1
|
Frantz SI, Small CM, Cresko WA, Singh ND. Ovarian transcriptional response to Wolbachia infection in D. melanogaster in the context of between-genotype variation in gene expression. G3 (BETHESDA, MD.) 2023; 13:jkad047. [PMID: 36857313 PMCID: PMC10151400 DOI: 10.1093/g3journal/jkad047] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 08/22/2022] [Accepted: 01/07/2023] [Indexed: 03/02/2023]
Abstract
Wolbachia is a maternally transmitted endosymbiotic bacteria that infects a wide variety of arthropod and nematode hosts. The effects of Wolbachia on host biology are far-reaching and include changes in host gene expression. However, previous work on the host transcriptional response has generally been investigated in the context of a single host genotype. Thus, the relative effect of Wolbachia infection versus vs. host genotype on gene expression is unknown. Here, we explicitly test the relative roles of Wolbachia infection and host genotype on host gene expression by comparing the ovarian transcriptomes of 4 strains of Drosophila melanogaster (D. melanogaster) infected and uninfected with Wolbachia. Our data suggest that infection explains a small amount of transcriptional variation, particularly in comparison to variation in gene expression among strains. However, infection specifically affects genes related to cell cycle, translation, and metabolism. We also find enrichment of cell division and recombination processes among genes with infection-associated differential expression. Broadly, the transcriptomic changes identified in this study provide novel understanding of the relative magnitude of the effect of Wolbachia infection on gene expression in the context of host genetic variation and also point to genes that are consistently differentially expressed in response to infection among multiple genotypes.
Collapse
Affiliation(s)
- Sophia I Frantz
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, 97403USA
| | - Clayton M Small
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, 97403USA
- Presidential Initiative in Data Science, University of Oregon, Eugene, OR, 97403USA
| | - William A Cresko
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, 97403USA
- Presidential Initiative in Data Science, University of Oregon, Eugene, OR, 97403USA
| | - Nadia D Singh
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, 97403USA
| |
Collapse
|
2
|
Yang Q, Yang XD, Liu MQ, Zeng C, Zhao HK, Xiang KW, Hou ZS, Wen HS, Li JF. Transcriptome analysis of liver, gill and intestine in rainbow trout (Oncorhynchus mykiss) symptomatically or asymptomatically infected with Vibrio anguillarum. FISH & SHELLFISH IMMUNOLOGY 2023; 135:108643. [PMID: 36871630 DOI: 10.1016/j.fsi.2023.108643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 02/16/2023] [Accepted: 02/23/2023] [Indexed: 06/18/2023]
Abstract
Rainbow trout (Oncorhynchus mykiss), an important economic cold-water fish worldwide, is severely threatened by viruses and bacteria in the farming industry. The vibriosis outbreak has caused a significant setback to aquaculture. Vibrio anguillarum, one of the common disease-causing vibriosis associated with severe lethal vibriosis in aquaculture, infects fish mainly by adsorption and invasion of the skin, gills, lateral line and intestine. To investigate the defense mechanism of rainbow trout against the pathogen after infection with Vibrio anguillarum, trout were intraperitoneally injected by Vibrio anguillarum and divided into symptomatic group (SG) and asymptomatic group (AG) according to the phenotype. RNA-Seq technology was used to evaluate the transcriptional signatures of liver, gill and intestine of trout injected with Vibrio anguillarum (SG and AG) and corresponding control groups (CG(A) and CG(B)). The GO and KEGG enrichment analyses were used to investigate the mechanisms underlying the differences in susceptibility to Vibrio anguillarum. Results showed that in SG, immunomodulatory genes in the cytokine network were activated and tissue function-related genes were down-regulated, while apoptosis mechanisms were activated. However, AG responded to Vibrio anguillarum infection by activating complement related immune defenses, while metabolism and function related genes were up-regulated. Conclusively, a rapid and effective immune and inflammatory response can successfully defend Vibrio anguillarum infection. However, a sustained inflammatory response can lead to tissue and organ damage and cause death. Our results may provide a theoretical basis for breeding rainbow trout for disease resistance.
Collapse
Affiliation(s)
- Qian Yang
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education (KLMME), Ocean University of China, Qingdao, China
| | - Xiao-Dong Yang
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education (KLMME), Ocean University of China, Qingdao, China
| | - Meng-Qun Liu
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education (KLMME), Ocean University of China, Qingdao, China
| | - Chu Zeng
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education (KLMME), Ocean University of China, Qingdao, China
| | - Hong-Kui Zhao
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education (KLMME), Ocean University of China, Qingdao, China
| | - Kai-Wen Xiang
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education (KLMME), Ocean University of China, Qingdao, China
| | - Zhi-Shuai Hou
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education (KLMME), Ocean University of China, Qingdao, China
| | - Hai-Shen Wen
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education (KLMME), Ocean University of China, Qingdao, China
| | - Ji-Fang Li
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education (KLMME), Ocean University of China, Qingdao, China.
| |
Collapse
|
3
|
Spector LP, Tiffany M, Ferraro NM, Abell NS, Montgomery SB, Kay MA. Evaluating the Genomic Parameters Governing rAAV-Mediated Homologous Recombination. Mol Ther 2021; 29:1028-1046. [PMID: 33248247 PMCID: PMC7934627 DOI: 10.1016/j.ymthe.2020.11.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 10/16/2020] [Accepted: 11/18/2020] [Indexed: 12/26/2022] Open
Abstract
Recombinant adeno-associated virus (rAAV) vectors have the unique ability to promote targeted integration of transgenes via homologous recombination at specified genomic sites, reaching frequencies of 0.1%-1%. We studied genomic parameters that influence targeting efficiencies on a large scale. To do this, we generated more than 1,000 engineered, doxycycline-inducible target sites in the human HAP1 cell line and infected this polyclonal population with a library of AAV-DJ targeting vectors, with each carrying a unique barcode. The heterogeneity of barcode integration at each target site provided an assessment of targeting efficiency at that locus. We compared targeting efficiency with and without target site transcription for identical chromosomal positions. Targeting efficiency was enhanced by target site transcription, while chromatin accessibility was associated with an increased likelihood of targeting. ChromHMM chromatin states characterizing transcription and enhancers in wild-type K562 cells were also associated with increased AAV-HR efficiency with and without target site transcription, respectively. Furthermore, the amenability of a site to targeting was influenced by the endogenous transcriptional level of intersecting genes. These results define important parameters that may not only assist in designing optimal targeting vectors for genome editing, but also provide new insights into the mechanism of AAV-mediated homologous recombination.
Collapse
Affiliation(s)
- Laura P Spector
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Matthew Tiffany
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA; Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Nicole M Ferraro
- Biomedical Informatics Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Nathan S Abell
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Stephen B Montgomery
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Mark A Kay
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA; Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA.
| |
Collapse
|
4
|
Luo B, Zhan Y, Luo M, Dong H, Liu J, Lin Y, Zhang J, Wang G, Verhoeyen E, Zhang Y, Zhang H. Engineering of α-PD-1 antibody-expressing long-lived plasma cells by CRISPR/Cas9-mediated targeted gene integration. Cell Death Dis 2020; 11:973. [PMID: 33184267 PMCID: PMC7661525 DOI: 10.1038/s41419-020-03187-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 10/25/2020] [Accepted: 10/27/2020] [Indexed: 12/11/2022]
Abstract
Long-lived plasma cells (LLPCs) are robust specialized antibody-secreting cells that mainly stay in the bone marrow and can persist a lifetime. As they can be generated by inducing the differentiation of B-lymphocytes, we investigated the possibility that human LLPCs might be engineered to express α-PD-1 monoclonal antibody to substitute recombinant α-PD-1 antitumor immunotherapy. To this end, we inserted an α-PD-1 cassette into the GAPDH locus through Cas9/sgRNA-guided specific integration in B-lymphocytes, which was mediated by an integrase-defective lentiviral vector. The edited B cells were capable of differentiating into LLPCs both in vitro and in vivo. Transcriptional profiling analysis confirmed that these cells were typical LLPCs. Importantly, these cells secreted de novo antibodies persistently, which were able to inhibit human melanoma growth via an antibody-mediated checkpoint blockade in xenograft-tumor mice. Our work suggests that the engineered LLPCs may be utilized as a vehicle to constantly produce special antibodies for long-term cellular immunotherapy to eradicate tumors and cellular reservoirs for various pathogens including human immunodeficiency virus type 1 (HIV-1) and hepatitis B virus (HBV).
Collapse
Affiliation(s)
- Baohong Luo
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, 510080, Guangzhou, Guangdong, China.,Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, 510080, Guangzhou, Guangdong, China.,Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, 510080, Guangzhou, Guangdong, China
| | - Yikang Zhan
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, 510080, Guangzhou, Guangdong, China.,Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, 510080, Guangzhou, Guangdong, China.,Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, 510080, Guangzhou, Guangdong, China
| | - Minqi Luo
- Department of Laboratory Medicine, Third Affiliated Hospital of Sun Yat-sen University, 510080, Guangzhou, Guangdong, China
| | - Huimin Dong
- Department of Laboratory Medicine, Third Affiliated Hospital of Sun Yat-sen University, 510080, Guangzhou, Guangdong, China
| | - Jun Liu
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, 510080, Guangzhou, Guangdong, China.,Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, 510080, Guangzhou, Guangdong, China.,Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, 510080, Guangzhou, Guangdong, China
| | - Yingtong Lin
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, 510080, Guangzhou, Guangdong, China.,Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, 510080, Guangzhou, Guangdong, China.,Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, 510080, Guangzhou, Guangdong, China
| | - Junsong Zhang
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, 510080, Guangzhou, Guangdong, China.,Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, 510080, Guangzhou, Guangdong, China.,Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, 510080, Guangzhou, Guangdong, China
| | - Guanwen Wang
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, 510080, Guangzhou, Guangdong, China.,Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, 510080, Guangzhou, Guangdong, China.,Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, 510080, Guangzhou, Guangdong, China
| | - Els Verhoeyen
- CIRI - International Center for Infectiology, Research team EVIR, Inserm, U1111, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, University of Lyon, Lyon, France.,Université Côte d'Azur, INSERM, C3M, 06204, Nice, France
| | - Yiwen Zhang
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, 510080, Guangzhou, Guangdong, China. .,Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, 510080, Guangzhou, Guangdong, China. .,Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, 510080, Guangzhou, Guangdong, China.
| | - Hui Zhang
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, 510080, Guangzhou, Guangdong, China. .,Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, 510080, Guangzhou, Guangdong, China. .,Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, 510080, Guangzhou, Guangdong, China.
| |
Collapse
|
5
|
The Regulatory Properties of the Ccr4-Not Complex. Cells 2020; 9:cells9112379. [PMID: 33138308 PMCID: PMC7692201 DOI: 10.3390/cells9112379] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 10/21/2020] [Accepted: 10/26/2020] [Indexed: 12/12/2022] Open
Abstract
The mammalian Ccr4–Not complex, carbon catabolite repression 4 (Ccr4)-negative on TATA-less (Not), is a large, highly conserved, multifunctional assembly of proteins that acts at different cellular levels to regulate gene expression. In the nucleus, it is involved in the regulation of the cell cycle, chromatin modification, activation and inhibition of transcription initiation, control of transcription elongation, RNA export, nuclear RNA surveillance, and DNA damage repair. In the cytoplasm, the Ccr4–Not complex plays a central role in mRNA decay and affects protein quality control. Most of our original knowledge of the Ccr4–Not complex is derived, primarily, from studies in yeast. More recent studies have shown that the mammalian complex has a comparable structure and similar properties. In this review, we summarize the evidence for the multiple roles of both the yeast and mammalian Ccr4–Not complexes, highlighting their similarities.
