1
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Chen X, Li J, Guan X, Bai Y, Wang K. Abnormal activation of genomic LINE1 elements caused by DNA demethylation contributes to lncRNA CASC9 overexpression in esophageal squamous cell carcinoma. Heliyon 2024; 10:e32857. [PMID: 38975080 PMCID: PMC11226909 DOI: 10.1016/j.heliyon.2024.e32857] [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: 09/12/2023] [Revised: 05/22/2024] [Accepted: 06/11/2024] [Indexed: 07/09/2024] Open
Abstract
Long noncoding RNA (lncRNA) cancer susceptibility 9 (CASC9) has been found to be overexpressed and functions as an oncogene in many cancer types. We investigated the molecular mechanism underlying CASC9 overexpression in esophageal squamous cell carcinoma (ESCC). Transcripts containing exons 2 and 6 and exons 4 and 6 showed the highest CASC9 expression levels in ESCC, no transcripts were detected in the normal esophageal epithelial Het1A cell line. The Long Interspersed Nuclear Element-1 (LINE1 or L1) element in the genome was found to participate in the evolution of lncRNA CASC9, the antisense promoter (ASP) of L1 provides the cis-regulatory elements necessary for CASC9 activation, and the antisense chain of L1 participates in the formation of exons of CASC9. The activation of the antisense promoter was due to the aberrant hypomethylation of L1 elements. An active enhancer element was identified in the downstream region of CASC9 gene by ChIP-seq and ChIP-qPCR. The interaction between ASP and the enhancer elements was confirmed by chromosome conformation capture (3C). Thus, our results suggest that the L1 ASP activation due to aberrant hypomethylation and downstream enhancer interaction plays a key role in the overexpression of lncRNA CASC9 in ESCC.
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Affiliation(s)
- Xuedan Chen
- Department of Medical Genetics, Department of Basic Medicine, Army Medical University, Chongqing 400038, China
| | - Juan Li
- Department of Medical Genetics, Department of Basic Medicine, Army Medical University, Chongqing 400038, China
- Jinfeng Laboratory, Chongqing 400038, China
| | - Xingying Guan
- Department of Medical Genetics, Department of Basic Medicine, Army Medical University, Chongqing 400038, China
| | - Yun Bai
- Department of Medical Genetics, Department of Basic Medicine, Army Medical University, Chongqing 400038, China
| | - Kai Wang
- Department of Medical Genetics, Department of Basic Medicine, Army Medical University, Chongqing 400038, China
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2
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Wang ZY, Ge LP, Ouyang Y, Jin X, Jiang YZ. Targeting transposable elements in cancer: developments and opportunities. Biochim Biophys Acta Rev Cancer 2024; 1879:189143. [PMID: 38936517 DOI: 10.1016/j.bbcan.2024.189143] [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: 12/07/2023] [Revised: 05/23/2024] [Accepted: 06/19/2024] [Indexed: 06/29/2024]
Abstract
Transposable elements (TEs), comprising nearly 50% of the human genome, have transitioned from being perceived as "genomic junk" to key players in cancer progression. Contemporary research links TE regulatory disruptions with cancer development, underscoring their therapeutic potential. Advances in long-read sequencing, computational analytics, single-cell sequencing, proteomics, and CRISPR-Cas9 technologies have enriched our understanding of TEs' clinical implications, notably their impact on genome architecture, gene regulation, and evolutionary processes. In cancer, TEs, including long interspersed element-1 (LINE-1), Alus, and long terminal repeat (LTR) elements, demonstrate altered patterns, influencing both tumorigenic and tumor-suppressive mechanisms. TE-derived nucleic acids and tumor antigens play critical roles in tumor immunity, bridging innate and adaptive responses. Given their central role in oncology, TE-targeted therapies, particularly through reverse transcriptase inhibitors and epigenetic modulators, represent a novel avenue in cancer treatment. Combining these TE-focused strategies with existing chemotherapy or immunotherapy regimens could enhance efficacy and offer a new dimension in cancer treatment. This review delves into recent TE detection advancements, explores their multifaceted roles in tumorigenesis and immune regulation, discusses emerging diagnostic and therapeutic approaches centered on TEs, and anticipates future directions in cancer research.
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Affiliation(s)
- Zi-Yu Wang
- Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Li-Ping Ge
- Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Yang Ouyang
- Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Xi Jin
- Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Yi-Zhou Jiang
- Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China.
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3
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Kojima S. Investigating mobile element variations by statistical genetics. Hum Genome Var 2024; 11:23. [PMID: 38816353 PMCID: PMC11140006 DOI: 10.1038/s41439-024-00280-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 04/17/2024] [Accepted: 04/24/2024] [Indexed: 06/01/2024] Open
Abstract
The integration of structural variations (SVs) in statistical genetics provides an opportunity to understand the genetic factors influencing complex human traits and disease. Recent advances in long-read technology and variant calling methods for short reads have improved the accurate discovery and genotyping of SVs, enabling their use in expression quantitative trait loci (eQTL) analysis and genome-wide association studies (GWAS). Mobile elements are DNA sequences that insert themselves into various genome locations. Insertional polymorphisms of mobile elements between humans, called mobile element variations (MEVs), contribute to approximately 25% of human SVs. We recently developed a variant caller that can accurately identify and genotype MEVs from biobank-scale short-read whole-genome sequencing (WGS) datasets and integrate them into statistical genetics. The use of MEVs in eQTL analysis and GWAS has a minimal impact on the discovery of genome loci associated with gene expression and disease; most disease-associated haplotypes can be identified by single nucleotide variations (SNVs). On the other hand, it helps make hypotheses about causal variants or effector variants. Focusing on MEVs, we identified multiple MEVs that contribute to differential gene expression and one of them is a potential cause of skin disease, emphasizing the importance of the integration of MEVs in medical genetics. Here, I will provide an overview of MEVs, MEV calling from WGS, and the integration of MEVs in statistical genetics. Finally, I will discuss the unanswered questions about MEVs, such as rare variants.
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Affiliation(s)
- Shohei Kojima
- Genome Immunobiology RIKEN Hakubi Research Team, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan.
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4
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Bjørnstad PM, Aaløkken R, Åsheim J, Sundaram AYM, Felde CN, Østby GH, Dalland M, Sjursen W, Carrizosa C, Vigeland MD, Sorte HS, Sheng Y, Ariansen SL, Grindedal EM, Gilfillan GD. A 39 kb structural variant causing Lynch Syndrome detected by optical genome mapping and nanopore sequencing. Eur J Hum Genet 2024; 32:513-520. [PMID: 38030917 PMCID: PMC11061271 DOI: 10.1038/s41431-023-01494-7] [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: 07/03/2023] [Revised: 10/19/2023] [Accepted: 11/06/2023] [Indexed: 12/01/2023] Open
Abstract
Lynch Syndrome (LS) is a hereditary cancer syndrome caused by pathogenic germline variants in one of the four mismatch repair (MMR) genes MLH1, MSH2, MSH6 and PMS2. It is characterized by a significantly increased risk of multiple cancer types, particularly colorectal and endometrial cancer, with autosomal dominant inheritance. Access to precise and sensitive methods for genetic testing is important, as early detection and prevention of cancer is possible when the variant is known. We present here two unrelated Norwegian families with family histories strongly suggestive of LS, where immunohistochemical and microsatellite instability analyses indicated presence of a pathogenic variant in MSH2, but targeted exon sequencing and multiplex ligation-dependent probe amplification (MLPA) were negative. Using Bionano optical genome mapping, we detected a 39 kb insertion in the MSH2 gene. Precise mapping of the insertion breakpoints and inserted sequence was performed by low-coverage whole-genome sequencing with an Oxford Nanopore MinION. The same variant was present in both families, and later found in other families from the same region of Norway, indicative of a founder event. To our knowledge, this is the first diagnosis of LS caused by a structural variant using these technologies. We suggest that structural variant detection be performed when LS is suspected but not confirmed with first-tier standard genetic testing.
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Affiliation(s)
- Pål Marius Bjørnstad
- Department Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Ragnhild Aaløkken
- Department Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - June Åsheim
- Department Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Arvind Y M Sundaram
- Department Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Caroline N Felde
- Department Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - G Henriette Østby
- Department Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Marianne Dalland
- Department Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Wenche Sjursen
- Department of Clinical & Molecular Medicine, NTNU and Department of Medical Genetics, St Olavs Hospital, Trondheim, Norway
| | - Christian Carrizosa
- Department Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Magnus D Vigeland
- Department Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
- Department of Forensic Sciences, Oslo University Hospital, 0372, Oslo, Norway
| | - Hanne S Sorte
- Department Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Ying Sheng
- Department Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Sarah L Ariansen
- Department Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Eli Marie Grindedal
- Department Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Gregor D Gilfillan
- Department Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway.
