PA 19104, USA
- Center for Genomic Sciences and Center for Advanced Microbial Processing, Institute of Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA 19102, USA
| |
Collapse
|
7
|
Singh M, MacKenzie D, Desai S, Batista N, Zhang D. Diagnostic Biomarkers and Therapeutic Targets of Alternative Lengthening of Telomeres-Positive Cancers. Genet Test Mol Biomarkers 2023; 27:123-125. [PMID: 37115645 DOI: 10.1089/gtmb.2023.29069.mas] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023] Open
|
8
|
Ding X, Han J, Van Winkle LS, Zhang QY. Detection of Transgene Location in the CYP2A13/2B6/2F1-transgenic Mouse Model using Optical Genome Mapping Technology. Drug Metab Dispos 2023; 51:46-53. [PMID: 36273825 PMCID: PMC9832375 DOI: 10.1124/dmd.122.001090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 10/01/2022] [Accepted: 10/04/2022] [Indexed: 01/14/2023] Open
Abstract
Most transgenic mouse models are generated through random integration of the transgene. The location of the transgene provides valuable information for assessing potential effects of the transgenesis on the host and for designing genotyping protocols that can amplify across the integration site, but it is challenging to identify. Here, we report the successful utility of optical genome mapping technology to identify the transgene insertion site in a CYP2A13/2B6/2F1-transgenic mouse model, which produces three human cytochrome P450 (P450) enzymes (CYP2A13, CYP2B6, and CYP2F1) that are encoded by neighboring genes on human chromosome 19. These enzymes metabolize many drugs, respiratory toxicants, and chemical carcinogens. Initial efforts to identify candidate insertion sites by whole genome sequencing was unsuccessful, apparently because the transgene is located in a region of the mouse genome that contains highly repetitive sequences. Subsequent utility of the optical genome mapping approach, which compares genome-wide marker distribution between the transgenic mouse genome and a reference mouse (GRCm38) or human (GRCh38) genome, localized the insertion site to mouse chromosome 14, between two marker positions at 4451324 base pair and 4485032 base pair. A transgene-mouse genome junction sequence was further identified through long-polymerase chain reaction amplification and DNA sequencing at GRCm38 Chr.14:4484726. The transgene insertion (∼2.4 megabase pair) contained 5-7 copies of the human transgenes, which replaced a 26.9-33.4 kilobase pair mouse genomic region, including exons 1-4 of Gm3182, a predicted and highly redundant gene. Finally, the sequencing results enabled the design of a new genotyping protocol that can distinguish between hemizygous and homozygous CYP2A13/2B6/2F1-transgenic mice. SIGNIFICANCE STATEMENT: This study characterizes the genomic structure of, and provides a new genotyping method for, a transgenic mouse model that expresses three human P450 enzymes, CYP2A13, CYP2B6, and CYP2F1, that are important in xenobiotic metabolism and toxicity. The demonstrated success in applying the optical genome mapping technology for identification of transgene insertion sites should encourage others to do the same for other transgenic models generated through random integration, including most of the currently available human P450 transgenic mouse models.
Collapse
Affiliation(s)
- Xinxin Ding
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, Arizona (X.D., J.H., Q.-Y.Z.) and Center for Health and the Environment and Department of Anatomy Physiology and Cell Biology, School of Veterinary Medicine, UC Davis, Davis, California (L.S.V.W.)
| | - John Han
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, Arizona (X.D., J.H., Q.-Y.Z.) and Center for Health and the Environment and Department of Anatomy Physiology and Cell Biology, School of Veterinary Medicine, UC Davis, Davis, California (L.S.V.W.)
| | - Laura S Van Winkle
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, Arizona (X.D., J.H., Q.-Y.Z.) and Center for Health and the Environment and Department of Anatomy Physiology and Cell Biology, School of Veterinary Medicine, UC Davis, Davis, California (L.S.V.W.)
| | - Qing-Yu Zhang
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, Arizona (X.D., J.H., Q.-Y.Z.) and Center for Health and the Environment and Department of Anatomy Physiology and Cell Biology, School of Veterinary Medicine, UC Davis, Davis, California (L.S.V.W.)
| |
Collapse
|
9
|
Adam E, Ranjan D, Riethman H. NPGREAT: assembly of human subtelomere regions with the use of ultralong nanopore reads and linked-reads. BMC Bioinformatics 2022; 23:545. [PMID: 36526983 PMCID: PMC9758922 DOI: 10.1186/s12859-022-05081-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 11/24/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Human subtelomeric DNA regulates the length and stability of adjacent telomeres that are critical for cellular function, and contains many gene/pseudogene families. Large evolutionarily recent segmental duplications and associated structural variation in human subtelomeres has made complete sequencing and assembly of these regions difficult to impossible for many loci, complicating or precluding a wide range of genetic analyses to investigate their function. RESULTS We present a hybrid assembly method, NanoPore Guided REgional Assembly Tool (NPGREAT), which combines Linked-Read data with mapped ultralong nanopore reads spanning subtelomeric segmental duplications to potentially overcome these difficulties. Linked-Read sets of DNA sequences identified by matches with 1-copy subtelomere sequence adjacent to segmental duplications are assembled and extended into the segmental duplication regions using Regional Extension of Assemblies using Linked-Reads (REXTAL). Mapped telomere-containing ultralong nanopore reads are then used to provide contiguity and correct orientation for matching REXTAL sequence contigs as well as identification/correction of any misassemblies. Our method was tested for a subset of representative subtelomeres with ultralong nanopore read coverage in the haploid human cell line CHM13. A 10X Linked-Read dataset from CHM13 was combined with ultralong nanopore reads from the same genome to provide improved subtelomere assemblies. Comparison of Nanopore-only assemblies using SHASTA with our NPGREAT assemblies in the distal-most subtelomere regions showed that NPGREAT produced higher-quality and more complete assemblies than SHASTA alone when these regions had low ultralong nanopore coverage (such as cases where large segmental duplications were immediately adjacent to (TTAGGG) tracts). CONCLUSION In genomic regions with large segmental duplications adjacent to telomeres, NPGREAT offers an alternative economical approach to improving assembly accuracy and coverage using linked-read datasets when more expensive HiFi datasets of 10-20 kb reads are unavailable.
Collapse
Affiliation(s)
- Eleni Adam
- grid.261368.80000 0001 2164 3177Department of Computer Science, Old Dominion University, Norfolk, VA USA
| | - Desh Ranjan
- grid.261368.80000 0001 2164 3177Department of Computer Science, Old Dominion University, Norfolk, VA USA
| | - Harold Riethman
- grid.261368.80000 0001 2164 3177Medical Diagnostic and Translational Sciences, Old Dominion University, Norfolk, VA USA
| |
Collapse
|
10
|
Uppuluri L, Wang Y, Young E, Wong JS, Abid HZ, Xiao M. Multiplex structural variant detection by whole-genome mapping and nanopore sequencing. Sci Rep 2022; 12:6512. [PMID: 35444207 PMCID: PMC9021263 DOI: 10.1038/s41598-022-10483-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 04/08/2022] [Indexed: 11/26/2022] Open
Abstract
Identification of structural variants (SVs) breakpoints is important in studying mutations, mutagenic causes, and functional impacts. Next-generation sequencing and whole-genome optical mapping are extensively used in SV discovery and characterization. However, multiple platforms and computational approaches are needed for comprehensive analysis, making it resource-intensive and expensive. Here, we propose a strategy combining optical mapping and cas9-assisted targeted nanopore sequencing to analyze SVs. Optical mapping can economically and quickly detect SVs across a whole genome but does not provide sequence-level information or precisely resolve breakpoints. Furthermore, since only a subset of all SVs is known to affect biology, we attempted to type a subset of all SVs using targeted nanopore sequencing. Using our approach, we resolved the breakpoints of five deletions, five insertions, and an inversion, in a single experiment.