Collapse
|
6
|
Rommel Fuentes R, Hesselink T, Nieuwenhuis R, Bakker L, Schijlen E, van Dooijeweert W, Diaz Trivino S, de Haan JR, Sanchez Perez G, Zhang X, Fransz P, de Jong H, van Dijk ADJ, de Ridder D, Peters SA. Meiotic recombination profiling of interspecific hybrid F1 tomato pollen by linked read sequencing. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 102:480-492. [PMID: 31820490 DOI: 10.1111/tpj.14640] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 11/25/2019] [Accepted: 12/04/2019] [Indexed: 06/10/2023]
Abstract
Genome wide screening of pooled pollen samples from a single interspecific F1 hybrid obtained from a cross between tomato, Solanum lycopersicum and its wild relative, Solanum pimpinellifolium using linked read sequencing of the haploid nuclei, allowed profiling of the crossover (CO) and gene conversion (GC) landscape. We observed a striking overlap between cold regions of CO in the male gametes and our previously established F6 recombinant inbred lines (RILs) population. COs were overrepresented in non-coding regions in the gene promoter and 5'UTR regions of genes. Poly-A/T and AT rich motifs were found enriched in 1 kb promoter regions flanking the CO sites. Non-crossover associated allelic and ectopic GCs were detected in most chromosomes, confirming that besides CO, GC represents also a source for genetic diversity and genome plasticity in tomato. Furthermore, we identified processed break junctions pointing at the involvement of both homology directed and non-homology directed repair pathways, suggesting a recombination machinery in tomato that is more complex than currently anticipated.
Collapse
Affiliation(s)
- Roven Rommel Fuentes
- Bioinformatics Group, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Thamara Hesselink
- Business Unit of Bioscience, Cluster Applied Bioinformatics, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Ronald Nieuwenhuis
- Business Unit of Bioscience, Cluster Applied Bioinformatics, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Linda Bakker
- Business Unit of Bioscience, Cluster Applied Bioinformatics, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Elio Schijlen
- Business Unit of Bioscience, Cluster Applied Bioinformatics, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Willem van Dooijeweert
- Centre for Genetic Resources, Wageningen University and Research, Wageningen, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Sara Diaz Trivino
- Business Unit of Bioscience, Cluster Applied Bioinformatics, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Jorn R de Haan
- Genetwister Technologies B.V., Nieuwe Kanaal 7b, 6709 PA, Wageningen, The Netherlands
| | - Gabino Sanchez Perez
- Genetwister Technologies B.V., Nieuwe Kanaal 7b, 6709 PA, Wageningen, The Netherlands
| | - Xinyue Zhang
- Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Paul Fransz
- Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Hans de Jong
- Laboratory of Genetics, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Aalt D J van Dijk
- Bioinformatics Group, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
- Biometris, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Dick de Ridder
- Bioinformatics Group, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Sander A Peters
- Business Unit of Bioscience, Cluster Applied Bioinformatics, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| |
Collapse
|
7
|
Zhang LH, Zhang XY, Hu T, Chen XY, Li JJ, Raida M, Sun N, Luo Y, Gao X. The SUMOylated METTL8 Induces R-loop and Tumorigenesis via m3C. iScience 2020; 23:100968. [PMID: 32199293 PMCID: PMC7082549 DOI: 10.1016/j.isci.2020.100968] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 02/08/2020] [Accepted: 03/03/2020] [Indexed: 01/26/2023] Open
Abstract
R-loops, three-stranded DNA-DNA:RNA hybrid structures, are best known for their deleterious effects on genome stability. The regulatory factors of this fundamental genetic structure remain unclear. Here, we reveal an epigenetic factor that controls R-loop stability. METTL8, a member of the methyltransferase-like protein family that methylates 3-methylcytidine (m3C), is a key factor in the R-loop regulating methyltransferase complex. Biochemical studies show that METTL8 forms a large SUMOylated nuclear RNA-binding protein complex (∼0.8 mega daltons) that contains well-reported R-loop related factors. Genetic ablation of METTL8 results in an overall reduction of R-loops in cells. Interaction assays indicated METTL8 binds to RNAs and is responsible for R-loop stability on selected gene regions. Our results demonstrate that the SUMOylated METTL8 promotes tumorigenesis by affecting genetic organization primarily in, or in close proximity to, the nucleolus and impacts the formation of regulatory R-loops through its methyltransferase activity on m3C. DNA:RNA hybrid structures are regulated by RNA methyltransferase via 3-methylcytidine SUMOylation stabilizes the RNA methyltransferase complex in the nucleus Dysregulation of DNA:RNA hybrids may induce tumorigenesis in mammalian cells
Collapse
Affiliation(s)
- Li-Hong Zhang
- Department of Biochemistry and Cancer Institute of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China; Key Laboratory of Cancer Prevention and Intervention of China National Ministry of Education, Hangzhou 310009, China
| | - Xue-Yun Zhang
- Department of Biochemistry and Cancer Institute of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China; Key Laboratory of Cancer Prevention and Intervention of China National Ministry of Education, Hangzhou 310009, China
| | - Tao Hu
- Department of Spine Surgery, Shanghai East Hospital, Tongji University, Shanghai 200092, China
| | - Xin-Yun Chen
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Jing-Jia Li
- Department of Biochemistry and Cancer Institute of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China; Key Laboratory of Cancer Prevention and Intervention of China National Ministry of Education, Hangzhou 310009, China
| | - Manfred Raida
- Life Sciences Institute, National University of Singapore, Singapore 117456, Singapore
| | - Ning Sun
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Yan Luo
- Department of Biochemistry and Cancer Institute of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China; Key Laboratory of Cancer Prevention and Intervention of China National Ministry of Education, Hangzhou 310009, China.
| | - Xiang Gao
- Department of Biochemistry and Cancer Institute of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China; Key Laboratory of Cancer Prevention and Intervention of China National Ministry of Education, Hangzhou 310009, China.
| |
Collapse
|
8
|
Abstract
The repair of DNA double-strand breaks occurs through a series of defined steps that are evolutionarily conserved and well-understood in most experimental organisms. However, it is becoming increasingly clear that repair does not occur in isolation from other DNA transactions. Transcription of DNA produces topological changes, RNA species, and RNA-dependent protein complexes that can dramatically influence the efficiency and outcomes of DNA double-strand break repair. The transcription-associated history of several double-strand break repair factors is reviewed here, with an emphasis on their roles in regulating R-loops and the emerging role of R-loops in coordination of repair events. Evidence for nucleolytic processing of R-loops is also discussed, as well as the molecular tools commonly used to measure RNA-DNA hybrids in cells.
Collapse
Affiliation(s)
- Tanya T Paull
- The Department of Molecular Biosciences and the Howard Hughes Medical Institute, The University of Texas at Austin, Austin, TX, USA
| |
Collapse
|
9
|
Sugaya K. Chromosome instability caused by mutations in the genes involved in transcription and splicing. RNA Biol 2019; 16:1521-1525. [PMID: 31385554 DOI: 10.1080/15476286.2019.1652523] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
Mutations in molecules involved in transcription and splicing can cause chromosome instability such as sister chromatid exchanges. We isolated and characterized responsible genes from mammalian temperature-sensitive mutant cells showing chromosome instability. A mutation in the largest subunit of RNA polymerase II affected DNA synthesis in S phase-arrested cells, resulting in abnormal induction of sister chromatid exchanges. The yeast mutant harboring a homologous mutation showed very similar phenotype to that of the mammalian mutant. A mutation in Smu1, which is involved in splicing, also affected DNA synthesis in S and G2 phase-arrested cells, resulting in abnormal induction of sister chromatid exchanges and chromosomal aberrations. These cells showed a connection between defects of RNA metabolism and induction of chromosome instability. Genome instability appeared to be caused by links between RNA metabolism and replication resulting in genomic recombination. RNA metabolism can be regarded as one possible driver of genome modification triggering genome evolution.
Collapse
Affiliation(s)
- Kimihiko Sugaya
- Department of Molecular Imaging and Theranostics, National Institute of Radiological Sciences (NIRS), National Institutes for Quantum and Radiological Science and Technology (QST) , Chiba , Japan.,Group of Quantum-state Controlled MRI, QST , Chiba , Japan
| |
Collapse
|
10
|
Summerer A, Schäfer E, Mautner VF, Messiaen L, Cooper DN, Kehrer-Sawatzki H. Ultra-deep amplicon sequencing indicates absence of low-grade mosaicism with normal cells in patients with type-1 NF1 deletions. Hum Genet 2018; 138:73-81. [PMID: 30478644 DOI: 10.1007/s00439-018-1961-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 11/20/2018] [Indexed: 11/26/2022]
Abstract
Different types of large NF1 deletion are distinguishable by breakpoint location and potentially also by the frequency of mosaicism with normal cells lacking the deletion. However, low-grade mosaicism with fewer than 10% normal cells has not yet been excluded for all NF1 deletion types since it is impossible to assess by the standard techniques used to identify such deletions, including MLPA and array analysis. Here, we used ultra-deep amplicon sequencing to investigate the presence of normal cells in the blood of 20 patients with type-1 NF1 deletions lacking mosaicism according to MLPA. The ultra-deep sequencing entailed the screening of 96 amplicons for heterozygous SNVs located within the NF1 deletion region. DNA samples from three previously identified patients with type-2 NF1 deletions and low-grade mosaicism with normal cells as determined by FISH or microsatellite marker analysis were used to validate our methodology. In these type-2 NF1 deletion samples, proportions of 5.3%, 6.6% and 15.0% normal cells, respectively, were detected by ultra-deep amplicon sequencing. However, using this highly sensitive method, none of the 20 patients with type-1 NF1 deletions included in our analysis exhibited low-grade mosaicism with normal cells in blood, thereby supporting the view that the vast majority of type-1 deletions are germline deletions.
Collapse
Affiliation(s)
- Anna Summerer
- Institute of Human Genetics, University of Ulm, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Eleonora Schäfer
- Institute of Human Genetics, University of Ulm, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Victor-Felix Mautner
- Department of Neurology, University Hospital Hamburg Eppendorf, 20246, Hamburg, Germany
| | - Ludwine Messiaen
- Department of Genetics, University of Alabama at Birmingham, Birmingham, USA
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK
| | | |
Collapse
|
11
|
Burgos-Morón E, Calderón-Montaño JM, Pastor N, Höglund A, Ruiz-Castizo Á, Domínguez I, López-Lázaro M, Hajji N, Helleday T, Mateos S, Orta ML. The Cockayne syndrome protein B is involved in the repair of 5-AZA-2'-deoxycytidine-induced DNA lesions. Oncotarget 2018; 9:35069-35084. [PMID: 30416680 PMCID: PMC6205548 DOI: 10.18632/oncotarget.26189] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 09/10/2018] [Indexed: 12/21/2022] Open
Abstract
The Cockayne Syndrome Protein B (CSB) plays an essential role in Transcription-Coupled Nucleotide Excision Repair (TC-NER) by recruiting repair proteins once transcription is blocked with a DNA lesion. In fact, CSB-deficient cells are unable to recover from transcription-blocking DNA lesions. 5-Aza-2′-deoxycytidine (5-azadC) is a nucleoside analogue that covalently traps DNA methyltransferases (DNMTs) onto DNA. This anticancer drug has a double mechanism of action: it reverts aberrant hypermethylation in tumour-suppressor genes, and it induces DNA damage. We have recently reported that Homologous Recombination and XRCC1/PARP play an important role in the repair of 5-azadC-induced DNA damage. However, the mechanisms involved in the repair of the DNMT adducts induced by azadC remain poorly understood. In this paper, we show for the first time the importance of CSB in the repair of azadC-induced DNA lesions. We propose a model in which CSB initiates a signalling pathway to repair transcription blocks induced by incorporated 5-azadC. Indeed, CSB-deficient cells treated with 5-azadC show a delay in the repair of trapped DNMT1, increased levels of DNA damage and reduced survival.
