301
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Ipsaro JJ, O'Brien PA, Bhattacharya S, Palmer AG, Joshua-Tor L. Asterix/Gtsf1 links tRNAs and piRNA silencing of retrotransposons. Cell Rep 2021; 34:108914. [PMID: 33789107 DOI: 10.1016/j.celrep.2021.108914] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 01/15/2021] [Accepted: 03/05/2021] [Indexed: 02/05/2023] Open
Abstract
The Piwi-interacting RNA (piRNA) pathway safeguards genomic integrity by silencing transposable elements (transposons) in the germline. While Piwi is the central piRNA factor, others including Asterix/Gtsf1 have also been demonstrated to be critical for effective silencing. Here, using enhanced crosslinking and immunoprecipitation (eCLIP) with a custom informatic pipeline, we show that Asterix/Gtsf1 specifically binds tRNAs in cellular contexts. We determined the structure of mouse Gtsf1 by NMR spectroscopy and identified the RNA-binding interface on the protein's first zinc finger, which was corroborated by biochemical analysis as well as cryo-EM structures of Gtsf1 in complex with co-purifying tRNA. Consistent with the known dependence of long terminal repeat (LTR) retrotransposons on tRNA primers, we demonstrate that LTR retrotransposons are, in fact, preferentially de-repressed in Asterix mutants. Together, these findings link Asterix/Gtsf1, tRNAs, and LTR retrotransposon silencing and suggest that Asterix exploits tRNA dependence to identify transposon transcripts and promote piRNA silencing.
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Affiliation(s)
- Jonathan J Ipsaro
- Howard Hughes Medical Institute, W.M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Paul A O'Brien
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, 650 West 168th Street, New York, NY 10032, USA
| | | | - Arthur G Palmer
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, 650 West 168th Street, New York, NY 10032, USA
| | - Leemor Joshua-Tor
- Howard Hughes Medical Institute, W.M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA.
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302
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Jönsson ME, Garza R, Sharma Y, Petri R, Södersten E, Johansson JG, Johansson PA, Atacho DA, Pircs K, Madsen S, Yudovich D, Ramakrishnan R, Holmberg J, Larsson J, Jern P, Jakobsson J. Activation of endogenous retroviruses during brain development causes an inflammatory response. EMBO J 2021; 40:e106423. [PMID: 33644903 PMCID: PMC8090857 DOI: 10.15252/embj.2020106423] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 01/22/2021] [Accepted: 01/26/2021] [Indexed: 01/09/2023] Open
Abstract
Endogenous retroviruses (ERVs) make up a large fraction of mammalian genomes and are thought to contribute to human disease, including brain disorders. In the brain, aberrant activation of ERVs is a potential trigger for an inflammatory response, but mechanistic insight into this phenomenon remains lacking. Using CRISPR/Cas9‐based gene disruption of the epigenetic co‐repressor protein Trim28, we found a dynamic H3K9me3‐dependent regulation of ERVs in proliferating neural progenitor cells (NPCs), but not in adult neurons. In vivo deletion of Trim28 in cortical NPCs during mouse brain development resulted in viable offspring expressing high levels of ERVs in excitatory neurons in the adult brain. Neuronal ERV expression was linked to activated microglia and the presence of ERV‐derived proteins in aggregate‐like structures. This study demonstrates that brain development is a critical period for the silencing of ERVs and provides causal in vivo evidence demonstrating that transcriptional activation of ERV in neurons results in an inflammatory response.
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Affiliation(s)
- Marie E Jönsson
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Raquel Garza
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Yogita Sharma
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Rebecca Petri
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Erik Södersten
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Jenny G Johansson
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Pia A Johansson
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Diahann Am Atacho
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Karolina Pircs
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Sofia Madsen
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund, Sweden
| | - David Yudovich
- Division of Molecular Medicine and Gene Therapy, Department of Laboratory Medicine and Lund Stem Cell Center, Lund University, Lund, Sweden
| | | | - Johan Holmberg
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Jonas Larsson
- Division of Molecular Medicine and Gene Therapy, Department of Laboratory Medicine and Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Patric Jern
- Science for Life Laboratory, Department for Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Johan Jakobsson
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund, Sweden
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303
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The RNA m 6A reader YTHDC1 silences retrotransposons and guards ES cell identity. Nature 2021; 591:322-326. [PMID: 33658714 DOI: 10.1038/s41586-021-03313-9] [Citation(s) in RCA: 214] [Impact Index Per Article: 53.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 01/29/2021] [Indexed: 02/07/2023]
Abstract
The RNA modification N6-methyladenosine (m6A) has critical roles in many biological processes1,2. However, the function of m6A in the early phase of mammalian development remains poorly understood. Here we show that the m6A reader YT521-B homology-domain-containing protein 1 (YTHDC1) is required for the maintenance of mouse embryonic stem (ES) cells in an m6A-dependent manner, and that its deletion initiates cellular reprogramming to a 2C-like state. Mechanistically, YTHDC1 binds to the transcripts of retrotransposons (such as intracisternal A particles, ERVK and LINE1) in mouse ES cells and its depletion results in the reactivation of these silenced retrotransposons, accompanied by a global decrease in SETDB1-mediated trimethylation at lysine 9 of histone H3 (H3K9me3). We further demonstrate that YTHDC1 and its target m6A RNAs act upstream of SETDB1 to repress retrotransposons and Dux, the master inducer of the two-cell stage (2C)-like program. This study reveals an essential role for m6A RNA and YTHDC1 in chromatin modification and retrotransposon repression.
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304
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Yin Y, Liu XZ, He X, Zhou LQ. Exogenous Coronavirus Interacts With Endogenous Retrotransposon in Human Cells. Front Cell Infect Microbiol 2021; 11:609160. [PMID: 33732659 PMCID: PMC7959850 DOI: 10.3389/fcimb.2021.609160] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 01/18/2021] [Indexed: 01/08/2023] Open
Abstract
There is an increased global outbreak of diseases caused by coronaviruses affecting respiratory tracts of birds and mammals. Recent dangerous coronaviruses are MERS-CoV, SARS-CoV, and SARS-CoV-2, causing respiratory illness and even failure of several organs. However, profound impact of coronavirus on host cells remains elusive. In this study, we analyzed transcriptome of MERS-CoV, SARS-CoV, and SARS-CoV-2 infected human lung-derived cells, and observed that infection of these coronaviruses all induced increase of retrotransposon expression with upregulation of TET genes. Upregulation of retrotransposon was also observed in SARS-CoV-2 infected human intestinal organoids. Retrotransposon upregulation may lead to increased genome instability and enhanced expression of genes with readthrough from retrotransposons. Therefore, people with higher basal level of retrotransposon such as cancer patients and aged people may have increased risk of symptomatic infection. Additionally, we show evidence supporting long-term epigenetic inheritance of retrotransposon upregulation. We also observed chimeric transcripts of retrotransposon and SARS-CoV-2 RNA for potential human genome invasion of viral fragments, with the front and the rear part of SARS-CoV-2 genome being easier to form chimeric RNA. Thus, we suggest that primers and probes for nucleic acid detection should be designed in the middle of virus genome to identify live virus with higher probability. In summary, we propose our hypothesis that coronavirus invades human cells and interacts with retrotransposon, eliciting more severe symptoms in patients with underlying diseases. In the treatment of patients with coronavirus infection, it may be necessary to pay more attention to the potential harm contributed by retrotransposon dysregulation.
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Affiliation(s)
- Ying Yin
- Department of Physiology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Center for Genomics and Proteomics Research, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Key Laboratory of Drug Target Research and Pharmacodynamic Evaluation, Huazhong University of Science and Technology, Wuhan, China
| | - Xiao-zhao Liu
- Department of Physiology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Center for Genomics and Proteomics Research, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Key Laboratory of Drug Target Research and Pharmacodynamic Evaluation, Huazhong University of Science and Technology, Wuhan, China
| | - Ximiao He
- Department of Physiology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Center for Genomics and Proteomics Research, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Key Laboratory of Drug Target Research and Pharmacodynamic Evaluation, Huazhong University of Science and Technology, Wuhan, China
| | - Li-quan Zhou
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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305
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Ma X, Liu C, Kong X, Liu J, Zhang S, Liang S, Luan W, Cao X. Extensive profiling of the expressions of tRNAs and tRNA-derived fragments (tRFs) reveals the complexities of tRNA and tRF populations in plants. SCIENCE CHINA-LIFE SCIENCES 2021; 64:495-511. [DOI: 10.1007/s11427-020-1891-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 01/19/2021] [Indexed: 12/13/2022]
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306
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Tsai SY, Huang F. Acetyltransferase Enok regulates transposon silencing and piRNA cluster transcription. PLoS Genet 2021; 17:e1009349. [PMID: 33524038 PMCID: PMC7877743 DOI: 10.1371/journal.pgen.1009349] [Citation(s) in RCA: 2] [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: 01/08/2020] [Revised: 02/11/2021] [Accepted: 01/07/2021] [Indexed: 11/19/2022] Open
Abstract
The piRNA pathway is a highly conserved mechanism to repress transposon activation in the germline in Drosophila and mammals. This pathway starts from transcribing piRNA clusters to generate long piRNA precursors. The majority of piRNA clusters lack conventional promoters, and utilize heterochromatin- and HP1D/Rhino-dependent noncanonical mechanisms for transcription. However, information regarding the transcriptional regulation of piRNA clusters is limited. Here, we report that the Drosophila acetyltransferase Enok, which can activate transcription by acetylating H3K23, is critical for piRNA production from 54% of piRNA clusters including 42AB, the major piRNA source. Surprisingly, we found that Enok not only promotes rhino expression by acetylating H3K23, but also directly enhances transcription of piRNA clusters by facilitating Rhino recruitment. Taken together, our study provides novel insights into the regulation of noncanonical transcription at piRNA clusters and transposon silencing. Roughly half of our genome is composed of transposons. Activation of those transposons in the germline will result in severe DNA damages and infertility. The PIWI-interacting RNA (piRNA) pathway, which is highly conserved between mammals and flies, is a key mechanism to suppress transposon activation in the germline. Here, we identified the fly acetyltransferase Enok as a novel regulator functioning in the early steps of this pathway. We found that Enok can promote the expression of three genes involved in piRNA production by acetylating histone H3 lysine 23 (H3K23). We also demonstrated that Enok regulates the recruitment of Rhi, a factor critical for transcription initiation at piRNA-generating loci, to a subset of those loci, and therefore enhances their transcription. Our findings reveal an upstream regulator in the piRNA pathway and advance our understanding regarding the molecular mechanism of transposon silencing.
