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Ferraj A, Audano PA, Balachandran P, Czechanski A, Flores JI, Radecki AA, Mosur V, Gordon DS, Walawalkar IA, Eichler EE, Reinholdt LG, Beck CR. Resolution of structural variation in diverse mouse genomes reveals chromatin remodeling due to transposable elements. CELL GENOMICS 2023; 3:100291. [PMID: 37228752 PMCID: PMC10203049 DOI: 10.1016/j.xgen.2023.100291] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 02/03/2023] [Accepted: 03/10/2023] [Indexed: 05/25/2023]
Abstract
Diverse inbred mouse strains are important biomedical research models, yet genome characterization of many strains is fundamentally lacking in comparison with humans. In particular, catalogs of structural variants (SVs) (variants ≥ 50 bp) are incomplete, limiting the discovery of causative alleles for phenotypic variation. Here, we resolve genome-wide SVs in 20 genetically distinct inbred mice with long-read sequencing. We report 413,758 site-specific SVs affecting 13% (356 Mbp) of the mouse reference assembly, including 510 previously unannotated coding variants. We substantially improve the Mus musculus transposable element (TE) callset, and we find that TEs comprise 39% of SVs and account for 75% of altered bases. We further utilize this callset to investigate how TE heterogeneity affects mouse embryonic stem cells and find multiple TE classes that influence chromatin accessibility. Our work provides a comprehensive analysis of SVs found in diverse mouse genomes and illustrates the role of TEs in epigenetic differences.
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Affiliation(s)
- Ardian Ferraj
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT 06032, USA
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Peter A. Audano
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | | | | | - Jacob I. Flores
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Alexander A. Radecki
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT 06032, USA
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Varun Mosur
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - David S. Gordon
- Howard Hughes Medical Institute and Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Isha A. Walawalkar
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT 06032, USA
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Evan E. Eichler
- Howard Hughes Medical Institute and Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | | | - Christine R. Beck
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT 06032, USA
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA
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2
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Miyasaka Y, Kobayashi T, Gotoh N, Kuga M, Kobayashi M, Horio F, Hashimoto K, Kawabe T, Ohno T. Neonatal lethality of mouse A/J-7 SM consomic strain is caused by an insertion mutation in the Dchs1 gene. Mamm Genome 2023; 34:32-43. [PMID: 36434174 DOI: 10.1007/s00335-022-09966-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 10/19/2022] [Indexed: 11/27/2022]
Abstract
Homosomic mice of the A/J-7SM consomic mouse strain that introduced the entire chromosome 7 (Chr 7) of SM/J into the A/J strain exhibited neonatal lethality. We tentatively maintained segregating inbred strains (A/J-7ASM and A/J-7DSM) in which the central portion of Chr 7 was heterozygous for the A/J and SM/J strains, and the centromeric and telomeric sides of Chr 7 were homozygous for the SM/J strain, instead of the A/J-7SM strain. Based on the chromosomal constitution of Chr 7 in A/J-7ASM and A/J-7DSM mice, the causative gene for neonatal lethality in homosomic mice was suggested to be located within an approximately 1.620 Mb region between D7Mit125 (104.879 Mb) and D7Mit355 (106.499 Mb) on Chr 7. RT-PCR analysis revealed that homosomic mice lacked dachsous cadherin-related 1 (Dchs1), which is located within the D7Mit125 to D7Mit355 region and functions in the regulation of planar cell polarity. Screening for mutations in Dchs1 indicated that homosomic mice possessed an early transposable (ETn)-like sequence in intron 1 of Dchs1. Moreover, an allelism test between Dchs1 ETn-like-insertion alleles detected in homosomic mice and CRISPR/Cas9-induced Dchs1 deletion alleles revealed that Dchs1 is a causative gene for neonatal lethality in homosomic mice. Based on these results, we concluded that in the A/J-7SM strain, ETn-like elements were inserted into intron 1 of SM/J-derived Dchs1 during strain development, which dramatically reduced Dchs1 expression, thus resulting in neonatal lethality in homosomic mice. Additionally, it was suggested that the timing of lethality in Dchs1 mutant mice is influenced by the genetic background.
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Affiliation(s)
- Yuki Miyasaka
- Division of Experimental Animals, Graduate School of Medicine, Nagoya University, 65 Tsurumai-Cho, Showa-Ku, Nagoya, Aichi, 466-8550, Japan.
| | - Takeshi Kobayashi
- Division of Experimental Animals, Graduate School of Medicine, Nagoya University, 65 Tsurumai-Cho, Showa-Ku, Nagoya, Aichi, 466-8550, Japan
| | - Naoya Gotoh
- Division of Experimental Animals, Graduate School of Medicine, Nagoya University, 65 Tsurumai-Cho, Showa-Ku, Nagoya, Aichi, 466-8550, Japan
| | - Masako Kuga
- Division of Experimental Animals, Graduate School of Medicine, Nagoya University, 65 Tsurumai-Cho, Showa-Ku, Nagoya, Aichi, 466-8550, Japan
| | - Misato Kobayashi
- Department of Nutritional Sciences, Nagoya University of Arts and Sciences, 57 Takenoyama, Iwasaki-Cho, Nisshin, Aichi, 470-0196, Japan
| | - Fumihiko Horio
- Department of Life Studies and Environmental Science, Nagoya Women's University, 3-40 Shioji-Cho, Mizuho-Ku, Nagoya, Aichi, 467-8610, Japan
| | - Katsunori Hashimoto
- Faculty of Medical Sciences, Shubun University, 6 Nikko-Cho, Ichinomiya, Aichi, 491-0938, Japan
| | - Tsutomu Kawabe
- Department of Pathophysiological Laboratory Sciences, Nagoya University Graduate School of Medicine, 1-1-20 Dikou-Minami, Higashi-Ku, Nagoya, Aichi, 461-8673, Japan
| | - Tamio Ohno
- Division of Experimental Animals, Graduate School of Medicine, Nagoya University, 65 Tsurumai-Cho, Showa-Ku, Nagoya, Aichi, 466-8550, Japan.
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3
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Adams DE, Heuer LS, Rojas M, Zhang W, Ridgway WM. Mutated Pkhd1 alone is sufficient to cause autoimmune biliary disease on the nonobese diabetic (NOD) genetic background. Immunogenetics 2023; 75:27-37. [PMID: 36097289 PMCID: PMC9468241 DOI: 10.1007/s00251-022-01276-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 08/27/2022] [Indexed: 01/21/2023]
Abstract
We previously reported that nonobese diabetic (NOD) congenic mice (NOD.c3c4 mice) developed an autoimmune biliary disease (ABD) with similarities to human primary biliary cholangitis (PBC), including anti-mitochondrial antibodies and organ-specific biliary lymphocytic infiltrates. We narrowed the possible contributory regions in a novel NOD.Abd3 congenic mouse to a B10 congenic region on chromosome 1 ("Abd3") and a mutated Pkhd1 gene (Pkhd1del36-67) upstream from Abd3, and we showed via backcrossing studies that the NOD genetic background was necessary for disease. Here, we show that NOD.Abd3 mice develop anti-PDC-E2 autoantibodies at high levels, and that placing the chromosome 1 interval onto a scid background eliminates disease, demonstrating the critical role of the adaptive immune system in pathogenesis. While the NOD genetic background is essential for disease, it was still unclear which of the two regions in the Abd3 locus were necessary and sufficient for disease. Here, using a classic recombinant breeding approach, we prove that the mutated Pkhd1del36-67 alone, on the NOD background, causes ABD. Further characterization of the mutant sequence demonstrated that the Pkhd1 gene is disrupted by an ETnII-beta retrotransposon inserted in intron 35 in an anti-sense orientation. Homozygous Pkhd1 mutations significantly affect viability, with the offspring skewed away from a Mendelian distribution towards NOD Pkhd1 homozygous or heterozygous genotypes. Cell-specific abnormalities, on a susceptible genetic background, can therefore induce an organ-specific autoimmunity directed to the affected cells. Future work will aim to characterize how mutant Pkhd1 can cause such an autoimmune response.
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Affiliation(s)
- David E Adams
- Division of Immunology, Allergy and Rheumatology, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
- Department of Internal Medicine, Cincinnati VA Medical Center, Cincinnati, OH, 45267, USA
| | - Luke S Heuer
- Department of Internal Medicine, Sacramento VA Medical Center, VA Northern California Health Care System, Mather, CA, 95655, USA
- Division of Rheumatology, Allergy and Clinical Immunology, University of California, Davis, CA, 95616, USA
| | - Manuel Rojas
- School of Medicine and Health Sciences, Doctoral Program in Biological and Biomedical Sciences, Center for Autoimmune Diseases Research (CREA), Universidad del Rosario, Bogota, Colombia
- Division of Rheumatology, Allergy and Clinical Immunology, University of California, Davis, CA, 95616, USA
| | - Weici Zhang
- Department of Internal Medicine, Sacramento VA Medical Center, VA Northern California Health Care System, Mather, CA, 95655, USA
- Division of Rheumatology, Allergy and Clinical Immunology, University of California, Davis, CA, 95616, USA
| | - William M Ridgway
- Department of Internal Medicine, Sacramento VA Medical Center, VA Northern California Health Care System, Mather, CA, 95655, USA.
- Division of Rheumatology, Allergy and Clinical Immunology, University of California, Davis, CA, 95616, USA.
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4
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Senft AD, Macfarlan TS. Transposable elements shape the evolution of mammalian development. Nat Rev Genet 2021; 22:691-711. [PMID: 34354263 DOI: 10.1038/s41576-021-00385-1] [Citation(s) in RCA: 95] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/11/2021] [Indexed: 02/06/2023]
Abstract
Transposable elements (TEs) promote genetic innovation but also threaten genome stability. Despite multiple layers of host defence, TEs actively shape mammalian-specific developmental processes, particularly during pre-implantation and extra-embryonic development and at the maternal-fetal interface. Here, we review how TEs influence mammalian genomes both directly by providing the raw material for genetic change and indirectly via co-evolving TE-binding Krüppel-associated box zinc finger proteins (KRAB-ZFPs). Throughout mammalian evolution, individual activities of ancient TEs were co-opted to enable invasive placentation that characterizes live-born mammals. By contrast, the widespread activity of evolutionarily young TEs may reflect an ongoing co-evolution that continues to impact mammalian development.
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Affiliation(s)
- Anna D Senft
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, The National Institutes of Health, Bethesda, MD, USA.
| | - Todd S Macfarlan
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, The National Institutes of Health, Bethesda, MD, USA.
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5
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Palazzo A, Marsano RM. Transposable elements: a jump toward the future of expression vectors. Crit Rev Biotechnol 2021; 41:792-808. [PMID: 33622117 DOI: 10.1080/07388551.2021.1888067] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Expression vectors (EVs) are artificial nucleic acid molecules with a modular structure that allows for the transcription of DNA sequences of interest in either cellular or cell-free environments. These vectors have emerged as cross-disciplinary tools with multiple applications in an expanding Life Sciences market. The cis-regulatory sequences (CRSs) that control the transcription in EVs are typically sourced from either viruses or from characterized genes. However, the recent advancement in transposable elements (TEs) technology provides attractive alternatives that may enable a significant improvement in the design of EVs. Commonly known as "jumping genes," due to their ability to move between genetic loci, TEs are constitutive components of both eukaryotic and prokaryotic genomes. TEs harbor native CRSs that allow the regulated transcription of transposition-related genes. However, some TE-related CRSs display striking characteristics, which provides the opportunity to reconsider TEs as lead actors in the design of EVs. In this article, we provide a synopsis of the transcriptional control elements commonly found in EVs together with an extensive discussion of their advantages and limitations. We also highlight the latest findings that may allow for the implementation of TE-derived sequences in the EVs feasible, possibly improving existing vectors. By introducing this new concept of TEs as a source of regulatory sequences, we aim to stimulate a profitable discussion of the potential advantages and benefits of developing a new generation of EVs based on the use of TE-derived control sequences.