Collapse
Affiliation(s)
- Estefanía Burgos-Morón
- Department of Pharmacology, Faculty of Pharmacy, University of Seville, 41012 Seville, Spain
| | | | - Nuria Pastor
- Department of Cell Biology, Faculty of Biology, University of Seville, 41012 Seville, Spain
| | - Andreas Höglund
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, S-171 21 Stockholm, Sweden.,Present address: Sprint Bioscience AB, 141 57 Huddinge, Sweden
| | - Ángel Ruiz-Castizo
- Department of Cell Biology, Faculty of Biology, University of Seville, 41012 Seville, Spain
| | - Inmaculada Domínguez
- Department of Cell Biology, Faculty of Biology, University of Seville, 41012 Seville, Spain
| | - Miguel López-Lázaro
- Department of Pharmacology, Faculty of Pharmacy, University of Seville, 41012 Seville, Spain
| | - Nabil Hajji
- Department of Medicine, Division of Experimental Medicine, Centre for Pharmacology & Therapeutics, Toxicology Unit, Imperial College London, Hammersmith Campus, London, W12 0NN UK
| | - Thomas Helleday
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, S-171 21 Stockholm, Sweden
| | - Santiago Mateos
- Department of Cell Biology, Faculty of Biology, University of Seville, 41012 Seville, Spain
| | - Manuel Luis Orta
- Department of Cell Biology, Faculty of Biology, University of Seville, 41012 Seville, Spain
| |
Collapse
|
12
|
Sivaramakrishnan P, Gordon AJE, Halliday JA, Herman C. How Acts of Infidelity Promote DNA Break Repair: Collision and Collusion Between DNA Repair and Transcription. Bioessays 2018; 40:e1800045. [PMID: 30091472 PMCID: PMC6334755 DOI: 10.1002/bies.201800045] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 07/07/2018] [Indexed: 12/20/2022]
Abstract
Transcription is a fundamental cellular process and the first step in gene regulation. Although RNA polymerase (RNAP) is highly processive, in growing cells the progression of transcription can be hindered by obstacles on the DNA template, such as damaged DNA. The authors recent findings highlight a trade-off between transcription fidelity and DNA break repair. While a lot of work has focused on the interaction between transcription and nucleotide excision repair, less is known about how transcription influences the repair of DNA breaks. The authors suggest that when the cell experiences stress from DNA breaks, the control of RNAP processivity affects the balance between preserving transcription integrity and DNA repair. Here, how the conflict between transcription and DNA double-strand break (DSB) repair threatens the integrity of both RNA and DNA are discussed. In reviewing this field, the authors speculate on cellular paradigms where this equilibrium is well sustained, and instances where the maintenance of transcription fidelity is favored over genome stability.
Collapse
Affiliation(s)
- Priya Sivaramakrishnan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Alasdair J E Gordon
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jennifer A Halliday
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Christophe Herman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Baylor College of Medicine, Dan L. Duncan Comprehensive Cancer Center, Houston, TX 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030, USA
| |
Collapse
|
13
|
Mikolaskova B, Jurcik M, Cipakova I, Kretova M, Chovanec M, Cipak L. Maintenance of genome stability: the unifying role of interconnections between the DNA damage response and RNA-processing pathways. Curr Genet 2018; 64:971-983. [PMID: 29497809 DOI: 10.1007/s00294-018-0819-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 02/23/2018] [Accepted: 02/27/2018] [Indexed: 01/14/2023]
Abstract
Endogenous and exogenous factors can severely affect the integrity of genetic information by inducing DNA damage and impairing genome stability. The protection of genome integrity is ensured by the so-called "DNA damage response" (DDR), a set of evolutionary-conserved events that, triggered upon DNA damage detection, arrests the cell cycle, and attempts DNA repair. Here, we review the role of the DDR proteins as post-transcriptional regulators of gene expression, in addition to their roles in DNA damage recognition, signaling, and repair. At the same time, we discuss recent insights into how pre-mRNA splicing factors go beyond their splicing activities and play direct functions in detecting, signaling, and repairing DNA damage. The importance of extensive two-way crosstalk and interaction between the RNA processing and the DDR stems from growing evidence that the defects of their communication lead to genomic instability.
Collapse
Affiliation(s)
- B Mikolaskova
- Department of Genetics, Biomedical Research Center, Cancer Research Institute, Slovak Academy of Sciences, Dubravska cesta 9, 845 05, Bratislava, Slovakia
| | - M Jurcik
- Department of Genetics, Biomedical Research Center, Cancer Research Institute, Slovak Academy of Sciences, Dubravska cesta 9, 845 05, Bratislava, Slovakia
| | - I Cipakova
- Department of Genetics, Biomedical Research Center, Cancer Research Institute, Slovak Academy of Sciences, Dubravska cesta 9, 845 05, Bratislava, Slovakia
| | - M Kretova
- Department of Genetics, Biomedical Research Center, Cancer Research Institute, Slovak Academy of Sciences, Dubravska cesta 9, 845 05, Bratislava, Slovakia
| | - M Chovanec
- Department of Genetics, Biomedical Research Center, Cancer Research Institute, Slovak Academy of Sciences, Dubravska cesta 9, 845 05, Bratislava, Slovakia
| | - L Cipak
- Department of Genetics, Biomedical Research Center, Cancer Research Institute, Slovak Academy of Sciences, Dubravska cesta 9, 845 05, Bratislava, Slovakia.
| |
Collapse
|
14
|
Multiple signaling kinases target Mrc1 to prevent genomic instability triggered by transcription-replication conflicts. Nat Commun 2018; 9:379. [PMID: 29371596 PMCID: PMC5785523 DOI: 10.1038/s41467-017-02756-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 12/21/2017] [Indexed: 02/05/2023] Open
Abstract
Conflicts between replication and transcription machineries represent a major source of genomic instability and cells have evolved strategies to prevent such conflicts. However, little is known regarding how cells cope with sudden increases of transcription while replicating. Here, we report the existence of a general mechanism for the protection of genomic integrity upon transcriptional outbursts in S phase that is mediated by Mrc1. The N-terminal phosphorylation of Mrc1 blocked replication and prevented transcription-associated recombination (TAR) and genomic instability during stress-induced gene expression in S phase. An unbiased kinome screening identified several kinases that phosphorylate Mrc1 at the N terminus upon different environmental stresses. Mrc1 function was not restricted to environmental cues but was also required when unscheduled transcription was triggered by low fitness states such as genomic instability or slow growth. Our data indicate that Mrc1 integrates multiple signals, thereby defining a general safeguard mechanism to protect genomic integrity upon transcriptional outbursts. During S phase of the cell cycle, transcription and replication need to be coordinated in order to avoid conflicts leading to potential genomic instability. Here, the authors find that Mrc1 integrates signals from different kinases to regulate replication during unscheduled transcription events.
Collapse
|
15
|
Lee T, Pelletier J. The biology of DHX9 and its potential as a therapeutic target. Oncotarget 2018; 7:42716-42739. [PMID: 27034008 PMCID: PMC5173168 DOI: 10.18632/oncotarget.8446] [Citation(s) in RCA: 115] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 03/16/2016] [Indexed: 12/25/2022] Open
Abstract
DHX9 is member of the DExD/H-box family of helicases with a “DEIH” sequence at its eponymous DExH-box motif. Initially purified from human and bovine cells and identified as a homologue of the Drosophila Maleless (MLE) protein, it is an NTP-dependent helicase consisting of a conserved helicase core domain, two double-stranded RNA-binding domains at the N-terminus, and a nuclear transport domain and a single-stranded DNA-binding RGG-box at the C-terminus. With an ability to unwind DNA and RNA duplexes, as well as more complex nucleic acid structures, DHX9 appears to play a central role in many cellular processes. Its functions include regulation of DNA replication, transcription, translation, microRNA biogenesis, RNA processing and transport, and maintenance of genomic stability. Because of its central role in gene regulation and RNA metabolism, there are growing implications for DHX9 in human diseases and their treatment. This review will provide an overview of the structure, biochemistry, and biology of DHX9, its role in cancer and other human diseases, and the possibility of targeting DHX9 in chemotherapy.
Collapse
Affiliation(s)
- Teresa Lee
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - Jerry Pelletier
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada.,Department of Oncology, McGill University, Montreal, Quebec, Canada.,Department of Rosalind and Morris Goodman Cancer Research Center, McGill University, Montreal, Quebec, Canada
| |
Collapse
|
16
|
Sakasai R, Isono M, Wakasugi M, Hashimoto M, Sunatani Y, Matsui T, Shibata A, Matsunaga T, Iwabuchi K. Aquarius is required for proper CtIP expression and homologous recombination repair. Sci Rep 2017; 7:13808. [PMID: 29061988 PMCID: PMC5653829 DOI: 10.1038/s41598-017-13695-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 09/26/2017] [Indexed: 01/01/2023] Open
Abstract
Accumulating evidence indicates that transcription is closely related to DNA damage formation and that the loss of RNA biogenesis factors causes genome instability. However, whether such factors are involved in DNA damage responses remains unclear. We focus here on the RNA helicase Aquarius (AQR), a known R-loop processing factor, and show that its depletion in human cells results in the accumulation of DNA damage during S phase, mediated by R-loop formation. We investigated the involvement of Aquarius in DNA damage responses and found that AQR knockdown decreased DNA damage-induced foci formation of Rad51 and replication protein A, suggesting that Aquarius contributes to homologous recombination (HR)-mediated repair of DNA double-strand breaks (DSBs). Interestingly, the protein level of CtIP, a DSB processing factor, was decreased in AQR-knockdown cells. Exogenous expression of Aquarius partially restored CtIP protein level; however, CtIP overproduction did not rescue defective HR in AQR-knockdown cells. In accordance with these data, Aquarius depletion sensitized cells to genotoxic agents. We propose that Aquarius contributes to the maintenance of genomic stability via regulation of HR by CtIP-dependent and -independent pathways.
Collapse
Affiliation(s)
- Ryo Sakasai
- Department of Biochemistry I, Kanazawa Medical University, Ishikawa, Japan
| | - Mayu Isono
- Education and Research Support Center, Gunma University, Ishikawa, Japan
| | - Mitsuo Wakasugi
- Faculty of Pharmacy, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Ishikawa, Japan
| | | | - Yumi Sunatani
- Department of Biochemistry I, Kanazawa Medical University, Ishikawa, Japan
| | - Tadashi Matsui
- Department of Biochemistry I, Kanazawa Medical University, Ishikawa, Japan
| | - Atsushi Shibata
- Education and Research Support Center, Gunma University, Ishikawa, Japan
| | - Tsukasa Matsunaga
- Faculty of Pharmacy, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Ishikawa, Japan
| | - Kuniyoshi Iwabuchi
- Department of Biochemistry I, Kanazawa Medical University, Ishikawa, Japan.
| |
Collapse
|
17
|
Demirci S, van Dijk ADJ, Sanchez Perez G, Aflitos SA, de Ridder D, Peters SA. Distribution, position and genomic characteristics of crossovers in tomato recombinant inbred lines derived from an interspecific cross between Solanum lycopersicum and Solanum pimpinellifolium. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 89:554-564. [PMID: 27797425 DOI: 10.1111/tpj.13406] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 10/21/2016] [Accepted: 10/21/2016] [Indexed: 05/20/2023]
Abstract
We determined the crossover (CO) distribution, frequency and genomic sequences involved in interspecies meiotic recombination by using parent-assigned variants of 52 F6 recombinant inbred lines obtained from a cross between tomato, Solanum lycopersicum, and its wild relative, Solanum pimpinellifolium. The interspecific CO frequency was 80% lower than reported for intraspecific tomato crosses. We detected regions showing a relatively high and low CO frequency, so-called hot and cold regions. Cold regions coincide to a large extent with the heterochromatin, although we found a limited number of smaller cold regions in the euchromatin. The CO frequency was higher at the distal ends of chromosomes than in pericentromeric regions and higher in short arm euchromatin. Hot regions of CO were detected in euchromatin, and COs were more often located in non-coding regions near the 5' untranslated region of genes than expected by chance. Besides overrepresented CCN repeats, we detected poly-A/T and AT-rich motifs enriched in 1-kb promoter regions flanking the CO sites. The most abundant sequence motifs at CO sites share weak similarity to transcription factor-binding sites, such as for the C2H2 zinc finger factors class and MADS box factors, while InterPro scans detected enrichment for genes possibly involved in the repair of DNA breaks.