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Affiliation(s)
- Shih-Ying Tsai
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Fu Huang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
- * E-mail:
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307
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Sun D, Layman TS, Jeong H, Chatterjee P, Grogan K, Merritt JR, Maney DL, Yi SV. Genome-wide variation in DNA methylation linked to developmental stage and chromosomal suppression of recombination in white-throated sparrows. Mol Ecol 2021; 30:3453-3467. [PMID: 33421223 PMCID: PMC8359194 DOI: 10.1111/mec.15793] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 11/25/2020] [Accepted: 01/04/2021] [Indexed: 12/14/2022]
Abstract
Much of our knowledge on regulatory impacts of DNA methylation has come from laboratory‐bred model organisms, which may not exhibit the full extent of variation found in wild populations. Here, we investigated naturally‐occurring variation in DNA methylation in a wild avian species, the white‐throated sparrow (Zonotrichia albicollis). This species offers exceptional opportunities for studying the link between genetic differentiation and phenotypic traits because of a nonrecombining chromosome pair linked to both plumage and behavioural phenotypes. Using novel single‐nucleotide resolution methylation maps and gene expression data, we show that DNA methylation and the expression of DNA methyltransferases are significantly higher in adults than in nestlings. Genes for which DNA methylation varied between nestlings and adults were implicated in development and cell differentiation and were located throughout the genome. In contrast, differential methylation between plumage morphs was concentrated in the nonrecombining chromosome pair. Interestingly, a large number of CpGs on the nonrecombining chromosome, localized to transposable elements, have undergone dramatic loss of DNA methylation since the split of the ZAL2 and ZAL2m chromosomes. Changes in methylation predicted changes in gene expression for both chromosomes. In summary, we demonstrate changes in genome‐wide DNA methylation that are associated with development and with specific functional categories of genes in white‐throated sparrows. Moreover, we observe substantial DNA methylation reprogramming associated with the suppression of recombination, with implications for genome integrity and gene expression divergence. These results offer an unprecedented view of ongoing epigenetic reprogramming in a wild population. see also the Perspective by Jordan A. Anderson and Jenny Tung.
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Affiliation(s)
- Dan Sun
- School of Biological Sciences, Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, USA.,Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, USA
| | - Thomas S Layman
- School of Biological Sciences, Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, USA
| | - Hyeonsoo Jeong
- School of Biological Sciences, Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, USA
| | - Paramita Chatterjee
- School of Biological Sciences, Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, USA
| | - Kathleen Grogan
- Department of Psychology, Emory University, Atlanta, GA, USA
| | | | - Donna L Maney
- Department of Psychology, Emory University, Atlanta, GA, USA
| | - Soojin V Yi
- School of Biological Sciences, Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, USA
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308
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Kaur D, Agrahari M, Singh SS, Mandal PK, Bhattacharya A, Bhattacharya S. Transcriptomic analysis of Entamoeba histolytica reveals domain-specific sense strand expression of LINE-encoded ORFs with massive antisense expression of RT domain. Plasmid 2021; 114:102560. [PMID: 33482228 DOI: 10.1016/j.plasmid.2021.102560] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 12/29/2020] [Accepted: 12/31/2020] [Indexed: 11/29/2022]
Abstract
LINEs are retrotransposable elements found in diverse organisms. Their activity is kept in check by several mechanisms, including transcriptional silencing. Here we have analyzed the transcription status of LINE1 copies in the early-branching parasitic protist Entamoeba histolytica. Full-length EhLINE1 encodes ORF1, and ORF2 with reverse transcriptase (RT) and endonuclease (EN) domains. RNA-Seq analysis of EhLINE1 copies (both truncated and full-length) showed unique features. Firstly, although 20/41 transcribed copies were full-length, we failed to detect any full-length transcripts. Rather, sense-strand transcripts mapped to the functional domains- ORF1, RT and EN. Secondly, there was strong antisense transcription specifically from RT domain. No antisense transcripts were seen from ORF1. Antisense RT transcripts did not encode known functional peptides. They could possibly be involved in attenuating translation of RT domain, as we failed to detect ORF2p, whereas ORF1p was detectable. Lack of full-length transcripts and strong antisense RT expression may serve to limit EhLINE1 retrotransposition.
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Affiliation(s)
- Devinder Kaur
- School of Environmental Sciences, Jawaharlal Nehru University, India
| | - Mridula Agrahari
- School of Environmental Sciences, Jawaharlal Nehru University, India
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309
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Cambier L, Stachelek K, Triska M, Jubran R, Huang M, Li W, Zhang J, Li J, Cobrinik D. Extracellular vesicle-associated repetitive element DNAs as candidate osteosarcoma biomarkers. Sci Rep 2021; 11:94. [PMID: 33420117 PMCID: PMC7794510 DOI: 10.1038/s41598-020-77398-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 10/29/2020] [Indexed: 12/21/2022] Open
Abstract
Osteosarcoma (OS) is the most common malignant bone tumor in children and young adults. Despite that high-risk factors have been identified, no test for early detection is available. This study aimed to identify circulating nucleic acid sequences associated with serum extracellular vesicle (EV) preparations at the time of OS diagnosis, as a step towards an OS early detection assay. Sequencing of small nucleic acids extracted from serum EV preparations revealed increased representation of diverse repetitive element sequences in OS patient versus control sera. Analysis of a validation cohort using qPCR of PEG-precipitated EV preparations revealed the over-representation of HSATI, HSATII, LINE1-P1, and Charlie 3 at the DNA but not RNA level, with receiver operating characteristic (ROC) area under the curve (AUC) ≥ 0.90. HSATI and HSATII DNAs co-purified with EVs prepared by precipitation and size exclusion chromatography but not by exosome immunocapture, indicative of packaging in a non-exosomal complex. The consistent over-representation of EV-associated repetitive element DNA sequences suggests their potential utility as biomarkers for OS and perhaps other cancers.
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Affiliation(s)
- Linda Cambier
- The Vision Center and The Saban Research Institute, Children's Hospital Los Angeles, 4650 Sunset Blvd, MS163, Los Angeles, CA, 90027, USA
| | - Kevin Stachelek
- The Vision Center and The Saban Research Institute, Children's Hospital Los Angeles, 4650 Sunset Blvd, MS163, Los Angeles, CA, 90027, USA.,Cancer Biology and Genomics Program, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA
| | - Martin Triska
- The Vision Center and The Saban Research Institute, Children's Hospital Los Angeles, 4650 Sunset Blvd, MS163, Los Angeles, CA, 90027, USA
| | - Rima Jubran
- Division of Hematology/Oncology, Children's Hospital Los Angeles, Los Angeles, CA, 90027, USA
| | - Manyu Huang
- Henan Luoyang Orthopedic Hospital (Henan Provincial Orthopedic Hospital)/Henan Provincial Orthopedic Institute, 82 Qiming Road, Luoyang, 471002, Henan, China
| | - Wuyin Li
- Henan Luoyang Orthopedic Hospital (Henan Provincial Orthopedic Hospital)/Henan Provincial Orthopedic Institute, 82 Qiming Road, Luoyang, 471002, Henan, China
| | - Jianying Zhang
- Department of Biological Science, The University of Texas at El Paso, El Paso, TX, 79968, USA
| | - Jitian Li
- Henan Luoyang Orthopedic Hospital (Henan Provincial Orthopedic Hospital)/Henan Provincial Orthopedic Institute, 82 Qiming Road, Luoyang, 471002, Henan, China. .,Department of Biological Science, The University of Texas at El Paso, El Paso, TX, 79968, USA.
| | - David Cobrinik
- The Vision Center and The Saban Research Institute, Children's Hospital Los Angeles, 4650 Sunset Blvd, MS163, Los Angeles, CA, 90027, USA. .,Cancer Biology and Genomics Program, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA. .,Department of Ophthalmology and Roski Eye Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA. .,Department of Biochemistry and Molecular Medicine and Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA.
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310
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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: 33] [Impact Index Per Article: 8.3] [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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311
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Lee YS, Maple R, Dürr J, Dawson A, Tamim S, Del Genio C, Papareddy R, Luo A, Lamb JC, Amantia S, Sylvester AW, Birchler JA, Meyers BC, Nodine MD, Rouster J, Gutierrez-Marcos J. A transposon surveillance mechanism that safeguards plant male fertility during stress. NATURE PLANTS 2021; 7:34-41. [PMID: 33398155 DOI: 10.1038/s41477-020-00818-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 11/05/2020] [Indexed: 06/12/2023]
Abstract
Although plants are able to withstand a range of environmental conditions, spikes in ambient temperature can impact plant fertility causing reductions in seed yield and notable economic losses1,2. Therefore, understanding the precise molecular mechanisms that underpin plant fertility under environmental constraints is critical to safeguarding future food production3. Here, we identified two Argonaute-like proteins whose activities are required to sustain male fertility in maize plants under high temperatures. We found that MALE-ASSOCIATED ARGONAUTE-1 and -2 associate with temperature-induced phased secondary small RNAs in pre-meiotic anthers and are essential to controlling the activity of retrotransposons in male meiocyte initials. Biochemical and structural analyses revealed how male-associated Argonaute activity and its interaction with retrotransposon RNA targets is modulated through the dynamic phosphorylation of a set of highly conserved, surface-located serine residues. Our results demonstrate that an Argonaute-dependent, RNA-guided surveillance mechanism is critical in plants to sustain male fertility under environmentally constrained conditions, by controlling the mutagenic activity of transposons in male germ cells.