Collapse
Affiliation(s)
- Lahari Uppuluri
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA.,Department of Mechanical Engineering and Mechanics, Drexel University, Philadelphia, PA, USA
| | - Yilin Wang
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA
| | - Eleanor Young
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA
| | - Jessica S Wong
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA
| | - Heba Z Abid
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA
| | - Ming Xiao
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA. .,Center for Genomic Sciences, Institute of Molecular Medicine and Infectious Disease, Drexel University, Philadelphia, PA, USA.
| |
Collapse
|
11
|
Wong JS, Jadhav T, Young E, Wang Y, Xiao M. Characterization of full-length LINE-1 insertions in 154 genomes. Genomics 2021; 113:3804-3810. [PMID: 34534648 DOI: 10.1016/j.ygeno.2021.09.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 08/18/2021] [Accepted: 09/11/2021] [Indexed: 10/20/2022]
Abstract
Long interspersed nuclear elements (LINEs) are retrotransposons that contribute to genetic variation in the human genome. LINE-1 elements in larger-scale studies are challenging to identify using sequencing technologies due to cost and scalability. We developed an approach using optical mapping for detection of full-length LINE-1 insertions and 10× sequencing for confirmation. We found 51 true positive full-length LINE-1 insertions, of which 4 are novel insertions, in NA12878. Repeating our analysis on a larger sample set representing 26 populations, we identified 329 full-length LINE-1 elements, of which 123 are novel. 24.8% of these 329 LINE-1 insertions were shared amongst all 5 superpopulations (AFR, AMR, EUR, EAS, SAS). The African superpopulation has a higher percentage of population-specific LINE-1 insertions than any other superpopulation. These data indicate that our approach can provide high-speed, cost-effective, and increased accuracy for LINE-1 detection. These data also provide an insight into variations of LINE-1 elements between different populations.
Collapse
Affiliation(s)
- Jessica S Wong
- School of Biomedical Engineering, Drexel University, Philadelphia, PA, United States of America
| | - Tanaya Jadhav
- School of Biomedical Engineering, Drexel University, Philadelphia, PA, United States of America
| | - Eleanor Young
- School of Biomedical Engineering, Drexel University, Philadelphia, PA, United States of America
| | - Yilin Wang
- School of Biomedical Engineering, Drexel University, Philadelphia, PA, United States of America
| | - Ming Xiao
- School of Biomedical Engineering, Drexel University, Philadelphia, PA, United States of America; Center for Genomic Sciences, Institute of Molecular Medicine and Infectious Disease, Drexel University, Philadelphia, PA, United States of America.
| |
Collapse
|
12
|
Uppuluri L, Jadhav T, Wang Y, Xiao M. Multicolor Whole-Genome Mapping in Nanochannels for Genetic Analysis. Anal Chem 2021; 93:9808-9816. [PMID: 34232611 DOI: 10.1021/acs.analchem.1c01373] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Analysis of structural variations (SVs) is important to understand mutations underlying genetic disorders and pathogenic conditions. However, characterizing SVs using short-read, high-throughput sequencing technology is difficult. Although long-read sequencing technologies are being increasingly employed in characterizing SVs, their low throughput and high costs discourage widespread adoption. Sequence motif-based optical mapping in nanochannels is useful in whole-genome mapping and SV detection, but it is not possible to precisely locate the breakpoints or estimate the copy numbers. We present here a universal multicolor mapping strategy in nanochannels combining conventional sequence-motif labeling system with Cas9-mediated target-specific labeling of any 20-base sequences (20mers) to create custom labels and detect new features. The sequence motifs are labeled with green fluorophores and the 20mers are labeled with red fluorophores. Using this strategy, it is possible to not only detect the SVs but also utilize custom labels to interrogate the features not accessible to motif-labeling, locate breakpoints, and precisely estimate copy numbers of genomic repeats. We validated our approach by quantifying the D4Z4 copy numbers, a known biomarker for facioscapulohumeral muscular dystrophy (FSHD) and estimating the telomere length, a clinical biomarker for assessing disease risk factors in aging-related diseases and malignant cancers. We also demonstrate the application of our methodology in discovering transposable long non-interspersed Elements 1 (LINE-1) insertions across the whole genome.
Collapse
Affiliation(s)
- Lahari Uppuluri
- School of Biomedical Engineering, Science and Health Systems, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania 19104, United States
| | - Tanaya Jadhav
- School of Biomedical Engineering, Science and Health Systems, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania 19104, United States
| | - Yilin Wang
- School of Biomedical Engineering, Science and Health Systems, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania 19104, United States
| | - Ming Xiao
- School of Biomedical Engineering, Science and Health Systems, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania 19104, United States.,Center for Genomic Sciences, Institute of Molecular Medicine and Infectious Disease, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania 19104, United States
| |
Collapse
|
13
|
Uppuluri L, Varapula D, Young E, Riethman H, Xiao M. Single-molecule telomere length characterization by optical mapping in nano-channel array: Perspective and review on telomere length measurement. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2021; 82:103562. [PMID: 33310082 PMCID: PMC8500550 DOI: 10.1016/j.etap.2020.103562] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 12/02/2020] [Accepted: 12/08/2020] [Indexed: 05/11/2023]
Abstract
In humans, the telomere consists of tandem 5'TTAGGG3' DNA repeats on both ends of all 46 chromosomes. Telomere shortening has been linked to aging and age-related diseases. Similarly, telomere length changes have been associated with chemical exposure, molecular-level DNA damage, and tumor development. Telomere elongation has been associated to tumor development, caused due to chemical exposure and molecular-level DNA damage. The methods used to study these effects mostly rely on average telomere length as a biomarker. The mechanisms regulating subtelomere-specific and haplotype-specific telomere lengths in humans remain understudied and poorly understood, primarily because of technical limitations in obtaining these data for all chromosomes. Recent studies have shown that it is the short telomeres that are crucial in preserving chromosome stability. The identity and frequency of specific critically short telomeres potentially is a useful biomarker for studying aging, age-related diseases, and cancer. Here, we will briefly review the role of telomere length, its measurement, and our recent single-molecule telomere length measurement assay. With this assay, one can measure individual telomere lengths as well as identify their physically linked subtelomeric DNA. This assay can also positively detect telomere loss, characterize novel subtelomeric variants, haplotypes, and previously uncharacterized recombined subtelomeres. We will also discuss its applications in aging cells and cancer cells, highlighting the utility of the single molecule telomere length assay.