Collapse
Affiliation(s)
- Sevgin Demirci
- Bioinformatics Group, Wageningen University and Research, Wageningen, The Netherlands
- Business Unit of Bioscience, Cluster Applied Bioinformatics, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Aalt D J van Dijk
- Business Unit of Bioscience, Cluster Applied Bioinformatics, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
- Biometris, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Gabino Sanchez Perez
- Bioinformatics Group, Wageningen University and Research, Wageningen, The Netherlands
- Business Unit of Bioscience, Cluster Applied Bioinformatics, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Saulo A Aflitos
- Business Unit of Bioscience, Cluster Applied Bioinformatics, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Dick de Ridder
- Bioinformatics Group, Wageningen University and Research, Wageningen, The Netherlands
| | - Sander A Peters
- Business Unit of Bioscience, Cluster Applied Bioinformatics, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| |
Collapse
|
18
|
Abstract
Chromosomal translocations are a hallmark of cancer. Unraveling the molecular mechanism of these rare genetic events requires a clear distinction between correlative and causative risk-determinants, where technical and analytical issues can be excluded. To meet this goal, we performed in-depth analyses of publicly available genome-wide datasets. In contrast to several recent reports, we demonstrate that chromosomal translocation risk is causally unrelated to promoter stalling (Spt5), transcriptional activity, or off-targeting activity of the activation-induced cytidine deaminase. Rather, an open chromatin configuration, which is not promoter-specific, explained the elevated translocation risk of promoter regions. Furthermore, the fact that gene size directly correlates with the translocation risk in mice and human cancers further demonstrated the general irrelevance of promoter-specific activities. Interestingly, a subset of translocations observed in cancer patients likely initiates from double-strand breaks induced by an access-independent process. Together, these unexpected and novel insights are fundamental in understanding the origin of chromosome translocations and, consequently, cancer.
Collapse
|
19
|
He X, Tan C, Wang F, Wang Y, Zhou R, Cui D, You W, Zhao H, Ren J, Feng B. Knock-in of large reporter genes in human cells via CRISPR/Cas9-induced homology-dependent and independent DNA repair. Nucleic Acids Res 2016; 44:e85. [PMID: 26850641 PMCID: PMC4872082 DOI: 10.1093/nar/gkw064] [Citation(s) in RCA: 220] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Revised: 01/23/2016] [Accepted: 01/25/2016] [Indexed: 12/23/2022] Open
Abstract
CRISPR/Cas9-induced site-specific DNA double-strand breaks (DSBs) can be repaired by homology-directed repair (HDR) or non-homologous end joining (NHEJ) pathways. Extensive efforts have been made to knock-in exogenous DNA to a selected genomic locus in human cells; which, however, has focused on HDR-based strategies and was proven inefficient. Here, we report that NHEJ pathway mediates efficient rejoining of genome and plasmids following CRISPR/Cas9-induced DNA DSBs, and promotes high-efficiency DNA integration in various human cell types. With this homology-independent knock-in strategy, integration of a 4.6 kb promoterless ires-eGFP fragment into the GAPDH locus yielded up to 20% GFP+ cells in somatic LO2 cells, and 1.70% GFP+ cells in human embryonic stem cells (ESCs). Quantitative comparison further demonstrated that the NHEJ-based knock-in is more efficient than HDR-mediated gene targeting in all human cell types examined. These data support that CRISPR/Cas9-induced NHEJ provides a valuable new path for efficient genome editing in human ESCs and somatic cells.
Collapse
Affiliation(s)
- Xiangjun He
- Key Laboratory for Regenerative Medicine, Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China CUHK-GIBH CAS Joint Research Laboratory on Stem Cell and Regenerative Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Chunlai Tan
- Key Laboratory for Regenerative Medicine, Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China CUHK-GIBH CAS Joint Research Laboratory on Stem Cell and Regenerative Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Feng Wang
- Key Laboratory for Regenerative Medicine, Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Yaofeng Wang
- Key Laboratory for Regenerative Medicine, Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China CUHK-GIBH CAS Joint Research Laboratory on Stem Cell and Regenerative Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China CUHK Shenzhen Research Institute, Shenzhen, 518057, China
| | - Rui Zhou
- Key Laboratory for Regenerative Medicine, Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China CUHK Shenzhen Research Institute, Shenzhen, 518057, China
| | - Dexuan Cui
- Key Laboratory for Regenerative Medicine, Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Wenxing You
- Key Laboratory for Regenerative Medicine, Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China CUHK-GIBH CAS Joint Research Laboratory on Stem Cell and Regenerative Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Hui Zhao
- Key Laboratory for Regenerative Medicine, Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China CUHK-GIBH CAS Joint Research Laboratory on Stem Cell and Regenerative Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China CUHK Shenzhen Research Institute, Shenzhen, 518057, China
| | - Jianwei Ren
- CUHK Shenzhen Research Institute, Shenzhen, 518057, China Department of Surgery, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Bo Feng
- Key Laboratory for Regenerative Medicine, Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China CUHK-GIBH CAS Joint Research Laboratory on Stem Cell and Regenerative Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China CUHK Shenzhen Research Institute, Shenzhen, 518057, China
| |
Collapse
|
20
|
Tokunaga A, Anai H, Hanada K. Mechanisms of gene targeting in higher eukaryotes. Cell Mol Life Sci 2016; 73:523-33. [PMID: 26507245 PMCID: PMC11108335 DOI: 10.1007/s00018-015-2073-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Revised: 10/14/2015] [Accepted: 10/14/2015] [Indexed: 10/22/2022]
Abstract
Targeted genome modifications using techniques that alter the genomic information of interest have contributed to multiple studies in both basic and applied biology. Traditionally, in gene targeting, the target-site integration of a targeting vector by homologous recombination is used. However, this strategy has several technical problems. The first problem is the extremely low frequency of gene targeting, which makes obtaining recombinant clones an extremely labor intensive task. The second issue is the limited number of biomaterials to which gene targeting can be applied. Traditional gene targeting hardly occurs in most of the human adherent cell lines. However, a new approach using designer nucleases that can introduce site-specific double-strand breaks in genomic DNAs has increased the efficiency of gene targeting. This new method has also expanded the number of biomaterials to which gene targeting could be applied. Here, we summarize various strategies for target gene modification, including a comparison of traditional gene targeting with designer nucleases.
Collapse
Affiliation(s)
- Akinori Tokunaga
- The Tokunaga Laboratory, Faculty of Medicine, Oita University, 1-1 Idaigaoka, Hasama-machi, Yufu, Oita, 879-5593, Japan
- Section of Physiology, Department of Integrative Aging Neuroscience, National Center for Geriatrics and Gerontology (NCGG), 7-430, Morioka-cho, Obu, Aichi, 474-8511, Japan
| | - Hirofumi Anai
- Clinical Engineering Research Center, Faculty of Medicine, Oita University, 1-1 Idaigaoka, Hasama-machi, Yufu, Oita, 879-5593, Japan
| | - Katsuhiro Hanada
- Clinical Engineering Research Center, Faculty of Medicine, Oita University, 1-1 Idaigaoka, Hasama-machi, Yufu, Oita, 879-5593, Japan.
| |
Collapse
|
21
|
Krause CD, Pestka S. Cut, copy, move, delete: The study of human interferon genes reveal multiple mechanisms underlying their evolution in amniotes. Cytokine 2015; 76:480-495. [PMID: 26228976 DOI: 10.1016/j.cyto.2015.07.019] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 07/21/2015] [Accepted: 07/21/2015] [Indexed: 11/15/2022]
Abstract
Interferons (IFNs) are rapidly evolving cytokines released when viral infections are detected in cells. Previous research suggests that genes encoding IFNs and their receptors duplicated extensively throughout vertebrate evolution. We present molecular genetic evidence that supports the use of nonallelic homologous recombination (NAHR) to expand select IFN genes during amniote evolution. The duplication of long regions of genome (encompassing at least one functional IFN gene) followed by the insertion of this genome fragment near its parent's location, is commonly observed in many amniote genomes. Duplicates inserted away from duplication hotspots are not as frequently perturbed with new duplicates, and tend to survive long periods of evolution, sometimes becoming new IFN subtypes. Although most duplicates are inserted parallel to and near the original sequence, the insertion of the Kelch-like 9 gene within the Type I IFN locus of placental mammals promoted antiparallel insertion of gene duplicates between the Kelch-like 9 and IFN-ε loci. Genetic exchange between highly similar Type I gene duplicates as well as between Type III IFN gene duplicates homogenized their diversification. Oddly, Type III IFN genes migrated long distances throughout the genome more frequently than did Type I IFN genes. The inter-chromosomal movement of Type I IFN genes in amniotes correlated with complete intron loss in their gene structure, and repeatedly occurred with occasional Type III IFN genes.
Collapse
Affiliation(s)
- Christopher D Krause
- Department of Biochemistry and Molecular Biology, Rutgers - Robert Wood Johnson Medical School, Piscataway, NJ, USA; Center for Molecular Biology and Biotechnology, Florida Atlantic University, Boca Raton, FL, USA.
| | - Sidney Pestka
- Department of Biochemistry and Molecular Biology, Rutgers - Robert Wood Johnson Medical School, Piscataway, NJ, USA; PBL Assay Sciences, Piscataway, NJ, USA
| |
Collapse
|
22
|
Abstract
Environmental agents are constantly challenging cells by damaging DNA, leading to the blockage of transcription elongation. How do cells deal with transcription-blockage and how is transcription restarted after the blocking lesions are removed? Here we review the processes responsible for the removal of transcription-blocking lesions, as well as mechanisms of transcription restart. We also discuss recent data suggesting that blocked RNA polymerases may not resume transcription from the site of the lesion following its removal but, rather, are forced to start over from the beginning of genes.
Collapse
|
23
|
Abstract
The rate and mechanism of protein sequence evolution have been central questions in evolutionary biology since the 1960s. Although the rate of protein sequence evolution depends primarily on the level of functional constraint, exactly what determines functional constraint has remained unclear. The increasing availability of genomic data has enabled much needed empirical examinations on the nature of functional constraint. These studies found that the evolutionary rate of a protein is predominantly influenced by its expression level rather than functional importance. A combination of theoretical and empirical analyses has identified multiple mechanisms behind these observations and demonstrated a prominent role in protein evolution of selection against errors in molecular and cellular processes.