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Affiliation(s)
- Yang-Seok Lee
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Robert Maple
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Julius Dürr
- School of Life Sciences, University of Warwick, Coventry, UK
| | | | - Saleh Tamim
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA
| | - Charo Del Genio
- Centre for Fluid and Complex Systems, School of Computing, Electronics and Mathematics, Coventry University, Coventry, UK
| | - Ranjith Papareddy
- Division of Plant Sciences, University of Missouri, Columbia, MO, USA
| | - Anding Luo
- Department of Molecular Biology, University of Wyoming, Laramie, WY, USA
| | - Jonathan C Lamb
- Division of Biological Sciences, University of Missouri, Columbia, MO, USA
- BayerCrop Science Division, St. Louis, MO, USA
| | - Stefano Amantia
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Anne W Sylvester
- Department of Molecular Biology, University of Wyoming, Laramie, WY, USA
| | - James A Birchler
- Division of Biological Sciences, University of Missouri, Columbia, MO, USA
| | - Blake C Meyers
- Division of Plant Sciences, University of Missouri, Columbia, MO, USA
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Michael D Nodine
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
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312
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Tsusaka T, Fukuda K, Shimura C, Kato M, Shinkai Y. The fibronectin type-III (FNIII) domain of ATF7IP contributes to efficient transcriptional silencing mediated by the SETDB1 complex. Epigenetics Chromatin 2020; 13:52. [PMID: 33256805 PMCID: PMC7706265 DOI: 10.1186/s13072-020-00374-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 11/13/2020] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND The histone methyltransferase SETDB1 (also known as ESET) represses genes and various types of transposable elements, such as endogenous retroviruses (ERVs) and integrated exogenous retroviruses, through a deposition of trimethylation on lysine 9 of histone H3 (H3K9me3) in mouse embryonic stem cells (mESCs). ATF7IP (also known as MCAF1 or AM), a binding partner of SETDB1, regulates the nuclear localization and enzymatic activities of SETDB1 and plays a crucial role in SETDB1-mediated transcriptional silencing. In this study, we further dissected the ATF7IP function with its truncated mutants in Atf7ip knockout (KO) mESCs. RESULTS We demonstrated that the SETDB1-interaction region within ATF7IP is essential for ATF7IP-dependent SETDB1 nuclear localization and silencing of both ERVs and integrated retroviral transgenes, whereas its C-terminal fibronectin type-III (FNIII) domain is dispensable for both these functions; rather, it has a role in efficient silencing mediated by the SETDB1 complex. Proteomic analysis identified a number of FNIII domain-interacting proteins, some of which have a consensus binding motif. We showed that one of the FNIII domain-binding proteins, ZMYM2, was involved in the efficient silencing of a transgene by ATF7IP. RNA-seq analysis of Atf7ip KO and WT or the FNIII domain mutant of ATF7IP-rescued Atf7ip KO mESCs showed that the FNIII domain mutant re-silenced most de-repressed SETDB1/ATF7IP-targeted ERVs compared to the WT. However, the silencing activity of the FNIII domain mutant was weaker than that of the ATF7IP WT, and some of the de-repressed germ cell-related genes in Atf7ip KO mESCs were not silenced by the FNIII domain mutant. Such germ cell-related genes are targeted and silenced by the MAX/MGA complex, and MGA was also identified as another potential binding molecule of the ATF7IP FNIII domain in the proteomic analysis. This suggests that the FNIII domain of ATF7IP acts as a binding hub of ATF7IP-interacting molecules possessing a specific interacting motif we named FAM and contributes to one layer of the SETDB1/ATF7IP complex-mediated silencing mechanisms. CONCLUSIONS Our findings contributed to further understanding the function of ATF7IP in the SETDB1 complex, revealed the role of the FNIII domain of ATF7IP in transcriptional silencing, and suggested a potential underlying molecular mechanism for it.
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Affiliation(s)
- Takeshi Tsusaka
- Cellular Memory Laboratory, RIKEN Cluster for Pioneering Research, Wako, 351-0198, Japan.,Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Department of Orthopedic Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Kei Fukuda
- Cellular Memory Laboratory, RIKEN Cluster for Pioneering Research, Wako, 351-0198, Japan
| | - Chikako Shimura
- Cellular Memory Laboratory, RIKEN Cluster for Pioneering Research, Wako, 351-0198, Japan
| | - Masaki Kato
- Cellular Memory Laboratory, RIKEN Cluster for Pioneering Research, Wako, 351-0198, Japan. .,Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, 230-0045, Japan.
| | - Yoichi Shinkai
- Cellular Memory Laboratory, RIKEN Cluster for Pioneering Research, Wako, 351-0198, Japan.
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313
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Greve G, Schüler J, Grüning BA, Berberich B, Stomper J, Zimmer D, Gutenkunst L, Bönisch U, Meier R, Blagitko-Dorfs N, Grishina O, Pfeifer D, Weichenhan D, Plass C, Lübbert M. Decitabine Induces Gene Derepression on Monosomic Chromosomes: In Vitro and In Vivo Effects in Adverse-Risk Cytogenetics AML. Cancer Res 2020; 81:834-846. [PMID: 33203699 DOI: 10.1158/0008-5472.can-20-1430] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 08/21/2020] [Accepted: 11/12/2020] [Indexed: 11/16/2022]
Abstract
Hypomethylating agents (HMA) have become the backbone of nonintensive acute myeloid leukemia/myelodysplastic syndrome (AML/MDS) treatment, also by virtue of their activity in patients with adverse genetics, for example, monosomal karyotypes, often with losses on chromosome 7, 5, or 17. No comparable activity is observed with cytarabine, a cytidine analogue without DNA-hypomethylating properties. As evidence exists for compounding hypermethylation and gene silencing of hemizygous tumor suppressor genes (TSG), we thus hypothesized that this effect may preferentially be reversed by the HMAs decitabine and azacitidine. An unbiased RNA-sequencing approach was developed to interrogate decitabine-induced transcriptome changes in AML cell lines with or without a deletion of chromosomes 7q, 5q or 17p. HMA treatment preferentially upregulated several hemizygous TSG in this genomic region, significantly derepressing endogenous retrovirus (ERV)3-1, with promoter demethylation, enhanced chromatin accessibility, and increased H3K4me3 levels. Decitabine globally reactivated multiple transposable elements, with activation of the dsRNA sensor RIG-I and interferon regulatory factor (IRF)7. Induction of ERV3-1 and RIG-I mRNA was also observed during decitabine treatment in vivo in serially sorted peripheral blood AML blasts. In patient-derived monosomal karyotype AML murine xenografts, decitabine treatment resulted in superior survival rates compared with cytarabine. Collectively, these data demonstrate preferential gene derepression and ERV reactivation in AML with chromosomal deletions, providing a mechanistic explanation that supports the clinical observation of superiority of HMA over cytarabine in this difficult-to-treat patient group. SIGNIFICANCE: These findings unravel the molecular mechanism underlying the intriguing clinical activity of HMAs in AML/MDS patients with chromosome 7 deletions and other monosomal karyotypes.See related commentary by O'Hagan et al., p. 813.
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Affiliation(s)
- Gabriele Greve
- Department of Medicine I, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Julia Schüler
- Charles River Discovery Research Services Germany GmbH, Freiburg, Germany
| | - Björn A Grüning
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany
| | - Bettina Berberich
- Department of Medicine I, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Julia Stomper
- Department of Medicine I, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Dennis Zimmer
- Department of Medicine I, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Lea Gutenkunst
- Department of Medicine I, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Ulrike Bönisch
- Deep Sequencing Facility, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Ruth Meier
- Department of Medicine I, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Clinic for Pediatric and Adolescent Medicine Klinikum Karlsruhe, Karlsruhe, Germany
| | - Nadja Blagitko-Dorfs
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Olga Grishina
- Clinical Trials Unit, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Dietmar Pfeifer
- Department of Medicine I, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Dieter Weichenhan
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christoph Plass
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Michael Lübbert
- Department of Medicine I, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany. .,DKTK Partner Site Freiburg, German Cancer Research Center (DKFZ), Heidelberg, Germany
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314
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Apoptosis in the fetal testis eliminates developmentally defective germ cell clones. Nat Cell Biol 2020; 22:1423-1435. [DOI: 10.1038/s41556-020-00603-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 10/12/2020] [Indexed: 01/22/2023]
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315
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Bloom JC, Schimenti JC. Sexually dimorphic DNA damage responses and mutation avoidance in the mouse germline. Genes Dev 2020; 34:1637-1649. [PMID: 33184219 PMCID: PMC7706705 DOI: 10.1101/gad.341602.120] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 10/07/2020] [Indexed: 12/20/2022]
Abstract
In this study, Bloom and Schimenti examine the response of primordial germ cells to DNA damage. Using both environmental and genetic stresses, the authors reveal the importance of the G1 checkpoint in preventing accumulation of complex mutations in the germline, and the differentiation of the DNA damage response during germ cell development. Germ cells specified during fetal development form the foundation of the mammalian germline. These primordial germ cells (PGCs) undergo rapid proliferation, yet the germline is highly refractory to mutation accumulation compared with somatic cells. Importantly, while the presence of endogenous or exogenous DNA damage has the potential to impact PGCs, there is little known about how these cells respond to stressors. To better understand the DNA damage response (DDR) in these cells, we exposed pregnant mice to ionizing radiation (IR) at specific gestational time points and assessed the DDR in PGCs. Our results show that PGCs prior to sex determination lack a G1 cell cycle checkpoint. Additionally, the response to IR-induced DNA damage differs between female and male PGCs post-sex determination. IR of female PGCs caused uncoupling of germ cell differentiation and meiotic initiation, while male PGCs exhibited repression of piRNA metabolism and transposon derepression. We also used whole-genome single-cell DNA sequencing to reveal that genetic rescue of DNA repair-deficient germ cells (Fancm−/−) leads to increased mutation incidence and biases. Importantly, our work uncovers novel insights into how PGCs exposed to DNA damage can become developmentally defective, leaving only those genetically fit cells to establish the adult germline.