Collapse
Affiliation(s)
- Lahari Uppuluri
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA
| | - Dharma Varapula
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA
| | - Eleanor Young
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA
| | - Harold Riethman
- Medical Diagnostic and Translational Sciences, Old Dominion University, Norfolk, VA, USA.
| | - Ming Xiao
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA; Institute of Molecular Medicine and Infectious Disease, School of Medicine, Drexel University, Philadelphia, PA, USA.
| |
Collapse
|
14
|
Abid HZ, Young E, McCaffrey J, Raseley K, Varapula D, Wang HY, Piazza D, Mell J, Xiao M. Customized optical mapping by CRISPR-Cas9 mediated DNA labeling with multiple sgRNAs. Nucleic Acids Res 2021; 49:e8. [PMID: 33231685 PMCID: PMC7826249 DOI: 10.1093/nar/gkaa1088] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 10/16/2020] [Accepted: 10/27/2020] [Indexed: 01/01/2023] Open
Abstract
Whole-genome mapping technologies have been developed as a complementary tool to provide scaffolds for genome assembly and structural variation analysis (1,2). We recently introduced a novel DNA labeling strategy based on a CRISPR-Cas9 genome editing system, which can target any 20bp sequences. The labeling strategy is specifically useful in targeting repetitive sequences, and sequences not accessible to other labeling methods. In this report, we present customized mapping strategies that extend the applications of CRISPR-Cas9 DNA labeling. We first design a CRISPR-Cas9 labeling strategy to interrogate and differentiate the single allele differences in NGG protospacer adjacent motifs (PAM sequence). Combined with sequence motif labeling, we can pinpoint the single-base differences in highly conserved sequences. In the second strategy, we design mapping patterns across a genome by selecting sets of specific single-guide RNAs (sgRNAs) for labeling multiple loci of a genomic region or a whole genome. By developing and optimizing a single tube synthesis of multiple sgRNAs, we demonstrate the utility of CRISPR-Cas9 mapping with 162 sgRNAs targeting the 2Mb Haemophilus influenzae chromosome. These CRISPR-Cas9 mapping approaches could be particularly useful for applications in defining long-distance haplotypes and pinpointing the breakpoints in large structural variants in complex genomes and microbial mixtures.
Collapse
MESH Headings
- Alleles
- Base Sequence
- Benzoxazoles/analysis
- CRISPR-Cas Systems
- Chromosome Mapping/methods
- Chromosomes, Bacterial/genetics
- Computer Simulation
- Conserved Sequence/genetics
- DNA-Directed RNA Polymerases
- Drug Resistance, Bacterial/genetics
- Fluorescent Dyes/analysis
- Gene Editing/methods
- Genome, Bacterial
- Genome, Human
- Haemophilus influenzae/drug effects
- Haemophilus influenzae/genetics
- Haplotypes/genetics
- Humans
- Lab-On-A-Chip Devices
- Nalidixic Acid/pharmacology
- Novobiocin/pharmacology
- Nucleotide Motifs/genetics
- Polymorphism, Single Nucleotide
- Quinolinium Compounds/analysis
- RNA, Guide, CRISPR-Cas Systems/chemical synthesis
- RNA, Guide, CRISPR-Cas Systems/genetics
- Repetitive Sequences, Nucleic Acid/genetics
- Sequence Alignment
- Staining and Labeling/methods
- Viral Proteins
Collapse
Affiliation(s)
- Heba Z Abid
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA
| | - Eleanor Young
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA
| | - Jennifer McCaffrey
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA
| | - Kaitlin Raseley
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA
| | - Dharma Varapula
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA
| | - Hung-Yi Wang
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA
| | - Danielle Piazza
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA
- Department of Microbiology and Immunology, College of Medicine, Drexel University, Philadelphia, PA, USA
- Center for Genomic Sciences, Institute of Molecular Medicine and Infectious Disease, Drexel University, Philadelphia, PA, USA
| | - Joshua Mell
- Department of Microbiology and Immunology, College of Medicine, Drexel University, Philadelphia, PA, USA
- Center for Genomic Sciences, Institute of Molecular Medicine and Infectious Disease, Drexel University, Philadelphia, PA, USA
| | - Ming Xiao
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA
- Center for Genomic Sciences, Institute of Molecular Medicine and Infectious Disease, Drexel University, Philadelphia, PA, USA
| |
Collapse
|
15
|
Lindrose AR, McLester-Davis LWY, Tristano RI, Kataria L, Gadalla SM, Eisenberg DTA, Verhulst S, Drury S. Method comparison studies of telomere length measurement using qPCR approaches: A critical appraisal of the literature. PLoS One 2021; 16:e0245582. [PMID: 33471860 PMCID: PMC7817045 DOI: 10.1371/journal.pone.0245582] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 01/05/2021] [Indexed: 12/16/2022] Open
Abstract
Use of telomere length (TL) as a biomarker for various environmental exposures and diseases has increased in recent years. Various methods have been developed to measure telomere length. Polymerase chain reaction (PCR)-based methods remain wide-spread for population-based studies due to the high-throughput capability. While several studies have evaluated the repeatability and reproducibility of different TL measurement methods, the results have been variable. We conducted a literature review of TL measurement cross-method comparison studies that included a PCR-based method published between January 1, 2002 and May 25, 2020. A total of 25 articles were found that matched the inclusion criteria. Papers were reviewed for quality of methodologic reporting of sample and DNA quality, PCR assay characteristics, sample blinding, and analytic approaches to determine final TL. Overall, methodologic reporting was low as assessed by two different reporting guidelines for qPCR-based TL measurement. There was a wide range in the reported correlation between methods (as assessed by Pearson’s r) and few studies utilized the recommended intra-class correlation coefficient (ICC) for assessment of assay repeatability and methodologic comparisons. The sample size for nearly all studies was less than 100, raising concerns about statistical power. Overall, this review found that the current literature on the relation between TL measurement methods is lacking in validity and scientific rigor. In light of these findings, we present reporting guidelines for PCR-based TL measurement methods and results of analyses of the effect of assay repeatability (ICC) on statistical power of cross-sectional and longitudinal studies. Additional cross-laboratory studies with rigorous methodologic and statistical reporting, adequate sample size, and blinding are essential to accurately determine assay repeatability and replicability as well as the relation between TL measurement methods.
Collapse
Affiliation(s)
- Alyssa R. Lindrose
- Department of Psychiatry and Behavioral Sciences, School of Medicine, Tulane University, New Orleans, Louisiana, United States of America
- * E-mail: (ARL); (SD)
| | | | - Renee I. Tristano
- School of Public Health and Tropical Medicine, Tulane University, New Orleans, Louisiana, United States of America
| | - Leila Kataria
- School of Science and Engineering, Tulane University, New Orleans, Louisiana, United States of America
| | - Shahinaz M. Gadalla
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Dan T. A. Eisenberg
- Department of Anthropology, Department of Biology, Center for Studies in Demography and Ecology, University of Washington, Seattle, Washington, United States of America
| | - Simon Verhulst
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Stacy Drury
- Department of Psychiatry and Behavioral Sciences, School of Medicine, Tulane University, New Orleans, Louisiana, United States of America
- Tulane Brain Institute, Tulane University, New Orleans, Louisiana, United States of America
- Department of Pediatrics, School of Medicine, Tulane University, New Orleans, Louisiana, United States of America
- * E-mail: (ARL); (SD)
| |
Collapse
|
16
|
Yuan Y, Chung CYL, Chan TF. Advances in optical mapping for genomic research. Comput Struct Biotechnol J 2020; 18:2051-2062. [PMID: 32802277 PMCID: PMC7419273 DOI: 10.1016/j.csbj.2020.07.018] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 07/08/2020] [Accepted: 07/24/2020] [Indexed: 12/28/2022] Open
Abstract
Recent advances in optical mapping have allowed the construction of improved genome assemblies with greater contiguity. Optical mapping also enables genome comparison and identification of large-scale structural variations. Association of these large-scale genomic features with biological functions is an important goal in plant and animal breeding and in medical research. Optical mapping has also been used in microbiology and still plays an important role in strain typing and epidemiological studies. Here, we review the development of optical mapping in recent decades to illustrate its importance in genomic research. We detail its applications and algorithms to show its specific advantages. Finally, we discuss the challenges required to facilitate the optimization of optical mapping and improve its future development and application.