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Mustafin RN, Khusnutdinova EK. Involvement of transposable elements in Alzheimer's disease pathogenesis. Vavilovskii Zhurnal Genet Selektsii 2024; 28:228-238. [PMID: 38680184 PMCID: PMC11043511 DOI: 10.18699/vjgb-24-27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 10/30/2023] [Accepted: 11/02/2023] [Indexed: 05/01/2024] Open
Abstract
Alzheimer's disease affects an average of 5 % of the population with a significant increase in prevalence with age, suggesting that the same mechanisms that underlie aging may influence this pathology. Investigation of these mechanisms is promising for effective methods of treatment and prevention of the disease. Possible participants in these mechanisms are transposons, which serve as drivers of epigenetic regulation, since they form species-specific distributions of non-coding RNA genes in genomes in evolution. Study of miRNA involvement in Alzheimer's disease pathogenesis is relevant, since the associations of protein-coding genes (APOE4, ABCA7, BIN1, CLU, CR1, PICALM, TREM2) with the disease revealed as a result of GWAS make it difficult to explain its complex pathogenesis. Specific expression changes of many genes were found in different brain parts of Alzheimer's patients, which may be due to global regulatory changes under the influence of transposons. Experimental and clinical studies have shown pathological activation of retroelements in Alzheimer's disease. Our analysis of scientific literature in accordance with MDTE DB revealed 28 miRNAs derived from transposons (17 from LINE, 5 from SINE, 4 from HERV, 2 from DNA transposons), the expression of which specifically changes in this disease (decreases in 17 and increases in 11 microRNA). Expression of 13 out of 28 miRNAs (miR-151a, -192, -211, -28, -31, -320c, -335, -340, -378a, -511, -576, -708, -885) also changes with aging and cancer development, which indicates the presence of possible common pathogenetic mechanisms. Most of these miRNAs originated from LINE retroelements, the pathological activation of which is associated with aging, carcinogenesis, and Alzheimer's disease, which supports the hypothesis that these three processes are based on the primary dysregulation of transposons that serve as drivers of epigenetic regulation of gene expression in ontogeny.
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Affiliation(s)
| | - E K Khusnutdinova
- Bashkir State Medical University, Ufa, Russia Institute of Biochemistry and Genetics - Subdivision of the Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa, Russia
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6
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Lee M, Ahmad SF, Xu J. Regulation and function of transposable elements in cancer genomes. Cell Mol Life Sci 2024; 81:157. [PMID: 38556602 PMCID: PMC10982106 DOI: 10.1007/s00018-024-05195-2] [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: 12/03/2023] [Revised: 02/28/2024] [Accepted: 03/01/2024] [Indexed: 04/02/2024]
Abstract
Over half of human genomic DNA is composed of repetitive sequences generated throughout evolution by prolific mobile genetic parasites called transposable elements (TEs). Long disregarded as "junk" or "selfish" DNA, TEs are increasingly recognized as formative elements in genome evolution, wired intimately into the structure and function of the human genome. Advances in sequencing technologies and computational methods have ushered in an era of unprecedented insight into how TE activity impacts human biology in health and disease. Here we discuss the current views on how TEs have shaped the regulatory landscape of the human genome, how TE activity is implicated in human cancers, and how recent findings motivate novel strategies to leverage TE activity for improved cancer therapy. Given the crucial role of methodological advances in TE biology, we pair our conceptual discussions with an in-depth review of the inherent technical challenges in studying repeats, specifically related to structural variation, expression analyses, and chromatin regulation. Lastly, we provide a catalog of existing and emerging assays and bioinformatic software that altogether are enabling the most sophisticated and comprehensive investigations yet into the regulation and function of interspersed repeats in cancer genomes.
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Affiliation(s)
- Michael Lee
- Department of Pediatrics, Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, TX, 75390, USA.
| | - Syed Farhan Ahmad
- Department of Pathology, Center of Excellence for Leukemia Studies, St. Jude Children's Research Hospital, 262 Danny Thomas Place - MS 345, Memphis, TN, 38105, USA
| | - Jian Xu
- Department of Pathology, Center of Excellence for Leukemia Studies, St. Jude Children's Research Hospital, 262 Danny Thomas Place - MS 345, Memphis, TN, 38105, USA.
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7
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Di Tommaso E, Giunta S. Dynamic interplay between human alpha-satellite DNA structure and centromere functions. Semin Cell Dev Biol 2024; 156:130-140. [PMID: 37926668 DOI: 10.1016/j.semcdb.2023.10.002] [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: 08/24/2023] [Revised: 10/04/2023] [Accepted: 10/10/2023] [Indexed: 11/07/2023]
Abstract
Maintenance of genome stability relies on functional centromeres for correct chromosome segregation and faithful inheritance of the genetic information. The human centromere is the primary constriction within mitotic chromosomes made up of repetitive alpha-satellite DNA hierarchically organized in megabase-long arrays of near-identical higher order repeats (HORs). Centromeres are epigenetically specified by the presence of the centromere-specific histone H3 variant, CENP-A, which enables the assembly of the kinetochore for microtubule attachment. Notably, centromeric DNA is faithfully inherited as intact haplotypes from the parents to the offspring without intervening recombination, yet, outside of meiosis, centromeres are akin to common fragile sites (CFSs), manifesting crossing-overs and ongoing sequence instability. Consequences of DNA changes within the centromere are just starting to emerge, with unclear effects on intra- and inter-generational inheritance driven by centromere's essential role in kinetochore assembly. Here, we review evidence of meiotic selection operating to mitigate centromere drive, as well as recent reports on centromere damage, recombination and repair during the mitotic cell division. We propose an antagonistic pleiotropy interpretation to reconcile centromere DNA instability as both driver of aneuploidy that underlies degenerative diseases, while also potentially necessary for the maintenance of homogenized HORs for centromere function. We attempt to provide a framework for this conceptual leap taking into consideration the structural interface of centromere-kinetochore interaction and present case scenarios for its malfunctioning. Finally, we offer an integrated working model to connect DNA instability, chromatin, and structural changes with functional consequences on chromosome integrity.
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Affiliation(s)
- Elena Di Tommaso
- Laboratory of Genome Evolution, Department of Biology & Biotechnology Charles Darwin, Sapienza University of Rome, Rome 00185, Italy
| | - Simona Giunta
- Laboratory of Genome Evolution, Department of Biology & Biotechnology Charles Darwin, Sapienza University of Rome, Rome 00185, Italy.
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8
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Chen X, Zhang F, Shi Y, Wang H, Chen M, Yang D, Wang L, Liu P, Xie F, Chen J, Fu A, Hu B, Wang B, Ouyang Z, Wu S, Lin Z, Cen Z, Luo W. Origin and evolution of pentanucleotide repeat expansions at the familial cortical myoclonic tremor with epilepsy type1 - SAMD12 locus. Eur J Hum Genet 2024:10.1038/s41431-024-01586-y. [PMID: 38467733 DOI: 10.1038/s41431-024-01586-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 02/23/2024] [Accepted: 02/28/2024] [Indexed: 03/13/2024] Open
Abstract
Familial cortical myoclonic tremor with epilepsy type 1 (FCMTE1) is caused by (TTTTA)exp(TTTCA)exp repeat expansions in SAMD12, while pure (TTTTA)exp is polymorphic. Our investigation focused on the origin and evolution of pure (TTTTA)exp and (TTTTA)exp(TTTCA)exp at this locus. We observed a founder effect between them. The phylogenetic analysis suggested that the (TTTTA)exp(TTTCA)exp might be generated from pure (TTTTA)exp through infrequent transformation events. Long-read sequencing revealed somatic generation of (TTTTA)exp(TTTCA)exp from pure (TTTTA)exp, likely via long segment (TTTCA) repeats insertion. Our findings indicate close relationships between the non-pathogenic (TTTTA)exp and the pathogenic (TTTTA)exp(TTTCA)exp, with dynamic interconversions. This sheds light on the genesis of pathogenic repeat expansions from ancestral premutation alleles. Our results may guide future studies in detecting novel repeat expansion disorders and elucidating repeat expansion mutational processes, thereby enhancing our understanding of human genomic variation.
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Affiliation(s)
- Xinhui Chen
- Department of Neurology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Fan Zhang
- Department of Neurology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Yihua Shi
- Department of Neurology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Haotian Wang
- Department of Neurology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Miao Chen
- Department of Neurology, Zhuji Affiliated Hospital of Wenzhou Medical University, Zhuji, China
| | - Dehao Yang
- Department of Neurology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Lebo Wang
- Department of Neurology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Peng Liu
- Department of Neurology, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, Zhejiang, China
| | - Fei Xie
- Department of Neurology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310020, Zhejiang, China
| | - Jiawen Chen
- Department of Neurology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Aisi Fu
- Wuhan Dgensee Clinical Laboratory Co., Ltd. Wuhan, Wuhan, 430075, China
| | - Ben Hu
- Center for Tumor Precision Diagnosis, Zhongnan Hospital of Wuhan University, Wuhan, 430062, China
| | - Bo Wang
- Department of Neurology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Zhiyuan Ouyang
- Department of Neurology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Sheng Wu
- Department of Neurology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Zhiru Lin
- Department of Neurology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Zhidong Cen
- Department of Neurology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China.
| | - Wei Luo
- Department of Neurology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China.