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Affiliation(s)
- Antonio Palazzo
- Laboratory of Translational Nanotechnology, "Istituto Tumori Giovanni Paolo II" I.R.C.C.S, Bari, Italy
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6
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Semi K, Takashima Y. Pluripotent stem cells for the study of early human embryology. Dev Growth Differ 2021; 63:104-115. [PMID: 33570781 PMCID: PMC8251740 DOI: 10.1111/dgd.12715] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 02/02/2021] [Accepted: 02/08/2021] [Indexed: 02/06/2023]
Abstract
Forty years have passed since the first pluripotent stem cells (PSCs), mouse embryonic stem cells (ESCs), were established. Since then, several PSCs have been reported, including human ESCs in 1998, mouse epiblast stem cells (EpiSCs) in 2007, induced PSCs (iPSCs) in 2006 and 2007, and naïve human PSCs in 2014. Naïve PSCs are thought to correspond to pre-implantation epiblast cells, whereas conventional (or primed) human PSCs correspond to post-implantation epiblast cells. Thus, naïve and primed PSCs are classified by their developmental stages and have stage-specific characteristics, despite sharing the common feature of pluripotency. In this review, we discuss the current status of PSCs and their use to model human peri-implantation development.
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Affiliation(s)
- Katsunori Semi
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Yasuhiro Takashima
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
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7
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Shao W, Wang T. Transcript assembly improves expression quantification of transposable elements in single-cell RNA-seq data. Genome Res 2021; 31:88-100. [PMID: 33355230 PMCID: PMC7849386 DOI: 10.1101/gr.265173.120] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 11/24/2020] [Indexed: 12/28/2022]
Abstract
Transposable elements (TEs) are an integral part of the host transcriptome. TE-containing noncoding RNAs (ncRNAs) show considerable tissue specificity and play important roles during development, including stem cell maintenance and cell differentiation. Recent advances in single-cell RNA-seq (scRNA-seq) revolutionized cell type-specific gene expression analysis. However, effective scRNA-seq quantification tools tailored for TEs are lacking, limiting our ability to dissect TE expression dynamics at single-cell resolution. To address this issue, we established a TE expression quantification pipeline that is compatible with scRNA-seq data generated across multiple technology platforms. We constructed TE-containing ncRNA references using bulk RNA-seq data and showed that quantifying TE expression at the transcript level effectively reduces noise. As proof of principle, we applied this strategy to mouse embryonic stem cells and successfully captured the expression profile of endogenous retroviruses in single cells. We further expanded our analysis to scRNA-seq data from early stages of mouse embryogenesis. Our results illustrated the dynamic TE expression at preimplantation stages and revealed 146 TE-containing ncRNA transcripts with substantial tissue specificity during gastrulation and early organogenesis.
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Affiliation(s)
- Wanqing Shao
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Ting Wang
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
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8
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Liu S, Yuan S, Gao X, Tao X, Yu W, Li X, Chen S, Xu A. Functional regulation of an ancestral RAG transposon ProtoRAG by a trans-acting factor YY1 in lancelet. Nat Commun 2020; 11:4515. [PMID: 32908127 PMCID: PMC7481187 DOI: 10.1038/s41467-020-18261-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 08/09/2020] [Indexed: 01/04/2023] Open
Abstract
The discovery of ancestral RAG transposons in early deuterostomia reveals the origin of vertebrate V(D)J recombination. Here, we analyze the functional regulation of a RAG transposon, ProtoRAG, in lancelet. We find that a specific interaction between the cis-acting element within the TIR sequences of ProtoRAG and a trans-acting factor, lancelet YY1-like (bbYY1), is important for the transcriptional regulation of lancelet RAG-like genes (bbRAG1L and bbRAG2L). Mechanistically, bbYY1 suppresses the transposition of ProtoRAG; meanwhile, bbYY1 promotes host DNA rejoins (HDJ) and TIR-TIR joints (TTJ) after TIR-dependent excision by facilitating the binding of bbRAG1L/2 L to TIR-containing DNA, and by interacting with the bbRAG1L/2 L complex. Our data thus suggest that bbYY1 has dual functions in fine-tuning the activity of ProtoRAG and maintaining the genome stability of the host.
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Affiliation(s)
- Song Liu
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, 510275, Guangzhou, People's Republic of China
| | - Shaochun Yuan
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, 510275, Guangzhou, People's Republic of China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, 266237, Qingdao, People's Republic of China.
| | - Xiaoman Gao
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, 510275, Guangzhou, People's Republic of China
| | - Xin Tao
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, 510275, Guangzhou, People's Republic of China
| | - Wenjuan Yu
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, 510275, Guangzhou, People's Republic of China
| | - Xu Li
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, 510275, Guangzhou, People's Republic of China
| | - Shangwu Chen
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, 510275, Guangzhou, People's Republic of China
| | - Anlong Xu
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, 510275, Guangzhou, People's Republic of China.
- School of Life Sciences, Beijing University of Chinese Medicine, 100029, Beijing, People's Republic of China.
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9
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Carter AC, Xu J, Nakamoto MY, Wei Y, Zarnegar BJ, Shi Q, Broughton JP, Ransom RC, Salhotra A, Nagaraja SD, Li R, Dou DR, Yost KE, Cho SW, Mistry A, Longaker MT, Khavari PA, Batey RT, Wuttke DS, Chang HY. Spen links RNA-mediated endogenous retrovirus silencing and X chromosome inactivation. eLife 2020; 9:e54508. [PMID: 32379046 PMCID: PMC7282817 DOI: 10.7554/elife.54508] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 05/05/2020] [Indexed: 12/12/2022] Open
Abstract
The Xist lncRNA mediates X chromosome inactivation (XCI). Here we show that Spen, an Xist-binding repressor protein essential for XCI , binds to ancient retroviral RNA, performing a surveillance role to recruit chromatin silencing machinery to these parasitic loci. Spen loss activates a subset of endogenous retroviral (ERV) elements in mouse embryonic stem cells, with gain of chromatin accessibility, active histone modifications, and ERV RNA transcription. Spen binds directly to ERV RNAs that show structural similarity to the A-repeat of Xist, a region critical for Xist-mediated gene silencing. ERV RNA and Xist A-repeat bind the RRM domains of Spen in a competitive manner. Insertion of an ERV into an A-repeat deficient Xist rescues binding of Xist RNA to Spen and results in strictly local gene silencing in cis. These results suggest that Xist may coopt transposable element RNA-protein interactions to repurpose powerful antiviral chromatin silencing machinery for sex chromosome dosage compensation.
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Affiliation(s)
- Ava C Carter
- Center for Personal Dynamic Regulomes, Stanford UniversityStanfordUnited States
| | - Jin Xu
- Center for Personal Dynamic Regulomes, Stanford UniversityStanfordUnited States
| | - Meagan Y Nakamoto
- Department of Biochemistry, University of ColoradoBoulderUnited States
| | - Yuning Wei
- Center for Personal Dynamic Regulomes, Stanford UniversityStanfordUnited States
| | - Brian J Zarnegar
- Department of Dermatology, Stanford University School of MedicineStanfordUnited States
| | - Quanming Shi
- Center for Personal Dynamic Regulomes, Stanford UniversityStanfordUnited States
| | - James P Broughton
- Center for Personal Dynamic Regulomes, Stanford UniversityStanfordUnited States
| | - Ryan C Ransom
- Department of Surgery, Division of Plastic and Reconstructive Surgery, Stanford University School of MedicineStanfordUnited States
| | - Ankit Salhotra
- Department of Surgery, Division of Plastic and Reconstructive Surgery, Stanford University School of MedicineStanfordUnited States
| | - Surya D Nagaraja
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford UniversityStanfordUnited States
| | - Rui Li
- Center for Personal Dynamic Regulomes, Stanford UniversityStanfordUnited States
| | - Diana R Dou
- Center for Personal Dynamic Regulomes, Stanford UniversityStanfordUnited States
| | - Kathryn E Yost
- Center for Personal Dynamic Regulomes, Stanford UniversityStanfordUnited States
| | - Seung-Woo Cho
- Center for Personal Dynamic Regulomes, Stanford UniversityStanfordUnited States
| | - Anil Mistry
- Novartis Institute for Biomedical ResearchCambridgeUnited States
| | - Michael T Longaker
- Department of Surgery, Division of Plastic and Reconstructive Surgery, Stanford University School of MedicineStanfordUnited States
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford UniversityStanfordUnited States
| | - Paul A Khavari
- Department of Dermatology, Stanford University School of MedicineStanfordUnited States
| | - Robert T Batey
- Department of Biochemistry, University of ColoradoBoulderUnited States
| | - Deborah S Wuttke
- Department of Biochemistry, University of ColoradoBoulderUnited States
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford UniversityStanfordUnited States
- Department of Dermatology, Stanford University School of MedicineStanfordUnited States
- Howard Hughes Medical Institute, Stanford UniversityStanfordUnited States
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10
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Endogenous Retroviruses Activity as a Molecular Signature of Neurodevelopmental Disorders. Int J Mol Sci 2019; 20:ijms20236050. [PMID: 31801288 PMCID: PMC6928979 DOI: 10.3390/ijms20236050] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 11/26/2019] [Accepted: 11/28/2019] [Indexed: 12/20/2022] Open
Abstract
Human endogenous retroviruses (HERVs) are genetic elements resulting from relics of ancestral infection of germline cells, now recognized as cofactors in the etiology of several complex diseases. Here we present a review of findings supporting the role of the abnormal HERVs activity in neurodevelopmental disorders. The derailment of brain development underlies numerous neuropsychiatric conditions, likely starting during prenatal life and carrying on during subsequent maturation of the brain. Autism spectrum disorders, attention deficit hyperactivity disorders, and schizophrenia are neurodevelopmental disorders that arise clinically during early childhood or adolescence, currently attributed to the interplay among genetic vulnerability, environmental risk factors, and maternal immune activation. The role of HERVs in human embryogenesis, their intrinsic responsiveness to external stimuli, and the interaction with the immune system support the involvement of HERVs in the derailed neurodevelopmental process. Although definitive proofs that HERVs are involved in neurobehavioral alterations are still lacking, both preclinical models and human studies indicate that the abnormal expression of ERVs could represent a neurodevelopmental disorders-associated biological trait in affected individuals and their parents.
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11
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Gagnier L, Belancio VP, Mager DL. Mouse germ line mutations due to retrotransposon insertions. Mob DNA 2019; 10:15. [PMID: 31011371 PMCID: PMC6466679 DOI: 10.1186/s13100-019-0157-4] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 04/01/2019] [Indexed: 12/24/2022] Open
Abstract
Transposable element (TE) insertions are responsible for a significant fraction of spontaneous germ line mutations reported in inbred mouse strains. This major contribution of TEs to the mutational landscape in mouse contrasts with the situation in human, where their relative contribution as germ line insertional mutagens is much lower. In this focussed review, we provide comprehensive lists of TE-induced mouse mutations, discuss the different TE types involved in these insertional mutations and elaborate on particularly interesting cases. We also discuss differences and similarities between the mutational role of TEs in mice and humans.