Collapse
Key Words
- 3D, three-dimensional
- DBG, de Bruijn graph
- DLS, direct label and strain
- DNA, deoxyribonucleic acid
- Genome assembly
- Hi-C, high-throughput chromosome conformation capture
- Mb, million base pair
- Next generation sequencing
- OLC, overlap-layout-consensus
- Optical mapping
- PCR, polymerase chain reaction
- PacBio, Pacific Biosciences
- SRS, short-read sequencing
- SV, structural variation
- Structural variation
- bp, base pair
- kb, kilobase pair
Collapse
Affiliation(s)
- Yuxuan Yuan
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
- State Key Laboratory for Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR, China
- AoE Centre for Genomic Studies on Plant-Environment Interaction for Sustainable Agriculture and Food Security, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Claire Yik-Lok Chung
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
- State Key Laboratory for Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Ting-Fung Chan
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
- State Key Laboratory for Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR, China
- AoE Centre for Genomic Studies on Plant-Environment Interaction for Sustainable Agriculture and Food Security, The Chinese University of Hong Kong, Hong Kong SAR, China
| |
Collapse
|
17
|
Abid HZ, McCaffrey J, Raseley K, Young E, Lassahn K, Varapula D, Riethman H, Xiao M. Single-molecule analysis of subtelomeres and telomeres in Alternative Lengthening of Telomeres (ALT) cells. BMC Genomics 2020; 21:485. [PMID: 32669102 PMCID: PMC7364475 DOI: 10.1186/s12864-020-06901-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 07/08/2020] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND Telomeric DNA is typically comprised of G-rich tandem repeat motifs and maintained by telomerase (Greider CW, Blackburn EH; Cell 51:887-898; 1987). In eukaryotes lacking telomerase, a variety of DNA repair and DNA recombination based pathways for telomere maintenance have evolved in organisms normally dependent upon telomerase for telomere elongation (Webb CJ, Wu Y, Zakian VA; Cold Spring Harb Perspect Biol 5:a012666; 2013); collectively called Alternative Lengthening of Telomeres (ALT) pathways. By measuring (TTAGGG) n tract lengths from the same large DNA molecules that were optically mapped, we simultaneously analyzed telomere length dynamics and subtelomere-linked structural changes at a large number of specific subtelomeric loci in the ALT-positive cell lines U2OS, SK-MEL-2 and Saos-2. RESULTS Our results revealed loci-specific ALT telomere features. For example, while each subtelomere included examples of single molecules with terminal (TTAGGG) n tracts as well as examples of recombinant telomeric single molecules, the ratio of these molecules was subtelomere-specific, ranging from 33:1 (19p) to 1:25 (19q) in U2OS. The Saos-2 cell line shows a similar percentage of recombinant telomeres. The frequency of recombinant subtelomeres of SK-MEL-2 (11%) is about half that of U2OS and Saos-2 (24 and 19% respectively). Terminal (TTAGGG) n tract lengths and heterogeneity levels, the frequencies of telomere signal-free ends, and the frequency and size of retained internal telomere-like sequences (ITSs) at recombinant telomere fusion junctions all varied according to the specific subtelomere involved in a particular cell line. Very large linear extrachromosomal telomere repeat (ECTR) DNA molecules were found in all three cell lines; these are in principle capable of templating synthesis of new long telomere tracts via break-induced repair (BIR) long-tract DNA synthesis mechanisms and contributing to the very long telomere tract length and heterogeneity characteristic of ALT cells. Many of longest telomere tracts (both end-telomeres and linear ECTRs) displayed punctate CRISPR/Cas9-dependent (TTAGGG) n labeling patterns indicative of interspersion of stretches of non-canonical telomere repeats. CONCLUSION Identifying individual subtelomeres and characterizing linked telomere (TTAGGG) n tract lengths and structural changes using our new single-molecule methodologies reveals the structural consequences of telomere damage, repair and recombination mechanisms in human ALT cells in unprecedented molecular detail and significant differences in different ALT-positive cell lines.
Collapse
Affiliation(s)
- Heba Z Abid
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA
| | - Jennifer McCaffrey
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA
| | - Kaitlin Raseley
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA
| | - Eleanor Young
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA
| | - Katy Lassahn
- School of Medical Diagnostic and Transnational Sciences, Old Dominion University, Norfolk, VA, USA
| | - Dharma Varapula
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA
| | - Harold Riethman
- School of Medical Diagnostic and Transnational Sciences, Old Dominion University, Norfolk, VA, USA.
| | - Ming Xiao
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA. .,Institute of Molecular Medicine and Infectious Disease, School of Medicine, Drexel University, Philadelphia, PA, USA.
| |
Collapse
|
18
|
Kahl VFS, Allen JAM, Nelson CB, Sobinoff AP, Lee M, Kilo T, Vasireddy RS, Pickett HA. Telomere Length Measurement by Molecular Combing. Front Cell Dev Biol 2020; 8:493. [PMID: 32612998 PMCID: PMC7308456 DOI: 10.3389/fcell.2020.00493] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 05/25/2020] [Indexed: 12/14/2022] Open
Abstract
Telomeres are repetitive regions of DNA bound by specialized proteins at the termini of linear chromosomes that prevent the natural chromosome ends from being recognized as DNA double strand breaks. Telomeric DNA is gradually eroded with each round of cell division, resulting in the accumulation of critically short or dysfunctional telomeres that eventually trigger cellular senescence. Consequently, telomere length is indicative of the proliferative capacity of a cell. Multiple methods exist to measure telomere length and telomere content, but a simple and reliable technique to accurately measure individual telomere lengths is currently lacking. We have developed the Telomere length Combing Assay (TCA) to measure telomere length on stretched DNA fibers. We used TCA to measure telomere erosion in primary human fibroblasts, and to detect telomere lengthening in response to activation of telomere maintenance pathways. TCA was also used to accurately measure telomere length in healthy individuals, and to identify critically short telomeres in patients with telomere biology disorders. TCA is performed on isolated DNA, negating the need for cycling cells. TCA is amenable to semi-automated image analysis, and can be fully automated using the Genomic Vision molecular combing platform. This not only precludes sampling bias, but also provides the potential for high-throughput applications and clinical development. TCA is a simple and versatile technique to measure the distribution of individual telomere lengths in a cell population, offering improved accuracy, and more detailed biological insight for telomere length measurement applications.