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9
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Wang Y, Chen Y, Gao J, Xie H, Guo Y, Yang J, Liu J, Chen Z, Li Q, Li M, Ren J, Wen L, Tang F. Mapping crossover events of mouse meiotic recombination by restriction fragment ligation-based Refresh-seq. Cell Discov 2024; 10:26. [PMID: 38443370 PMCID: PMC10915157 DOI: 10.1038/s41421-023-00638-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 12/11/2023] [Indexed: 03/07/2024] Open
Abstract
Single-cell whole-genome sequencing methods have undergone great improvements over the past decade. However, allele dropout, which means the inability to detect both alleles simultaneously in an individual diploid cell, largely restricts the application of these methods particularly for medical applications. Here, we develop a new single-cell whole-genome sequencing method based on third-generation sequencing (TGS) platform named Refresh-seq (restriction fragment ligation-based genome amplification and TGS). It is based on restriction endonuclease cutting and ligation strategy in which two alleles in an individual cell can be cut into equal fragments and tend to be amplified simultaneously. As a new single-cell long-read genome sequencing method, Refresh-seq features much lower allele dropout rate compared with SMOOTH-seq. Furthermore, we apply Refresh-seq to 688 sperm cells and 272 female haploid cells (secondary polar bodies and parthenogenetic oocytes) from F1 hybrid mice. We acquire high-resolution genetic map of mouse meiosis recombination at low sequencing depth and reveal the sexual dimorphism in meiotic crossovers. We also phase the structure variations (deletions and insertions) in sperm cells and female haploid cells with high precision. Refresh-seq shows great performance in screening aneuploid sperm cells and oocytes due to the low allele dropout rate and has great potential for medical applications such as preimplantation genetic diagnosis.
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Affiliation(s)
- Yan Wang
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
| | - Yijun Chen
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Junpeng Gao
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
- Emergency Center, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Haoling Xie
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
| | - Yuqing Guo
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
| | - Jingwei Yang
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
| | - Jun'e Liu
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
| | - Zonggui Chen
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
- Changping Laboratory, Beijing, China
| | - Qingqing Li
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
| | - Mengyao Li
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
| | - Jie Ren
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
| | - Lu Wen
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
| | - Fuchou Tang
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing, China.
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China.
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.
- Changping Laboratory, Beijing, China.
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10
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Magliacane Trotta S, Adinolfi A, D'Orsi L, Panico S, Mercadante G, Mehlen P, Ambati J, De Falco S, Tarallo V. Cancer-derived exosomal Alu RNA promotes colorectal cancer progression. Exp Mol Med 2024; 56:700-710. [PMID: 38486106 PMCID: PMC10984964 DOI: 10.1038/s12276-024-01166-6] [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: 07/14/2023] [Revised: 11/10/2023] [Accepted: 11/29/2023] [Indexed: 04/04/2024] Open
Abstract
Inflammation plays a crucial role in cancer progression, but the relevance of the inflammasome remains unclear. Alu RNA was the first endogenous nucleic acid shown to activate the NLRP3 (nucleotide-binding domain leucine-rich repeat containing 3) inflammasome. Here, we showed that Alu RNA can induce epithelial-to-mesenchymal transition (EMT) through NLRP3 inflammasome activation and IL-1β release in colorectal cancer (CRC) cells. Alu RNA is stored, transported and transferred to CRC cells by exosomes. Exosomal Alu RNA promotes tumorigenesis by inducing invasion, metastasis and EMT via NLRP3 inflammasome activation. Consistent with these data, we found that significantly increased Alu RNA expression correlates with the induction of NLRP3 priming in human CRC patients. Furthermore, the level of Alu RNA in circulating exosomes correlates with CRC progression in a preclinical model. These findings reveal the direct involvement of Alu RNA in cancer pathogenesis, and its presence in CRC cell-derived exosomes could be used as a noninvasive diagnostic biomarker.
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Affiliation(s)
- Sara Magliacane Trotta
- Angiogenesis Lab, Institute of Genetics and Biophysics 'Adriano Buzzati-Traverso' - CNR, 80131, Naples, Italy
| | - Antonio Adinolfi
- Angiogenesis Lab, Institute of Genetics and Biophysics 'Adriano Buzzati-Traverso' - CNR, 80131, Naples, Italy
| | - Luca D'Orsi
- Angiogenesis Lab, Institute of Genetics and Biophysics 'Adriano Buzzati-Traverso' - CNR, 80131, Naples, Italy
- BIOVIIIx srl, Via Alessandro Manzoni 1, 80123, Napoli, Italy
| | - Sonia Panico
- Angiogenesis Lab, Institute of Genetics and Biophysics 'Adriano Buzzati-Traverso' - CNR, 80131, Naples, Italy
| | - Grazia Mercadante
- Angiogenesis Lab, Institute of Genetics and Biophysics 'Adriano Buzzati-Traverso' - CNR, 80131, Naples, Italy
| | - Patrick Mehlen
- Apoptosis, Cancer and Development Laboratory, Equipe labellisée 'La Ligue', LabEx DEVweCAN, Centre de Recherche en Cancérologie de Lyon, INSERM U1052-CNRS UMR5286, Université de Lyon, Centre Léon Bérard, 69008, Lyon, France
| | - Jayakrishna Ambati
- Center for Advanced Vision Science; Department of Ophthalmology; Department of Pathology; Department of Microbiology, Immunology, and Cancer Biology, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Sandro De Falco
- Angiogenesis Lab, Institute of Genetics and Biophysics 'Adriano Buzzati-Traverso' - CNR, 80131, Naples, Italy
- BIOVIIIx srl, Via Alessandro Manzoni 1, 80123, Napoli, Italy
| | - Valeria Tarallo
- Angiogenesis Lab, Institute of Genetics and Biophysics 'Adriano Buzzati-Traverso' - CNR, 80131, Naples, Italy.
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11
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Toda T, Bedrosian TA, Schafer ST, Cuoco MS, Linker SB, Ghassemzadeh S, Mitchell L, Whiteley JT, Novaresi N, McDonald AH, Gallina IS, Yoon H, Hester ME, Pena M, Lim C, Suljic E, AlFatah Mansour A, Boulard M, Parylak SL, Gage FH. Long interspersed nuclear elements safeguard neural progenitors from precocious differentiation. Cell Rep 2024; 43:113774. [PMID: 38349791 PMCID: PMC10948021 DOI: 10.1016/j.celrep.2024.113774] [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: 11/12/2022] [Revised: 11/30/2023] [Accepted: 01/24/2024] [Indexed: 02/15/2024] Open
Abstract
Long interspersed nuclear element-1 (L1 or LINE-1) is a highly abundant mobile genetic element in both humans and mice, comprising almost 20% of each genome. L1s are silenced by several mechanisms, as their uncontrolled expression has the potential to induce genomic instability. However, L1s are paradoxically expressed at high levels in differentiating neural progenitor cells. Using in vitro and in vivo techniques to modulate L1 expression, we report that L1s play a critical role in both human and mouse brain development by regulating the rate of neural differentiation in a reverse-transcription-independent manner.
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Affiliation(s)
- Tomohisa Toda
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA; Laboratory of Neural Epigenomics, Institute of Medical Physics and Micro-tissue Engineering, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany; Nuclear Architecture in Neural Plasticity and Aging Laboratory, German Center for Neurodegenerative Diseases, 01307 Dresden, Germany.
| | - Tracy A Bedrosian
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA; Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Simon T Schafer
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA; Department of Psychiatry and Psychotherapy, School of Medicine and Health, Technical University of Munich, Munich, Germany; TUM Center for Organoid Systems (COS), Munich Institute of Biomedical Engineering, Garching, Germany
| | - Michael S Cuoco
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA; Computational Neural DNA Dynamics Lab, Department of Cognitive Science, University of California, San Diego, San Diego, CA, USA; Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, San Diego, CA, USA
| | - Sara B Linker
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Saeed Ghassemzadeh
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Lisa Mitchell
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Jack T Whiteley
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Nicole Novaresi
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Aidan H McDonald
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Iryna S Gallina
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Hyojung Yoon
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Mark E Hester
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Monique Pena
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA; Department of Psychiatry and Psychotherapy, School of Medicine and Health, Technical University of Munich, Munich, Germany; TUM Center for Organoid Systems (COS), Munich Institute of Biomedical Engineering, Garching, Germany
| | - Christina Lim
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Emelia Suljic
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Abed AlFatah Mansour
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Matthieu Boulard
- Epigenetics & Neurobiology Unit, EMBL Rome, European Molecular Biology Laboratory, Via Ramarini 32, 00015 Monterotondo, Italy
| | - Sarah L Parylak
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Fred H Gage
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA.