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Affiliation(s)
- Jordana C Bloom
- Department of Biomedical Sciences,, Cornell University, Ithaca, New York 14853, USA.,Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
| | - John C Schimenti
- Department of Biomedical Sciences,, Cornell University, Ithaca, New York 14853, USA.,Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
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316
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Tunbak H, Enriquez-Gasca R, Tie CHC, Gould PA, Mlcochova P, Gupta RK, Fernandes L, Holt J, van der Veen AG, Giampazolias E, Burns KH, Maillard PV, Rowe HM. The HUSH complex is a gatekeeper of type I interferon through epigenetic regulation of LINE-1s. Nat Commun 2020; 11:5387. [PMID: 33144593 PMCID: PMC7609715 DOI: 10.1038/s41467-020-19170-5] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 09/28/2020] [Indexed: 12/20/2022] Open
Abstract
The Human Silencing Hub (HUSH) complex is necessary for epigenetic repression of LINE-1 elements. We show that HUSH-depletion in human cell lines and primary fibroblasts leads to induction of interferon-stimulated genes (ISGs) through JAK/STAT signaling. This effect is mainly attributed to MDA5 and RIG-I sensing of double-stranded RNAs (dsRNAs). This coincides with upregulation of primate-conserved LINE-1s, as well as increased expression of full-length hominid-specific LINE-1s that produce bidirectional RNAs, which may form dsRNA. Notably, LTRs nearby ISGs are derepressed likely rendering these genes more responsive to interferon. LINE-1 shRNAs can abrogate the HUSH-dependent response, while overexpression of an engineered LINE-1 construct activates interferon signaling. Finally, we show that the HUSH component, MPP8 is frequently downregulated in diverse cancers and that its depletion leads to DNA damage. These results suggest that LINE-1s may drive physiological or autoinflammatory responses through dsRNA sensing and gene-regulatory roles and are controlled by the HUSH complex.
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Affiliation(s)
- Hale Tunbak
- Centre for Immunobiology, Blizard Institute, Queen Mary University of London, London, E1 2AT, UK
| | - Rocio Enriquez-Gasca
- Centre for Immunobiology, Blizard Institute, Queen Mary University of London, London, E1 2AT, UK
| | | | - Poppy A Gould
- Centre for Immunobiology, Blizard Institute, Queen Mary University of London, London, E1 2AT, UK
| | - Petra Mlcochova
- Department of Medicine, University of Cambridge, CB2 0AF, Cambridge, UK
| | - Ravindra K Gupta
- Department of Medicine, University of Cambridge, CB2 0AF, Cambridge, UK
| | - Liane Fernandes
- Centre for Immunobiology, Blizard Institute, Queen Mary University of London, London, E1 2AT, UK
| | - James Holt
- Centre for Immunobiology, Blizard Institute, Queen Mary University of London, London, E1 2AT, UK
| | - Annemarthe G van der Veen
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Leiden University Medical Centre, Department of Immunohematology and Blood Transfusion, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | | | - Kathleen H Burns
- Department of Pathology, John Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Pierre V Maillard
- Centre for Immunobiology, Blizard Institute, Queen Mary University of London, London, E1 2AT, UK
| | - Helen M Rowe
- Centre for Immunobiology, Blizard Institute, Queen Mary University of London, London, E1 2AT, UK.
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317
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Lefkopoulos S, Polyzou A, Derecka M, Bergo V, Clapes T, Cauchy P, Jerez-Longres C, Onishi-Seebacher M, Yin N, Martagon-Calderón NA, Potts KS, Klaeylé L, Liu F, Bowman TV, Jenuwein T, Mione MC, Trompouki E. Repetitive Elements Trigger RIG-I-like Receptor Signaling that Regulates the Emergence of Hematopoietic Stem and Progenitor Cells. Immunity 2020; 53:934-951.e9. [DOI: 10.1016/j.immuni.2020.10.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 06/23/2020] [Accepted: 09/30/2020] [Indexed: 02/06/2023]
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318
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Linker SB, Randolph-Moore L, Kottilil K, Qiu F, Jaeger BN, Barron J, Gage FH. Identification of bona fide B2 SINE retrotransposon transcription through single-nucleus RNA-seq of the mouse hippocampus. Genome Res 2020; 30:1643-1654. [PMID: 33122305 PMCID: PMC7605253 DOI: 10.1101/gr.262196.120] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 09/29/2020] [Indexed: 12/21/2022]
Abstract
Currently, researchers rely on generalized methods to quantify transposable element (TE) RNA expression, such as RT-qPCR and RNA-seq, that do not distinguish between TEs expressed from their own promoter (bona fide) and TEs that are transcribed from a neighboring gene promoter such as within an intron or exon. This distinction is important owing to the differing functional roles of TEs depending on whether they are independently transcribed. Here we report a simple strategy to examine bona fide TE expression, termed BonaFide-TEseq. This approach can be used with any template-switch based library such as Smart-seq2 or the single-cell 5' gene expression kit from 10x, extending its utility to single-cell RNA-sequencing. This approach does not require TE-specific enrichment, enabling the simultaneous examination of TEs and protein-coding genes. We show that TEs identified through BonaFide-TEseq are expressed from their own promoter, rather than captured as internal products of genes. We reveal the utility of BonaFide-TEseq in the analysis of single-cell data and show that short-interspersed nuclear elements (SINEs) show cell type-specific expression profiles in the mouse hippocampus. We further show that, in response to a brief exposure of home-cage mice to a novel stimulus, SINEs are activated in dentate granule neurons in a time course that is similar to that of protein-coding immediate early genes. This work provides a simple alternative approach to assess bona fide TE transcription at single-cell resolution and provides a proof-of-concept using this method to identify SINE activation in a context that is relevant for normal learning and memory.
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Affiliation(s)
- Sara B Linker
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Lynne Randolph-Moore
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Kalyani Kottilil
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Fan Qiu
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Baptiste N Jaeger
- Laboratory of Neural Plasticity, Faculty of Medicine and Science, Brain Research Institute, University of Zurich, 8057 Zurich, Switzerland
| | - Jerika Barron
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, California 94143, USA
| | - Fred H Gage
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
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319
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Posttranscriptional regulation of human endogenous retroviruses by RNA-binding motif protein 4, RBM4. Proc Natl Acad Sci U S A 2020; 117:26520-26530. [PMID: 33020268 DOI: 10.1073/pnas.2005237117] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The human genome encodes for over 1,500 RNA-binding proteins (RBPs), which coordinate regulatory events on RNA transcripts. Most studies of RBPs have concentrated on their action on host protein-encoding mRNAs, which constitute a minority of the transcriptome. A widely neglected subset of our transcriptome derives from integrated retroviral elements, termed endogenous retroviruses (ERVs), that comprise ∼8% of the human genome. Some ERVs have been shown to be transcribed under physiological and pathological conditions, suggesting that sophisticated regulatory mechanisms to coordinate and prevent their ectopic expression exist. However, it is unknown how broadly RBPs and ERV transcripts directly interact to provide a posttranscriptional layer of regulation. Here, we implemented a computational pipeline to determine the correlation of expression between individual RBPs and ERVs from single-cell or bulk RNA-sequencing data. One of our top candidates for an RBP negatively regulating ERV expression was RNA-binding motif protein 4 (RBM4). We used photoactivatable ribonucleoside-enhanced cross-linking and immunoprecipitation to demonstrate that RBM4 indeed bound ERV transcripts at CGG consensus elements. Loss of RBM4 resulted in an elevated transcript level of bound ERVs of the HERV-K and -H families, as well as increased expression of HERV-K envelope protein. We pinpointed RBM4 regulation of HERV-K to a CGG-containing element that is conserved in the LTRs of HERV-K-10, -K-11, and -K-20, and validated the functionality of this site using reporter assays. In summary, we systematically identified RBPs that may regulate ERV function and demonstrate a role for RBM4 in controlling ERV expression.
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320
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OneStopRNAseq: A Web Application for Comprehensive and Efficient Analyses of RNA-Seq Data. Genes (Basel) 2020; 11:genes11101165. [PMID: 33023248 PMCID: PMC7650687 DOI: 10.3390/genes11101165] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 09/22/2020] [Accepted: 09/29/2020] [Indexed: 01/21/2023] Open
Abstract
Over the past decade, a large amount of RNA sequencing (RNA-seq) data were deposited in public repositories, and more are being produced at an unprecedented rate. However, there are few open source tools with point-and-click interfaces that are versatile and offer streamlined comprehensive analysis of RNA-seq datasets. To maximize the capitalization of these vast public resources and facilitate the analysis of RNA-seq data by biologists, we developed a web application called OneStopRNAseq for the one-stop analysis of RNA-seq data. OneStopRNAseq has user-friendly interfaces and offers workflows for common types of RNA-seq data analyses, such as comprehensive data-quality control, differential analysis of gene expression, exon usage, alternative splicing, transposable element expression, allele-specific gene expression quantification, and gene set enrichment analysis. Users only need to select the desired analyses and genome build, and provide a Gene Expression Omnibus (GEO) accession number or Dropbox links to sequence files, alignment files, gene-expression-count tables, or rank files with the corresponding metadata. Our pipeline facilitates the comprehensive and efficient analysis of private and public RNA-seq data.
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321
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Host Gene Regulation by Transposable Elements: The New, the Old and the Ugly. Viruses 2020; 12:v12101089. [PMID: 32993145 PMCID: PMC7650545 DOI: 10.3390/v12101089] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 09/14/2020] [Accepted: 09/23/2020] [Indexed: 12/12/2022] Open
Abstract
The human genome has been under selective pressure to evolve in response to emerging pathogens and other environmental challenges. Genome evolution includes the acquisition of new genes or new isoforms of genes and changes to gene expression patterns. One source of genome innovation is from transposable elements (TEs), which carry their own promoters, enhancers and open reading frames and can act as ‘controlling elements’ for our own genes. TEs include LINE-1 elements, which can retrotranspose intracellularly and endogenous retroviruses (ERVs) that represent remnants of past retroviral germline infections. Although once pathogens, ERVs also represent an enticing source of incoming genetic material that the host can then repurpose. ERVs and other TEs have coevolved with host genes for millions of years, which has allowed them to become embedded within essential gene expression programmes. Intriguingly, these host genes are often subject to the same epigenetic control mechanisms that evolved to combat the TEs that now regulate them. Here, we illustrate the breadth of host gene regulation through TEs by focusing on examples of young (The New), ancient (The Old), and disease-causing (The Ugly) TE integrants.