Collapse
Affiliation(s)
- Jianzhi Zhang
- Department of Ecology and Evolutionary Biology, University of Michigan, 830 North University Avenue, Ann Arbor, Michigan 48109, USA
| | - Jian-Rong Yang
- Department of Ecology and Evolutionary Biology, University of Michigan, 830 North University Avenue, Ann Arbor, Michigan 48109, USA
| |
Collapse
|
24
|
RECQ5-dependent SUMOylation of DNA topoisomerase I prevents transcription-associated genome instability. Nat Commun 2015; 6:6720. [PMID: 25851487 DOI: 10.1038/ncomms7720] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Accepted: 02/23/2015] [Indexed: 02/07/2023] Open
Abstract
DNA topoisomerase I (TOP1) has an important role in maintaining DNA topology by relaxing supercoiled DNA. Here we show that the K391 and K436 residues of TOP1 are SUMOylated by the PIAS1-SRSF1 E3 ligase complex in the chromatin fraction containing active RNA polymerase II (RNAPIIo). This modification is necessary for the binding of TOP1 to RNAPIIo and for the recruitment of RNA splicing factors to the actively transcribed chromatin, thereby reducing the formation of R-loops that lead to genome instability. RECQ5 helicase promotes TOP1 SUMOylation by facilitating the interaction between PIAS1, SRSF1 and TOP1. Unexpectedly, the topoisomerase activity is compromised by K391/K436 SUMOylation, and this provides the first in vivo evidence that TOP1 activity is negatively regulated at transcriptionally active chromatin to prevent TOP1-induced DNA damage. Therefore, our data provide mechanistic insight into how TOP1 SUMOylation contributes to genome maintenance during transcription.
Collapse
|
25
|
Batenburg NL, Thompson EL, Hendrickson EA, Zhu XD. Cockayne syndrome group B protein regulates DNA double-strand break repair and checkpoint activation. EMBO J 2015; 34:1399-416. [PMID: 25820262 DOI: 10.15252/embj.201490041] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Accepted: 03/11/2015] [Indexed: 11/09/2022] Open
Abstract
Mutations of CSB account for the majority of Cockayne syndrome (CS), a devastating hereditary disorder characterized by physical impairment, neurological degeneration and segmental premature aging. Here we report the generation of a human CSB-knockout cell line. We find that CSB facilitates HR and represses NHEJ. Loss of CSB or a CS-associated CSB mutation abrogating its ATPase activity impairs the recruitment of BRCA1, RPA and Rad51 proteins to damaged chromatin but promotes the formation of 53BP1-Rif1 damage foci in S and G2 cells. Depletion of 53BP1 rescues the formation of BRCA1 damage foci in CSB-knockout cells. In addition, knockout of CSB impairs the ATM- and Chk2-mediated DNA damage responses, promoting a premature entry into mitosis. Furthermore, we show that CSB accumulates at sites of DNA double-strand breaks (DSBs) in a transcription-dependent manner. The kinetics of DSB-induced chromatin association of CSB is distinct from that of its UV-induced chromatin association. These results reveal novel, important functions of CSB in regulating the DNA DSB repair pathway choice as well as G2/M checkpoint activation.
Collapse
Affiliation(s)
| | - Elizabeth L Thompson
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Eric A Hendrickson
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Xu-Dong Zhu
- Department of Biology, McMaster University, Hamilton, ON, Canada
| |
Collapse
|
26
|
Hamperl S, Cimprich KA. The contribution of co-transcriptional RNA:DNA hybrid structures to DNA damage and genome instability. DNA Repair (Amst) 2014; 19:84-94. [PMID: 24746923 PMCID: PMC4051866 DOI: 10.1016/j.dnarep.2014.03.023] [Citation(s) in RCA: 189] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Accurate DNA replication and DNA repair are crucial for the maintenance of genome stability, and it is generally accepted that failure of these processes is a major source of DNA damage in cells. Intriguingly, recent evidence suggests that DNA damage is more likely to occur at genomic loci with high transcriptional activity. Furthermore, loss of certain RNA processing factors in eukaryotic cells is associated with increased formation of co-transcriptional RNA:DNA hybrid structures known as R-loops, resulting in double-strand breaks (DSBs) and DNA damage. However, the molecular mechanisms by which R-loop structures ultimately lead to DNA breaks and genome instability is not well understood. In this review, we summarize the current knowledge about the formation, recognition and processing of RNA:DNA hybrids, and discuss possible mechanisms by which these structures contribute to DNA damage and genome instability in the cell.
Collapse
Affiliation(s)
- Stephan Hamperl
- Department of Chemical, Systems Biology, Stanford University School of Medicine, 318 Campus Drive, Stanford, CA 94305-5441, USA
| | - Karlene A Cimprich
- Department of Chemical, Systems Biology, Stanford University School of Medicine, 318 Campus Drive, Stanford, CA 94305-5441, USA.
| |
Collapse
|
27
|
Abstract
Poly (ADP-ribose) polymerase-1 (PARP1) is an abundant, ubiquitously expressed NAD(+)-dependent nuclear enzyme that has prognostic value for a multitude of human cancers. PARP1 activity serves to poly (ADP-ribose)-ylate the vast majority of known client proteins and affects a number of cellular and biologic outcomes, by mediating the DNA damage response (DDR), base-excision repair (BER), and DNA strand break (DSB) pathways. PARP1 is also critically important for the maintenance of genomic integrity, as well as chromatin dynamics and transcriptional regulation. Evidence also indicates that PARP-directed therapeutics are "synthetic lethal" in BRCA1/2-deficient model systems. Strikingly, recent studies have unearthed exciting new transcriptional-regulatory roles for PARP1, which has profound implications for human malignancies and will be reviewed herein.
Collapse
Affiliation(s)
| | - Karen E Knudsen
- Kimmel Cancer Center, Departments of Cancer Biology, Urology, and Radiation Oncology, Thomas Jefferson University, Philadelphia, Pennsylvania
| |
Collapse
|
28
|
Hosono Y, Abe T, Ishiai M, Islam MN, Arakawa H, Wang W, Takeda S, Ishii Y, Takata M, Seki M, Enomoto T. Tumor suppressor RecQL5 controls recombination induced by DNA crosslinking agents. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1843:1002-12. [PMID: 24418621 DOI: 10.1016/j.bbamcr.2014.01.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Revised: 12/15/2013] [Accepted: 01/02/2014] [Indexed: 12/20/2022]
Abstract
RecQ family DNA helicases function in the maintenance of genome stability. Mice deficient in RecQL5, one of five RecQ helicases, show a cancer predisposition phenotype, suggesting that RecQL5 plays a tumor suppressor role. RecQL5 interacts with Rad51, a key factor in homologous recombination (HR), and displaces Rad51 from Rad51-single stranded DNA (ssDNA) filaments in vitro. However, the precise roles of RecQL5 in the cell remain elusive. Here, we present evidence suggesting that RecQL5 is involved in DNA interstrand crosslink (ICL) repair. Chicken DT40 RECQL5 gene knockout (KO) cells showed sensitivity to ICL-inducing agents such as cisplatin (CDDP) and mitomycin C (MMC) and a higher number of chromosome aberrations in the presence of MMC than wild-type cells. The phenotypes of RECQL5 KO cells resembled those of Fanconi anemia gene KO cells. Genetic analysis using corresponding gene knockout cells showed that RecQL5 is involved in the FANCD1 (BRCA2)-dependent ICL repair pathway in which Rad51-ssDNA filament formation is promoted by BRCA2. The disappearance but not appearance of Rad51-foci was delayed in RECQL5 KO cells after MMC treatment. Deletion of Rad54, which processes the Rad51-ssDNA filament in HR, in RECQL5 KO cells increased sensitivity to CDDP and further delayed the disappearance of Rad51-foci, suggesting that RecQL5 and Rad54 have different effects on the Rad51-ssDNA filament. Furthermore, the frequency and variation of CDDP-induced gene conversion at the immunoglobulin locus were increased in RECQL5 KO cells. These results suggest that RecQL5 plays a role in regulating the incidence and quality of ICL-induced recombination.
Collapse
Affiliation(s)
- Yoshifumi Hosono
- Molecular Cell Biology Laboratory, Graduate School of Pharmaceutical Sciences, Tohoku University, Aoba 6-3, Aramaki, Aoba-ku, Sendai 980-8578, Japan
| | - Takuya Abe
- IFOM, the FIRC Institute for Molecular Oncology Foundation, IFOM-IEO Campus, Via Adamello 16, 20139 Milan, Italy
| | - Masamichi Ishiai
- Laboratory of DNA Damage Signaling, Department of Late Effect Studies, Radiation Biology Center, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - M Nurul Islam
- Laboratory of Genetics, NIA, National Institutes of Health, NIH Biomedical Research Center, Baltimore, MD 21224, USA; Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Hiroshi Arakawa
- IFOM, the FIRC Institute for Molecular Oncology Foundation, IFOM-IEO Campus, Via Adamello 16, 20139 Milan, Italy
| | - Weidong Wang
- Laboratory of Genetics, NIA, National Institutes of Health, NIH Biomedical Research Center, Baltimore, MD 21224, USA
| | - Shunichi Takeda
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yutaka Ishii
- Shujitsu University, School of Pharmacy, Nishigawara, Naka-ku, Okayama 703-8516, Japan
| | - Minoru Takata
- Laboratory of DNA Damage Signaling, Department of Late Effect Studies, Radiation Biology Center, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Masayuki Seki
- Molecular Cell Biology Laboratory, Graduate School of Pharmaceutical Sciences, Tohoku University, Aoba 6-3, Aramaki, Aoba-ku, Sendai 980-8578, Japan; Department of Biochemistry, Tohoku Pharmaceutical University, 4-1, Komatsushima 4-chome, Aoba-ku, Sendai, Miyagi 981-8558, Japan.
| | - Takemi Enomoto
- Molecular Cell Biology Laboratory, Research Institute of Pharmaceutical Sciences, Faculty of Pharmacy, Musashino University, 1-1-20 Shinmachi, Nishitokyo-shi, Tokyo 202-8585, Japan.
| |
Collapse
|
29
|
Transcription-replication collision increases recombination efficiency between plasmids. Plasmid 2013; 70:406-11. [PMID: 24161752 DOI: 10.1016/j.plasmid.2013.10.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Revised: 10/04/2013] [Accepted: 10/14/2013] [Indexed: 11/23/2022]
Abstract
It has been proposed that the stalling of the replication forks can induce homologous recombination in several organisms, and that arrested replication forks may offer nuclease targets, thereby providing a substrate for proteins involved in double-strand repair. In this article, we constructed a plasmid with the potential for transcription-replication collision (TRC), in which DNA replication and RNA transcription occur on the same DNA template simultaneously. Theoretically, transcription will impede DNA replication and increase homologous recombination. To validate this hypothesis, another plasmid was constructed that contained a homologous sequence with the exception of some mutated sites. Co-transfection of these two plasmids into 293T cells resulted in increased recombination frequency. The ratio of these two plasmids also affected the recombination frequency. Moreover, we found high expression levels of RAD51, which indicated that the increase in the recombination rate was probably via the homologous recombination pathway. These results indicate that mutant genes in plasmids can be repaired by TRC-induced recombination.