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12
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Liu Y, Tan Y, Zhang Z, Yi M, Zhu L, Peng W. The interaction between ageing and Alzheimer's disease: insights from the hallmarks of ageing. Transl Neurodegener 2024; 13:7. [PMID: 38254235 PMCID: PMC10804662 DOI: 10.1186/s40035-024-00397-x] [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: 09/13/2023] [Revised: 12/31/2023] [Accepted: 01/02/2024] [Indexed: 01/24/2024] Open
Abstract
Ageing is a crucial risk factor for Alzheimer's disease (AD) and is characterised by systemic changes in both intracellular and extracellular microenvironments that affect the entire body instead of a single organ. Understanding the specific mechanisms underlying the role of ageing in disease development can facilitate the treatment of ageing-related diseases, such as AD. Signs of brain ageing have been observed in both AD patients and animal models. Alleviating the pathological changes caused by brain ageing can dramatically ameliorate the amyloid beta- and tau-induced neuropathological and memory impairments, indicating that ageing plays a crucial role in the pathophysiological process of AD. In this review, we summarize the impact of several age-related factors on AD and propose that preventing pathological changes caused by brain ageing is a promising strategy for improving cognitive health.
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Affiliation(s)
- Yuqing Liu
- Department of Integrated Traditional Chinese and Western Medicine, The Second Xiangya Hospital, Central South University, No.139 Middle Renmin Road, Changsha, 410011, Hunan, People's Republic of China
- National Clinical Research Center for Metabolic Diseases, Changsha, 410011, People's Republic of China
| | - Yejun Tan
- School of Mathematics, University of Minnesota Twin Cities, Minneapolis, MN, 55455, USA
| | - Zheyu Zhang
- Department of Integrated Traditional Chinese and Western Medicine, The Second Xiangya Hospital, Central South University, No.139 Middle Renmin Road, Changsha, 410011, Hunan, People's Republic of China
- National Clinical Research Center for Metabolic Diseases, Changsha, 410011, People's Republic of China
| | - Min Yi
- Department of Integrated Traditional Chinese and Western Medicine, The Second Xiangya Hospital, Central South University, No.139 Middle Renmin Road, Changsha, 410011, Hunan, People's Republic of China
- National Clinical Research Center for Metabolic Diseases, Changsha, 410011, People's Republic of China
| | - Lemei Zhu
- Academician Workstation, Changsha Medical University, Changsha, 410219, People's Republic of China
| | - Weijun Peng
- Department of Integrated Traditional Chinese and Western Medicine, The Second Xiangya Hospital, Central South University, No.139 Middle Renmin Road, Changsha, 410011, Hunan, People's Republic of China.
- National Clinical Research Center for Metabolic Diseases, Changsha, 410011, People's Republic of China.
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13
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Smolka M, Paulin LF, Grochowski CM, Horner DW, Mahmoud M, Behera S, Kalef-Ezra E, Gandhi M, Hong K, Pehlivan D, Scholz SW, Carvalho CMB, Proukakis C, Sedlazeck FJ. Detection of mosaic and population-level structural variants with Sniffles2. Nat Biotechnol 2024:10.1038/s41587-023-02024-y. [PMID: 38168980 PMCID: PMC11217151 DOI: 10.1038/s41587-023-02024-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 10/11/2023] [Indexed: 01/05/2024]
Abstract
Calling structural variations (SVs) is technically challenging, but using long reads remains the most accurate way to identify complex genomic alterations. Here we present Sniffles2, which improves over current methods by implementing a repeat aware clustering coupled with a fast consensus sequence and coverage-adaptive filtering. Sniffles2 is 11.8 times faster and 29% more accurate than state-of-the-art SV callers across different coverages (5-50×), sequencing technologies (ONT and HiFi) and SV types. Furthermore, Sniffles2 solves the problem of family-level to population-level SV calling to produce fully genotyped VCF files. Across 11 probands, we accurately identified causative SVs around MECP2, including highly complex alleles with three overlapping SVs. Sniffles2 also enables the detection of mosaic SVs in bulk long-read data. As a result, we identified multiple mosaic SVs in brain tissue from a patient with multiple system atrophy. The identified SV showed a remarkable diversity within the cingulate cortex, impacting both genes involved in neuron function and repetitive elements.
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Affiliation(s)
- Moritz Smolka
- Human Genome Sequencing Center Baylor College of Medicine, Houston, TX, USA
| | - Luis F Paulin
- Human Genome Sequencing Center Baylor College of Medicine, Houston, TX, USA
| | | | - Dominic W Horner
- Department of Clinical and Movement Neurosciences, Royal Free Campus, Queen Square Institute of Neurology, University College London, London, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Medhat Mahmoud
- Human Genome Sequencing Center Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Sairam Behera
- Human Genome Sequencing Center Baylor College of Medicine, Houston, TX, USA
| | - Ester Kalef-Ezra
- Department of Clinical and Movement Neurosciences, Royal Free Campus, Queen Square Institute of Neurology, University College London, London, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Mira Gandhi
- Pacific Northwest Research Institute (PNRI), Seattle, WA, USA
| | - Karl Hong
- Bionano Genomics, San Diego, CA, USA
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Division of Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Sonja W Scholz
- Neurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
- Department of Neurology, Johns Hopkins University Medical Center, Baltimore, MD, USA
| | - Claudia M B Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Pacific Northwest Research Institute (PNRI), Seattle, WA, USA
| | - Christos Proukakis
- Department of Clinical and Movement Neurosciences, Royal Free Campus, Queen Square Institute of Neurology, University College London, London, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center Baylor College of Medicine, Houston, TX, USA.
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA.
- Department of Computer Science, Rice University, Houston, TX, USA.
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14
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Wambach JA, Wegner DJ, Kitzmiller J, White FV, Heins HB, Yang P, Paul AJ, Granadillo JL, Eghtesady P, Kuklinski C, Turner T, Fairman K, Stone K, Wilson T, Breman A, Smith J, Schroeder MC, Neidich JA, Whitsett JA, Cole FS. Homozygous, Intragenic Tandem Duplication of SFTPB Causes Neonatal Respiratory Failure. Am J Respir Cell Mol Biol 2024; 70:78-80. [PMID: 38156804 PMCID: PMC10768837 DOI: 10.1165/rcmb.2023-0156le] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024] Open
Affiliation(s)
| | | | | | | | | | - Ping Yang
- Washington University School of MedicineSt. Louis, Missouri
| | | | | | | | | | - Tiffany Turner
- Indiana University School of MedicineIndianapolis, Indiana
| | - Korre Fairman
- Indiana University School of MedicineIndianapolis, Indiana
| | - Kristyne Stone
- Indiana University School of MedicineIndianapolis, Indiana
| | | | - Amy Breman
- Indiana University School of MedicineIndianapolis, Indiana
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15
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Volpe E, Corda L, Tommaso ED, Pelliccia F, Ottalevi R, Licastro D, Guarracino A, Capulli M, Formenti G, Tassone E, Giunta S. The complete diploid reference genome of RPE-1 identifies human phased epigenetic landscapes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.01.565049. [PMID: 38168337 PMCID: PMC10760208 DOI: 10.1101/2023.11.01.565049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Comparative analysis of recent human genome assemblies highlights profound sequence divergence that peaks within polymorphic loci such as centromeres. This raises the question about the adequacy of relying on human reference genomes to accurately analyze sequencing data derived from experimental cell lines. Here, we generated the complete diploid genome assembly for the human retinal epithelial cells (RPE-1), a widely used non-cancer laboratory cell line with a stable karyotype, to use as matched reference for multi-omics sequencing data analysis. Our RPE1v1.0 assembly presents completely phased haplotypes and chromosome-level scaffolds that span centromeres with ultra-high base accuracy (>QV60). We mapped the haplotype-specific genomic variation specific to this cell line including t(Xq;10q), a stable 73.18 Mb duplication of chromosome 10 translocated onto the microdeleted chromosome X telomere t(Xq;10q). Polymorphisms between haplotypes of the same genome reveals genetic and epigenetic variation for all chromosomes, especially at centromeres. The RPE-1 assembly as matched reference genome improves mapping quality of multi-omics reads originating from RPE-1 cells with drastic reduction in alignments mismatches compared to using the most complete human reference to date (CHM13). Leveraging the accuracy achieved using a matched reference, we were able to identify the kinetochore sites at base pair resolution and show unprecedented variation between haplotypes. This work showcases the use of matched reference genomes for multiomics analyses and serves as the foundation for a call to comprehensively assemble experimentally relevant cell lines for widespread application.