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Affiliation(s)
- Liane Gagnier
- Terry Fox Laboratory, BC Cancer and Department of Medical Genetics, University of British Columbia, V5Z1L3, Vancouver, BC Canada
| | - Victoria P. Belancio
- Department of Structural and Cellular Biology, Tulane University School of Medicine, Tulane Cancer Center, Tulane Center for Aging, New Orleans, LA 70112 USA
| | - Dixie L. Mager
- Terry Fox Laboratory, BC Cancer and Department of Medical Genetics, University of British Columbia, V5Z1L3, Vancouver, BC Canada
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12
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Jung YD, Lee HE, Jo A, Hiroo I, Cha HJ, Kim HS. Activity analysis of LTR12C as an effective regulatory element of the RAE1 gene. Gene 2017; 634:22-28. [PMID: 28867566 DOI: 10.1016/j.gene.2017.08.037] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 08/24/2017] [Indexed: 10/18/2022]
Abstract
Ribonucleic acid export 1 (RAE1) plays an important role in the export of mature mRNAs from the nucleus to the cytoplasm. Long terminal repeats (LTRs) became integrated into the human genome during primate evolution. One such repeat element, LTR12C, lies within a predicted regulatory region located upstream of the RAE1 gene. We examined the transcriptional activity of LTR12C by using the luciferase assay, and showed that the tandem repeat region (TRR) located within LTR12C was required for its regulatory function. A bioinformatics analysis revealed that the LTR12C element had multiple transcription factor binding sites specific for nuclear transcription factor Y (NF-Y), and the promoter activity of LTR12C was significantly decreased after NF-Y knockdown. Additionally, we discovered novel data indicating that LTR12C was initially inserted into the gorilla genome. Taken together, our results reveal that the TRR of LTR12C has powerful regulatory activity due to its NF-Y binding sites, and the integration of the LTR12C element into the primate genome during evolution may have affected RAE1 transcription.
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Affiliation(s)
- Yi-Deun Jung
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience & Biotechnology, Daejeon 34141, Republic of Korea
| | - Hee-Eun Lee
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 609-735, Republic of Korea; Institute of Systems Biology, Pusan National University, Busan 46241, Republic of Korea
| | - Ara Jo
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 609-735, Republic of Korea; Institute of Systems Biology, Pusan National University, Busan 46241, Republic of Korea
| | - Imai Hiroo
- Molecular Biology Section, Department of Cellular and Molecular Biology, Primate Research Institute, Kyoto University, Inuyama, Aichi, Japan
| | - Hee-Jae Cha
- Department of Parasitology and Genetics, College of Medicine, Kosin University, Busan, Republic of Korea
| | - Heui-Soo Kim
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 609-735, Republic of Korea; Institute of Systems Biology, Pusan National University, Busan 46241, Republic of Korea.
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13
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Campos-Sánchez R, Cremona MA, Pini A, Chiaromonte F, Makova KD. Integration and Fixation Preferences of Human and Mouse Endogenous Retroviruses Uncovered with Functional Data Analysis. PLoS Comput Biol 2016; 12:e1004956. [PMID: 27309962 PMCID: PMC4911145 DOI: 10.1371/journal.pcbi.1004956] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 04/29/2016] [Indexed: 01/24/2023] Open
Abstract
Endogenous retroviruses (ERVs), the remnants of retroviral infections in the germ line, occupy ~8% and ~10% of the human and mouse genomes, respectively, and affect their structure, evolution, and function. Yet we still have a limited understanding of how the genomic landscape influences integration and fixation of ERVs. Here we conducted a genome-wide study of the most recently active ERVs in the human and mouse genome. We investigated 826 fixed and 1,065 in vitro HERV-Ks in human, and 1,624 fixed and 242 polymorphic ETns, as well as 3,964 fixed and 1,986 polymorphic IAPs, in mouse. We quantitated >40 human and mouse genomic features (e.g., non-B DNA structure, recombination rates, and histone modifications) in ±32 kb of these ERVs' integration sites and in control regions, and analyzed them using Functional Data Analysis (FDA) methodology. In one of the first applications of FDA in genomics, we identified genomic scales and locations at which these features display their influence, and how they work in concert, to provide signals essential for integration and fixation of ERVs. The investigation of ERVs of different evolutionary ages (young in vitro and polymorphic ERVs, older fixed ERVs) allowed us to disentangle integration vs. fixation preferences. As a result of these analyses, we built a comprehensive model explaining the uneven distribution of ERVs along the genome. We found that ERVs integrate in late-replicating AT-rich regions with abundant microsatellites, mirror repeats, and repressive histone marks. Regions favoring fixation are depleted of genes and evolutionarily conserved elements, and have low recombination rates, reflecting the effects of purifying selection and ectopic recombination removing ERVs from the genome. In addition to providing these biological insights, our study demonstrates the power of exploiting multiple scales and localization with FDA. These powerful techniques are expected to be applicable to many other genomic investigations.
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Affiliation(s)
- Rebeca Campos-Sánchez
- Genetics Graduate Program, The Huck Institutes of the Life Sciences, Penn State University, University Park, Pennsylvania, United States of America
| | - Marzia A. Cremona
- MOX—Modeling and Scientific Computing, Department of Mathematics, Politecnico di Milano, Milano, Italy
- Department of Statistics, Penn State University, University Park, Pennsylvania, United States of America
| | - Alessia Pini
- MOX—Modeling and Scientific Computing, Department of Mathematics, Politecnico di Milano, Milano, Italy
| | - Francesca Chiaromonte
- Department of Statistics, Penn State University, University Park, Pennsylvania, United States of America
- Center for Medical Genomics, The Huck Institutes of the Life Sciences, Penn State University, University Park, Pennsylvania, United States of America
| | - Kateryna D. Makova
- Center for Medical Genomics, The Huck Institutes of the Life Sciences, Penn State University, University Park, Pennsylvania, United States of America
- Department of Biology, Penn State University, University Park, Pennsylvania, United States of America
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14
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Soliai MM, Meyer SE, Udall JA, Elzinga DE, Hermansen RA, Bodily PM, Hart AA, Coleman CE. De novo genome assembly of the fungal plant pathogen Pyrenophora semeniperda. PLoS One 2014; 9:e87045. [PMID: 24475219 PMCID: PMC3903604 DOI: 10.1371/journal.pone.0087045] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 12/18/2013] [Indexed: 12/31/2022] Open
Abstract
Pyrenophora semeniperda (anamorph Drechslera campulata) is a necrotrophic fungal seed pathogen that has a wide host range within the Poaceae. One of its hosts is cheatgrass (Bromus tectorum), a species exotic to the United States that has invaded natural ecosystems of the Intermountain West. As a natural pathogen of cheatgrass, P. semeniperda has potential as a biocontrol agent due to its effectiveness at killing seeds within the seed bank; however, few genetic resources exist for the fungus. Here, the genome of P. semeniperda isolate assembled from sequence reads of 454 pyrosequencing is presented. The total assembly is 32.5 Mb and includes 11,453 gene models encoding putative proteins larger than 24 amino acids. The models represent a variety of putative genes that are involved in pathogenic pathways typically found in necrotrophic fungi. In addition, extensive rearrangements, including inter- and intrachromosomal rearrangements, were found when the P. semeniperda genome was compared to P. tritici-repentis, a related fungal species.
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Affiliation(s)
- Marcus M. Soliai
- Plant and Wildlife Sciences, Brigham Young University, Provo, Utah, United States of America
| | - Susan E. Meyer
- USDA Forest Service, Rocky Mountain Research Station, Shrub Sciences Laboratory, Provo, Utah, United States of America
| | - Joshua A. Udall
- Plant and Wildlife Sciences, Brigham Young University, Provo, Utah, United States of America
| | - David E. Elzinga
- Plant and Wildlife Sciences, Brigham Young University, Provo, Utah, United States of America
| | - Russell A. Hermansen
- Plant and Wildlife Sciences, Brigham Young University, Provo, Utah, United States of America
| | - Paul M. Bodily
- Plant and Wildlife Sciences, Brigham Young University, Provo, Utah, United States of America
| | - Aaron A. Hart
- Plant and Wildlife Sciences, Brigham Young University, Provo, Utah, United States of America
| | - Craig E. Coleman
- Plant and Wildlife Sciences, Brigham Young University, Provo, Utah, United States of America
- * E-mail:
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15
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Lehoczky JA, Thomas PE, Patrie KM, Owens KM, Villarreal LM, Galbraith K, Washburn J, Johnson CN, Gavino B, Borowsky AD, Millen KJ, Wakenight P, Law W, Van Keuren ML, Gavrilina G, Hughes ED, Saunders TL, Brihn L, Nadeau JH, Innis JW. A novel intergenic ETnII-β insertion mutation causes multiple malformations in polypodia mice. PLoS Genet 2013; 9:e1003967. [PMID: 24339789 PMCID: PMC3854779 DOI: 10.1371/journal.pgen.1003967] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Accepted: 10/04/2013] [Indexed: 11/28/2022] Open
Abstract
Mouse early transposon insertions are responsible for ∼10% of spontaneous mutant phenotypes. We previously reported the phenotypes and genetic mapping of Polypodia, (Ppd), a spontaneous, X-linked dominant mutation with profound effects on body plan morphogenesis. Our new data shows that mutant mice are not born in expected Mendelian ratios secondary to loss after E9.5. In addition, we refined the Ppd genetic interval and discovered a novel ETnII-β early transposon insertion between the genes for Dusp9 and Pnck. The ETn inserted 1.6 kb downstream and antisense to Dusp9 and does not disrupt polyadenylation or splicing of either gene. Knock-in mice engineered to carry the ETn display Ppd characteristic ectopic caudal limb phenotypes, showing that the ETn insertion is the Ppd molecular lesion. Early transposons are actively expressed in the early blastocyst. To explore the consequences of the ETn on the genomic landscape at an early stage of development, we compared interval gene expression between wild-type and mutant ES cells. Mutant ES cell expression analysis revealed marked upregulation of Dusp9 mRNA and protein expression. Evaluation of the 5′ LTR CpG methylation state in adult mice revealed no correlation with the occurrence or severity of Ppd phenotypes at birth. Thus, the broad range of phenotypes observed in this mutant is secondary to a novel intergenic ETn insertion whose effects include dysregulation of nearby interval gene expression at early stages of development. Mobile genetic elements, particularly early transposons (ETn), cause malformations by inserting within genes leading to disruption of exons, splicing or polyadenylation. Few mutagenic early transposon insertions have been found outside genes and the effects of such insertions on surrounding gene regulation is poorly understood. We discovered a novel intergenic ETnII-β insertion in the mouse mutant Polypodia (Ppd). We reproduced the mutant phenotype after engineering the mutation in wild-type cells with homologous recombination, proving that this early transposon insertion is Ppd. Mutant mice are not born in expected Mendelian ratios secondary to loss after E9.5. Embryonic stem cells from mutant mice show upregulated transcription of an adjacent gene, Dusp9. Thus, at an early and critical stage of development, dysregulated gene transcription is one consequence of the insertion mutation. DNA methylation of the ETn 5′ LTR is not correlated with phenotypic outcome in mutant mice. Polypodia is an example of an intergenic mobile element insertion in mice causing dramatic morphogenetic defects and fetal death.