Collapse
|
30
|
Noble R, Christodoulou Z, Kyes S, Pinches R, Newbold CI, Recker M. The antigenic switching network of Plasmodium falciparum and its implications for the immuno-epidemiology of malaria. eLife 2013; 2:e01074. [PMID: 24062941 PMCID: PMC3778436 DOI: 10.7554/elife.01074] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Accepted: 08/19/2013] [Indexed: 12/23/2022] Open
Abstract
Antigenic variation in the human malaria parasite Plasmodium falciparum involves sequential and mutually exclusive expression of members of the var multi-gene family and appears to follow a non-random pattern. In this study, using a detailed in vitro gene transcription analysis of the culture-adapted HB3 strain of P. falciparum, we show that antigenic switching is governed by a global activation hierarchy favouring short and highly diverse genes in central chromosomal location. Longer and more conserved genes, which have previously been associated with severe infection in immunologically naive hosts, are rarely activated, however, implying an in vivo fitness advantage possibly through adhesion-dependent survival rates. We further show that a gene’s activation rate is positively associated sequence diversity, which could offer important new insights into the evolution and maintenance of antigenic diversity in P. falciparum malaria. DOI:http://dx.doi.org/10.7554/eLife.01074.001 Our ability to acquire immunity to a disease depends on our immune system learning to recognise foreign molecules—called antigens—that are specific to the disease-causing virus, bacterium or parasite. However, some pathogens, such as the malaria-causing parasite Plasmodium falciparum, get around this defence through a process called antigenic variation. This involves the parasite switching between different antigens over the course of an infection, preventing the host immune system from learning to recognise them and leading to infections that last many weeks or even months. The main antigen in P. falciparum is a protein called PfEMP1, which is encoded by a family of genes called var (‘variable’). Var genes have evolved to be highly diverse, and different parasites have different repertoires of around 50–60 var genes. This ensures that there are a huge number of distinct variants of the PfEMP1 antigen available within the population, allowing the malaria parasite to maintain long-lasting infections and also to infect the same individuals again and again. Previous work has shown that the expression of var genes is not random, but it is not clear what determines which genes are expressed at any given time. Now, Noble et al. have performed a detailed investigation of antigenic switching in P. falciparum. Using clonal parasites, they closely monitored the expression of the entire var gene repertoire during many generations of parasite culture. They observed that although different cultures initially expressed distinct var genes, most of them ended up expressing two particular genes—var27 and var29—at high levels, indicating a hard-wired gene ‘activation hierarchy’. Noble et al. found that whenever the parasites switched antigens, var genes that were centrally located on chromosomes—such as var27 and var29—were more likely to be activated than those at the ends of chromosomes. Moreover, var genes that were highly diverse were more likely to be activated than more conserved genes: this is the first evidence linking var gene evolution with gene activation probabilities. Together, these factors gave rise to the proposed activation hierarchy, which favours genes optimised for immune evasion and aids their continued evolution and diversification. Further work is now needed to identify the molecular mechanisms that control antigenic switching and to determine whether these could represent new therapeutic targets for malaria. DOI:http://dx.doi.org/10.7554/eLife.01074.002
Collapse
Affiliation(s)
- Robert Noble
- Department of Zoology , University of Oxford , Oxford , United Kingdom
| | | | | | | | | | | |
Collapse
|
31
|
Telomeric RNA-DNA hybrids affect telomere-length dynamics and senescence. Nat Struct Mol Biol 2013; 20:1199-205. [DOI: 10.1038/nsmb.2662] [Citation(s) in RCA: 210] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Accepted: 08/06/2013] [Indexed: 12/27/2022]
|
32
|
Duch A, de Nadal E, Posas F. Dealing with transcriptional outbursts during S phase to protect genomic integrity. J Mol Biol 2013; 425:4745-55. [PMID: 24021813 DOI: 10.1016/j.jmb.2013.08.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Revised: 08/16/2013] [Accepted: 08/23/2013] [Indexed: 10/26/2022]
Abstract
Transcription during S phase needs to be spatially and temporally regulated to prevent collisions between the transcription and replication machineries. Cells have evolved a number of mechanisms to make both processes compatible under normal growth conditions. When conflict management fails, the head-on encounter between RNA and DNA polymerases results in genomic instability unless conflict resolution mechanisms are activated. Nevertheless, there are specific situations in which cells need to dramatically change their transcriptional landscape to adapt to environmental challenges. Signal transduction pathways, such as stress-activated protein kinases (SAPKs), serve to regulate gene expression in response to environmental insults. Prototypical members of SAPKs are the yeast Hog1 and mammalian p38. In response to stress, p38/Hog1 SAPKs control transcription and also regulate cell cycle progression. When yeast cells are stressed during S phase, Hog1 promotes gene induction and, remarkably, also delays replication by directly affecting early origin firing and fork progression. Therefore, by delaying replication, Hog1 plays a key role in preventing conflicts between RNA and DNA polymerases. In this review, we focus on the genomic determinants and mechanisms that make compatible transcription with replication during S phase to prevent genomic instability, especially in response to environmental changes.
Collapse
Affiliation(s)
- Alba Duch
- Cell Signaling Unit, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, E-08003 Barcelona, Spain
| | | | | |
Collapse
|
33
|
Carofiglio F, Inagaki A, de Vries S, Wassenaar E, Schoenmakers S, Vermeulen C, van Cappellen WA, Sleddens-Linkels E, Grootegoed JA, te Riele HPJ, de Massy B, Baarends WM. SPO11-independent DNA repair foci and their role in meiotic silencing. PLoS Genet 2013; 9:e1003538. [PMID: 23754961 PMCID: PMC3675022 DOI: 10.1371/journal.pgen.1003538] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Accepted: 04/16/2013] [Indexed: 11/19/2022] Open
Abstract
In mammalian meiotic prophase, the initial steps in repair of SPO11-induced DNA double-strand breaks (DSBs) are required to obtain stable homologous chromosome pairing and synapsis. The X and Y chromosomes pair and synapse only in the short pseudo-autosomal regions. The rest of the chromatin of the sex chromosomes remain unsynapsed, contains persistent meiotic DSBs, and the whole so-called XY body undergoes meiotic sex chromosome inactivation (MSCI). A more general mechanism, named meiotic silencing of unsynapsed chromatin (MSUC), is activated when autosomes fail to synapse. In the absence of SPO11, many chromosomal regions remain unsynapsed, but MSUC takes place only on part of the unsynapsed chromatin. We asked if spontaneous DSBs occur in meiocytes that lack a functional SPO11 protein, and if these might be involved in targeting the MSUC response to part of the unsynapsed chromatin. We generated mice carrying a point mutation that disrupts the predicted catalytic site of SPO11 (Spo11(YF/YF)), and blocks its DSB-inducing activity. Interestingly, we observed foci of proteins involved in the processing of DNA damage, such as RAD51, DMC1, and RPA, both in Spo11(YF/YF) and Spo11 knockout meiocytes. These foci preferentially localized to the areas that undergo MSUC and form the so-called pseudo XY body. In SPO11-deficient oocytes, the number of repair foci increased during oocyte development, indicating the induction of S phase-independent, de novo DNA damage. In wild type pachytene oocytes we observed meiotic silencing in two types of pseudo XY bodies, one type containing DMC1 and RAD51 foci on unsynapsed axes, and another type containing only RAD51 foci, mainly on synapsed axes. Taken together, our results indicate that in addition to asynapsis, persistent SPO11-induced DSBs are important for the initiation of MSCI and MSUC, and that SPO11-independent DNA repair foci contribute to the MSUC response in oocytes.
Collapse
Affiliation(s)
- Fabrizia Carofiglio
- Department of Reproduction and Development, Erasmus MC - University Medical Center, Rotterdam, The Netherlands
| | - Akiko Inagaki
- Department of Reproduction and Development, Erasmus MC - University Medical Center, Rotterdam, The Netherlands
| | - Sandra de Vries
- Division of Molecular Biology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Evelyne Wassenaar
- Department of Reproduction and Development, Erasmus MC - University Medical Center, Rotterdam, The Netherlands
| | - Sam Schoenmakers
- Department of Obstetrics and Gynaecology, Erasmus MC - University Medical Center, Rotterdam, The Netherlands
| | - Christie Vermeulen
- Division of Molecular Biology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Wiggert A. van Cappellen
- Department of Reproduction and Development, Erasmus MC - University Medical Center, Rotterdam, The Netherlands
- Erasmus Optical Imaging Centre, Department of Pathology, Erasmus MC - University Medical Center, Rotterdam, The Netherlands
| | - Esther Sleddens-Linkels
- Department of Reproduction and Development, Erasmus MC - University Medical Center, Rotterdam, The Netherlands
| | - J. Anton Grootegoed
- Department of Reproduction and Development, Erasmus MC - University Medical Center, Rotterdam, The Netherlands
| | - Hein P. J. te Riele
- Division of Molecular Biology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Bernard de Massy
- Institut de Génétique Humaine, CNRS UPR 1142, Montpellier, France
| | - Willy M. Baarends
- Department of Reproduction and Development, Erasmus MC - University Medical Center, Rotterdam, The Netherlands
- * E-mail:
| |
Collapse
|
34
|
Popuri V, Tadokoro T, Croteau DL, Bohr VA. Human RECQL5: guarding the crossroads of DNA replication and transcription and providing backup capability. Crit Rev Biochem Mol Biol 2013; 48:289-99. [PMID: 23627586 DOI: 10.3109/10409238.2013.792770] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
DNA helicases are ubiquitous enzymes that catalyze unwinding of duplex DNA and function in all metabolic processes in which access to single-stranded DNA is required, including DNA replication, repair, recombination and RNA transcription. RecQ helicases are a conserved family of DNA helicases that display highly specialized and vital roles in the maintenance of genome stability. Mutations in three of the five human RecQ helicases, BLM, WRN and RECQL4 are associated with the genetic disorders Bloom syndrome, Werner syndrome and Rothmund-Thomson syndrome that are characterized by chromosomal instability, premature aging and predisposition to cancer. The biological role of human RECQL5 is only partially understood and RECQL5 has not yet been associated with any human disease. Illegitimate recombination and replication stress are hallmarks of human cancers and common instigators for genomic instability and cell death. Recql5 knockout mice are cancer prone and show increased chromosomal instability. Recql5-deficient mouse embryonic fibroblasts are sensitive to camptothecin and display elevated levels of sister chromatid exchanges. Unlike other human RecQ helicases, RECQL5 is recruited to single-stranded DNA breaks and is also proposed to play an essential role in RNA transcription. Here, we review the established roles of RECQL5 at the cross roads of DNA replication, recombination and transcription, and propose that human RECQL5 provides important backup functions in the absence of other DNA helicases.
Collapse
Affiliation(s)
- Venkateswarlu Popuri
- Laboratory of Molecular Gerontology, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | | | | | | |
Collapse
|
35
|
Gaillard H, Herrera-Moyano E, Aguilera A. Transcription-associated genome instability. Chem Rev 2013; 113:8638-61. [PMID: 23597121 DOI: 10.1021/cr400017y] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Hélène Gaillard
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla , Av. Américo Vespucio s/n, 41092 Seville, Spain
| | | | | |
Collapse
|
36
|
Alexander MP, Begins KJ, Crall WC, Holmes MP, Lippert MJ. High levels of transcription stimulate transversions at GC base pairs in yeast. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2013; 54:44-53. [PMID: 23055242 PMCID: PMC5013542 DOI: 10.1002/em.21740] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2012] [Revised: 08/18/2012] [Accepted: 08/22/2012] [Indexed: 06/01/2023]
Abstract
High-levels of transcription through a gene stimulate spontaneous mutation rate, a phenomenon termed transcription-associated mutation (TAM). While transcriptional effects on specific mutation classes have been identified using forward mutation and frameshift-reversion assays, little is yet known about transcription-associated base substitutions in yeast. To address this issue, we developed a new base substitution reversion assay (the lys2-TAG allele). We report a 22-fold increase in overall reversion rate in the high- relative to the low-transcription strain (from 2.1- to 47- × 10(-9) ). While all detectable base substitution types increased in the high-transcription strain, G→T and G→C transversions increased disproportionately by 58- and 52-fold, respectively. To assess a potential role of DNA damage in the TAM events, we measured mutation rates and spectra in individual strains defective in the repair of specific DNA lesions or null for the error-prone translesion DNA polymerase zeta (Pol zeta). Results exclude a role of 8-oxoGuanine, general oxidative damage, or apurinic/apyrimidinic sites in the generation of TAM G→T and G→C transversions. In contrast, the TAM transversions at GC base pairs depend on Pol zeta for occurrence implicating DNA damage, other than oxidative lesions or AP sites, in the TAM mechanism. Results further indicate that transcription-dependent G→T transversions in yeast differ mechanistically from equivalent events in E. coli reported by others. Given their occurrences in repair-proficient cells, transcription-associated G→T and G→C events represent a novel type of transcription-associated mutagenesis in normal cells with potentially important implications for evolution and genetic disease.