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Affiliation(s)
- Emilia Volpe
- Giunta Laboratory of Genome Evolution, Department of Biology and Biotechnologies Charles Darwin, University of Rome “Sapienza”, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Luca Corda
- Giunta Laboratory of Genome Evolution, Department of Biology and Biotechnologies Charles Darwin, University of Rome “Sapienza”, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Elena Di Tommaso
- Giunta Laboratory of Genome Evolution, Department of Biology and Biotechnologies Charles Darwin, University of Rome “Sapienza”, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Franca Pelliccia
- Giunta Laboratory of Genome Evolution, Department of Biology and Biotechnologies Charles Darwin, University of Rome “Sapienza”, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Riccardo Ottalevi
- Department of Bioinformatic, Dante Genomics Corp Inc., 667 Madison Avenue, New York, NY 10065 USA and S.s.17, 67100, L’Aquila, Italy
| | | | - Andrea Guarracino
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Mattia Capulli
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, L’Aquila, Italy
| | - Giulio Formenti
- The Rockefeller University, 1230 York Avenue, 10065 New York, USA
| | - Evelyne Tassone
- Giunta Laboratory of Genome Evolution, Department of Biology and Biotechnologies Charles Darwin, University of Rome “Sapienza”, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Simona Giunta
- Giunta Laboratory of Genome Evolution, Department of Biology and Biotechnologies Charles Darwin, University of Rome “Sapienza”, Piazzale Aldo Moro 5, 00185 Rome, Italy
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16
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Mendez-Dorantes C, Burns KH. LINE-1 retrotransposition and its deregulation in cancers: implications for therapeutic opportunities. Genes Dev 2023; 37:948-967. [PMID: 38092519 PMCID: PMC10760644 DOI: 10.1101/gad.351051.123] [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] [Indexed: 12/28/2023]
Abstract
Long interspersed element 1 (LINE-1) is the only protein-coding transposon that is active in humans. LINE-1 propagates in the genome using RNA intermediates via retrotransposition. This activity has resulted in LINE-1 sequences occupying approximately one-fifth of our genome. Although most copies of LINE-1 are immobile, ∼100 copies are retrotransposition-competent. Retrotransposition is normally limited via epigenetic silencing, DNA repair, and other host defense mechanisms. In contrast, LINE-1 overexpression and retrotransposition are hallmarks of cancers. Here, we review mechanisms of LINE-1 regulation and how LINE-1 may promote genetic heterogeneity in tumors. Finally, we discuss therapeutic strategies to exploit LINE-1 biology in cancers.
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Affiliation(s)
- Carlos Mendez-Dorantes
- Department of Pathology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA;
- Department of Pathology, Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
| | - Kathleen H Burns
- Department of Pathology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA;
- Department of Pathology, Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
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17
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Choo ZN, Behr JM, Deshpande A, Hadi K, Yao X, Tian H, Takai K, Zakusilo G, Rosiene J, Da Cruz Paula A, Weigelt B, Setton J, Riaz N, Powell SN, Busam K, Shoushtari AN, Ariyan C, Reis-Filho J, de Lange T, Imieliński M. Most large structural variants in cancer genomes can be detected without long reads. Nat Genet 2023; 55:2139-2148. [PMID: 37945902 PMCID: PMC10703688 DOI: 10.1038/s41588-023-01540-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 09/19/2023] [Indexed: 11/12/2023]
Abstract
Short-read sequencing is the workhorse of cancer genomics yet is thought to miss many structural variants (SVs), particularly large chromosomal alterations. To characterize missing SVs in short-read whole genomes, we analyzed 'loose ends'-local violations of mass balance between adjacent DNA segments. In the landscape of loose ends across 1,330 high-purity cancer whole genomes, most large (>10-kb) clonal SVs were fully resolved by short reads in the 87% of the human genome where copy number could be reliably measured. Some loose ends represent neotelomeres, which we propose as a hallmark of the alternative lengthening of telomeres phenotype. These pan-cancer findings were confirmed by long-molecule profiles of 38 breast cancer and melanoma cases. Our results indicate that aberrant homologous recombination is unlikely to drive the majority of large cancer SVs. Furthermore, analysis of mass balance in short-read whole genome data provides a surprisingly complete picture of cancer chromosomal structure.
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Affiliation(s)
- Zi-Ning Choo
- New York Genome Center, New York, NY, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
- Tri-institutional MD PhD Program, Weill Cornell Medicine, New York, NY, USA
- Physiology and Biophysics PhD Program, Weill Cornell Medicine, New York, NY, USA
| | - Julie M Behr
- New York Genome Center, New York, NY, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
- Tri-institutional PhD Program in Computational Biology and Medicine, New York, NY, USA
| | - Aditya Deshpande
- New York Genome Center, New York, NY, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
- Tri-institutional PhD Program in Computational Biology and Medicine, New York, NY, USA
| | - Kevin Hadi
- New York Genome Center, New York, NY, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
- Physiology and Biophysics PhD Program, Weill Cornell Medicine, New York, NY, USA
| | - Xiaotong Yao
- New York Genome Center, New York, NY, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
- Tri-institutional PhD Program in Computational Biology and Medicine, New York, NY, USA
| | - Huasong Tian
- New York Genome Center, New York, NY, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
- Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY, USA
| | - Kaori Takai
- Laboratory of Cell Biology and Genetics, Rockefeller University, New York, NY, USA
| | - George Zakusilo
- Laboratory of Cell Biology and Genetics, Rockefeller University, New York, NY, USA
| | - Joel Rosiene
- New York Genome Center, New York, NY, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | | | - Britta Weigelt
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jeremy Setton
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nadeem Riaz
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Simon N Powell
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Klaus Busam
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | | | | | - Titia de Lange
- Laboratory of Cell Biology and Genetics, Rockefeller University, New York, NY, USA
| | - Marcin Imieliński
- New York Genome Center, New York, NY, USA.
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA.
- Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY, USA.
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA.
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18
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Chen M, Bie L, Ying J. Cancer cell-intrinsic PD-1: Its role in malignant progression and immunotherapy. Biomed Pharmacother 2023; 167:115514. [PMID: 37716115 DOI: 10.1016/j.biopha.2023.115514] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 09/08/2023] [Accepted: 09/12/2023] [Indexed: 09/18/2023] Open
Abstract
Programmed cell death protein-1 (PD-1), also called CD279, is coded by the PDCD1 gene and is constitutively expressed on the surface of immune cells. As a receptor and immune checkpoint, PD-1 can bind to programmed death ligand-1/programmed death ligand-2 (PD-L1/PD-L2) in tumor cells, leading to tumor immune evasion. Anti-PD-1 and anti-PD-L1 are important components in tumor immune therapy. PD-1 is also expressed as an intrinsic variant (iPD-1) in cancer cells where it plays important roles in malignant progression as proposed by recent studies. However, iPD-1 has received much less attention compared to PD-1 expressed on immune cells although there is an unmet medical need for fully elucidating the mechanisms of actions to achieve the best response in tumor immunotherapy. iPD-1 suppresses tumorigenesis in non-small cell lung cancer (NSCLC) and colon cancer, whereas it promotes tumorigenesis in melanoma, hepatocellular carcinoma (HCC), pancreatic ductal adenocarcinoma (PDAC), thyroid cancer (TC), glioblastoma (GBM), and triple-negative breast cancer (TNBC). In this review, we focus on the role of iPD-1 in tumorigenesis and development and its molecular mechanisms. We also deeply discuss nivolumab-based combined therapy in common tumor therapy. iPD-1 may explain the different therapeutic effects of anti-PD-1 treatment and provide critical information for use in combined anti-tumor approaches.
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Affiliation(s)
- Muhua Chen
- Department of Hepato-Pancreato-Biliary & Gastric Medical Oncology, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China.
| | - Lei Bie
- Department of Thoracic Surgery, Wuhan No.1 Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Jieer Ying
- Department of Hepato-Pancreato-Biliary & Gastric Medical Oncology, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China.
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19
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Dileep V, Boix CA, Mathys H, Marco A, Welch GM, Meharena HS, Loon A, Jeloka R, Peng Z, Bennett DA, Kellis M, Tsai LH. Neuronal DNA double-strand breaks lead to genome structural variations and 3D genome disruption in neurodegeneration. Cell 2023; 186:4404-4421.e20. [PMID: 37774679 PMCID: PMC10697236 DOI: 10.1016/j.cell.2023.08.038] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 04/02/2023] [Accepted: 08/29/2023] [Indexed: 10/01/2023]
Abstract
Persistent DNA double-strand breaks (DSBs) in neurons are an early pathological hallmark of neurodegenerative diseases including Alzheimer's disease (AD), with the potential to disrupt genome integrity. We used single-nucleus RNA-seq in human postmortem prefrontal cortex samples and found that excitatory neurons in AD were enriched for somatic mosaic gene fusions. Gene fusions were particularly enriched in excitatory neurons with DNA damage repair and senescence gene signatures. In addition, somatic genome structural variations and gene fusions were enriched in neurons burdened with DSBs in the CK-p25 mouse model of neurodegeneration. Neurons enriched for DSBs also had elevated levels of cohesin along with progressive multiscale disruption of the 3D genome organization aligned with transcriptional changes in synaptic, neuronal development, and histone genes. Overall, this study demonstrates the disruption of genome stability and the 3D genome organization by DSBs in neurons as pathological steps in the progression of neurodegenerative diseases.