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322
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Shadle SC, Bennett SR, Wong CJ, Karreman NA, Campbell AE, van der Maarel SM, Bass BL, Tapscott SJ. DUX4-induced bidirectional HSATII satellite repeat transcripts form intranuclear double-stranded RNA foci in human cell models of FSHD. Hum Mol Genet 2020; 28:3997-4011. [PMID: 31630170 DOI: 10.1093/hmg/ddz242] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 09/19/2019] [Accepted: 10/03/2019] [Indexed: 12/29/2022] Open
Abstract
The DUX4 transcription factor is normally expressed in the cleavage-stage embryo and regulates genes involved in embryonic genome activation. Misexpression of DUX4 in skeletal muscle, however, is toxic and causes facioscapulohumeral muscular dystrophy (FSHD). We recently showed DUX4-induced toxicity is due, in part, to the activation of the double-stranded RNA (dsRNA) response pathway and the accumulation of intranuclear dsRNA foci. Here, we determined the composition of DUX4-induced dsRNAs. We found that a subset of DUX4-induced dsRNAs originate from inverted Alu repeats embedded within the introns of DUX4-induced transcripts and from DUX4-induced dsRNA-forming intergenic transcripts enriched for endogenous retroviruses, Alu and LINE-1 elements. However, these repeat classes were also represented in dsRNAs from cells not expressing DUX4. In contrast, pericentric human satellite II (HSATII) repeats formed a class of dsRNA specific to the DUX4 expressing cells. Further investigation revealed that DUX4 can initiate the bidirectional transcription of normally heterochromatin-silenced HSATII repeats. DUX4-induced HSATII RNAs co-localized with DUX4-induced nuclear dsRNA foci and with intranuclear aggregation of EIF4A3 and ADAR1. Finally, gapmer-mediated knockdown of HSATII transcripts depleted DUX4-induced intranuclear ribonucleoprotein aggregates and decreased DUX4-induced cell death, suggesting that HSATII-formed dsRNAs contribute to DUX4 toxicity.
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Affiliation(s)
- Sean C Shadle
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.,Molecular and Cellular Biology Program, University of Washington, Seattle, WA 91805, USA
| | - Sean R Bennett
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Chao-Jen Wong
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Nancy A Karreman
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Amy E Campbell
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | | | - Brenda L Bass
- Department of Biochemistry, University of Utah, Salt Lake City, UT 84112, USA
| | - Stephen J Tapscott
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
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323
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GeneTEFlow: A Nextflow-based pipeline for analysing gene and transposable elements expression from RNA-Seq data. PLoS One 2020; 15:e0232994. [PMID: 32866155 PMCID: PMC7458328 DOI: 10.1371/journal.pone.0232994] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 08/02/2020] [Indexed: 11/19/2022] Open
Abstract
Transposable elements (TEs) are mobile genetic elements in eukaryotic genomes. Recent research highlights the important role of TEs in the embryogenesis, neurodevelopment, and immune functions. However, there is a lack of a one-stop and easy to use computational pipeline for expression analysis of both genes and locus-specific TEs from RNA-Seq data. Here, we present GeneTEFlow, a fully automated, reproducible and platform-independent workflow, for the comprehensive analysis of gene and locus-specific TEs expression from RNA-Seq data employing Nextflow and Docker technologies. This application will help researchers more easily perform integrated analysis of both gene and TEs expression, leading to a better understanding of roles of gene and TEs regulation in human diseases. GeneTEFlow is freely available at https://github.com/zhongw2/GeneTEFlow.
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324
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Panda K, Slotkin RK. Long-Read cDNA Sequencing Enables a "Gene-Like" Transcript Annotation of Transposable Elements. THE PLANT CELL 2020; 32:2687-2698. [PMID: 32647069 PMCID: PMC7474280 DOI: 10.1105/tpc.20.00115] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 06/11/2020] [Accepted: 06/25/2020] [Indexed: 05/05/2023]
Abstract
Transcript-based annotations of genes facilitate both genome-wide analyses and detailed single-locus research. In contrast, transposable element (TE) annotations are rudimentary, consisting of information only on TE location and type. The repetitiveness and limited annotation of TEs prevent the ability to distinguish between potentially functional expressed elements and degraded copies. To improve genome-wide TE bioinformatics, we performed long-read sequencing of cDNAs from Arabidopsis (Arabidopsis thaliana) lines deficient in multiple layers of TE repression. These uniquely mapping transcripts were used to identify the set of TEs able to generate polyadenylated RNAs and create a new transcript-based annotation of TEs that we have layered upon the existing high-quality community standard annotation. We used this annotation to reduce the bioinformatic complexity associated with multimapping reads from short-read RNA sequencing experiments, and we show that this improvement is expanded in a TE-rich genome such as maize (Zea mays). Our TE annotation also enables the testing of specific standing hypotheses in the TE field. We demonstrate that inaccurate TE splicing does not trigger small RNA production, and the cell more strongly targets DNA methylation to TEs that have the potential to make mRNAs. This work provides a transcript-based TE annotation for Arabidopsis and maize, which serves as a blueprint to reduce the bioinformatic complexity associated with repetitive TEs in any organism.
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Affiliation(s)
- Kaushik Panda
- Donald Danforth Plant Science Center, St. Louis, 63132 Missouri
| | - R Keith Slotkin
- Donald Danforth Plant Science Center, St. Louis, 63132 Missouri
- Division of Biological Sciences, University of Missouri, Columbia, 63132 Missouri
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325
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Gutzat R, Rembart K, Nussbaumer T, Hofmann F, Pisupati R, Bradamante G, Daubel N, Gaidora A, Lettner N, Donà M, Nordborg M, Nodine M, Mittelsten Scheid O. Arabidopsis shoot stem cells display dynamic transcription and DNA methylation patterns. EMBO J 2020; 39:e103667. [PMID: 32815560 PMCID: PMC7560203 DOI: 10.15252/embj.2019103667] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 07/15/2020] [Accepted: 07/27/2020] [Indexed: 12/18/2022] Open
Abstract
In plants, aerial organs originate continuously from stem cells in the center of the shoot apical meristem. Descendants of stem cells in the subepidermal layer are progenitors of germ cells, giving rise to male and female gametes. In these cells, mutations, including insertions of transposable elements or viruses, must be avoided to preserve genome integrity across generations. To investigate the molecular characteristics of stem cells in Arabidopsis, we isolated their nuclei and analyzed stage‐specific gene expression and DNA methylation in plants of different ages. Stem cell expression signatures are largely defined by developmental stage but include a core set of stem cell‐specific genes, among which are genes implicated in epigenetic silencing. Transiently increased expression of transposable elements in meristems prior to flower induction correlates with increasing CHG methylation during development and decreased CHH methylation, before stem cells enter the reproductive lineage. These results suggest that epigenetic reprogramming may occur at an early stage in this lineage and could contribute to genome protection in stem cells during germline development.
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Affiliation(s)
- Ruben Gutzat
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
| | - Klaus Rembart
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
| | - Thomas Nussbaumer
- Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Falko Hofmann
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
| | - Rahul Pisupati
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
| | - Gabriele Bradamante
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
| | - Nina Daubel
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
| | - Angelika Gaidora
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
| | - Nicole Lettner
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
| | - Mattia Donà
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
| | - Magnus Nordborg
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
| | - Michael Nodine
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
| | - Ortrun Mittelsten Scheid
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
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326
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Li Z, Hua X, Serra-Cardona A, Xu X, Gan S, Zhou H, Yang WS, Chen CL, Xu RM, Zhang Z. DNA polymerase α interacts with H3-H4 and facilitates the transfer of parental histones to lagging strands. SCIENCE ADVANCES 2020; 6:eabb5820. [PMID: 32923642 PMCID: PMC7449674 DOI: 10.1126/sciadv.abb5820] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 07/14/2020] [Indexed: 05/03/2023]
Abstract
How parental histones, the carriers of epigenetic modifications, are deposited onto replicating DNA remains poorly understood. Here, we describe the eSPAN method (enrichment and sequencing of protein-associated nascent DNA) in mouse embryonic stem (ES) cells and use it to detect histone deposition onto replicating DNA strands with a relatively small number of cells. We show that DNA polymerase α (Pol α), which synthesizes short primers for DNA synthesis, binds histone H3-H4 preferentially. A Pol α mutant defective in histone binding in vitro impairs the transfer of parental H3-H4 to lagging strands in both yeast and mouse ES cells. Last, dysregulation of both coding genes and noncoding endogenous retroviruses is detected in mutant ES cells defective in parental histone transfer. Together, we report an efficient eSPAN method for analysis of DNA replication-linked processes in mouse ES cells and reveal the mechanism of Pol α in parental histone transfer.