Collapse
Affiliation(s)
| | | | | | | | - Malcolm J. Lippert
- Correspondence to: Malcolm J. Lippert, Saint Michael's College, Biology Department, Box 283, 1 Winooski Park, Colchester, VT 05439, USA.
| |
Collapse
|
37
|
Otto B, Gruner K, Heinlein C, Wegwitz F, Nollau P, Ylstra B, Pantel K, Schumacher U, Baumbusch LO, Martin-Subero JI, Siebert R, Wagener C, Streichert T, Deppert W, Tolstonog GV. Low-grade and high-grade mammary carcinomas in WAP-T transgenic mice are independent entities distinguished by Met expression. Int J Cancer 2012; 132:1300-10. [DOI: 10.1002/ijc.27783] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Accepted: 08/03/2012] [Indexed: 12/15/2022]
|
38
|
Lin YL, Pasero P. Interference between DNA replication and transcription as a cause of genomic instability. Curr Genomics 2012; 13:65-73. [PMID: 22942676 PMCID: PMC3269018 DOI: 10.2174/138920212799034767] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2011] [Revised: 10/03/2011] [Accepted: 10/06/2011] [Indexed: 11/22/2022] Open
Abstract
Replication and transcription are key aspects of DNA metabolism that take place on the same template and potentially interfere with each other. Conflicts between these two activities include head-on or co-directional collisions between DNA and RNA polymerases, which can lead to the formation of DNA breaks and chromosome rearrangements. To avoid these deleterious consequences and prevent genomic instability, cells have evolved multiple mechanisms preventing replication forks from colliding with the transcription machinery. Yet, recent reports indicate that interference between replication and transcription is not limited to physical interactions between polymerases and that other cotranscriptional processes can interfere with DNA replication. These include DNA-RNA hybrids that assemble behind elongating RNA polymerases, impede fork progression and promote homologous recombination. Here, we discuss recent evidence indicating that R-loops represent a major source of genomic instability in all organisms, from bacteria to human, and are potentially implicated in cancer development.
Collapse
Affiliation(s)
- Yea-Lih Lin
- Institute of Human Genetics, CNRS-UPR1142, Montpellier, France
| | | |
Collapse
|
39
|
Bauer M, Goldstein M, Heylmann D, Kaina B. Human monocytes undergo excessive apoptosis following temozolomide activating the ATM/ATR pathway while dendritic cells and macrophages are resistant. PLoS One 2012; 7:e39956. [PMID: 22768182 PMCID: PMC3386965 DOI: 10.1371/journal.pone.0039956] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2012] [Accepted: 05/29/2012] [Indexed: 11/18/2022] Open
Abstract
Immunodeficiency is a severe therapy-limiting side effect of anticancer chemotherapy resulting from sensitivity of immunocompetent cells to DNA damaging agents. A central role in the immune system is played by monocytes that differentiate into macrophages and dendritic cells (DCs). In this study we compared human monocytes isolated from peripheral blood and cytokine matured macrophages and DCs derived from them and assessed the mechanism of toxicity of the DNA methylating anticancer drug temozolomide (TMZ) in these cell populations. We observed that monocytes, but not DCs and macrophages, were highly sensitive to the killing effect of TMZ. Studies on DNA damage and repair revealed that the initial DNA incision was efficient in monocytes while the re-ligation step of base excision repair (BER) can not be accomplished, resulting in an accumulation of DNA single-strand breaks (SSBs). Furthermore, monocytes accumulated DNA double-strand breaks (DSBs) following TMZ treatment, while DCs and macrophages were able to repair DSBs. Monocytes lack the DNA repair proteins XRCC1, ligase IIIα and PARP-1 whose expression is restored during differentiation into macrophages and DCs following treatment with GM-CSF and GM-CSF plus IL-4, respectively. These proteins play a key role both in BER and DSB repair by B-NHEJ, which explains the accumulation of DNA breaks in monocytes following TMZ treatment. Although TMZ provoked an upregulation of XRCC1 and ligase IIIα, BER was not enhanced likely because PARP-1 was not upregulated. Accordingly, inhibition of PARP-1 did not sensitize monocytes, but monocyte-derived DCs in which strong PARP activation was observed. TMZ induced in monocytes the DNA damage response pathways ATM-Chk2 and ATR-Chk1 resulting in p53 activation. Finally, upon activation of the Fas-receptor and the mitochondrial pathway apoptosis was executed in a caspase-dependent manner. The downregulation of DNA repair in monocytes, resulting in their selective killing by TMZ, might impact on the immune response during cancer chemotherapy.
Collapse
Affiliation(s)
- Martina Bauer
- Department of Toxicology, University Medical Center, Mainz, Germany
| | | | - Daniel Heylmann
- Department of Toxicology, University Medical Center, Mainz, Germany
| | - Bernd Kaina
- Department of Toxicology, University Medical Center, Mainz, Germany
| |
Collapse
|
40
|
Poveda AM, Le Clech M, Pasero P. Transcription and replication: breaking the rules of the road causes genomic instability. Transcription 2012; 1:99-102. [PMID: 21326900 DOI: 10.4161/trns.1.2.12665] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2010] [Revised: 06/13/2010] [Accepted: 06/14/2010] [Indexed: 11/19/2022] Open
Abstract
Replication and transcription machineries progress at high speed on the same DNA template, which inevitably causes traffic accidents. Problems are not only caused by frontal collisions between polymerases, but also by cotranscriptional R-loops. These RNA-DNA hybrids induce genomic instability by blocking fork progression and could be implicated in the development of cancer.
Collapse
|
41
|
Xu L, Kuo J, Liu JK, Wong TY. Bacterial phylogenetic tree construction based on genomic translation stop signals. MICROBIAL INFORMATICS AND EXPERIMENTATION 2012; 2:6. [PMID: 22651236 PMCID: PMC3466146 DOI: 10.1186/2042-5783-2-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2012] [Accepted: 04/15/2012] [Indexed: 11/10/2022]
Abstract
Background The efficiencies of the stop codons TAA, TAG, and TGA in protein synthesis termination are not the same. These variations could allow many genes to be regulated. There are many similar nucleotide trimers found on the second and third reading-frames of a gene. They are called premature stop codons (PSC). Like stop codons, the PSC in bacterial genomes are also highly bias in terms of their quantities and qualities on the genes. Phylogenetically related species often share a similar PSC profile. We want to know whether the selective forces that influence the stop codons and the PSC usage biases in a genome are related. We also wish to know how strong these trimers in a genome are related to the natural history of the bacterium. Knowing these relations may provide better knowledge in the phylogeny of bacteria Results A 16SrRNA-alignment tree of 19 well-studied α-, β- and γ-Proteobacteria Type species is used as standard reference for bacterial phylogeny. The genomes of sixty-one bacteria, belonging to the α-, β- and γ-Proteobacteria subphyla, are used for this study. The stop codons and PSC are collectively termed “Translation Stop Signals” (TSS). A gene is represented by nine scalars corresponding to the numbers of counts of TAA, TAG, and TGA on each of the three reading-frames of that gene. “Translation Stop Signals Ratio” (TSSR) is the ratio between the TSS counts. Four types of TSSR are investigated. The TSSR-1, TSSR-2 and TSSR-3 are each a 3-scalar series corresponding respectively to the average ratio of TAA: TAG: TGA on the first, second, and third reading-frames of all genes in a genome. The Genomic-TSSR is a 9-scalar series representing the ratio of distribution of all TSS on the three reading-frames of all genes in a genome. Results show that bacteria grouped by their similarities based on TSSR-1, TSSR-2, or TSSR-3 values could only partially resolve the phylogeny of the species. However, grouping bacteria based on thier Genomic-TSSR values resulted in clusters of bacteria identical to those bacterial clusters of the reference tree. Unlike the 16SrRNA method, the Genomic-TSSR tree is also able to separate closely related species/strains at high resolution. Species and strains separated by the Genomic-TSSR grouping method are often in good agreement with those classified by other taxonomic methods. Correspondence analysis of individual genes shows that most genes in a bacterial genome share a similar TSSR value. However, within a chromosome, the Genic-TSSR values of genes near the replication origin region (Ori) are more similar to each other than those genes near the terminus region (Ter). Conclusion The translation stop signals on the three reading-frames of the genes on a bacterial genome are interrelated, possibly due to frequent off-frame recombination facilitated by translational-associated recombination (TSR). However, TSR may not occur randomly in a bacterial chromosome. Genes near the Ori region are often highly expressed and a bacterium always maintains multiple copies of Ori. Frequent collisions between DNA- polymerase and RNA-polymerase would create many DNA strand-breaks on the genes; whereas DNA strand-break induced homologues-recombination is more likely to take place between genes with similar sequence. Thus, localized recombination could explain why the TSSR of genes near the Ori region are more similar to each other. The quantity and quality of these TSS in a genome strongly reflect the natural history of a bacterium. We propose that the Genomic- TSSR can be used as a subjective biomarker to represent the phyletic status of a bacterium.
Collapse
Affiliation(s)
- Lijing Xu
- Department of Biological Sciences, Bioinformatics Program, The University of Memphis, Memphis, TN, USA
| | - Jimmy Kuo
- Department of Planning and Research, National Museum of Marine Biology and Aquarium, Pingtung, Taiwan
| | - Jong-Kang Liu
- Department of Biological Sciences, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Tit-Yee Wong
- Department of Biological Sciences, Bioinformatics Program, The University of Memphis, Memphis, TN, USA
| |
Collapse
|
42
|
Cesarini E, D'Alfonso A, Camilloni G. H4K16 acetylation affects recombination and ncRNA transcription at rDNA in Saccharomyces cerevisiae. Mol Biol Cell 2012; 23:2770-81. [PMID: 22621897 PMCID: PMC3395664 DOI: 10.1091/mbc.e12-02-0095] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Transcription-associated recombination (TAR) is crucial for stability among repeated units of rDNA. Several histone deacetylases and a chromatin architectural component control the synthesis of ncRNA and rDNA recombination. The only acetylation state of histone H4 at Lys-16 is sufficient to regulate TAR at rDNA. Transcription-associated recombination is an important process involved in several aspects of cell physiology. In the ribosomal DNA (rDNA) of Saccharomyces cerevisiae, RNA polymerase II transcription–dependent recombination has been demonstrated among the repeated units. In this study, we investigate the mechanisms controlling this process at the chromatin level. On the basis of a small biased screening, we found that mutants of histone deacetylases and chromatin architectural proteins alter both the amount of Pol II–dependent noncoding transcripts and recombination products at rDNA in a coordinated manner. Of interest, chromatin immunoprecipitation analyses in these mutants revealed a corresponding variation of the histone H4 acetylation along the rDNA repeat, particularly at Lys-16. Here we provide evidence that a single, rapid, and reversible posttranslational modification—the acetylation of the H4K16 residue—is involved in the coordination of transcription and recombination at rDNA.