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Affiliation(s)
- Jessica A. Lehoczky
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Peedikayil E. Thomas
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
- Pediatrics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Kevin M. Patrie
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Kailey M. Owens
- Pediatrics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Lisa M. Villarreal
- Pediatrics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Kenneth Galbraith
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Joe Washburn
- Biomedical Research Core Facilities, DNA Sequencing Core Lab, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Craig N. Johnson
- Biomedical Research Core Facilities, DNA Sequencing Core Lab, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Bryant Gavino
- Murine Molecular Constructs Laboratory-MMCL Mouse Biology Program, University of California, Davis, California, United States of America
| | - Alexander D. Borowsky
- University of California, Davis, Center for Comparative Medicine and Comprehensive Cancer Center, Department of Pathology and Laboratory Medicine, Davis, California, United States of America
| | - Kathleen J. Millen
- Division of Genetic Medicine, Department of Pediatrics, Seattle Children's Hospital, Seattle, Washington, United States of America
| | - Paul Wakenight
- Division of Genetic Medicine, Department of Pediatrics, Seattle Children's Hospital, Seattle, Washington, United States of America
| | - William Law
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Margaret L. Van Keuren
- Transgenic Animal Model Core Lab, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Galina Gavrilina
- Transgenic Animal Model Core Lab, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Elizabeth D. Hughes
- Transgenic Animal Model Core Lab, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Thomas L. Saunders
- Transgenic Animal Model Core Lab, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Lesil Brihn
- Department of Genetics, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Joseph H. Nadeau
- Pacific Northwest Research Institute, Seattle, Washington, United States of America
| | - Jeffrey W. Innis
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
- Pediatrics, University of Michigan, Ann Arbor, Michigan, United States of America
- * E-mail:
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16
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Lexa M, Kejnovský E, Steflová P, Konvalinová H, Vorlícková M, Vyskot B. Quadruplex-forming sequences occupy discrete regions inside plant LTR retrotransposons. Nucleic Acids Res 2013; 42:968-78. [PMID: 24106085 PMCID: PMC3902901 DOI: 10.1093/nar/gkt893] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Retrotransposons with long terminal repeats (LTR) form a significant proportion of eukaryotic genomes, especially in plants. They have gag and pol genes and several regulatory regions necessary for transcription and reverse transcription. We searched for potential quadruplex-forming sequences (PQSs) and potential triplex-forming sequences (PTSs) in 18 377 full-length LTR retrotransposons collected from 21 plant species. We found that PQSs were often located in LTRs, both upstream and downstream of promoters from which the whole retrotransposon is transcribed. Upstream-located guanine PQSs were dominant in the minus DNA strand, whereas downstream-located guanine PQSs prevailed in the plus strand, indicating their role both at transcriptional and post-transcriptional levels. Our circular dichroism spectroscopy measurements confirmed that these PQSs readily adopted guanine quadruplex structures-some of them were paralell-stranded, while others were anti-parallel-stranded. The PQS often formed doublets at a mutual distance of up to 400 bp. PTSs were most abundant in 3'UTR (but were also present in 5'UTR). We discuss the potential role of quadruplexes and triplexes as the regulators of various processes participating in LTR retrotransposon life cycle and as potential recombination sites during post-insertional retrotransposon-based genome rearrangements.
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Affiliation(s)
- Matej Lexa
- Department of Information Technologies, Faculty of Informatics, Masaryk University, Botanicka 68a, 60200 Brno, Czech Republic, Laboratory of Genome Dynamics, CEITEC - Central European Institute of Technology, Masaryk University, Zerotinovo nam 9, 60177 Brno, Czech Republic, Department of Plant Developmental Genetics, Institute of Biophysics ASCR, Kralovopolska 135, 61265 Brno, Czech Republic, Laboratory of CD Spectroscopy, CEITEC - Central European Institute of Technology, Masaryk University, Zerotinovo nam 9, 60177 Brno, Czech Republic and Department of CD Spectroscopy of Nucleic Acids, Institute of Biophysics ASCR, Kralovopolska 135, 61265 Brno, Czech Republic
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17
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Duan JJ, Qiu W, Xu SL, Wang B, Ye XZ, Ping YF, Zhang X, Bian XW, Yu SC. Strategies for isolating and enriching cancer stem cells: well begun is half done. Stem Cells Dev 2013; 22:2221-39. [PMID: 23540661 DOI: 10.1089/scd.2012.0613] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Cancer stem cells (CSCs) constitute a subpopulation of cancer cells that have the potential for self-renewal, multipotent differentiation, and tumorigenicity. Studies on CSC biology and CSC-targeted therapies depend on CSC isolation and/or enrichment methodologies. Scientists have conducted extensive research in this field since John Dick's group successfully isolated CSCs based on the expression of the CD34 and CD38 surface markers. Progress in CSC research has been greatly facilitated by the enrichment and isolation of these cells. In this review, we summarize the current strategies used in our and other laboratories for CSC isolation and enrichment, including methods based on stem cell surface markers, intracellular enzyme activity, the concentration of reactive oxygen species, the mitochondrial membrane potential, promoter-driven fluorescent protein expression, autofluorescence, suspension/adherent culture, cell division, the identification of side population cells, resistance to cytotoxic compounds or hypoxia, invasiveness/adhesion, immunoselection, and physical property. Although many challenges remain to be overcome, it is reasonable to believe that more reliable, efficient, and convenient methods will be developed in the near future.
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Affiliation(s)
- Jiang-Jie Duan
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University, Chongqing, People's Republic of China
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18
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Vlangos CN, Siuniak AN, Robinson D, Chinnaiyan AM, Lyons RH, Cavalcoli JD, Keegan CE. Next-generation sequencing identifies the Danforth's short tail mouse mutation as a retrotransposon insertion affecting Ptf1a expression. PLoS Genet 2013; 9:e1003205. [PMID: 23437000 PMCID: PMC3578742 DOI: 10.1371/journal.pgen.1003205] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2012] [Accepted: 11/14/2012] [Indexed: 11/29/2022] Open
Abstract
The semidominant Danforth's short tail (Sd) mutation arose spontaneously in the 1920s. The homozygous Sd phenotype includes severe malformations of the axial skeleton with an absent tail, kidney agenesis, anal atresia, and persistent cloaca. The Sd mutant phenotype mirrors features seen in human caudal malformation syndromes including urorectal septum malformation, caudal regression, VACTERL association, and persistent cloaca. The Sd mutation was previously mapped to a 0.9 cM region on mouse chromosome 2qA3. We performed Sanger sequencing of exons and intron/exon boundaries mapping to the Sd critical region and did not identify any mutations. We then performed DNA enrichment/capture followed by next-generation sequencing (NGS) of the critical genomic region. Standard bioinformatic analysis of paired-end sequence data did not reveal any causative mutations. Interrogation of reads that had been discarded because only a single end mapped correctly to the Sd locus identified an early transposon (ETn) retroviral insertion at the Sd locus, located 12.5 kb upstream of the Ptf1a gene. We show that Ptf1a expression is significantly upregulated in Sd mutant embryos at E9.5. The identification of the Sd mutation will lead to improved understanding of the developmental pathways that are misregulated in human caudal malformation syndromes. Birth defects are the leading cause of infant mortality in the United States, accounting for 1 in 5 infant deaths annually. Birth defects that affect development of the caudal portion of the embryo can include malformations of the spine, such as spina bifida, and malformations of the kidneys and lower gastrointestinal tract. Little is known regarding the genetic causes of human caudal birth defects. The Danforth's short tail (Sd) mouse shares many similarities with these caudal birth defects that occur in humans. In this manuscript, we used next-generation sequencing to identify the genetic cause of the Sd mouse phenotype. We found that the Sd mutation is a retrotransposon insertion that inappropriately turns on a nearby gene that is normally important for pancreas development. Future studies of Sd mice will help us understand the pathogenesis of caudal birth defects in humans.
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Affiliation(s)
- Christopher N. Vlangos
- Department of Pediatrics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Amanda N. Siuniak
- Department of Pediatrics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Dan Robinson
- Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Arul M. Chinnaiyan
- Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Robert H. Lyons
- Biological Chemistry Department, University of Michigan, Ann Arbor, Michigan, United States of America
- University of Michigan DNA Sequencing Core, University of Michigan, Ann Arbor, Michigan, United States of America
| | - James D. Cavalcoli
- Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Catherine E. Keegan
- Department of Pediatrics, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
- * E-mail:
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19
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Jung YD, Ha HS, Park SJ, Oh KB, Im GS, Kim TH, Seong HH, Kim HS. Identification and promoter analysis of PERV LTR subtypes in NIH-miniature pig. Mol Cells 2013; 35:99-105. [PMID: 23456331 PMCID: PMC3887905 DOI: 10.1007/s10059-013-2289-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2011] [Revised: 11/20/2012] [Accepted: 12/11/2012] [Indexed: 11/28/2022] Open
Abstract
Porcine endogenous retroviruses (PERVs) are integrated into the genomes of all pigs. Since some PERVs can also infect human cells, they represent a potential risk for xenotransplantation involving pig cells or organs. The long terminal repeat (LTR) elements of PERVs show promoter activity that can affect human functional genes; therefore, we examined these elements in this study. We detected several expressed LTRs in the NIH-miniature pig liver, among which we identified 9 different subtypes. When these LTRs were compared, distinct structures that contained several insertion and deletion (INDEL) events and tandem repeats were identified in the U3 region. The transcriptional activity of the 9 LTR subtypes was analyzed in the PK15 porcine cell line and in the HepG2 and Hep3B human liver cell lines, and transcriptional regulation was found to be different in the 3 cell lines. The D LTR subtype was found to have stronger promoter activity than all other types in 4 different human cell lines (HepG2, Hep3B, U251, and 293). Using computational approaches, the D type was shown to contain 4 transcription factor-binding sites distinct from those in the U3 regions of the other subtypes. Therefore, deletion mutants were constructed and examined by a transient transfection luciferase assay. The results of this analysis indicated that the binding site for the Hand1:E47 transcription factor might play a positive role in the transcriptional regulation of PERV LTR subtype D in human liver cell lines.
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Affiliation(s)
- Yi-Deun Jung
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 609-735,
Korea
| | | | - Sang-Je Park
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 609-735,
Korea
| | | | | | | | | | - Heui-Soo Kim
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 609-735,
Korea
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20
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Grabundzija I, Wang J, Sebe A, Erdei Z, Kajdi R, Devaraj A, Steinemann D, Szuhai K, Stein U, Cantz T, Schambach A, Baum C, Izsvák Z, Sarkadi B, Ivics Z. Sleeping Beauty transposon-based system for cellular reprogramming and targeted gene insertion in induced pluripotent stem cells. Nucleic Acids Res 2012; 41:1829-47. [PMID: 23275558 PMCID: PMC3561994 DOI: 10.1093/nar/gks1305] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The discovery of direct cell reprogramming and induced pluripotent stem (iPS) cell technology opened up new avenues for the application of non-viral, transposon-based gene delivery systems. The Sleeping Beauty (SB) transposon is highly advanced for versatile genetic manipulations in mammalian cells. We established iPS cell reprogramming of mouse embryonic fibroblasts and human foreskin fibroblasts by transposition of OSKM (Oct4, Sox2, Klf4 and c-Myc) and OSKML (OSKM + Lin28) expression cassettes mobilized by the SB100X hyperactive transposase. The efficiency of iPS cell derivation with SB transposon system was in the range of that obtained with retroviral vectors. Co-expression of the miRNA302/367 cluster together with OSKM significantly improved reprogramming efficiency and accelerated the temporal kinetics of reprogramming. The iPS cells displayed a stable karyotype, and hallmarks of pluripotency including expression of stem cell markers and the ability to differentiate into embryoid bodies in vitro. We demonstrate Cre recombinase-mediated exchange allowing simultaneous removal of the reprogramming cassette and targeted knock-in of an expression cassette of interest into the transposon-tagged locus in mouse iPS cells. This strategy would allow correction of a genetic defect by site-specific insertion of a therapeutic gene construct into ‘safe harbor’ sites in the genomes of autologous, patient-derived iPS cells.