Collapse
Affiliation(s)
- Vivian F S Kahl
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Joshua A M Allen
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Christopher B Nelson
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Alexander P Sobinoff
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Michael Lee
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Tatjana Kilo
- Department of Hematology, Children's Hospital at Westmead, Sydney Children's Hospitals Network, Sydney, NSW, Australia
| | - Raja S Vasireddy
- Department of Hematology, Children's Hospital at Westmead, Sydney Children's Hospitals Network, Sydney, NSW, Australia
| | - Hilda A Pickett
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| |
Collapse
|
19
|
Human subtelomeric DNA methylation: regulation and roles in telomere function. Curr Opin Genet Dev 2020; 60:9-16. [PMID: 32109830 DOI: 10.1016/j.gde.2020.02.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 01/21/2020] [Accepted: 02/02/2020] [Indexed: 12/26/2022]
Abstract
Subtelomeres are the regions at chromosome ends, immediately adjacent to the terminal telomeric repeats. The majority of human subtelomeres are CpG-rich in their distal two kilobases, and are methylated during early embryonic development by the de novo DNA methyltransferase DNMT3B. The biological relevance of subtelomeric DNA methylation is highlighted by the presence of promoters for the long non-coding TERRA transcripts in these CpG-rich regions. Indeed, deviant subtelomeric methylation has been linked with abnormal telomeric phenotypes, as most strikingly found in ICF syndrome. Here we review recent studies that explore new aspects of subtelomeric methylation regulation and demonstrate the significance of maintaining proper DNA methylation at the extreme distal human subtelomeric regions.
Collapse
|
20
|
Saint-Leandre B, Levine MT. The Telomere Paradox: Stable Genome Preservation with Rapidly Evolving Proteins. Trends Genet 2020; 36:232-242. [PMID: 32155445 DOI: 10.1016/j.tig.2020.01.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 01/08/2020] [Accepted: 01/13/2020] [Indexed: 01/08/2023]
Abstract
Telomeres ensure chromosome length homeostasis and protection from catastrophic end-to-end chromosome fusions. All eukaryotes require this essential, strictly conserved telomere-dependent genome preservation. However, recent evolutionary analyses of mammals, plants, and flies report pervasive rapid evolution of telomere proteins. The causes of this paradoxical observation - that unconserved machinery underlies an essential, conserved function - remain enigmatic. Indeed, these fast-evolving telomere proteins bind, extend, and protect telomeric DNA, which itself evolves slowly in most systems. We hypothesize that the universally fast-evolving subtelomere - the telomere-adjacent, repetitive sequence - is a primary driver of the 'telomere paradox'. Under this model, radical sequence changes in the subtelomere perturb subtelomere-dependent, telomere functions. Compromised telomere function then spurs adaptation of telomere proteins to maintain telomere length homeostasis and protection. We propose an experimental framework that leverages both protein divergence and subtelomeric sequence divergence to test the hypothesis that subtelomere sequence evolution shapes recurrent innovation of telomere machinery.
Collapse
Affiliation(s)
- Bastien Saint-Leandre
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA; Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Mia T Levine
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA; Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA.
| |
Collapse
|
21
|
Young E, Abid HZ, Kwok PY, Riethman H, Xiao M. Comprehensive Analysis of Human Subtelomeres by Whole Genome Mapping. PLoS Genet 2020; 16:e1008347. [PMID: 31986135 PMCID: PMC7004388 DOI: 10.1371/journal.pgen.1008347] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 02/06/2020] [Accepted: 10/15/2019] [Indexed: 12/03/2022] Open
Abstract
Detailed comprehensive knowledge of the structures of individual long-range telomere-terminal haplotypes are needed to understand their impact on telomere function, and to delineate the population structure and evolution of subtelomere regions. However, the abundance of large evolutionarily recent segmental duplications and high levels of large structural variations have complicated both the mapping and sequence characterization of human subtelomere regions. Here, we use high throughput optical mapping of large single DNA molecules in nanochannel arrays for 154 human genomes from 26 populations to present a comprehensive look at human subtelomere structure and variation. The results catalog many novel long-range subtelomere haplotypes and determine the frequencies and contexts of specific subtelomeric duplicons on each chromosome arm, helping to clarify the currently ambiguous nature of many specific subtelomere structures as represented in the current reference sequence (HG38). The organization and content of some duplicons in subtelomeres appear to show both chromosome arm and population-specific trends. Based upon these trends we estimate a timeline for the spread of these duplication blocks.
Collapse
Affiliation(s)
- Eleanor Young
- School of Biomedical Engineering, Drexel University, Philadelphia, PA, United States of America
| | - Heba Z. Abid
- School of Biomedical Engineering, Drexel University, Philadelphia, PA, United States of America
| | - Pui-Yan Kwok
- Cardiovascular Research Institute, University of California–San Francisco, San Francisco, CA, United States of America
- Department of Dermatology, University of California–San Francisco, San Francisco, CA, United States of America
- Institute for Human Genetics, University of California–San Francisco, San Francisco, CA, United States of America
| | - Harold Riethman
- Medical Diagnostic & Translational Sciences, Old Dominium University, Norfolk, VA, United States of America
| | - Ming Xiao
- School of Biomedical Engineering, Drexel University, Philadelphia, PA, United States of America
- Institute of Molecular Medicine and Infectious Disease in the School of Medicine, Drexel University, Philadelphia, PA, United States of America
| |
Collapse
|
22
|
Varapula D, LaBouff E, Raseley K, Uppuluri L, Ehrlich GD, Noh M, Xiao M. A micropatterned substrate for on-surface enzymatic labelling of linearized long DNA molecules. Sci Rep 2019; 9:15059. [PMID: 31636335 PMCID: PMC6803683 DOI: 10.1038/s41598-019-51507-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 10/02/2019] [Indexed: 12/22/2022] Open
Abstract
Optical mapping of linearized DNA molecules is a promising new technology for sequence assembly and scaffolding, large structural variant detection, and diagnostics. This is currently achieved either using nanochannel confinement or by stretching single DNA molecules on a solid surface. While the first method necessitates DNA labelling before linearization, the latter allows for modification post-linearization, thereby affording increased process flexibility. Each method is constrained by various physical and chemical limitations. One of the most common techniques for linearization of DNA uses a hydrophobic surface and a receding meniscus, termed molecular combing. Here, we report the development of a microfabricated surface that can not only comb the DNA molecules efficiently but also provides for sequence-specific enzymatic fluorescent DNA labelling. By modifying a glass surface with two contrasting functionalities, such that DNA binds selectively to one of the two regions, we can control DNA extension, which is known to be critical for sequence-recognition by an enzyme. Moreover, the surface modification provides enzymatic access to the DNA backbone, as well as minimizing non-specific fluorescent dye adsorption. These enhancements make the designed surface suitable for large-scale and high-resolution single DNA molecule studies.
Collapse
Affiliation(s)
- Dharma Varapula
- School of Biomedical Engineering, Drexel University, Philadelphia, PA, 19104, USA
| | - Eric LaBouff
- School of Biomedical Engineering, Drexel University, Philadelphia, PA, 19104, USA
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, 19102, USA
- Center for Genomic Sciences and Center for Advanced Microbial Processing, Institute of Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, 19102, USA
| | - Kaitlin Raseley
- School of Biomedical Engineering, Drexel University, Philadelphia, PA, 19104, USA
| | - Lahari Uppuluri
- Department of Mechanical Engineering and Mechanics, Drexel University, Philadelphia, PA, 19104, USA
| | - Garth D Ehrlich
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, 19102, USA
- Center for Genomic Sciences and Center for Advanced Microbial Processing, Institute of Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, 19102, USA
- Department of Otolaryngology Head and Neck Surgery, Drexel University College of Medicine, Philadelphia, PA, 19102, USA
| | - Moses Noh
- Department of Mechanical Engineering and Mechanics, Drexel University, Philadelphia, PA, 19104, USA
| | - Ming Xiao
- School of Biomedical Engineering, Drexel University, Philadelphia, PA, 19104, USA.