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Affiliation(s)
- Zhiming Li
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Pediatrics, Columbia University Medical Center, New York, NY 10032, USA
- Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA
| | - Xu Hua
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Pediatrics, Columbia University Medical Center, New York, NY 10032, USA
- Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA
| | - Albert Serra-Cardona
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Pediatrics, Columbia University Medical Center, New York, NY 10032, USA
- Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA
| | - Xiaowei Xu
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Pediatrics, Columbia University Medical Center, New York, NY 10032, USA
- Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA
| | - Songlin Gan
- National Laboratory of Biomacromolecules, Chinese Academy of Sciences Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- School of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hui Zhou
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Pediatrics, Columbia University Medical Center, New York, NY 10032, USA
- Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA
| | - Wen-Si Yang
- National Laboratory of Biomacromolecules, Chinese Academy of Sciences Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- School of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chun-long Chen
- Curie Institute, PSL Research University, CNRS UMR 3244, F-75005, Paris, France
- Sorbonne University, F-75005 Paris, France
| | - Rui-Ming Xu
- National Laboratory of Biomacromolecules, Chinese Academy of Sciences Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- School of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhiguo Zhang
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Pediatrics, Columbia University Medical Center, New York, NY 10032, USA
- Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA
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327
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Goodier JL, Soares AO, Pereira GC, DeVine LR, Sanchez L, Cole RN, García-Pérez JL. C9orf72-associated SMCR8 protein binds in the ubiquitin pathway and with proteins linked with neurological disease. Acta Neuropathol Commun 2020; 8:110. [PMID: 32678027 PMCID: PMC7364817 DOI: 10.1186/s40478-020-00982-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 06/26/2020] [Indexed: 02/08/2023] Open
Abstract
A pathogenic GGGCCC hexanucleotide expansion in the first intron/promoter region of the C9orf72 gene is the most common mutation associated with amyotrophic lateral sclerosis (ALS). The C9orf72 gene product forms a complex with SMCR8 (Smith-Magenis Syndrome Chromosome Region, Candidate 8) and WDR41 (WD Repeat domain 41) proteins. Recent studies have indicated roles for the complex in autophagy regulation, vesicle trafficking, and immune response in transgenic mice, however a direct connection with ALS etiology remains unclear. With the aim of increasing understanding of the multi-functional C9orf72-SMCR8-WDR41 complex, we determined by mass spectrometry analysis the proteins that directly associate with SMCR8. SMCR8 protein binds many components of the ubiquitin-proteasome system, and we demonstrate its poly-ubiquitination without obvious degradation. Evidence is also presented for localization of endogenous SMCR8 protein to cytoplasmic stress granules. However, in several cell lines we failed to reproduce previous observations that C9orf72 protein enters these granules. SMCR8 protein associates with many products of genes associated with various Mendelian neurological disorders in addition to ALS, implicating SMCR8-containing complexes in a range of neuropathologies. We reinforce previous observations that SMCR8 and C9orf72 protein levels are positively linked, and now show in vivo that SMCR8 protein levels are greatly reduced in brain tissues of C9orf72 gene expansion carrier individuals. While further study is required, these data suggest that SMCR8 protein level might prove a useful biomarker for the C9orf72 expansion in ALS.
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Affiliation(s)
- John L. Goodier
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Alisha O. Soares
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Gavin C. Pereira
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Lauren R. DeVine
- Mass Spectrometry and Proteomics Facility, Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Laura Sanchez
- GENYO. Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, Granada, Spain
| | - Robert N. Cole
- Mass Spectrometry and Proteomics Facility, Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Jose Luis García-Pérez
- GENYO. Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, Granada, Spain
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine (IGMM), University of Edinburgh, Western General Hospital, Edinburgh, UK
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328
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LaRocca TJ, Cavalier AN, Wahl D. Repetitive elements as a transcriptomic marker of aging: Evidence in multiple datasets and models. Aging Cell 2020; 19:e13167. [PMID: 32500641 PMCID: PMC7412685 DOI: 10.1111/acel.13167] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 04/21/2020] [Accepted: 05/05/2020] [Indexed: 12/27/2022] Open
Abstract
Transcriptomic markers of aging can be useful for studying age‐related processes and diseases. However, noncoding repetitive element (RE) transcripts, which may play an important role in aging, are commonly overlooked in transcriptome studies—and their potential as a transcriptomic marker of aging has not been evaluated. Here, we used multiple RNA‐seq datasets generated from human samples and Caenorhabditis elegans and found that most RE transcripts (a) accumulate progressively with aging; (b) can be used to accurately predict age; and (c) may be a good marker of biological age. The strong RE/aging correlations we observed are consistent with growing evidence that RE transcripts contribute directly to aging and disease.
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Affiliation(s)
- Thomas J. LaRocca
- Department of Health and Exercise Science Center for Healthy Aging Colorado State University Fort Collins CO USA
| | - Alyssa N. Cavalier
- Department of Health and Exercise Science Center for Healthy Aging Colorado State University Fort Collins CO USA
| | - Devin Wahl
- Department of Health and Exercise Science Center for Healthy Aging Colorado State University Fort Collins CO USA
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329
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Lanciano S, Cristofari G. Measuring and interpreting transposable element expression. Nat Rev Genet 2020; 21:721-736. [PMID: 32576954 DOI: 10.1038/s41576-020-0251-y] [Citation(s) in RCA: 205] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/19/2020] [Indexed: 12/21/2022]
Abstract
Transposable elements (TEs) are insertional mutagens that contribute greatly to the plasticity of eukaryotic genomes, influencing the evolution and adaptation of species as well as physiology or disease in individuals. Measuring TE expression helps to understand not only when and where TE mobilization can occur but also how this process alters gene expression, chromatin accessibility or cellular signalling pathways. Although genome-wide gene expression assays such as RNA sequencing include transposon-derived transcripts, most computational analytical tools discard or misinterpret TE-derived reads. Emerging approaches are improving the identification of expressed TE loci and helping to discriminate TE transcripts that permit TE mobilization from chimeric gene-TE transcripts or pervasive transcription. Here we review the main challenges associated with the detection of TE expression, including mappability, insertional and internal sequence polymorphisms, and the diversity of the TE transcriptional landscape, as well as the different experimental and computational strategies to solve them.
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330
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Bravo JI, Nozownik S, Danthi PS, Benayoun BA. Transposable elements, circular RNAs and mitochondrial transcription in age-related genomic regulation. Development 2020; 147:dev175786. [PMID: 32527937 PMCID: PMC10680986 DOI: 10.1242/dev.175786] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Our understanding of the molecular regulation of aging and age-related diseases is still in its infancy, requiring in-depth characterization of the molecular landscape shaping these complex phenotypes. Emerging classes of molecules with promise as aging modulators include transposable elements, circRNAs and the mitochondrial transcriptome. Analytical complexity means that these molecules are often overlooked, even though they exhibit strong associations with aging and, in some cases, may directly contribute to its progress. Here, we review the links between these novel factors and age-related phenotypes, and we suggest tools that can be easily incorporated into existing pipelines to better understand the aging process.
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Affiliation(s)
- Juan I Bravo
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
- Graduate Program in the Biology of Aging, University of Southern California, Los Angeles, CA 90089, USA
| | - Séverine Nozownik
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
- Magistère européen de Génétique, Université Paris Diderot-Paris 7, Paris 75014, France
| | - Prakroothi S Danthi
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Bérénice A Benayoun
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
- Neuroscience Graduate Program, University of Southern California, Los Angeles, CA 90089, USA
- USC Norris Comprehensive Cancer Center, Epigenetics and Gene Regulation, Los Angeles, CA 90089, USA
- USC Stem Cell Initiative, Los Angeles, CA 90089, USA
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331
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Pisano MP, Grandi N, Tramontano E. High-Throughput Sequencing is a Crucial Tool to Investigate the Contribution of Human Endogenous Retroviruses (HERVs) to Human Biology and Development. Viruses 2020; 12:E633. [PMID: 32545287 PMCID: PMC7354619 DOI: 10.3390/v12060633] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 06/07/2020] [Accepted: 06/10/2020] [Indexed: 01/19/2023] Open
Abstract
Human Endogenous retroviruses (HERVs) are remnants of ancient retroviral infections that represent a large fraction of our genome. Their transcriptional activity is finely regulated in early developmental stages and their expression is modulated in different cell types and tissues. Such activity has an impact on human physiology and pathology that is only partially understood up to date. Novel high-throughput sequencing tools have recently allowed for a great advancement in elucidating the various HERV expression patterns in different tissues as well as the mechanisms controlling their transcription, and overall, have helped in gaining better insights in an all-inclusive understanding of the impact of HERVs in biology of the host.
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Affiliation(s)
- Maria Paola Pisano
- Laboratory of Molecular Virology, Department of Life and Environmental Sciences, University of Cagliari, 09042 Cagliari, Italy; (M.P.P.); (N.G.)
| | - Nicole Grandi
- Laboratory of Molecular Virology, Department of Life and Environmental Sciences, University of Cagliari, 09042 Cagliari, Italy; (M.P.P.); (N.G.)
| | - Enzo Tramontano
- Laboratory of Molecular Virology, Department of Life and Environmental Sciences, University of Cagliari, 09042 Cagliari, Italy; (M.P.P.); (N.G.)
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, 09042 Cagliari, Italy
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332
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de Cubas AA, Dunker W, Zaninovich A, Hongo RA, Bhatia A, Panda A, Beckermann KE, Bhanot G, Ganesan S, Karijolich J, Rathmell WK. DNA hypomethylation promotes transposable element expression and activation of immune signaling in renal cell cancer. JCI Insight 2020; 5:137569. [PMID: 32493845 PMCID: PMC7308050 DOI: 10.1172/jci.insight.137569] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 04/29/2020] [Indexed: 12/20/2022] Open
Abstract
Recently, we reported that expression of endogenous retroviruses (ERVs) is associated with response to immune checkpoint blockade (ICB) in renal cell carcinoma (RCC). We show that decitabine, a DNA hypomethylating agent, activates transposable element (TE) expression (LINE1 and ERVs ERV3-2 and ERV4700) and antiviral signaling to potentially enhance response to ICB in kidney cancer cell lines and primary cells. KO of RIGI and MDA5 dsRNA sensors attenuated activation of antiviral signaling associated with DNA hypomethylation, and RIGI and MDA5 IPs showed increased ERV binding with decitabine treatment. Bioinformatic analyses showed the decitabine-induced signature could be associated with increased immune infiltration and response to ICB. Cytokine secretion induced by decitabine could modestly improve T cell activation and robustly enhanced T cell migration. In a small retrospective cohort of metastatic clear cell RCC (ccRCC) patients treated with anti-PD1/PDL1 blockade, activation of some antiviral genes was significantly higher in responders. Thus, we identified a potential strategy to induce TE expression through inhibition of DNA methylation in modulating T cell action via regulation of the innate antiviral pathway.