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Affiliation(s)
- Vishnu Dileep
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Carles A Boix
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Hansruedi Mathys
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Asaf Marco
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Gwyneth M Welch
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Hiruy S Meharena
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Anjanet Loon
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ritika Jeloka
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Zhuyu Peng
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | - Manolis Kellis
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Li-Huei Tsai
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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20
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Omichi N, Kishita Y, Nakama M, Sasai H, Terazawa A, Kobayashi E, Fushimi T, Sugiyama Y, Ichimoto K, Nitta KR, Yatsuka Y, Ohtake A, Murayama K, Okazaki Y. Novel ITPA variants identified by whole genome sequencing and RNA sequencing. J Hum Genet 2023; 68:649-652. [PMID: 37246162 DOI: 10.1038/s10038-023-01156-y] [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: 02/26/2023] [Revised: 04/20/2023] [Accepted: 04/21/2023] [Indexed: 05/30/2023]
Abstract
Approximately 80% of rare diseases have a genetic cause, and an accurate genetic diagnosis is necessary for disease management, prognosis prediction, and genetic counseling. Whole-exome sequencing (WES) is a cost-effective approach for exploring the genetic cause, but several cases often remain undiagnosed. We combined whole genome sequencing (WGS) and RNA sequencing (RNA-seq) to identify the pathogenic variants in an unsolved case using WES. RNA-seq revealed aberrant exon 4 and exon 6 splicing of ITPA. WGS showed a previously unreported splicing donor variant, c.263+1G>A, and a novel heterozygous deletion, including exon 6. Detailed examination of the breakpoint indicated the deletion caused by recombination between Alu elements in different introns. The proband was found to have developmental and epileptic encephalopathies caused by variants in the ITPA gene. The combination of WGS and RNA-seq may be effective in diagnosing conditions in proband who could not be diagnosed using WES.
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Affiliation(s)
- Nanako Omichi
- Department of Life Science, Faculty of Science and Engineering, Kindai University, Osaka, Japan
| | - Yoshihito Kishita
- Department of Life Science, Faculty of Science and Engineering, Kindai University, Osaka, Japan
- Diagnostics and Therapeutic of Intractable Diseases, Intractable Disease Research Center, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Mina Nakama
- Department of Life Science, Faculty of Science and Engineering, Kindai University, Osaka, Japan
- Clinical Genetics Center, Gifu University Hospital, Gifu, Japan
- Department of Pediatrics, Graduate School of Medicine, Gifu University, Gifu, Japan
| | - Hideo Sasai
- Clinical Genetics Center, Gifu University Hospital, Gifu, Japan
- Department of Pediatrics, Graduate School of Medicine, Gifu University, Gifu, Japan
- Department of Applied Genomics, Kazusa DNA Research Institute, Chiba, Japan
| | - Atsushi Terazawa
- Department of Pediatric Cardiology, Gifu Prefectural General Medical Center, Gifu, Japan
| | - Emiko Kobayashi
- Department of Pediatrics, Gifu Prefectural General Medical Center, Gifu, Japan
| | - Takuya Fushimi
- Department of Metabolism, Chiba Children's Hospital, Chiba, Japan
| | - Yohei Sugiyama
- Department of Metabolism, Chiba Children's Hospital, Chiba, Japan
| | - Keiko Ichimoto
- Department of Metabolism, Chiba Children's Hospital, Chiba, Japan
| | - Kazuhiro R Nitta
- Diagnostics and Therapeutic of Intractable Diseases, Intractable Disease Research Center, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Yukiko Yatsuka
- Diagnostics and Therapeutic of Intractable Diseases, Intractable Disease Research Center, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Akira Ohtake
- Department of Pediatrics and Clinical Genomics, Saitama Medical University, Moroyama, Saitama, Japan
- Center for Intractable Diseases, Saitama Medical University Hospital, Moroyama, Saitama, Japan
| | - Kei Murayama
- Diagnostics and Therapeutic of Intractable Diseases, Intractable Disease Research Center, Graduate School of Medicine, Juntendo University, Tokyo, Japan
- Department of Metabolism, Chiba Children's Hospital, Chiba, Japan
- Center for Medical Genetics, Chiba Children's Hospital, Chiba, Japan
| | - Yasushi Okazaki
- Diagnostics and Therapeutic of Intractable Diseases, Intractable Disease Research Center, Graduate School of Medicine, Juntendo University, Tokyo, Japan.
- Laboratory for Comprehensive Genomic Analysis, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan.
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21
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Reitz D, Djeghmoum Y, Watson RA, Rajput P, Argueso JL, Heyer WD, Piazza A. Delineation of two multi-invasion-induced rearrangement pathways that differently affect genome stability. Genes Dev 2023; 37:621-639. [PMID: 37541760 PMCID: PMC10499017 DOI: 10.1101/gad.350618.123] [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: 03/10/2023] [Accepted: 07/14/2023] [Indexed: 08/06/2023]
Abstract
Punctuated bursts of structural genomic variations (SVs) have been described in various organisms, but their etiology remains incompletely understood. Homologous recombination (HR) is a template-guided mechanism of repair of DNA double-strand breaks and stalled or collapsed replication forks. We recently identified a DNA break amplification and genome rearrangement pathway originating from the endonucleolytic processing of a multi-invasion (MI) DNA joint molecule formed during HR. Genome-wide approaches confirmed that multi-invasion-induced rearrangement (MIR) frequently leads to several repeat-mediated SVs and aneuploidies. Using molecular and genetic analysis and a novel, highly sensitive proximity ligation-based assay for chromosomal rearrangement quantification, we further delineate two MIR subpathways. MIR1 is a universal pathway occurring in any sequence context, which generates secondary breaks and frequently leads to additional SVs. MIR2 occurs only if recombining donors exhibit substantial homology and results in sequence insertion without additional breaks or SVs. The most detrimental MIR1 pathway occurs late on a subset of persisting DNA joint molecules in a PCNA/Polδ-independent manner, unlike recombinational DNA synthesis. This work provides a refined mechanistic understanding of these HR-based SV formation pathways and shows that complex repeat-mediated SVs can occur without displacement DNA synthesis. Sequence signatures for inferring MIR1 from long-read data are proposed.
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Affiliation(s)
- Diedre Reitz
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, California 95616, USA
| | - Yasmina Djeghmoum
- Laboratory of Biology and Modelling of the Cell (UMR5239), Ecole Normale Supérieure de Lyon, 69007 Lyon, France
| | - Ruth A Watson
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, Colorado 80523, USA
| | - Pallavi Rajput
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, California 95616, USA
| | - Juan Lucas Argueso
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, Colorado 80523, USA
| | - Wolf-Dietrich Heyer
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, California 95616, USA;
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, California 95616, USA
| | - Aurèle Piazza
- Laboratory of Biology and Modelling of the Cell (UMR5239), Ecole Normale Supérieure de Lyon, 69007 Lyon, France;
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22
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Zhang M, Sun W, You X, Xu D, Wang L, Yang J, Li E, He S. LINE-1 repression in Epstein-Barr virus-associated gastric cancer through viral-host genome interaction. Nucleic Acids Res 2023; 51:4867-4880. [PMID: 36942479 PMCID: PMC10250212 DOI: 10.1093/nar/gkad203] [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: 12/14/2022] [Revised: 03/07/2023] [Accepted: 03/12/2023] [Indexed: 03/23/2023] Open
Abstract
Long INterspersed Element 1 (LINE-1 or L1) acts as a major remodeling force in genome regulation and evolution. Accumulating evidence shows that virus infection impacts L1 expression, potentially impacting host antiviral response and diseases. The underlying regulation mechanism is unclear. Epstein-Barr virus (EBV), a double-stranded DNA virus linked to B-cell and epithelial malignancies, is known to have viral-host genome interaction, resulting in transcriptional rewiring in EBV-associated gastric cancer (EBVaGC). By analyzing publicly available datasets from the Gene Expression Omnibus (GEO), we found that EBVaGC has L1 transcriptional repression compared with EBV-negative gastric cancer (EBVnGC). More specifically, retrotransposition-associated young and full-length L1s (FL-L1s) were among the most repressed L1s. Epigenetic alterations, especially increased H3K9me3, were observed on FL-L1s. H3K9me3 deposition was potentially attributed to increased TASOR expression, a key component of the human silencing hub (HUSH) complex for H3K9 trimethylation. The 4C- and HiC-seq data indicated that the viral DNA interacted in the proximity of the TASOR enhancer, strengthening the loop formation between the TASOR enhancer and its promoter. These results indicated that EBV infection is associated with increased H3K9me3 deposition, leading to L1 repression. This study uncovers a regulation mechanism of L1 expression by chromatin topology remodeling associated with viral-host genome interaction in EBVaGC.