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Affiliation(s)
- Ivana Grabundzija
- Max Delbrück Center for Molecular Medicine, Robert Rössle Strasse 10, 13125 Berlin, Germany
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21
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Lai CB, Mager DL. Role of runt-related transcription factor 3 (RUNX3) in transcription regulation of natural cytotoxicity receptor 1 (NCR1/NKp46), an activating natural killer (NK) cell receptor. J Biol Chem 2012; 287:7324-34. [PMID: 22253448 DOI: 10.1074/jbc.m111.306936] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Natural cytotoxicity receptor 1 (NCR1), also known as NKp46, is a natural killer (NK) lymphocyte-activating receptor. It is involved in major aspects of NK immune function and shows a high degree of lineage specificity in blood and bone marrow. The nature of its NK-restricted expression is not well understood. In this study, we confirm that human NCR1 NK-specific expression is achieved at the mRNA level. We found two key cis-regulatory elements in the immediate vicinity upstream of the gene. One element acts as an essential promoter, whereas the other acts as a tissue-dependent enhancer/repressor. This latter regulatory element contains a runt related-transcription factor (RUNX) recognition motif that preferentially binds RUNX3. Interfering with RUNX proteins using a dominant negative form results in decreased Ncr1 expression. RUNX3 overexpression had the opposite effect. These findings shed light on the role of RUNX3 in the control of an important NK-activating receptor.
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Affiliation(s)
- C Benjamin Lai
- Terry Fox Laboratory, British Columbia Cancer Agency and Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V5Z1L3, Canada
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22
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Sciamanna I, Vitullo P, Curatolo A, Spadafora C. A reverse transcriptase-dependent mechanism is essential for murine preimplantation development. Genes (Basel) 2011; 2:360-73. [PMID: 24710196 PMCID: PMC3924816 DOI: 10.3390/genes2020360] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Revised: 05/06/2011] [Accepted: 05/10/2011] [Indexed: 11/26/2022] Open
Abstract
LINE-1 (Long Interspersed Nuclear elements) and HERVs (Human Endogenous Retroviruses) are two families of retrotransposons which together account for about 28% of the human genome. Genes harbored within LINE-1 and HERV retrotransposons, particularly that encoding the reverse transcriptase (RT) enzyme, are generally expressed at low levels in differentiated cells, but their expression is up-regulated in embryonic tissues and transformed cells. Here we review evidence indicating that the LINE-1-encoded RT plays regulatory roles in early embryonic development. Indeed, antisense-mediated inhibition of expression of a highly expressed LINE-1 family in mouse zygotes caused developmental arrest at the two- or four-cell embryo stages. Development is also arrested when the embryo endogenous RT activity is pharmacologically inhibited by nevirapine, an RT inhibitor currently employed in AIDS treatment. The arrest of embryonic development is irreversible even after RT inhibition is removed and it is associated with subverted gene expression profiles. These data indicate an early requirement for LINE-1-encoded RT to support early developmental progression. Consistent with this, recent findings indicate that a reverse transcription wave is triggered in the zygote a few hours after fertilization and is propagated at least through the first two rounds of cell division. On the whole these findings suggest that reverse transcription is strictly required in early embryos as a key component of a novel RT-dependent mechanism that regulated the proper unfolding of the developmental program.
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Affiliation(s)
- Ilaria Sciamanna
- Italian National Institute of Health (ISS), Viale Regina Elena 299, 00161 Rome, Italy.
| | - Patrizia Vitullo
- Italian National Institute of Health (ISS), Viale Regina Elena 299, 00161 Rome, Italy.
| | - Angela Curatolo
- Italian National Institute of Health (ISS), Viale Regina Elena 299, 00161 Rome, Italy.
| | - Corrado Spadafora
- Italian National Institute of Health (ISS), Viale Regina Elena 299, 00161 Rome, Italy.
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23
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Expression of the human endogenous retrovirus (HERV) group HML-2/HERV-K does not depend on canonical promoter elements but is regulated by transcription factors Sp1 and Sp3. J Virol 2011; 85:3436-48. [PMID: 21248046 DOI: 10.1128/jvi.02539-10] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
After fixation in the human genome, human endogenous retroviruses (HERVs) are bona fide cellular genes despite their exogenous origin. To be able to spread within the germ line and the early embryo, the ancient retroviral promoters must have adapted to the requirements for expression in these cell types. We describe that in contrast to the case for current exogenous retroviruses, which replicate in specific somatic cells, the long terminal repeat (LTR) of the human endogenous retrovirus HERV-K acts as a TATA- and initiator element-independent promoter with a variable transcription start site. We present evidence that the HERV-K LTR is regulated by the transcription factors Sp1 and Sp3. Mutating specific GC boxes, which are binding sites for Sp proteins, and knocking down Sp1 and Sp3 by use of small interfering RNA (siRNA) significantly reduced the promoter activity. Binding of Sp1 and Sp3 to the promoter region was confirmed using electrophoretic mobility shift assays (EMSAs) and chromatin immunoprecipitation (ChIP). Our data explain why certain HERV-K proviruses have lost promoter competence. Since vertebrate promoters lacking canonical core promoter elements are common but poorly studied, understanding the HERV-K promoter not only will provide insight into the regulation of endogenous retroviruses but also can serve as a paradigm for understanding the regulation of this class of cellular genes.
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Park SJ, Huh JW, Kim DS, Ha HS, Jung YD, Ahn K, Oh KB, Park EW, Chang KT, Kim HS. Analysis of the molecular and regulatory properties of active porcine endogenous retrovirus gamma-1 long terminal repeats in kidney tissues of the NIH-Miniature pig. Mol Cells 2010; 30:319-25. [PMID: 20811814 DOI: 10.1007/s10059-010-0121-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2010] [Revised: 06/10/2010] [Accepted: 06/28/2010] [Indexed: 11/26/2022] Open
Abstract
The pig genome contains the gamma 1 family of porcine endogenous retroviruses (PERVs), which are a major obstacle to the development of successful xenotransplantation from pig to human. Long terminal repeats (LTRs) found in PERVs are known to be essential elements for the control of the transcriptional activity of single virus by different transcription factors (TFs). To identify transcribed PERV LTR elements, RT-PCR and DNA sequencing analyses were performed. Twenty-nine actively transcribed LTR elements were identified in the kidney tissues of the NIH-Miniature pig. These elements were divided into two major groups (I and II), and four minor groups (I-1, I-2, I-3, and II-1), by the presence of insertion and deletion (INDEL) sequences. Group I elements showed strong transcriptional activity compared to group II elements. Four different LTR elements (PL1, PL2, PL3, and PL4) as representative of the groups were analyzed by using a transient transfection assay. The regulation of their promoter activity was investigated by treatment with M.SssI (CpG DNA methyltransferase) and garcinol (histone acetyltransferase inhibitor). The transcriptional activity of PERV LTR elements was significantly reduced by treatment with M.SssI. These data indicate that transcribed PERV LTR elements harbor sufficient promoter activity to regulate the transcription of a single virus, and the transcriptional activity of PERV LTRs may be controlled by DNA methylation events.
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Affiliation(s)
- Sang-Je Park
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan, 609-735, Korea
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Identification of E74-like factor 1 (ELF1) as a transcriptional regulator of the Hox cofactor MEIS1. Exp Hematol 2010; 38:798-8, 808.e1-2. [PMID: 20600580 DOI: 10.1016/j.exphem.2010.06.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2010] [Revised: 06/01/2010] [Accepted: 06/04/2010] [Indexed: 11/22/2022]
Abstract
OBJECTIVE Myeloid ectropic viral integration site 1 (MEIS1) is a Hox cofactor known for its role in development and is strongly linked to normal and leukemic hematopoiesis. Although previous studies have focused on identifying protein partners of MEIS1 and its transcriptionally regulated targets, little is known about the upstream transcriptional regulators of this tightly regulated gene. Understanding the regulation of MEIS1 is important to understanding normal hematopoiesis and leukemogenesis. MATERIALS AND METHODS Here we describe our studies focusing on the evolutionary conserved putative MEIS1 promoter region. Phylogenetic sequence analysis and reporter assays in MEIS1-expressing (K562) and nonexpressing (HL60) leukemic cell line models were used to identify key regulatory regions and potential transcription factor binding sites within the candidate promoter region followed by functional and expression studies of one identified regulator in both cell lines and primary human cord blood and leukemia samples. RESULTS Chromatin status of MEIS1 promoter region is associated with MEIS1 expression. Truncation and mutation studies coupled with reporter assays revealed that a conserved ETS family member binding site located 289 bp upstream of the annotated human MEIS1 transcription start site is required for promoter activity. Of the three ETS family members tested, only ELF1 was enriched on the MEIS1 promoter as assessed by both electrophoretic mobility shift assay and chromatin immunoprecipitation experiments in K562. This finding was confirmed in MEIS1-expressing primary human samples. Moreover, small interfering RNA-mediated knockdown of ELF1 in K562 cells was associated with a decreased MEIS1 expression. CONCLUSIONS We conclude that the ETS transcription factor ELF1 is an important positive regulator of MEIS1 expression.
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Brunmeir R, Lagger S, Simboeck E, Sawicka A, Egger G, Hagelkruys A, Zhang Y, Matthias P, Miller WJ, Seiser C. Epigenetic regulation of a murine retrotransposon by a dual histone modification mark. PLoS Genet 2010; 6:e1000927. [PMID: 20442873 PMCID: PMC2861705 DOI: 10.1371/journal.pgen.1000927] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2009] [Accepted: 03/29/2010] [Indexed: 12/15/2022] Open
Abstract
Large fractions of eukaryotic genomes contain repetitive sequences of which the vast majority is derived from transposable elements (TEs). In order to inactivate those potentially harmful elements, host organisms silence TEs via methylation of transposon DNA and packaging into chromatin associated with repressive histone marks. The contribution of individual histone modifications in this process is not completely resolved. Therefore, we aimed to define the role of reversible histone acetylation, a modification commonly associated with transcriptional activity, in transcriptional regulation of murine TEs. We surveyed histone acetylation patterns and expression levels of ten different murine TEs in mouse fibroblasts with altered histone acetylation levels, which was achieved via chemical HDAC inhibition with trichostatin A (TSA), or genetic inactivation of the major deacetylase HDAC1. We found that one LTR retrotransposon family encompassing virus-like 30S elements (VL30) showed significant histone H3 hyperacetylation and strong transcriptional activation in response to TSA treatment. Analysis of VL30 transcripts revealed that increased VL30 transcription is due to enhanced expression of a limited number of genomic elements, with one locus being particularly responsive to HDAC inhibition. Importantly, transcriptional induction of VL30 was entirely dependent on the activation of MAP kinase pathways, resulting in serine 10 phosphorylation at histone H3. Stimulation of MAP kinase cascades together with HDAC inhibition led to simultaneous phosphorylation and acetylation (phosphoacetylation) of histone H3 at the VL30 regulatory region. The presence of the phosphoacetylation mark at VL30 LTRs was linked with full transcriptional activation of the mobile element. Our data indicate that the activity of different TEs is controlled by distinct chromatin modifications. We show that activation of a specific mobile element is linked to a dual epigenetic mark and propose a model whereby phosphoacetylation of histone H3 is crucial for full transcriptional activation of VL30 elements. The majority of genomic sequences in higher eukaryotes do not contain protein coding genes. Large fractions are covered by repetitive sequences, many of which are derived from transposable elements (TEs). These selfish genes, only containing sequences necessary for self-propagation, can multiply and change their location within the genome, threatening host genome integrity and provoking mutational bursts. Therefore host organisms have evolved a diverse repertoire of defence mechanisms to counteract and silence these genomic parasites. One way is to package DNA sequences containing TEs into transcriptionally inert heterochromatin, which is partly achieved via chemical modification of the packaging proteins associated with DNA, the histones. To better understand the contribution of histone acetylation in the activation of TEs, we treated mouse fibroblasts with a specific histone deacetylase inhibitor. By monitoring the expression of ten different types of murine mobile elements, we identified a defined subset of VL30 transposons specifically reactivated upon increased histone acetylation. Importantly, phosphorylation of histone H3, a modification that is triggered by stress, is required for acetylation-dependent activation of VL30 elements. We present a model where concomitant histone phosphorylation and acetylation cooperate in the transcriptional induction of VL30 elements.