- Center for Genomic Sciences and Center for Advanced Microbial Processing, Institute of Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, 19102, USA.
| |
Collapse
|
23
|
Adam E, Islam T, Ranjan D, Riethman H. Nanopore Guided Assembly of Segmental Duplications near Telomeres. PROCEEDINGS. IEEE INTERNATIONAL SYMPOSIUM ON BIOINFORMATICS AND BIOENGINEERING 2019; 2019:19243617. [PMID: 33868775 PMCID: PMC8049597 DOI: 10.1109/bibe.2019.00020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Human subtelomere regions are highly enriched in large segmental duplications and structural variants, leading to many gaps and misassemblies in these regions. We develop a novel method, NPGREAT (NanoPore Guided REgional Assembly Tool), which combines Nanopore ultralong read datasets and short-read assemblies derived from 10x linked-reads to efficiently assemble these subtelomere regions into a single continuous sequence. We show that with the use of ultralong Nanopore reads as a guide, the highly accurate shorter linked-read sequence contigs are correctly oriented, ordered, spaced and extended. In the rare cases where a linked-read sequence contig contains inaccurately assembled segments, the use of Nanopore reads allows for detection and correction of this error. We tested NPGREAT on four representative subtelomeres of the NA12878 human genome (10p, 16p, 19q and 20p). The results demonstrate that the final computed assembly of each subtelomere is accurate and complete.
Collapse
Affiliation(s)
- Eleni Adam
- Department of Computer Science, Old Dominion University, Norfolk, VA, USA
| | - Tunazzina Islam
- Department of Computer Science, Purdue University, West Lafayette, IN, USA
| | - Desh Ranjan
- Department of Computer Science, Old Dominion University, Norfolk, VA, USA
| | - Harold Riethman
- School of Medical Diagnostic & Translational Sciences, Old Dominion University, Norfolk, VA, USA
| |
Collapse
|
24
|
Leung AKY, Liu MCJ, Li L, Lai YYY, Chu C, Kwok PY, Ho PL, Yip KY, Chan TF. OMMA enables population-scale analysis of complex genomic features and phylogenomic relationships from nanochannel-based optical maps. Gigascience 2019; 8:giz079. [PMID: 31289833 PMCID: PMC6615982 DOI: 10.1093/gigascience/giz079] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Revised: 01/13/2019] [Accepted: 06/16/2019] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Optical mapping is an emerging technology that complements sequencing-based methods in genome analysis. It is widely used in improving genome assemblies and detecting structural variations by providing information over much longer (up to 1 Mb) reads. Current standards in optical mapping analysis involve assembling optical maps into contigs and aligning them to a reference, which is limited to pairwise comparison and becomes bias-prone when analyzing multiple samples. FINDINGS We present a new method, OMMA, that extends optical mapping to the study of complex genomic features by simultaneously interrogating optical maps across many samples in a reference-independent manner. OMMA captures and characterizes complex genomic features, e.g., multiple haplotypes, copy number variations, and subtelomeric structures when applied to 154 human samples across the 26 populations sequenced in the 1000 Genomes Project. For small genomes such as pathogenic bacteria, OMMA accurately reconstructs the phylogenomic relationships and identifies functional elements across 21 Acinetobacter baumannii strains. CONCLUSIONS With the increasing data throughput of optical mapping system, the use of this technology in comparative genome analysis across many samples will become feasible. OMMA is a timely solution that can address such computational need. The OMMA software is available at https://github.com/TF-Chan-Lab/OMTools.
Collapse
Affiliation(s)
| | - Melissa Chun-Jiao Liu
- Carol Yu Center for Infection and Department of Microbiology, The University of Hong Kong, Queen Mary Hospital, Pok Fu Lam, Hong Kong
| | - Le Li
- Department of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Yvonne Yuk-Yin Lai
- Cardiovascular Research Institute, University of California, San Francisco, CA 94153, USA
- Institute of Human Genetics, University of California, San Francisco, CA 94153, USA
| | - Catherine Chu
- Cardiovascular Research Institute, University of California, San Francisco, CA 94153, USA
- Institute of Human Genetics, University of California, San Francisco, CA 94153, USA
| | - Pui-Yan Kwok
- Cardiovascular Research Institute, University of California, San Francisco, CA 94153, USA
- Institute of Human Genetics, University of California, San Francisco, CA 94153, USA
| | - Pak-Leung Ho
- Carol Yu Center for Infection and Department of Microbiology, The University of Hong Kong, Queen Mary Hospital, Pok Fu Lam, Hong Kong
| | - Kevin Y Yip
- Department of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, Hong Kong
- Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Ting-Fung Chan
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
- Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Shatin, Hong Kong
| |
Collapse
|
25
|
Yoshimura J, Ichikawa K, Shoura MJ, Artiles KL, Gabdank I, Wahba L, Smith CL, Edgley ML, Rougvie AE, Fire AZ, Morishita S, Schwarz EM. Recompleting the Caenorhabditis elegans genome. Genome Res 2019; 29:1009-1022. [PMID: 31123080 PMCID: PMC6581061 DOI: 10.1101/gr.244830.118] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 03/11/2019] [Indexed: 01/14/2023]
Abstract
Caenorhabditis elegans was the first multicellular eukaryotic genome sequenced to apparent completion. Although this assembly employed a standard C. elegans strain (N2), it used sequence data from several laboratories, with DNA propagated in bacteria and yeast. Thus, the N2 assembly has many differences from any C. elegans available today. To provide a more accurate C. elegans genome, we performed long-read assembly of VC2010, a modern strain derived from N2. Our VC2010 assembly has 99.98% identity to N2 but with an additional 1.8 Mb including tandem repeat expansions and genome duplications. For 116 structural discrepancies between N2 and VC2010, 97 structures matching VC2010 (84%) were also found in two outgroup strains, implying deficiencies in N2. Over 98% of N2 genes encoded unchanged products in VC2010; moreover, we predicted ≥53 new genes in VC2010. The recompleted genome of C. elegans should be a valuable resource for genetics, genomics, and systems biology.