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Affiliation(s)
- Mengyu Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, Medical School, Nanjing University, Nanjing 210093, China
- Jiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University, Nanjing 210093, China
- Yancheng Medical Research Center, Medical School, Nanjing University, Yancheng 224000, China
| | - Weikang Sun
- State Key Laboratory of Pharmaceutical Biotechnology, Medical School, Nanjing University, Nanjing 210093, China
- Jiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University, Nanjing 210093, China
| | - Xiaoxin You
- State Key Laboratory of Pharmaceutical Biotechnology, Medical School, Nanjing University, Nanjing 210093, China
- Jiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University, Nanjing 210093, China
| | - Dongge Xu
- State Key Laboratory of Pharmaceutical Biotechnology, Medical School, Nanjing University, Nanjing 210093, China
- Jiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University, Nanjing 210093, China
| | - Lingling Wang
- State Key Laboratory of Pharmaceutical Biotechnology, Medical School, Nanjing University, Nanjing 210093, China
- Jiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University, Nanjing 210093, China
| | - Jingping Yang
- State Key Laboratory of Pharmaceutical Biotechnology, Medical School, Nanjing University, Nanjing 210093, China
- Jiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University, Nanjing 210093, China
| | - Erguang Li
- State Key Laboratory of Pharmaceutical Biotechnology, Medical School, Nanjing University, Nanjing 210093, China
- Jiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University, Nanjing 210093, China
- Institute of Medical Virology, Nanjing Drum Tower Hospital, Medical School, Nanjing University, Nanjing 210093, China
- Shenzhen Research Institute of Nanjing University, Shenzhen 518000, China
| | - Susu He
- State Key Laboratory of Pharmaceutical Biotechnology, Medical School, Nanjing University, Nanjing 210093, China
- Jiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University, Nanjing 210093, China
- Yancheng Medical Research Center, Medical School, Nanjing University, Yancheng 224000, China
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23
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Mongia P, Toyofuku N, Pan Z, Xu R, Kinoshita Y, Oki K, Takahashi H, Ogura Y, Hayashi T, Nakagawa T. Fission yeast Srr1 and Skb1 promote isochromosome formation at the centromere. Commun Biol 2023; 6:551. [PMID: 37237082 DOI: 10.1038/s42003-023-04925-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 05/09/2023] [Indexed: 05/28/2023] Open
Abstract
Rad51 maintains genome integrity, whereas Rad52 causes non-canonical homologous recombination leading to gross chromosomal rearrangements (GCRs). Here we find that fission yeast Srr1/Ber1 and Skb1/PRMT5 promote GCRs at centromeres. Genetic and physical analyses show that srr1 and skb1 mutations reduce isochromosome formation mediated by centromere inverted repeats. srr1 increases DNA damage sensitivity in rad51 cells but does not abolish checkpoint response, suggesting that Srr1 promotes Rad51-independent DNA repair. srr1 and rad52 additively, while skb1 and rad52 epistatically reduce GCRs. Unlike srr1 or rad52, skb1 does not increase damage sensitivity. Skb1 regulates cell morphology and cell cycle with Slf1 and Pom1, respectively, but neither Slf1 nor Pom1 causes GCRs. Mutating conserved residues in the arginine methyltransferase domain of Skb1 greatly reduces GCRs. These results suggest that, through arginine methylation, Skb1 forms aberrant DNA structures leading to Rad52-dependent GCRs. This study has uncovered roles for Srr1 and Skb1 in GCRs at centromeres.
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Affiliation(s)
- Piyusha Mongia
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
- Forefront Research Center, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
| | - Naoko Toyofuku
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
| | - Ziyi Pan
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
- Forefront Research Center, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
| | - Ran Xu
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
- Forefront Research Center, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
| | - Yakumo Kinoshita
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
- Forefront Research Center, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
| | - Keitaro Oki
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
| | - Hiroki Takahashi
- Medical Mycology Research Center, Chiba University, Chiba, 260-8673, Japan
| | - Yoshitoshi Ogura
- Division of Microbiology, Department of Infectious Medicine, Kurume University School of Medicine, Kurume, Fukuoka, 830-0011, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan
| | - Takuro Nakagawa
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan.
- Forefront Research Center, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan.
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24
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Zapater LJ, Rodriguez-Fos E, Planas-Felix M, Lewis S, Cameron D, Demarest P, Nabila A, Zhao J, Bergin P, Reed C, Yamada M, Pagnozzi A, Nava C, Bourel-Ponchel E, Neilson DE, Dursun A, Özgül RK, Akar HT, Socci ND, Hayes M, Rabadan R, Torrents D, Kruer MC, Toth M, Kentsis A. A transposase-derived gene required for human brain development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.28.538770. [PMID: 37163102 PMCID: PMC10168387 DOI: 10.1101/2023.04.28.538770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
DNA transposable elements and transposase-derived genes are present in most living organisms, including vertebrates, but their function is largely unknown. PiggyBac Transposable Element Derived 5 (PGBD5) is an evolutionarily conserved vertebrate DNA transposase-derived gene with retained nuclease activity in cells. Vertebrate brain development is known to be associated with prominent neuronal cell death and DNA breaks, but their causes and functions are not well understood. Here, we show that PGBD5 contributes to normal brain development in mice and humans, where its deficiency causes disorder of intellectual disability, movement and seizures. In mice, Pgbd5 is required for the developmental induction of post-mitotic DNA breaks and recurrent somatic genome rearrangements in neurons. Together, these studies nominate PGBD5 as the long-hypothesized neuronal DNA nuclease required for brain function in mammals.
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Affiliation(s)
- Luz Jubierre Zapater
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10021
- Tow Center for Developmental Oncology, Department of Pediatrics, Memorial Sloan Kettering Cancer Center; New York, United States, 10021
| | | | | | - Sara Lewis
- Pediatric Movement Disorders Program, Barrow Neurological Institute, Phoenix Children’s Hospital and Departments of Child Health, Neurology, Genetics and Cellular & Molecular Medicine, Phoenix, AZ
| | - Daniel Cameron
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10021
- Tow Center for Developmental Oncology, Department of Pediatrics, Memorial Sloan Kettering Cancer Center; New York, United States, 10021
| | - Phillip Demarest
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10021
| | - Anika Nabila
- Department of Pharmacology, Weill Cornell Medical College, New York, NY, 10021
| | - Junfei Zhao
- Program for Mathematical Genomics, Departments of Systems Biology and Biomedical Informatics, Columbia University, New York, NY
| | - Paul Bergin
- Department of Pharmacology, Weill Cornell Medical College, New York, NY, 10021
| | - Casie Reed
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10021
| | - Makiko Yamada
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10021
- Tow Center for Developmental Oncology, Department of Pediatrics, Memorial Sloan Kettering Cancer Center; New York, United States, 10021
| | - Alex Pagnozzi
- CSIRO Health and Biosecurity, The Australian e-Health Research Centre, Brisbane, Australia
| | - Caroline Nava
- Assistance Publique-Hôpitaux de Paris, Département de Génétique, Hôpital Pitié-Salpêtrière, Paris, France
| | - Emilie Bourel-Ponchel
- Research Group on Multimodal Analysis of Brain Function, University of Picardie Jules Verne, France
- Pediatric Neurophysiology Unit, Amiens Picardie University Hospital, France
| | | | - Ali Dursun
- Hacettepe University, Faculty of Medicine & Institute of Child Health, Department of Pediatric Metabolism, Ankara, Turkey
| | - R. Köksal Özgül
- Hacettepe University, Faculty of Medicine & Institute of Child Health, Department of Pediatric Metabolism, Ankara, Turkey
| | - Halil Tuna Akar
- Hacettepe University, Faculty of Medicine & Institute of Child Health, Department of Pediatric Metabolism, Ankara, Turkey
| | - Nicholas D. Socci
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10021
| | - Matthew Hayes
- Department of Physics and Computer Science, Xavier University of Louisiana, New Orleans, LA
| | - Raul Rabadan
- Program for Mathematical Genomics, Departments of Systems Biology and Biomedical Informatics, Columbia University, New York, NY
| | - David Torrents
- Barcelona Supercomputing Center (BSC), Barcelona, Spain, 08034
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | | | - Miklos Toth
- Department of Pharmacology, Weill Cornell Medical College, New York, NY, 10021
| | - Alex Kentsis
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10021
- Tow Center for Developmental Oncology, Department of Pediatrics, Memorial Sloan Kettering Cancer Center; New York, United States, 10021
- Department of Pharmacology, Weill Cornell Medical College, New York, NY, 10021
- Departments of Pediatrics, Pharmacology, and Physiology & Biophysics, Weill Cornell Graduate School of Medical Sciences, Cornell University; New York, United States
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25
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Sharif J, Koseki H, Parrish NF. Bridging multiple dimensions: roles of transposable elements in higher-order genome regulation. Curr Opin Genet Dev 2023; 80:102035. [PMID: 37028152 DOI: 10.1016/j.gde.2023.102035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 03/01/2023] [Accepted: 03/05/2023] [Indexed: 04/09/2023]
Abstract
Transposable elements (TEs) such as endogenous retroviruses (ERVs), long interspersed nuclear elements (LINEs), and short interspersed nuclear elements (SINEs) occupy nearly half of typical mammalian genomes. Previous studies show that these parasitic elements, especially LINEs and ERVs, provide important activities promoting host germ cell and placental development, preimplantation embryogenesis, and maintenance of pluripotent stem cells. Despite being the most numerically abundant type of TEs in the genome, the consequences of SINEs on host genome regulation are less well characterized than those of ERVs and LINEs. Interestingly, recent findings reveal that SINEs recruit the key architectural protein CTCF (CCCTC-binding factor), indicating a role of these elements for 3D genome regulation. Higher-order nuclear structures are linked with important cellular functions such as gene regulation and DNA replication. SINEs and other TEs, therefore, may mediate distinct physiological processes with benefits to the host by modulating the 3D genome.