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Affiliation(s)
- Reinhard Brunmeir
- Max F. Perutz Laboratories, Medical University of Vienna, Vienna Biocenter, Vienna, Austria
| | - Sabine Lagger
- Max F. Perutz Laboratories, Medical University of Vienna, Vienna Biocenter, Vienna, Austria
| | - Elisabeth Simboeck
- Max F. Perutz Laboratories, Medical University of Vienna, Vienna Biocenter, Vienna, Austria
| | - Anna Sawicka
- Max F. Perutz Laboratories, Medical University of Vienna, Vienna Biocenter, Vienna, Austria
| | - Gerda Egger
- Department of Clinical Pathology, Medical University of Vienna, Vienna, Austria
| | - Astrid Hagelkruys
- Max F. Perutz Laboratories, Medical University of Vienna, Vienna Biocenter, Vienna, Austria
| | - Yu Zhang
- Friedrich Miescher Institute for Biomedical Research, Novartis Research Foundation, Basel, Switzerland
| | - Patrick Matthias
- Friedrich Miescher Institute for Biomedical Research, Novartis Research Foundation, Basel, Switzerland
| | - Wolfgang J. Miller
- Laboratories of Genome Dynamics, Center of Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
- * E-mail: (CS); (WJM)
| | - Christian Seiser
- Max F. Perutz Laboratories, Medical University of Vienna, Vienna Biocenter, Vienna, Austria
- * E-mail: (CS); (WJM)
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Matsui T, Leung D, Miyashita H, Maksakova IA, Miyachi H, Kimura H, Tachibana M, Lorincz MC, Shinkai Y. Proviral silencing in embryonic stem cells requires the histone methyltransferase ESET. Nature 2010; 464:927-31. [PMID: 20164836 DOI: 10.1038/nature08858] [Citation(s) in RCA: 569] [Impact Index Per Article: 40.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2009] [Accepted: 01/16/2010] [Indexed: 12/13/2022]
Abstract
Endogenous retroviruses (ERVs), retrovirus-like elements with long terminal repeats, are widely dispersed in the euchromatic compartment in mammalian cells, comprising approximately 10% of the mouse genome. These parasitic elements are responsible for >10% of spontaneous mutations. Whereas DNA methylation has an important role in proviral silencing in somatic and germ-lineage cells, an additional DNA-methylation-independent pathway also functions in embryonal carcinoma and embryonic stem (ES) cells to inhibit transcription of the exogenous gammaretrovirus murine leukaemia virus (MLV). Notably, a recent genome-wide study revealed that ERVs are also marked by histone H3 lysine 9 trimethylation (H3K9me3) and H4K20me3 in ES cells but not in mouse embryonic fibroblasts. However, the role that these marks have in proviral silencing remains unexplored. Here we show that the H3K9 methyltransferase ESET (also called SETDB1 or KMT1E) and the Krüppel-associated box (KRAB)-associated protein 1 (KAP1, also called TRIM28) are required for H3K9me3 and silencing of endogenous and introduced retroviruses specifically in mouse ES cells. Furthermore, whereas ESET enzymatic activity is crucial for HP1 binding and efficient proviral silencing, the H4K20 methyltransferases Suv420h1 and Suv420h2 are dispensable for silencing. Notably, in DNA methyltransferase triple knockout (Dnmt1(-/-)Dnmt3a(-/-)Dnmt3b(-/-)) mouse ES cells, ESET and KAP1 binding and ESET-mediated H3K9me3 are maintained and ERVs are minimally derepressed. We propose that a DNA-methylation-independent pathway involving KAP1 and ESET/ESET-mediated H3K9me3 is required for proviral silencing during the period early in embryogenesis when DNA methylation is dynamically reprogrammed.
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Affiliation(s)
- Toshiyuki Matsui
- Experimental Research Center for Infectious Diseases, Institute for Virus Research, Kyoto University, 53 Shogoin, Kawara-cho, Sakyo-ku, Kyoto 606-8507, Japan
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Hotta A, Cheung AYL, Farra N, Garcha K, Chang WY, Pasceri P, Stanford WL, Ellis J. EOS lentiviral vector selection system for human induced pluripotent stem cells. Nat Protoc 2010; 4:1828-44. [PMID: 20010937 DOI: 10.1038/nprot.2009.201] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Generation of induced pluripotent stem (iPS) cells from patients has exciting applications for studying molecular mechanisms of diseases, screening drugs and ultimately for use in cell therapies. However, the low efficiency and heterogeneous nature of reprogramming is a major impediment to the generation of personalized iPS cell lines. We reported in Nature Methods (6, 370-376, 2009) the first selection system to enrich for reprogrammed human iPS cells. Using a lentiviral vector that specifically expresses the enhanced green fluorescence protein and puromycin resistance genes in pluripotent stem cells, it is now possible to mark and enrich for human iPS cell colonies expressing endogenous pluripotency markers. In this study, we describe a detailed protocol for the production of the pluripotent state-specific lentiviral vector and the selection system for the induction of healthy and disease-specific human iPS cells. Overall, preparation of the selection system takes 2 weeks, and the generation of human iPS cells takes approximately 2 months.
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Affiliation(s)
- Akitsu Hotta
- Developmental and Stem Cell Biology Program, SickKids, Toronto, Ontario, Canada
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Carstea AC, Pirity MK, Dinnyes A. Germline competence of mouse ES and iPS cell lines: Chimera technologies and genetic background. World J Stem Cells 2009; 1:22-9. [PMID: 21607104 PMCID: PMC3097913 DOI: 10.4252/wjsc.v1.i1.22] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2009] [Revised: 12/14/2009] [Accepted: 12/21/2009] [Indexed: 02/06/2023] Open
Abstract
In mice, gene targeting by homologous recombination continues to play an essential role in the understanding of functional genomics. This strategy allows precise location of the site of transgene integration and is most commonly used to ablate gene expression ("knock-out"), or to introduce mutant or modified alleles at the locus of interest ("knock-in"). The efficacy of producing live, transgenic mice challenges our understanding of this complex process, and of the factors which influence germline competence of embryonic stem cell lines. Increasingly, evidence indicates that culture conditions and in vitro manipulation can affect the germline-competence of Embryonic Stem cell (ES cell) lines by accumulation of chromosome abnormalities and/or epigenetic alterations of the ES cell genome. The effectiveness of ES cell derivation is greatly strain-dependent and it may also influence the germline transmission capability. Recent technical improvements in the production of germline chimeras have been focused on means of generating ES cells lines with a higher germline potential. There are a number of options for generating chimeras from ES cells (ES chimera mice); however, each method has its advantages and disadvantages. Recent developments in induced pluripotent stem (iPS) cell technology have opened new avenues for generation of animals from genetically modified somatic cells by means of chimera technologies. The aim of this review is to give a brief account of how the factors mentioned above are influencing the germline transmission capacity and the developmental potential of mouse pluripotent stem cell lines. The most recent methods for generating specifically ES and iPS chimera mice, including the advantages and disadvantages of each method are also discussed.
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Affiliation(s)
- Ana Claudia Carstea
- Ana Claudia Carstea, Genetic Reprogramming Group, Agricultural Biotechnology Center, Szent Györgyi A u. 4, H-2100 Gödöllö, Hungary
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Human endogenous retroviral long terminal repeat sequences as cell type-specific promoters in retroviral vectors. J Virol 2009; 83:12643-50. [PMID: 19741000 DOI: 10.1128/jvi.00858-09] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The human genome contains more than half a million human endogenous retrovirus (HERV) long terminal repeats (LTRs) that can be regarded as mobile regulatory modules. Many of these HERV LTRs have been recruited during evolution as transcriptional control elements for cellular gene expression. We have cloned LTR sequences from two HERV families, HERV-H and HERV-L, differing widely in their activity and tissue specificity into a murine leukemia virus (MLV)-based promoter conversion vector (ProCon). Various human cell lines were infected with the HERV-MLV hybrid vectors, and cell type-specific expression of the reporter gene was compared with the promoter specificity of the corresponding HERV LTRs in transient-transfection assays. Transcription start site analysis of HERV-MLV hybrid vectors revealed preferential use of the HERV promoter initiation site. Our data show that HERV LTRs function in the context of retroviral vectors in certain cell types and have the potential to be useful as cell type-specific promoters in vector construction.
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31
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Yeung ML, Bennasser Y, Watashi K, Le SY, Houzet L, Jeang KT. Pyrosequencing of small non-coding RNAs in HIV-1 infected cells: evidence for the processing of a viral-cellular double-stranded RNA hybrid. Nucleic Acids Res 2009; 37:6575-86. [PMID: 19729508 PMCID: PMC2770672 DOI: 10.1093/nar/gkp707] [Citation(s) in RCA: 191] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Small non-coding RNAs of 18-25 nt in length can regulate gene expression through the RNA interference (RNAi) pathway. To characterize small RNAs in HIV-1-infected cells, we performed linker-ligated cloning followed by high-throughput pyrosequencing. Here, we report the composition of small RNAs in HIV-1 productively infected MT4 T-cells. We identified several HIV-1 small RNA clones and a highly abundant small 18-nt RNA that is antisense to the HIV-1 primer-binding site (PBS). This 18-nt RNA apparently originated from the dsRNA hybrid formed by the HIV-1 PBS and the 3' end of the human cellular tRNAlys3. It was found to associate with the Ago2 protein, suggesting its possible function in the cellular RNAi machinery for targeting HIV-1.
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Affiliation(s)
- Man Lung Yeung
- Molecular Virology Section, Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892-0460, USA
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Rouhi A, Lai CB, Cheng TP, Takei F, Yokoyama WM, Mager DL. Evidence for high bi-allelic expression of activating Ly49 receptors. Nucleic Acids Res 2009; 37:5331-42. [PMID: 19605564 PMCID: PMC2760814 DOI: 10.1093/nar/gkp592] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Stochastic expression is a hallmark of the Ly49 family that encode the main MHC class-I-recognizing receptors of mouse natural killer (NK) cells. This highly polygenic and polymorphic family includes both activating and inhibitory receptor genes and is one of genome's fastest evolving loci. The inhibitory Ly49 genes are expressed in a stochastic mono-allelic manner, possibly under the control of an upstream bi-directional early promoter and show mono-allelic DNA methylation patterns. To date, no studies have directly addressed the transcriptional regulation of the activating Ly49 receptors. Our study shows differences in DNA methylation pattern between activating and inhibitory genes in C57BL/6 and F1 hybrid mouse strains. We also show a bias towards bi-allelic expression of the activating receptors based on allele-specific single-cell RT–PCR in F1 hybrid NK cells for Ly49d and Ly49H expression in Ly49h+/− mice. Furthermore, we have identified a region of high sequence identity with possible transcriptional regulatory capacity for the activating Ly49 genes. Our results also point to a likely difference between NK and T-cells in their ability to transcribe the activating Ly49 genes. These studies highlight the complex regulation of this rapidly evolving gene family of central importance in mouse NK cell function.