Collapse
Affiliation(s)
- Jun Yoshimura
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8583, Japan
| | - Kazuki Ichikawa
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8583, Japan
| | - Massa J Shoura
- Department of Pathology, Stanford University, Stanford, California 94305, USA
| | - Karen L Artiles
- Department of Pathology, Stanford University, Stanford, California 94305, USA
| | - Idan Gabdank
- Department of Genetics, Stanford University, Stanford, California 94305, USA
| | - Lamia Wahba
- Department of Pathology, Stanford University, Stanford, California 94305, USA
| | - Cheryl L Smith
- Department of Pathology, Stanford University, Stanford, California 94305, USA.,Department of Genetics, Stanford University, Stanford, California 94305, USA
| | - Mark L Edgley
- Department of Zoology and Michael Smith Laboratories, University of British Columbia, Vancouver V6T 1Z3, British Columbia, Canada
| | - Ann E Rougvie
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota 55454, USA
| | - Andrew Z Fire
- Department of Pathology, Stanford University, Stanford, California 94305, USA.,Department of Genetics, Stanford University, Stanford, California 94305, USA
| | - Shinichi Morishita
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8583, Japan
| | - Erich M Schwarz
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
| |
Collapse
|
26
|
Nguyen K, Broucqsault N, Chaix C, Roche S, Robin JD, Vovan C, Gerard L, Mégarbané A, Urtizberea JA, Bellance R, Barnérias C, David A, Eymard B, Fradin M, Manel V, Sacconi S, Tiffreau V, Zagnoli F, Cuisset JM, Salort-Campana E, Attarian S, Bernard R, Lévy N, Magdinier F. Deciphering the complexity of the 4q and 10q subtelomeres by molecular combing in healthy individuals and patients with facioscapulohumeral dystrophy. J Med Genet 2019; 56:590-601. [PMID: 31010831 DOI: 10.1136/jmedgenet-2018-105949] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 02/28/2019] [Accepted: 03/24/2019] [Indexed: 12/13/2022]
Abstract
BACKGROUND Subtelomeres are variable regions between telomeres and chromosomal-specific regions. One of the most studied pathologies linked to subtelomeric imbalance is facioscapulohumeral dystrophy (FSHD). In most cases, this disease involves shortening of an array of D4Z4 macrosatellite elements at the 4q35 locus. The disease also segregates with a specific A-type haplotype containing a degenerated polyadenylation signal distal to the last repeat followed by a repetitive array of β-satellite elements. This classification applies to most patients with FSHD. A subset of patients called FSHD2 escapes this definition and carries a mutation in the SMCHD1 gene. We also recently described patients carrying a complex rearrangement consisting of a cis-duplication of the distal 4q35 locus identified by molecular combing. METHODS Using this high-resolution technology, we further investigated the organisation of the 4q35 region linked to the disease and the 10q26 locus presenting with 98% of homology in controls and patients. RESULTS Our analyses reveal a broad variability in size of the different elements composing these loci highlighting the complexity of these subtelomeres and the difficulty for genomic assembly. Out of the 1029 DNA samples analysed in our centre in the last 7 years, we also identified 54 cases clinically diagnosed with FSHD carrying complex genotypes. This includes mosaic patients, patients with deletions of the proximal 4q region and 23 cases with an atypical chromosome 10 pattern, infrequently found in the control population and never reported before. CONCLUSION Overall, this work underlines the complexity of these loci challenging the diagnosis and genetic counselling for this disease.
Collapse
Affiliation(s)
- Karine Nguyen
- Medical Genetics, Assistance Publique Hopitaux de Marseille, Marseille, France.,Aix Marseille Univ, INSERM, MMG, Marseille Medical Genetics U1251, Marseille, France
| | - Natacha Broucqsault
- Aix Marseille Univ, INSERM, MMG, Marseille Medical Genetics U1251, Marseille, France
| | - Charlene Chaix
- Medical Genetics, Assistance Publique Hopitaux de Marseille, Marseille, France
| | - Stephane Roche
- Aix Marseille Univ, INSERM, MMG, Marseille Medical Genetics U1251, Marseille, France
| | - Jérôme D Robin
- Aix Marseille Univ, INSERM, MMG, Marseille Medical Genetics U1251, Marseille, France
| | - Catherine Vovan
- Medical Genetics, Assistance Publique Hopitaux de Marseille, Marseille, France
| | - Laurene Gerard
- Medical Genetics, Assistance Publique Hopitaux de Marseille, Marseille, France
| | | | - Jon Andoni Urtizberea
- Pôle Soins de suite et réadaptation handicaps lourds et maladies rares neurologiques, Hôpital Marin, Assistance publique des hopitaux de Paris, Hendaye, France
| | - Remi Bellance
- Hopital Pierre Zobda-Quitman, Fort-de-France, France
| | - Christine Barnérias
- Service de Neurologie infantile, Université Paris Descartes, Sorbonne Paris Cité, Hôpital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France.,Centre de Référence de Maladies Neuromusculaires Garches-Necker-Mondor-Hendaye (GNMH), Réseau National Français de la Filière Neuromusculaire (FILNEMUS), Paris, France
| | | | - Bruno Eymard
- Assistance Publique - Hopitaux de Paris, Paris, Île-de-France, France
| | - Melanie Fradin
- Service de Génétique Médicale, Centre De Référence Anomalies du Développement, CHU de Rennes, Rennes, France
| | - Véronique Manel
- Centre référent maladies neuromusculaires rares, Hospices Civils de Lyon, Hôpital Femme Mère Enfant, Bron, France
| | - Sabrina Sacconi
- Peripheral Nervous System, Muscle and ALS Department, Université Côte d'Azur, Nice, France.,Institute for Research on Cancer and Aging of Nice, Université Côte d'Azur, Faculty of Medicine, Nice, France
| | - Vincent Tiffreau
- Centre de Référence des Maladies Neuromusculaires, service de Médecine Physique et de Réadaptation, Centre hospitalier régionale de Lille, Lille, France
| | - Fabien Zagnoli
- Centre de Référence des Maladies Neuromusculaires, CHU Morvan, Brest, France
| | | | - Emmanuelle Salort-Campana
- Aix Marseille Univ, INSERM, MMG, Marseille Medical Genetics U1251, Marseille, France.,Centre de reference des maladies neuromusculaires, Assistance Publique Hopitaux de Marseille, Marseille, France
| | - Shahram Attarian
- Aix Marseille Univ, INSERM, MMG, Marseille Medical Genetics U1251, Marseille, France.,Centre de reference des maladies neuromusculaires, Assistance Publique Hopitaux de Marseille, Marseille, France
| | - Rafaëlle Bernard
- Medical Genetics, Assistance Publique Hopitaux de Marseille, Marseille, France.,Aix Marseille Univ, INSERM, MMG, Marseille Medical Genetics U1251, Marseille, France
| | - Nicolas Lévy
- Medical Genetics, Assistance Publique Hopitaux de Marseille, Marseille, France.,Aix Marseille Univ, INSERM, MMG, Marseille Medical Genetics U1251, Marseille, France
| | - Frederique Magdinier
- Aix Marseille Univ, INSERM, MMG, Marseille Medical Genetics U1251, Marseille, France
| |
Collapse
|
27
|
Parivesh A, Barseghyan H, Délot E, Vilain E. Translating genomics to the clinical diagnosis of disorders/differences of sex development. Curr Top Dev Biol 2019; 134:317-375. [PMID: 30999980 PMCID: PMC7382024 DOI: 10.1016/bs.ctdb.2019.01.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The medical and psychosocial challenges faced by patients living with Disorders/Differences of Sex Development (DSD) and their families can be alleviated by a rapid and accurate diagnostic process. Clinical diagnosis of DSD is limited by a lack of standardization of anatomical and endocrine phenotyping and genetic testing, as well as poor genotype/phenotype correlation. Historically, DSD genes have been identified through positional cloning of disease-associated variants segregating in families and validation of candidates in animal and in vitro modeling of variant pathogenicity. Owing to the complexity of conditions grouped under DSD, genome-wide scanning methods are better suited for identifying disease causing gene variant(s) and providing a clinical diagnosis. Here, we review a number of established genomic tools (karyotyping, chromosomal microarrays and exome sequencing) used in clinic for DSD diagnosis, as well as emerging genomic technologies such as whole-genome (short-read) sequencing, long-read sequencing, and optical mapping used for novel DSD gene discovery. These, together with gene expression and epigenetic studies can potentiate the clinical diagnosis of DSD diagnostic rates and enhance the outcomes for patients and families.