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Affiliation(s)
- Aguirre A. de Cubas
- Division of Hematology and Oncology, Department of Medicine, Vanderbilt-Ingram Cancer Center, and
| | - William Dunker
- Department of Pathology, Microbiology, and Immunology, Vanderbilt Center for Immunobiology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Andrew Zaninovich
- Division of Hematology and Oncology, Department of Medicine, Vanderbilt-Ingram Cancer Center, and
| | - Rachel A. Hongo
- Division of Hematology and Oncology, Department of Medicine, Vanderbilt-Ingram Cancer Center, and
| | - Anuj Bhatia
- Division of Hematology and Oncology, Department of Medicine, Vanderbilt-Ingram Cancer Center, and
| | - Anshuman Panda
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey, USA
| | - Kathryn E. Beckermann
- Division of Hematology and Oncology, Department of Medicine, Vanderbilt-Ingram Cancer Center, and
| | - Gyan Bhanot
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey, USA
- Department of Physics and Astronomy and
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey, USA
- Moores Cancer Center at UCSD Health, La Jolla, California, USA
| | - Shridar Ganesan
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey, USA
- Department of Medicine, Rutgers Robert Wood Johnson Medical School, Rutgers University, Piscataway, New Jersey, USA
| | - John Karijolich
- Department of Pathology, Microbiology, and Immunology, Vanderbilt Center for Immunobiology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - W. Kimryn Rathmell
- Division of Hematology and Oncology, Department of Medicine, Vanderbilt-Ingram Cancer Center, and
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333
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Yates-Stewart AD, Daron J, Wijeratne S, Shahid S, Edgington HA, Slotkin RK, Michel A. Soybean aphids adapted to host-plant resistance by down regulating putative effectors and up regulating transposable elements. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2020; 121:103363. [PMID: 32201218 DOI: 10.1016/j.ibmb.2020.103363] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 03/06/2020] [Accepted: 03/15/2020] [Indexed: 06/10/2023]
Abstract
In agricultural systems, crops equipped with host-plant resistance (HPR) have enhanced protection against pests, and are used as a safe and sustainable tool in pest management. In soybean, HPR can control the soybean aphid (Aphis glycines), but certain aphid populations have overcome this resistance (i.e., virulence). The molecular mechanisms underlying aphid virulence to HPR are unknown, but likely involve effector proteins that are secreted by aphids to modulate plant defenses. Another mechanism to facilitate adaptation is through the activity of transposable elements, which can become activated by stress. In this study, we performed RNA sequencing of virulent and avirulent soybean aphids fed susceptible or resistant (Rag1 + Rag2) soybean. Our goal was to better understand the molecular mechanisms underlying soybean aphid virulence. Our data showed that virulent aphids mostly down regulate putative effector genes relative to avirulent aphids, especially when aphids were fed susceptible soybean. Decreased expression of effectors may help evade HPR plant defenses. Virulent aphids also transcriptionally up regulate a diverse set of transposable elements and nearby genes, which is consistent with stress adaptation. Our work demonstrates two mechanisms of pest adaptation to resistance, and identifies effector gene targets for future functional testing.
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Affiliation(s)
| | - Josquin Daron
- CNRS, Centre National de la Recherche Scientifique, Montpellier, France
| | - Saranga Wijeratne
- The Ohio State University, Molecular and Cellular Imaging Center, OARDC, Wooster, OH, USA
| | - Saima Shahid
- Donald Danforth Plant Science Center, St, Louis, MO, USA
| | - Hilary A Edgington
- The Ohio State University, Department of Entomology, CFAES Wooster Campus, Wooster, OH, USA
| | - R Keith Slotkin
- Donald Danforth Plant Science Center, St, Louis, MO, USA; Division of Biological Sciences, University of Missouri, Columbia, MO, USA
| | - Andy Michel
- The Ohio State University, Center for Applied Plant Sciences, Wooster, OH, USA; The Ohio State University, Department of Entomology, CFAES Wooster Campus, Wooster, OH, USA.
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334
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poly(UG)-tailed RNAs in genome protection and epigenetic inheritance. Nature 2020; 582:283-288. [PMID: 32499657 PMCID: PMC8396162 DOI: 10.1038/s41586-020-2323-8] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 04/16/2020] [Indexed: 12/17/2022]
Abstract
Mobile genetic elements threaten genome integrity in all organisms. MUT-2/RDE-3 is a ribonucleotidyltransferase required for transposon silencing and RNA interference (RNAi) in C. elegans1–4. When tethered to RNAs in heterologous expression systems, RDE-3 can add long stretches of alternating non-templated uridine (U) and guanosine (G) ribonucleotides to the 3’ termini of these RNAs (poly(UG) or pUG tails)5. Here we show that, in its natural context in C. elegans, RDE-3 adds pUG tails to targets of RNAi, as well as to transposon RNAs. pUG tails with more than 16 perfectly alternating 3’ U and G nucleotides convert RNA fragments into agents of gene silencing. pUG tails promote gene silencing by recruiting RNA-dependent RNA polymerases (RdRPs), which use pUG-tailed RNAs (pUG RNAs) as templates to synthesize small interfering RNAs (siRNAs). Our results show that cycles of pUG RNA–templated siRNA synthesis and siRNA-directed mRNA pUGylation underlie dsRNA-directed transgenerational epigenetic inheritance in the C. elegans germline. We speculate that this pUG RNA/siRNA silencing loop allows parents to inoculate progeny against the expression of unwanted or parasitic genetic elements
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335
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Lynch-Sutherland CF, Chatterjee A, Stockwell PA, Eccles MR, Macaulay EC. Reawakening the Developmental Origins of Cancer Through Transposable Elements. Front Oncol 2020; 10:468. [PMID: 32432029 PMCID: PMC7214541 DOI: 10.3389/fonc.2020.00468] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 03/16/2020] [Indexed: 12/12/2022] Open
Abstract
Transposable elements (TEs) have an established role as important regulators of early human development, functioning as tissue-specific genes and regulatory elements. Functional TEs are highly active during early development, and interact with important developmental genes, some of which also function as oncogenes. Dedifferentiation is a hallmark of cancer, and is characterized by genetic and epigenetic changes that enable proliferation, self-renewal and a metabolism reminiscent of embryonic stem cells. There is also compelling evidence suggesting that the path to dedifferentiation in cancer can contribute to invasion and metastasis. TEs are frequently expressed in cancer, and recent work has identified a newly proposed mechanism involving extensive recruitment of TE-derived promoters to drive expression of oncogenes and subsequently promote oncogenesis—a process termed onco-exaptation. However, the mechanism by which this phenomenon occurs, and the extent to which it contributes to oncogenesis remains unknown. Initial hypotheses have proposed that onco-exaptation events are cancer-specific and arise randomly due to the dysregulated and hypomethylated state of cancer cells and abundance of TEs across the genome. However, we suspect that exaptation-like events may not just arise due to chance activation of novel regulatory relationships as proposed previously, but as a result of the reestablishment of early developmental regulatory relationships. Dedifferentiation in cancer is well-documented, along with expression of TEs. The known interactions between TEs and pluripotency factors such as NANOG and OCTt4 during early development, along with the expression of some placental-specific TE-derived transcripts in cancer support a possible link between TEs and dedifferentiation of tumor cells. Thus, we hypothesize that onco-exaptation events can be associated with the epigenetic reawakening of early developmental TEs to regulate expression of oncogenes and promote oncogenesis. We also suspect that activation of these early developmental regulatory TEs may promote dedifferentiation, although at this stage it is hard to predict whether TE activation is one of the initial drivers of dedifferentiation. We expect that developmental TE activation occurs as a result of the establishment of an epigenetic landscape in cancer that resembles that of early development and that developmental TE activation may also enable cancers to exploit early developmental pathways, repurposing them to promote malignancy.
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Affiliation(s)
| | - Aniruddha Chatterjee
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand
| | - Peter A Stockwell
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Michael R Eccles
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand
| | - Erin C Macaulay
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
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336
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Marasca F, Gasparotto E, Polimeni B, Vadalà R, Ranzani V, Bodega B. The Sophisticated Transcriptional Response Governed by Transposable Elements in Human Health and Disease. Int J Mol Sci 2020; 21:ijms21093201. [PMID: 32366056 PMCID: PMC7247572 DOI: 10.3390/ijms21093201] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 04/29/2020] [Accepted: 04/29/2020] [Indexed: 01/15/2023] Open
Abstract
Transposable elements (TEs), which cover ~45% of the human genome, although firstly considered as “selfish” DNA, are nowadays recognized as driving forces in eukaryotic genome evolution. This capability resides in generating a plethora of sophisticated RNA regulatory networks that influence the cell type specific transcriptome in health and disease. Indeed, TEs are transcribed and their RNAs mediate multi-layered transcriptional regulatory functions in cellular identity establishment, but also in the regulation of cellular plasticity and adaptability to environmental cues, as occurs in the immune response. Moreover, TEs transcriptional deregulation also evolved to promote pathogenesis, as in autoimmune and inflammatory diseases and cancers. Importantly, many of these findings have been achieved through the employment of Next Generation Sequencing (NGS) technologies and bioinformatic tools that are in continuous improvement to overcome the limitations of analyzing TEs sequences. However, they are highly homologous, and their annotation is still ambiguous. Here, we will review some of the most recent findings, questions and improvements to study at high resolution this intriguing portion of the human genome in health and diseases, opening the scenario to novel therapeutic opportunities.
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Affiliation(s)
- Federica Marasca
- Fondazione INGM, Istituto Nazionale di Genetica Molecolare “Enrica e Romeo Invernizzi”, 20122 Milan, Italy; (F.M.); (E.G.); (B.P.); (R.V.); (V.R.)
| | - Erica Gasparotto
- Fondazione INGM, Istituto Nazionale di Genetica Molecolare “Enrica e Romeo Invernizzi”, 20122 Milan, Italy; (F.M.); (E.G.); (B.P.); (R.V.); (V.R.)
| | - Benedetto Polimeni
- Fondazione INGM, Istituto Nazionale di Genetica Molecolare “Enrica e Romeo Invernizzi”, 20122 Milan, Italy; (F.M.); (E.G.); (B.P.); (R.V.); (V.R.)
| | - Rebecca Vadalà
- Fondazione INGM, Istituto Nazionale di Genetica Molecolare “Enrica e Romeo Invernizzi”, 20122 Milan, Italy; (F.M.); (E.G.); (B.P.); (R.V.); (V.R.)