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Affiliation(s)
- Arefeh Rouhi
- The Terry Fox laboratory, British Columbia Cancer Agency, University of British Columbia, Vancouver, BC, Canada
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Hotta A, Cheung AYL, Farra N, Vijayaragavan K, Séguin CA, Draper JS, Pasceri P, Maksakova IA, Mager DL, Rossant J, Bhatia M, Ellis J. Isolation of human iPS cells using EOS lentiviral vectors to select for pluripotency. Nat Methods 2009; 6:370-6. [PMID: 19404254 DOI: 10.1038/nmeth.1325] [Citation(s) in RCA: 222] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2009] [Accepted: 03/30/2009] [Indexed: 01/13/2023]
Abstract
Induced pluripotent stem (iPS) cells may be of use in regenerative medicine. However, the low efficiency of reprogramming is a major impediment to the generation of patient-specific iPS cell lines. Here we report the first selection system for the isolation of human iPS cells. We developed the EOS (Early Transposon promoter and Oct-4 (Pou5f1) and Sox2 enhancers) lentiviral vector to specifically express in mouse and human embryonic stem cells but not in primary fibroblasts. The bicistronic EOS vector marked emerging mouse and human iPS cell colonies with EGFP, and we used puromycin selection to aid the isolation of iPS cell lines that expressed endogenous pluripotency markers. These lines differentiated into cell types from all three germ layers. Reporter expression was extinguished upon differentiation and therefore monitored the residual pluripotent cells that form teratomas. Finally, we used EOS selection to establish Rett syndrome-specific mouse and human iPS cell lines with known mutations in MECP2.
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Affiliation(s)
- Akitsu Hotta
- Developmental and Stem Cell Biology Program, Toronto, Ontario, Canada
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Lai CB, Zhang Y, Rogers SL, Mager DL. Creation of the two isoforms of rodent NKG2D was driven by a B1 retrotransposon insertion. Nucleic Acids Res 2009; 37:3032-43. [PMID: 19304755 PMCID: PMC2685100 DOI: 10.1093/nar/gkp174] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The mouse gene for the natural killer (NK) cell-activating receptor Nkg2d produces two protein isoforms, NKG2D-S and NKG2D-L, which differ by 13 amino acids at the N-terminus and have different signalling capabilities. These two isoforms are produced through differential splicing, but their regulation has not been investigated. In this study, we show that rat Nkg2d has the same splicing pattern as that of the mouse, and we mapped transcriptional start sites in both species. We found that the splice forms arise from alternative promoters and that the NKG2D-L promoter is derived from a rodent B1 retrotransposon that inserted before mouse–rat divergence. This B1 insertion is associated with loss of a nearby splice acceptor site that subsequently allowed creation of the short NKG2D isoform found in mouse but not human. Transient reporter assays indicate that the B1 element is a strong promoter with no inherent lymphoid tissue-specificity. We have also identified different binding sites for the ETS family member GABP within both the mouse and rat B1 elements that are necessary for high-promoter activity and for full Nkg2d-L expression. These findings demonstrate that a retroelement insertion has led to gene-regulatory change and functional diversification of rodent NKG2D.
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Affiliation(s)
- C Benjamin Lai
- Department of Medical Genetics, Terry Fox Laboratory, British Columbia Cancer Agency, University of British Columbia, Vancouver, BC, Canada
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Preferential epigenetic suppression of the autonomous MusD over the nonautonomous ETn mouse retrotransposons. Mol Cell Biol 2009; 29:2456-68. [PMID: 19273603 DOI: 10.1128/mcb.01383-08] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nonautonomous retrotransposon subfamilies are often amplified in preference to their coding-competent relatives. However, the mechanisms responsible for such replicative success are poorly understood. Here, we demonstrate that the autonomous MusD long terminal repeat (LTR) retrotransposons are subject to greater epigenetic silencing than their nonautonomous cousins, the early transposons (ETns), which are expressed at a 170-fold-higher level than MusD in mouse embryonic stem (ES) cells. We show that, in ES cells, 5' LTRs and the downstream region of MusD elements are more heavily methylated and are associated with less-activating and more-repressive histone modifications than the highly similar ETnII sequences. The internal region of MusD likely contributes to their silencing, as transgenes with MusD, compared to those with ETnII sequences, show reduced reporter gene expression and a higher level of repressive histone marks. Genomic distribution patterns of MusD and ETn elements are consistent with stronger selection against MusD elements within introns, suggesting that MusD-associated silencing marks can negatively impact genes. We propose a model in which nonautonomous retrotransposons may gain transcriptional and retrotranspositional advantages over their coding-competent counterparts by elimination of the CpG-rich retroviral sequence targeting the autonomous subfamilies for silencing.
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Fukai E, Dobrowolska AD, Madsen LH, Madsen EB, Umehara Y, Kouchi H, Hirochika H, Stougaard J. Transposition of a 600 thousand-year-old LTR retrotransposon in the model legume Lotus japonicus. PLANT MOLECULAR BIOLOGY 2008; 68:653-63. [PMID: 18802778 DOI: 10.1007/s11103-008-9397-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2008] [Accepted: 09/01/2008] [Indexed: 05/08/2023]
Abstract
We have identified a new Ty3-gypsy retrotransposon family named LORE2 (Lotus retrotransposon 2) and documented its activity in the model legume Lotus japonicus. Three new LORE2 insertions were found in symbiotic mutant alleles isolated from a plant population, established by tissue culture mediated transformation of the L. japonicus Gifu accession. Low transcriptional and transpositional activities of LORE2 in cultured cells suggested that the LORE2 transpositions identified in the three symbiotic mutants occurred in intact plants, not in callus. Tracing of the transpositional events identified two active LORE2 members in Gifu. One of them named LORE2A possesses a deletion in its coding region and polymorphisms between intraelemental LTRs. LORE2A is thus an aged element, estimated as 600 thousand years old. Our findings indicate that plant genomes carry more cryptic LTR retrotransposons, i.e., aged yet active, than estimated before, and that these cryptic elements may have contributed to plant genome dynamics, for example, the burst of transpositions reported in several plant species.
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Affiliation(s)
- Eigo Fukai
- National Institute of Agrobiological Science, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan.
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Abstract
Up to 10% of the mouse genome is comprised of endogenous retrovirus (ERV) sequences, and most represent the remains of ancient germ line infections. Our knowledge of the three distinct classes of ERVs is inversely correlated with their copy number, and their characterization has benefited from the availability of divergent wild mouse species and subspecies, and from ongoing analysis of the Mus genome sequence. In contrast to human ERVs, which are nearly all extinct, active mouse ERVs can still be found in all three ERV classes. The distribution and diversity of ERVs has been shaped by host-virus interactions over the course of evolution, but ERVs have also been pivotal in shaping the mouse genome by altering host genes through insertional mutagenesis, by adding novel regulatory and coding sequences, and by their co-option by host cells as retroviral resistance genes. We review mechanisms by which an adaptive coexistence has evolved. (Part of a multi-author review).
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Affiliation(s)
- C. Stocking
- Heinrich-Pette-Institute, Martinistrasse 52, 20251 Hamburg, Germany
| | - C. A. Kozak
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 4 Center Drive MSC 0460, Bethesda, Maryland, 20892-0460 USA
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Transcription of HERV-E and HERV-E-related sequences in malignant and non-malignant human haematopoietic cells. Virology 2008; 382:37-45. [PMID: 18929381 DOI: 10.1016/j.virol.2008.09.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2008] [Revised: 07/10/2008] [Accepted: 09/03/2008] [Indexed: 02/07/2023]
Abstract
Infection of a human T-cell leukaemia cell line (HSB-2) with HHV-6 led to the induction of exosome-like-particles attached to newly formed HHV-6 enveloped particles and to amplification of a 1642 bp molecule consisting of a partial human endogenous retrovirus (HERV)-E polymerase gene and repetitive sequences. We initiated an analysis of transcriptional patterns of predicted genes from HERV-E sequences in normal and malignant haematopoietic cells. Transcription patterns of regions corresponding to gag, pol and env genes at different chromosomal loci varied among cell types tested. Several specific transcripts were only observed in malignant haematopoietic cells and transcriptional activity varied among different malignant cell types. A transcript of 7.1 kb spanning the complete gag, pol and env gene region, originating from chromosome 8p23, was identified in normal peripheral blood cells and cells of the chronic myeloid leukaemia cell line K562. Our study describes new active HERV-E sequences and new loci throughout the human genome.
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Doering CJ, Rehak R, Bonfield S, Peloquin JB, Stell WK, Mema SC, Sauvé Y, McRory JE. Modified Ca(v)1.4 expression in the Cacna1f(nob2) mouse due to alternative splicing of an ETn inserted in exon 2. PLoS One 2008; 3:e2538. [PMID: 18596967 PMCID: PMC2432030 DOI: 10.1371/journal.pone.0002538] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2008] [Accepted: 05/15/2008] [Indexed: 01/19/2023] Open
Abstract
The Cacna1fnob2 mouse is reported to be a naturally occurring null mutation for the Cav1.4 calcium channel gene and the phenotype of this mouse is not identical to that of the targeted gene knockout model. We found two mRNA species in the Cacna1fnob2 mouse: approximately 90% of the mRNA represents a transcript with an in-frame stop codon within exon 2 of CACNA1F, while approximately 10% of the mRNA represents a transcript in which alternative splicing within the ETn element has removed the stop codon. This latter mRNA codes for full length Cav1.4 protein, detectable by Western blot analysis that is predicted to differ from wild type Cav1.4 protein in a region of approximately 22 amino acids in the N-terminal portion of the protein. Electrophysiological analysis with either mouse Cav1.4wt or Cav1.4nob2 cDNA revealed that the alternatively spliced protein does not differ from wild type with respect to activation and inactivation characteristics; however, while the wild type N-terminus interacted with filamin proteins in a biochemical pull-down experiment, the alternatively spliced N-terminus did not. The Cacna1fnob2 mouse electroretinogram displayed reduced b-wave and oscillatory potential amplitudes, and the retina was morphologically disorganized, with substantial reduction in thickness of the outer plexiform layer and sprouting of bipolar cell dendrites ectopically into the outer nuclear layer. Nevertheless, the spatial contrast sensitivity (optokinetic response) of Cacna1fnob2 mice was generally similar to that of wild type mice. These results suggest the Cacna1fnob2 mouse is not a CACNA1F knockout model. Rather, alternative splicing within the ETn element can lead to full-length Cav1.4 protein, albeit at reduced levels, and the functional Cav1.4 mutant may be incapable of interacting with cytoskeletal filamin proteins. These changes, do not alter the ability of the Cacna1fnob2 mouse to detect and follow moving sine-wave gratings compared to their wild type counterparts.