Collapse
Affiliation(s)
- Elisa Cesarini
- Dipartimento di Biologia e Biotecnologie, Università di Roma La Sapienza, 00185 Rome, Italy
| | | | | |
Collapse
|
43
|
Abstract
Alterations in genome sequence and structure contribute to somatic disease, affect the fitness of subsequent generations and drive evolutionary processes. The crucial roles of highly accurate replication and efficient repair in maintaining overall genome integrity are well-known, but the more localized stability costs that are associated with transcribing DNA into RNA molecules are less appreciated. Here we review the diverse ways in which the essential process of transcription alters the underlying DNA template and thereby modifies the genetic landscape.
Collapse
|
44
|
Yenerall P, Krupa B, Zhou L. Mechanisms of intron gain and loss in Drosophila. BMC Evol Biol 2011; 11:364. [PMID: 22182367 PMCID: PMC3296678 DOI: 10.1186/1471-2148-11-364] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2011] [Accepted: 12/19/2011] [Indexed: 12/02/2022] Open
Abstract
Background It is widely accepted that orthologous genes have lost or gained introns throughout evolution. However, the specific mechanisms that generate these changes have proved elusive. Introns are known to affect nearly every level of gene expression. Therefore, understanding their mechanism of evolution after their initial fixation in eukaryotes is pertinent to understanding the means by which organisms develop greater regulation and complexity. Results To investigate possible mechanisms of intron gain and loss, we identified 189 intron gain and 297 intron loss events among 11 Drosophila species. We then investigated these events for signatures of previously proposed mechanisms of intron gain and loss. This work constitutes the first comprehensive study into the specific mechanisms that may generate intron gains and losses in Drosophila. We report evidence of intron gain via transposon insertion; the first intron loss that may have occurred via non-homologous end joining; intron gains via the repair of a double strand break; evidence of intron sliding; and evidence that internal or 5' introns may not frequently be deleted via the self-priming of reverse transcription during mRNA-mediated intron loss. Our data also suggest that the transcription process may promote or result in intron gain. Conclusion Our findings support the occurrence of intron gain via transposon insertion, repair of double strand breaks, as well as intron loss via non-homologous end joining. Furthermore, our data suggest that intron gain may be enabled by or due to transcription, and we shed further light on the exact mechanism of mRNA-mediated intron loss.
Collapse
Affiliation(s)
- Paul Yenerall
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | | | | |
Collapse
|
45
|
Klein IA, Resch W, Jankovic M, Oliveira T, Yamane A, Nakahashi H, Di Virgilio M, Bothmer A, Nussenzweig A, Robbiani DF, Casellas R, Nussenzweig MC. Translocation-capture sequencing reveals the extent and nature of chromosomal rearrangements in B lymphocytes. Cell 2011; 147:95-106. [PMID: 21962510 DOI: 10.1016/j.cell.2011.07.048] [Citation(s) in RCA: 286] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2011] [Revised: 07/14/2011] [Accepted: 07/27/2011] [Indexed: 02/06/2023]
Abstract
Chromosomal rearrangements, including translocations, require formation and joining of DNA double strand breaks (DSBs). These events disrupt the integrity of the genome and are frequently involved in producing leukemias, lymphomas and sarcomas. Despite the importance of these events, current understanding of their genesis is limited. To examine the origins of chromosomal rearrangements we developed Translocation Capture Sequencing (TC-Seq), a method to document chromosomal rearrangements genome-wide, in primary cells. We examined over 180,000 rearrangements obtained from 400 million B lymphocytes, revealing that proximity between DSBs, transcriptional activity and chromosome territories are key determinants of genome rearrangement. Specifically, rearrangements tend to occur in cis and to transcribed genes. Finally, we find that activation-induced cytidine deaminase (AID) induces the rearrangement of many genes found as translocation partners in mature B cell lymphoma.
Collapse
Affiliation(s)
- Isaac A Klein
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
46
|
Common fragile sites: mechanisms of instability revisited. Trends Genet 2011; 28:22-32. [PMID: 22094264 DOI: 10.1016/j.tig.2011.10.003] [Citation(s) in RCA: 207] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2011] [Revised: 10/05/2011] [Accepted: 10/05/2011] [Indexed: 12/22/2022]
Abstract
Common fragile sites (CFSs) are large chromosomal regions prone to breakage upon replication stress that are considered a driving force of oncogenesis. CFSs were long believed to contain sequences blocking fork progression, thus impeding replication completion and leading to DNA breaks upon chromosome condensation. However, recent studies show that delayed completion of DNA replication instead depends on a regional paucity in initiation events. Because the distribution and the timing of these events are cell type dependent, different chromosomal regions can be committed to fragility in different cell types. These new data reveal the epigenetic nature of CFSs and open the way to a reevaluation of the role played by these sites in the formation of chromosome rearrangements found in tumors from different tissues.
Collapse
|
47
|
Lagerwerf S, Vrouwe MG, Overmeer RM, Fousteri MI, Mullenders LHF. DNA damage response and transcription. DNA Repair (Amst) 2011; 10:743-50. [PMID: 21622031 DOI: 10.1016/j.dnarep.2011.04.024] [Citation(s) in RCA: 122] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A network of DNA damage surveillance systems is triggered by sensing of DNA lesions and the initiation of a signal transduction cascade that activates genome-protection pathways including nucleotide excision repair (NER). NER operates through coordinated assembly of repair factors into pre- and post-incision complexes. Recent work identifies RPA as a key regulator of the transition from dual incision to repair-synthesis in UV-irradiated non-cycling cells, thereby averting the generation of unprocessed repair intermediates. These intermediates could lead to recombinogenic events and trigger a persistent ATR-dependent checkpoint signaling. It is now evident that DNA damage signaling is not limited to NER proficient cells. ATR-dependent checkpoint activation also occurs in UV-exposed non-cycling repair deficient cells coinciding with the formation of endonuclease APE1-mediated DNA strand breaks. In addition, the encounter of elongating RNA polymerase II (RNAPIIo) with DNA damage lesions and its persistent stalling provides a strong DNA damage signaling leading to cell cycle arrest, apoptosis and increased mutagenesis. The mechanism underlying the strong and strand specific induction of UV-induced mutations in NER deficient cells has been recently resolved by the finding that gene transcription itself increases UV-induced mutagenesis in a strand specific manner via increased deamination of cytosines. The cell removes the RNAPIIo-blocking DNA lesions by transcription-coupled repair (TC-NER) without displacement of the DNA damage stalled RNAPIIo. Deficiency in TC-NER associates with mutations in the CSA and CSB genes giving rise to the rare human disorder Cockayne syndrome (CS). CSB functions as a repair coupling factor to attract NER proteins, chromatin remodelers and the CSA-E3-ubiquitin ligase complex to the stalled RNAPIIo; CSA is dispensable for attraction of NER proteins, yet in cooperation with CSB is required to recruit XAB2, the nucleosomal binding protein HMGN1 and TFIIS. The molecular mechanisms by which these proteins bring about efficient TC-NER and trigger signaling after transcription arrest remain elusive; particularly the role of chromatin remodeling in TC-NER needs to be clarified in the context of anticipated structural changes that allow repair and transcription restart.
Collapse
Affiliation(s)
- Saskia Lagerwerf
- Department of Toxicogenetics, Leiden University Medical Center, 2333 RC Leiden, The Netherlands
| | | | | | | | | |
Collapse
|
48
|
Human DHX9 helicase preferentially unwinds RNA-containing displacement loops (R-loops) and G-quadruplexes. DNA Repair (Amst) 2011; 10:654-65. [PMID: 21561811 DOI: 10.1016/j.dnarep.2011.04.013] [Citation(s) in RCA: 164] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2010] [Revised: 04/08/2011] [Accepted: 04/11/2011] [Indexed: 02/02/2023]
Abstract
Human DHX9 helicase, also known as nuclear DNA helicase II (NDH II) and RNA helicase A (RHA), belongs to the SF2 superfamily of nucleic acid unwinding enzymes. DHX9 melts simple DNA-DNA, RNA-RNA, and DNA-RNA strands with a 3'-5' polarity; despite this little is known about its substrate specificity. Here, we used partial duplex DNA consisting of M13mp18 DNA and oligonucleotide-based replication and recombination intermediates. We show that DHX9 unwinds DNA- and RNA-containing forks, DNA- and RNA-containing displacement loops (D- and R-loops), and also G-quadruplexes. With these substrates, DHX9 behaved similarly as the RecQ helicase WRN. In contrast to WRN, DHX9 melted RNA-hybrids considerably faster than the corresponding DNA-DNA strands. DHX9 preferably unwound R-loops and DNA-based G-quadruplexes indicating that these structures may be biologically relevant. DHX9 also unwound RNA-based G-quadruplexes that have been reported to occur in human transcripts. It is believed that an improper dissolution of co-transcriptionally formed D-loops, R-loops, and DNA- or RNA-based G-quadruplexes represent potential roadblocks for transcription and thereby enhance transcription associated recombination events. By unwinding these structures, DHX9 may significantly contribute to transcriptional activation and also to the maintenance of genomic stability.
Collapse
|
49
|
Transcription inhibition by DRB potentiates recombinational repair of UV lesions in mammalian cells. PLoS One 2011; 6:e19492. [PMID: 21573160 PMCID: PMC3088672 DOI: 10.1371/journal.pone.0019492] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2010] [Accepted: 04/07/2011] [Indexed: 01/04/2023] Open
Abstract
Homologous recombination (HR) is intricately associated with replication, transcription and DNA repair in all organisms studied. However, the interplay between all these processes occurring simultaneously on the same DNA molecule is still poorly understood. Here, we study the interplay between transcription and HR during ultraviolet light (UV)-induced DNA damage in mammalian cells. Our results show that inhibition of transcription with 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole (DRB) increases the number of UV-induced DNA lesions (γH2AX, 53BP1 foci formation), which correlates with a decrease in the survival of wild type or nucleotide excision repair defective cells. Furthermore, we observe an increase in RAD51 foci formation, suggesting HR is triggered in response to an increase in UV-induced DSBs, while inhibiting transcription. Unexpectedly, we observe that DRB fails to sensitise HR defective cells to UV treatment. Thus, increased RAD51 foci formation correlates with increased cell death, suggesting the existence of a futile HR repair of UV-induced DSBs which is linked to transcription inhibition.
Collapse
|
50
|
Spatiotemporally different DNA repair systems participate in Epstein-Barr virus genome maturation. J Virol 2011; 85:6127-35. [PMID: 21490093 DOI: 10.1128/jvi.00258-11] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Productive replication of Epstein-Barr virus occurs in discrete sites in nuclei, called replication compartments, where viral DNA replication proteins and host homologous recombinational repair (HRR) and mismatch repair (MMR) factors are recruited. Three-dimensional (3D) surface reconstruction imaging clarified the spatial arrangements of these factors within the replication compartments. Subnuclear domains, designated BMRF1 cores, which were highly enriched in viral polymerase processivity factor BMRF1 could be identified inside the replication compartments. Pulse-chase experiments revealed that newly synthesized viral genomes organized around the BMRF1 cores were transferred inward. HRR factors could be demonstrated mainly outside BMRF1 cores, where de novo synthesis of viral DNA was ongoing, whereas MMR factors were found predominantly inside. These results imply that de novo synthesis of viral DNA is coupled with HRR outside the cores, followed by MMR inside cores for quality control of replicated viral genomes. Thus, our approach unveiled a viral genome manufacturing plant.
Collapse
|