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Affiliation(s)
- Jafar Sharif
- Laboratory of Developmental Genetics, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
| | - Haruhiko Koseki
- Laboratory of Developmental Genetics, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; Department of Cellular and Molecular Medicine, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan
| | - Nicholas F Parrish
- Genome Immunobiology RIKEN Hakubi Research Team, RIKEN Center for Integrative Medical Sciences and RIKEN Cluster for Pioneering Research, Yokohama, Japan.
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26
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Reitz D, Djeghmoum Y, Watson RA, Rajput P, Argueso JL, Heyer WD, Piazza A. Delineation of two multi-invasion-induced rearrangement pathways that differently affect genome stability. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.15.532751. [PMID: 36993162 PMCID: PMC10055120 DOI: 10.1101/2023.03.15.532751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Punctuated bursts of structural genomic variations (SVs) have been described in various organisms, but their etiology remains incompletely understood. Homologous recombination (HR) is a template-guided mechanism of repair of DNA double-strand breaks and stalled or collapsed replication forks. We recently identified a DNA break amplification and genome rearrangement pathway originating from the endonucleolytic processing of a multi-invasion (MI) DNA joint molecule formed during HR. Genome-wide sequencing approaches confirmed that multi-invasion-induced rearrangement (MIR) frequently leads to several repeat-mediated SVs and aneuploidies. Using molecular and genetic analysis, and a novel, highly sensitive proximity ligation-based assay for chromosomal rearrangement quantification, we further delineate two MIR sub-pathways. MIR1 is a universal pathway occurring in any sequence context, which generates secondary breaks and frequently leads to additional SVs. MIR2 occurs only if recombining donors exhibit substantial homology, and results in sequence insertion without additional break or SV. The most detrimental MIR1 pathway occurs late on a subset of persisting DNA joint molecules in a PCNA/Polδ-independent manner, unlike recombinational DNA synthesis. This work provides a refined mechanistic understanding of these HR-based SV formation pathways and shows that complex repeat-mediated SVs can occur without displacement DNA synthesis. Sequence signatures for inferring MIR1 from long-read data are proposed.
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Affiliation(s)
- Diedre Reitz
- Department of Microbiology and Molecular Genetics, One Shields Ave, University of California, Davis, CA 95616, USA
| | - Yasmina Djeghmoum
- Univ Lyon, ENS, UCBL, CNRS, INSERM, Laboratory of Biology and Modelling of the Cell, UMR5239, U 1210, F-69364, Lyon, France
| | - Ruth A. Watson
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO 80523
| | - Pallavi Rajput
- Department of Microbiology and Molecular Genetics, One Shields Ave, University of California, Davis, CA 95616, USA
| | - Juan Lucas Argueso
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO 80523
| | - Wolf-Dietrich Heyer
- Department of Microbiology and Molecular Genetics, One Shields Ave, University of California, Davis, CA 95616, USA
- Department of Molecular and Cellular Biology, One Shields Ave, University of California, Davis, CA 95616, USA
| | - Aurèle Piazza
- Univ Lyon, ENS, UCBL, CNRS, INSERM, Laboratory of Biology and Modelling of the Cell, UMR5239, U 1210, F-69364, Lyon, France
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27
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Pascarella G, Straniero L, Frith M, Carninci P. Capture-seq protocol and TE-reX pipeline guidelines for detection of recombination of repeat elements in short- and long-DNA reads libraries. STAR Protoc 2023. [DOI: 10.1016/j.xpro.2022.102027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
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28
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Gasparotto E, Burattin FV, Di Gioia V, Panepuccia M, Ranzani V, Marasca F, Bodega B. Transposable Elements Co-Option in Genome Evolution and Gene Regulation. Int J Mol Sci 2023; 24:ijms24032610. [PMID: 36768929 PMCID: PMC9917352 DOI: 10.3390/ijms24032610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/26/2023] [Accepted: 01/28/2023] [Indexed: 01/31/2023] Open
Abstract
The genome is no longer deemed as a fixed and inert item but rather as a moldable matter that is continuously evolving and adapting. Within this frame, Transposable Elements (TEs), ubiquitous, mobile, repetitive elements, are considered an alive portion of the genomes to date, whose functions, although long considered "dark", are now coming to light. Here we will review that, besides the detrimental effects that TE mobilization can induce, TEs have shaped genomes in their current form, promoting genome sizing, genomic rearrangements and shuffling of DNA sequences. Although TEs are mostly represented in the genomes by evolutionarily old, short, degenerated, and sedentary fossils, they have been thoroughly co-opted by the hosts as a prolific and original source of regulatory instruments for the control of gene transcription and genome organization in the nuclear space. For these reasons, the deregulation of TE expression and/or activity is implicated in the onset and progression of several diseases. It is likely that we have just revealed the outermost layers of TE functions. Further studies on this portion of the genome are required to unlock novel regulatory functions that could also be exploited for diagnostic and therapeutic approaches.
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Affiliation(s)
- Erica Gasparotto
- Fondazione INGM, Istituto Nazionale di Genetica Molecolare “Enrica e Romeo Invernizzi”, 20122 Milan, Italy
- SEMM, European School of Molecular Medicine, 20139 Milan, Italy
| | - Filippo Vittorio Burattin
- Fondazione INGM, Istituto Nazionale di Genetica Molecolare “Enrica e Romeo Invernizzi”, 20122 Milan, Italy
- Department of Biosciences, University of Milan, 20133 Milan, Italy
| | - Valeria Di Gioia
- Fondazione INGM, Istituto Nazionale di Genetica Molecolare “Enrica e Romeo Invernizzi”, 20122 Milan, Italy
- SEMM, European School of Molecular Medicine, 20139 Milan, Italy
| | - Michele Panepuccia
- Fondazione INGM, Istituto Nazionale di Genetica Molecolare “Enrica e Romeo Invernizzi”, 20122 Milan, Italy
| | - Valeria Ranzani
- Fondazione INGM, Istituto Nazionale di Genetica Molecolare “Enrica e Romeo Invernizzi”, 20122 Milan, Italy
| | - Federica Marasca
- Fondazione INGM, Istituto Nazionale di Genetica Molecolare “Enrica e Romeo Invernizzi”, 20122 Milan, Italy
- Department of Clinical Sciences and Community Health, University of Milan, 20122 Milan, Italy
| | - Beatrice Bodega
- Fondazione INGM, Istituto Nazionale di Genetica Molecolare “Enrica e Romeo Invernizzi”, 20122 Milan, Italy
- Department of Biosciences, University of Milan, 20133 Milan, Italy
- Correspondence:
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Shuffling the yeast genome using CRISPR/Cas9-generated DSBs that target the transposable Ty1 elements. PLoS Genet 2023; 19:e1010590. [PMID: 36701275 PMCID: PMC9879454 DOI: 10.1371/journal.pgen.1010590] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 12/21/2022] [Indexed: 01/27/2023] Open
Abstract
Although homologous recombination between transposable elements can drive genomic evolution in yeast by facilitating chromosomal rearrangements, the details of the underlying mechanisms are not fully clarified. In the genome of the yeast Saccharomyces cerevisiae, the most common class of transposon is the retrotransposon Ty1. Here, we explored how Cas9-induced double-strand breaks (DSBs) directed to Ty1 elements produce genomic alterations in this yeast species. Following Cas9 induction, we observed a significant elevation of chromosome rearrangements such as deletions, duplications and translocations. In addition, we found elevated rates of mitotic recombination, resulting in loss of heterozygosity. Using Southern analysis coupled with short- and long-read DNA sequencing, we revealed important features of recombination induced in retrotransposons. Almost all of the chromosomal rearrangements reflect the repair of DSBs at Ty1 elements by non-allelic homologous recombination; clustered Ty elements were hotspots for chromosome rearrangements. In contrast, a large proportion (about three-fourths) of the allelic mitotic recombination events have breakpoints in unique sequences. Our analysis suggests that some of the latter events reflect extensive processing of the broken ends produced in the Ty element that extend into unique sequences resulting in break-induced replication. Finally, we found that haploid and diploid strain have different preferences for the pathways used to repair double-stranded DNA breaks. Our findings demonstrate the importance of DNA lesions in retrotransposons in driving genome evolution.
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Miné-Hattab J, Liu S, Taddei A. Repair Foci as Liquid Phase Separation: Evidence and Limitations. Genes (Basel) 2022; 13:1846. [PMID: 36292731 PMCID: PMC9602295 DOI: 10.3390/genes13101846] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 09/29/2022] [Accepted: 09/29/2022] [Indexed: 07/26/2023] Open
Abstract
In response to DNA double strand breaks (DSB), repair proteins accumulate at damaged sites, forming membrane-less condensates or "foci". The formation of these foci and their disassembly within the proper time window are essential for genome integrity. However, how these membrane-less sub-compartments are formed, maintained and disassembled remains unclear. Recently, several studies across different model organisms proposed that DNA repair foci form via liquid phase separation. In this review, we discuss the current research investigating the physical nature of repair foci. First, we present the different models of condensates proposed in the literature, highlighting the criteria to differentiate them. Second, we discuss evidence of liquid phase separation at DNA repair sites and the limitations of this model to fully describe structures formed in response to DNA damage. Finally, we discuss the origin and possible function of liquid phase separation for DNA repair processes.
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