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Affiliation(s)
- Clinton J. Doering
- Hotchkiss Brain Institute, University of Calgary, Calgary, Canada
- Lions Centre for Retinal Degeneration Research, University of Calgary, Calgary, Canada
| | - Renata Rehak
- Hotchkiss Brain Institute, University of Calgary, Calgary, Canada
| | - Stephan Bonfield
- Cell Biology and Anatomy / Surgery, University of Calgary, Calgary, Canada
- Lions Centre for Retinal Degeneration Research, University of Calgary, Calgary, Canada
| | - Jean B. Peloquin
- Hotchkiss Brain Institute, University of Calgary, Calgary, Canada
- Lions Centre for Retinal Degeneration Research, University of Calgary, Calgary, Canada
| | - William K. Stell
- Hotchkiss Brain Institute, University of Calgary, Calgary, Canada
- Cell Biology and Anatomy / Surgery, University of Calgary, Calgary, Canada
- Lions Centre for Retinal Degeneration Research, University of Calgary, Calgary, Canada
| | - Silvina C. Mema
- Department of Ophthalmology, University of Alberta, Edmonton, Canada
| | - Yves Sauvé
- Department of Ophthalmology, University of Alberta, Edmonton, Canada
| | - John E. McRory
- Hotchkiss Brain Institute, University of Calgary, Calgary, Canada
- Lions Centre for Retinal Degeneration Research, University of Calgary, Calgary, Canada
- * E-mail:
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Genome-wide assessments reveal extremely high levels of polymorphism of two active families of mouse endogenous retroviral elements. PLoS Genet 2008; 4:e1000007. [PMID: 18454193 PMCID: PMC2265474 DOI: 10.1371/journal.pgen.1000007] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2007] [Accepted: 01/15/2008] [Indexed: 11/19/2022] Open
Abstract
Endogenous retroviral elements (ERVs) in mice are significant genomic mutagens, causing ∼10% of all reported spontaneous germ line mutations in laboratory strains. The majority of these mutations are due to insertions of two high copy ERV families, the IAP and ETn/MusD elements. This significant level of ongoing retrotranspositional activity suggests that inbred mice are highly variable in content of these two ERV groups. However, no comprehensive genome-wide studies have been performed to assess their level of polymorphism. Here we compared three test strains, for which sufficient genomic sequence is available, to each other and to the reference C57BL/6J genome and detected very high levels of insertional polymorphism for both ERV families, with an estimated false discovery rate of only 0.4%. Specifically, we found that at least 60% of IAP and 25% of ETn/MusD elements detected in any strain are absent in one or more of the other three strains. The polymorphic nature of a set of 40 ETn/MusD elements found within gene introns was confirmed using genomic PCR on DNA from a panel of mouse strains. For some cases, we detected gene-splicing abnormalities involving the ERV and obtained additional evidence for decreased gene expression in strains carrying the insertion. In total, we identified nearly 700 polymorphic IAP or ETn/MusD ERVs or solitary LTRs that reside in gene introns, providing potential candidates that may contribute to gene expression differences among strains. These extreme levels of polymorphism suggest that ERV insertions play a significant role in genetic drift of mouse lines. The laboratory mouse is the most widely used mammal for biological research. Hundreds of inbred mouse strains have been developed that vary in characteristics such as susceptibility to cancer or other diseases. There is much interest in uncovering differences between strains that result in different traits and, to aid this effort, millions of single nucleotide differences or polymorphisms between strains have been cataloged. To date, there has been less emphasis placed on other sources of genetic variation. In this study, we have conducted a genome-wide analysis to examine the level of polymorphism of mouse endogenous retroviral sequences (ERVs). ERVs are derived from infectious retroviruses that now exist in the genome and are inherited as part of chromosomes. Unlike in humans, genomic insertions of ERVs cause many new mutations in mice but their extent of variation between strains has been difficult to study because of their high copy numbers. By comparing genomic sequences of four common mouse strains, we found very high levels of polymorphism for two large active families of ERVs. Moreover, we documented nearly 700 polymorphic ERVs located within gene introns and found evidence that some of these affect gene transcript levels. This study demonstrates that ERV polymorphisms are a major source of genetic variability among mouse strains and likely contribute to strain-specific traits.
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Kano H, Kurahashi H, Toda T. Genetically regulated epigenetic transcriptional activation of retrotransposon insertion confers mouse dactylaplasia phenotype. Proc Natl Acad Sci U S A 2007; 104:19034-9. [PMID: 17984064 PMCID: PMC2141903 DOI: 10.1073/pnas.0705483104] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2007] [Indexed: 01/17/2023] Open
Abstract
Dactylaplasia, characterized by missing central digital rays, is an inherited mouse limb malformation that depends on two genetic loci. The first locus, Dac, is an insertional mutation around the dactylin gene that is inherited as a semidominant trait. The second locus is an unlinked modifier, mdac/Mdac, that is polymorphic among inbred strains. Mdac dominantly suppresses the dactylaplasia phenotype in mice carrying Dac. However, little is known about either locus or the nature of their interaction. Here we show that Dac is a LTR retrotransposon insertion caused by the type D mouse endogenous provirus element (MusD). This insertion exhibits different epigenetic states and spatiotemporally expresses depending on the mdac/Mdac modifier background. In dactylaplasia mutants (Dac/+ mdac/mdac), the LTRs of the insertion contained unmethylated CpGs and active chromatin. Furthermore, MusD elements expressed ectopically at the apical ectodermal ridge of limb buds, accompanying the dactylaplasia phenotype. On the other hand, in Dac mutants carrying Mdac (Dac/+ Mdac/mdac), the 5' LTR of the insertion was heavily methylated and enriched with inactive chromatin, correlating with inhibition of the dactylaplasia phenotype. Ectopic expression was not observed in the presence of Mdac, which we refined to a 9.4-Mb region on mouse chromosome 13. We report a pathogenic mutation caused by MusD. Our findings indicate that ectopic expression from the MusD insertion correlates with the dactylaplasia phenotype and that Mdac acts as a defensive factor to protect the host genome from pathogenic MusD insertions.
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Affiliation(s)
- Hiroki Kano
- *Division of Clinical Genetics, Department of Medical Genetics, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan; and
| | - Hiroki Kurahashi
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake 470-1192, Japan
| | - Tatsushi Toda
- *Division of Clinical Genetics, Department of Medical Genetics, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan; and
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RNA sequence analysis defines Dicer's role in mouse embryonic stem cells. Proc Natl Acad Sci U S A 2007; 104:18097-102. [PMID: 17989215 DOI: 10.1073/pnas.0709193104] [Citation(s) in RCA: 262] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Short RNA expression was analyzed from Dicer-positive and Dicer-knockout mouse embryonic [corrected] stem (ES) cells, using high-throughput pyrosequencing. A correlation of miRNA quantification with sequencing frequency estimates that there are 110,000 miRNAs per ES cell, the majority of which can be accounted for by six distinct miRNA loci. Four of these miRNA loci or their human homologues have demonstrated roles in cell cycle regulation or oncogenesis, suggesting that a major function of the miRNA pathway in ES cells may be to shape their distinct cell cycle. Forty-six previously uncharacterized miRNAs were identified, most of which are expressed at low levels and are less conserved than the set of known miRNAs. Low-abundance short RNAs matching all classes of repetitive elements were present in cells lacking Dicer, although the production of some SINE- and simple repeat-associated short RNAs appeared to be Dicer-dependent. These and other Dicer-dependent sequences resembled miRNAs. At a depth of sequencing that approaches the total number of 5' phosphorylated short RNAs per cell, miRNAs appeared to be Dicer's only substrate. The results presented suggest a model in which repeat-associated miRNAs serve as host defenses against repetitive elements, a function canonically ascribed to other classes of short RNA.
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Lerat E, Birot AM, Samarut J, Mey A. Maintenance in the Chicken Genome of the Retroviral-like cENS Gene Family Specifically Expressed in Early Embryos. J Mol Evol 2007; 65:215-27. [PMID: 17671751 DOI: 10.1007/s00239-007-9001-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2006] [Accepted: 05/18/2007] [Indexed: 02/05/2023]
Abstract
Embryonic stem (ES) cells are important developmental cells that appear very early during development and subsequently give rise to all the cell lineages of the future adult organism. In these cells a limited subset of transcription factors is expressed that are well conserved among species and essential for the fate of the stem cell. The transcriptome analysis of ES cells from chicken has revealed a gene family, cENS, that is specifically expressed in ES cells and in early embryos and is repressed during the differentiation process. This family is characterized by displaying retroviral structures and shares no homology with other species' genes. These characteristics are probably not restricted to the chicken genome and raise the question of whether similar genes are present and have been maintained in other species. We have examined the different copies of this gene in the sequenced chicken genome to investigate its dynamics and its evolution. We have distinguished two groups of cENS-related copies. The first group, resulting from recent transposition events, contains the transcribed ENS-1 and ENS-3 plus copies subjected to negative selection pressures. The second group contains degenerate copies that were integrated into the genome earlier. Comparison with copies previously isolated from three Galliformes showed that they are also subjected to selection pressures. We also detected numerous solo-LTRs containing the ENS-1 promoter that may control the expression of host genes. Taken together, these findings suggest a function sustained by a neogene of retroviral origin during the early stages of chicken development.
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Affiliation(s)
- Emmanuelle Lerat
- Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon, Université Lyon 1, CNRS, UMR 5558, Villeurbanne, France.
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Ramírez MA, Pericuesta E, Fernandez-Gonzalez R, Moreira P, Pintado B, Gutierrez-Adan A. Transcriptional and post-transcriptional regulation of retrotransposons IAP and MuERV-L affect pluripotency of mice ES cells. Reprod Biol Endocrinol 2006; 4:55. [PMID: 17090336 PMCID: PMC1636644 DOI: 10.1186/1477-7827-4-55] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2006] [Accepted: 11/08/2006] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND In the mouse, culture of embryonic stem (ES) cells may decrease their pluripotency and give rise to foetal abnormalities in recipient embryos. These abnormalities are frequently associated with both, chromosome abnormalities or epigenetic alteration of imprinting genes; however, little is known about the epigenetic stability of endogenous retrotransposable elements (REs). In our laboratory, we came across a R1 ES cell line, which at passage 27, lost the ability of germline transmission and started inducing the kinky tail phenotype in all chimeric animals produced with it. METHODS In order to investigate whether this phenotype was associated with chromosome alteration, inadvertent differentiation, or epigenetic modification, we characterized and compared this R1 ES cell line at passage 27 with an early passage and with a second ES cell line C57/CBAF1 generated in our laboratory. We assessed: i) karyotype; ii) expression of pluripotent and differentiation markers, iii) mRNA transcription by qRT-PCR of two REs, intracisternal-A particle (IAP) and murine endogenous-retrovirus-L (MuERV-L), and iv) methylation of IAP and MuERV-L. RESULTS The R1 ES cell at passage 27, presented normal morphology, karyotype, and expression of genetic markers characteristic of pluripotent; however, it was detected an altered mRNA transcription of sense and antisense RNA strands of both REs, concomitantly with an altered methylation pattern for the IAP element but not for MuERV-L. These results indicate that besides methylation, other post-transcriptional processes are involved in gene silencing of some REs; and that culture of ES cells may decrease their pluripotency by producing inadvertent alterations in the expression of REs without significantly affecting the morphology, chromosome structure, and expression of pluripotent or differentiation markers. CONCLUSION Inadvertent REs instability may have important consequences for the use of ES cells in transgenesis (chimera formation) or in cell therapy.
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Affiliation(s)
- Miguel A Ramírez
- Departamento de Reproducción Animal, INIA, Ctra. De La Coruña Km 5,9, Madrid 28040, España
| | - Eva Pericuesta
- Departamento de Reproducción Animal, INIA, Ctra. De La Coruña Km 5,9, Madrid 28040, España
| | | | - Pedro Moreira
- Departamento de Reproducción Animal, INIA, Ctra. De La Coruña Km 5,9, Madrid 28040, España
| | - Belen Pintado
- Departamento de Reproducción Animal, INIA, Ctra. De La Coruña Km 5,9, Madrid 28040, España
| | - Alfonso Gutierrez-Adan
- Departamento de Reproducción Animal, INIA, Ctra. De La Coruña Km 5,9, Madrid 28040, España
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