Collapse
Affiliation(s)
- Abhinav Parivesh
- Center for Genetic Medicine Research, Children's National Medical Center, Washington, DC, United States
| | - Hayk Barseghyan
- Center for Genetic Medicine Research, Children's National Medical Center, Washington, DC, United States; Department of Genomics and Precision Medicine, The George Washington University, Washington, DC, United States
| | - Emmanuèle Délot
- Center for Genetic Medicine Research, Children's National Medical Center, Washington, DC, United States; Department of Genomics and Precision Medicine, The George Washington University, Washington, DC, United States.
| | - Eric Vilain
- Center for Genetic Medicine Research, Children's National Medical Center, Washington, DC, United States; Department of Genomics and Precision Medicine, The George Washington University, Washington, DC, United States.
| |
Collapse
|
28
|
Bocklandt S, Hastie A, Cao H. Bionano Genome Mapping: High-Throughput, Ultra-Long Molecule Genome Analysis System for Precision Genome Assembly and Haploid-Resolved Structural Variation Discovery. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1129:97-118. [DOI: 10.1007/978-981-13-6037-4_7] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
|
29
|
Zhao Z, Tan Q, Zhan X, Lin J, Fan Z, Xiao K, Li B, Liao Y, Huang X. Cascaded Electrochemiluminescence Signal Amplifier for the Detection of Telomerase Activity from Tumor Cells and Tissues. Am J Cancer Res 2018; 8:5625-5633. [PMID: 30555568 PMCID: PMC6276299 DOI: 10.7150/thno.27680] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 08/16/2018] [Indexed: 12/26/2022] Open
Abstract
Telomerase is closely linked to the physiological transformation of tumor cells and is commonly overexpressed in most types of tumor cells. Therefore, telomerase has become a potential biomarker for the process of tumorigenesis, progression, prognosis and metastasis. Thus, it is important to develop a simple, accurate and reliable method for detecting telomerase activity. As a high signal-to-noise ratio mode, electrochemiluminescence (ECL) has been widely applied in the field of biomedical analysis. Here, our objective was to construct an improved ECL signal amplifier for the detection of telomerase activity. Methods: A cascaded ECL signal amplifier was constructed to detect telomerase activity with high selectivity via controllable construction of a lysine-based dendric Ru(bpy)3 2+ polymer (DRP). The sensitivity, specificity and performance index were simultaneously evaluated by standard substance and cell and tissue samples. Results: With this cascaded ECL signal amplifier, high sensitivities of 100, 50, and 100 cells for three tumor cell lines (A549, MCF7 and HepG2 cell lines) were simultaneously achieved, and desirable specificity was also obtained. Furthermore, the excellent performance of this platform was also demonstrated in the detection of telomerase in tumor cells and tissues. Conclusion: This cascaded ECL signal amplifier has the potential to be a technological innovation in the field of telomerase activity detection.
Collapse
|
30
|
Affiliation(s)
- Chao-Yung Wang
- Department of Cardiology, Chang Gung Memorial Hospital, and Chang Gung University College of Medicine, Taoyuan, Taiwan
| |
Collapse
|
31
|
Pontremoli C, Forni D, Cagliani R, Pozzoli U, Clerici M, Sironi M. Evolutionary rates of mammalian telomere-stability genes correlate with karyotype features and female germline expression. Nucleic Acids Res 2018; 46:7153-7168. [PMID: 29893967 PMCID: PMC6101625 DOI: 10.1093/nar/gky494] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 05/17/2018] [Accepted: 05/22/2018] [Indexed: 12/26/2022] Open
Abstract
Telomeres protect the ends of eukaryotic chromosomes and are essential for cell viability. In mammals, telomere dynamics vary with life history traits (e.g. body mass and longevity), suggesting differential selection depending on physiological characteristics. Telomeres, in analogy to centromeric regions, also represent candidate meiotic drivers and subtelomeric DNA evolves rapidly. We analyzed the evolutionary history of mammalian genes implicated in telomere homeostasis (TEL genes). We detected widespread positive selection and we tested two alternative hypotheses: (i) fast evolution is driven by changes in life history traits; (ii) a conflict with selfish DNA elements at the female meiosis represents the underlying selective pressure. By accounting for the phylogenetic relationships among mammalian species, we show that life history traits do not contribute to shape diversity of TEL genes. Conversely, the evolutionary rate of TEL genes correlates with expression levels during meiosis and episodes of positive selection across mammalian species are associated with karyotype features (number of chromosome arms). We thus propose a telomere drive hypothesis, whereby (sub)telomeres and telomere-binding proteins are engaged in an intra-genomic conflict similar to the one described for centromeres.
Collapse
Affiliation(s)
- Chiara Pontremoli
- Bioinformatics, Scientific Institute IRCCS E. MEDEA, 23842 Bosisio Parini, Italy
| | - Diego Forni
- Bioinformatics, Scientific Institute IRCCS E. MEDEA, 23842 Bosisio Parini, Italy
| | - Rachele Cagliani
- Bioinformatics, Scientific Institute IRCCS E. MEDEA, 23842 Bosisio Parini, Italy
| | - Uberto Pozzoli
- Bioinformatics, Scientific Institute IRCCS E. MEDEA, 23842 Bosisio Parini, Italy
| | - Mario Clerici
- Department of Physiopathology and Transplantation, University of Milan, 20090 Milan, Italy
- Don C. Gnocchi Foundation ONLUS, IRCCS, 20148 Milan, Italy
| | - Manuela Sironi
- Bioinformatics, Scientific Institute IRCCS E. MEDEA, 23842 Bosisio Parini, Italy
| |
Collapse
|
32
|
CRISPR-based strategies for studying regulatory elements and chromatin structure in mammalian gene control. Mamm Genome 2018; 29:205-228. [PMID: 29196861 PMCID: PMC9881389 DOI: 10.1007/s00335-017-9727-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 11/27/2017] [Indexed: 01/31/2023]
Abstract
The development of high-throughput methods has enabled the genome-wide identification of putative regulatory elements in a wide variety of mammalian cells at an unprecedented resolution. Extensive genomic studies have revealed the important role of regulatory elements and genetic variation therein in disease formation and risk. In most cases, there is only correlative evidence for the roles of these elements and non-coding changes within these elements in pathogenesis. With the advent of genome- and epigenome-editing tools based on the CRISPR technology, it is now possible to test the functional relevance of the regulatory elements and alterations on a genomic scale. Here, we review the various CRISPR-based strategies that have been developed to functionally validate the candidate regulatory elements in mammals as well as the non-coding genetic variants found to be associated with human disease. We also discuss how these synthetic biology tools have helped to elucidate the role of three-dimensional nuclear architecture and higher-order chromatin organization in shaping functional genome and controlling gene expression.
Collapse
|