- Translational and Molecular Medicine, DIMET, University of Milan-Bicocca, 20900 Monza, Italy
| | - Valeria Ranzani
- Fondazione INGM, Istituto Nazionale di Genetica Molecolare “Enrica e Romeo Invernizzi”, 20122 Milan, Italy; (F.M.); (E.G.); (B.P.); (R.V.); (V.R.)
| | - Beatrice Bodega
- Fondazione INGM, Istituto Nazionale di Genetica Molecolare “Enrica e Romeo Invernizzi”, 20122 Milan, Italy; (F.M.); (E.G.); (B.P.); (R.V.); (V.R.)
- Correspondence:
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Corrêa RL, Sanz-Carbonell A, Kogej Z, Müller SY, Ambrós S, López-Gomollón S, Gómez G, Baulcombe DC, Elena SF. Viral Fitness Determines the Magnitude of Transcriptomic and Epigenomic Reprograming of Defense Responses in Plants. Mol Biol Evol 2020; 37:1866-1881. [DOI: 10.1093/molbev/msaa091] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Abstract
Although epigenetic factors may influence the expression of defense genes in plants, their role in antiviral responses and the impact of viral adaptation and evolution in shaping these interactions are still poorly explored. We used two isolates of turnip mosaic potyvirus with varying degrees of adaptation to Arabidopsis thaliana to address these issues. One of the isolates was experimentally evolved in the plant and presented increased load and virulence relative to the ancestral isolate. The magnitude of the transcriptomic responses was larger for the evolved isolate and indicated a role of innate immunity systems triggered by molecular patterns and effectors in the infection process. Several transposable elements located in different chromatin contexts and epigenetic-related genes were also affected. Correspondingly, mutant plants having loss or gain of repressive marks were, respectively, more tolerant and susceptible to turnip mosaic potyvirus, with a more efficient response against the ancestral isolate. In wild-type plants, both isolates induced similar levels of cytosine methylation changes, including in and around transposable elements and stress-related genes. Results collectively suggested that apart from RNA silencing and basal immunity systems, DNA methylation and histone modification pathways may also be required for mounting proper antiviral defenses and that the effectiveness of this type of regulation strongly depends on the degree of viral adaptation to the host.
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Affiliation(s)
- Régis L Corrêa
- Instituto de Biología Integrativa de Sistemas (I2SysBio), Consejo Superior de Investigaciones Científicas (CSIC)—Universitat de València, Paterna, Valencia, Spain
- Department of Genetics, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Alejandro Sanz-Carbonell
- Instituto de Biología Integrativa de Sistemas (I2SysBio), Consejo Superior de Investigaciones Científicas (CSIC)—Universitat de València, Paterna, Valencia, Spain
| | - Zala Kogej
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
- Instituto de Biología Integrativa de Sistemas (I2SysBio), Consejo Superior de Investigaciones Científicas (CSIC)—Universitat de València, Paterna, Valencia, Spain
| | - Sebastian Y Müller
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Silvia Ambrós
- Instituto de Biología Integrativa de Sistemas (I2SysBio), Consejo Superior de Investigaciones Científicas (CSIC)—Universitat de València, Paterna, Valencia, Spain
| | - Sara López-Gomollón
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Gustavo Gómez
- Instituto de Biología Integrativa de Sistemas (I2SysBio), Consejo Superior de Investigaciones Científicas (CSIC)—Universitat de València, Paterna, Valencia, Spain
| | - David C Baulcombe
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Santiago F Elena
- Instituto de Biología Integrativa de Sistemas (I2SysBio), Consejo Superior de Investigaciones Científicas (CSIC)—Universitat de València, Paterna, Valencia, Spain
- The Santa Fe Institute, Santa Fe, NM
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338
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The UCSC repeat browser allows discovery and visualization of evolutionary conflict across repeat families. Mob DNA 2020; 11:13. [PMID: 32266012 PMCID: PMC7110667 DOI: 10.1186/s13100-020-00208-w] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 03/10/2020] [Indexed: 01/12/2023] Open
Abstract
Background Nearly half the human genome consists of repeat elements, most of which are retrotransposons, and many of which play important biological roles. However repeat elements pose several unique challenges to current bioinformatic analyses and visualization tools, as short repeat sequences can map to multiple genomic loci resulting in their misclassification and misinterpretation. In fact, sequence data mapping to repeat elements are often discarded from analysis pipelines. Therefore, there is a continued need for standardized tools and techniques to interpret genomic data of repeats. Results We present the UCSC Repeat Browser, which consists of a complete set of human repeat reference sequences derived from annotations made by the commonly used program RepeatMasker. The UCSC Repeat Browser also provides an alignment from the human genome to these references, uses it to map the standard human genome annotation tracks, and presents all of them as a comprehensive interface to facilitate work with repetitive elements. It also provides processed tracks of multiple publicly available datasets of particular interest to the repeat community, including ChIP-seq datasets for KRAB Zinc Finger Proteins (KZNFs) – a family of proteins known to bind and repress certain classes of repeats. We used the UCSC Repeat Browser in combination with these datasets, as well as RepeatMasker annotations in several non-human primates, to trace the independent trajectories of species-specific evolutionary battles between LINE 1 retroelements and their repressors. Furthermore, we document at https://repeatbrowser.ucsc.edu how researchers can map their own human genome annotations to these reference repeat sequences. Conclusions The UCSC Repeat Browser allows easy and intuitive visualization of genomic data on consensus repeat elements, circumventing the problem of multi-mapping, in which sequencing reads of repeat elements map to multiple locations on the human genome. By developing a reference consensus, multiple datasets and annotation tracks can easily be overlaid to reveal complex evolutionary histories of repeats in a single interactive window. Specifically, we use this approach to retrace the history of several primate specific LINE-1 families across apes, and discover several species-specific routes of evolution that correlate with the emergence and binding of KZNFs.
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339
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O'Neill K, Brocks D, Hammell MG. Mobile genomics: tools and techniques for tackling transposons. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190345. [PMID: 32075565 PMCID: PMC7061981 DOI: 10.1098/rstb.2019.0345] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/20/2019] [Indexed: 12/22/2022] Open
Abstract
Next-generation sequencing approaches have fundamentally changed the types of questions that can be asked about gene function and regulation. With the goal of approaching truly genome-wide quantifications of all the interaction partners and downstream effects of particular genes, these quantitative assays have allowed for an unprecedented level of detail in exploring biological interactions. However, many challenges remain in our ability to accurately describe and quantify the interactions that take place in those hard to reach and extremely repetitive regions of our genome comprised mostly of transposable elements (TEs). Tools dedicated to TE-derived sequences have lagged behind, making the inclusion of these sequences in genome-wide analyses difficult. Recent improvements, both computational and experimental, allow for the better inclusion of TE sequences in genomic assays and a renewed appreciation for the importance of TE biology. This review will discuss the recent improvements that have been made in the computational analysis of TE-derived sequences as well as the areas where such analysis still proves difficult. This article is part of a discussion meeting issue 'Crossroads between transposons and gene regulation'.
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Affiliation(s)
- Kathryn O'Neill
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - David Brocks
- Department of Computer Science and Applied Mathematics, The Weizmann Institute of Science, Rehovot, Israel
| | - Molly Gale Hammell
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
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340
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Venkei ZG, Choi CP, Feng S, Chen C, Jacobsen SE, Kim JK, Yamashita YM. A kinesin Klp10A mediates cell cycle-dependent shuttling of Piwi between nucleus and nuage. PLoS Genet 2020; 16:e1008648. [PMID: 32168327 PMCID: PMC7094869 DOI: 10.1371/journal.pgen.1008648] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 03/25/2020] [Accepted: 02/03/2020] [Indexed: 12/26/2022] Open
Abstract
The piRNA pathway protects germline genomes from selfish genetic elements (e.g. transposons) through their transcript cleavage in the cytoplasm and/or their transcriptional silencing in the nucleus. Here, we describe a mechanism by which the nuclear and cytoplasmic arms of the piRNA pathway are linked. We find that during mitosis of Drosophila spermatogonia, nuclear Piwi interacts with nuage, the compartment that mediates the cytoplasmic arm of the piRNA pathway. At the end of mitosis, Piwi leaves nuage to return to the nucleus. Dissociation of Piwi from nuage occurs at the depolymerizing microtubules of the central spindle, mediated by a microtubule-depolymerizing kinesin, Klp10A. Depletion of klp10A delays the return of Piwi to the nucleus and affects piRNA production, suggesting the role of nuclear-cytoplasmic communication in piRNA biogenesis. We propose that cell cycle-dependent communication between the nuclear and cytoplasmic arms of the piRNA pathway may play a previously unappreciated role in piRNA regulation. The piRNA pathway that defends germline from selfish elements operates in two subpathways, one mediated by Piwi in Drosophila to silence transcription of targets in the nucleus and the other mediated by Aub and Ago3 to cleave transcripts of targets in the cytoplasm. How these two subpathways might coordinate with each other, particularly at the cell biological level, remains elusive. This study shows that Piwi interacts with Aub/Ago3 specifically in mitosis in nuage, the organelle that serves as the platform for piRNA cytoplasmic subpathway. Piwi returns to the nucleus at the end of mitosis, and our study suggests that dissociation of Piwi from nuage is facilitated by microtubule depolymerization by a kinesin Klp10A at the central spindle. We propose that cell-cycle-dependent interaction of two piRNA subpathways may play an important role in piRNA production.
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Affiliation(s)
- Zsolt G. Venkei
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Charlotte P. Choi
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Suhua Feng
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, California, United States of America
- Eli and Edyth Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, California, United States of America
| | - Cuie Chen
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Steven E. Jacobsen
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, California, United States of America
- Eli and Edyth Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, California, United States of America
- Howard Hughes Medical Institute, University of California, Los Angeles, California, United States of America
| | - John K. Kim
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Yukiko M. Yamashita
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
- Howard Hughes Medical Institute, University of Michigan Ann Arbor, Michigan, United States of America
- * E-mail:
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341
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Sybirna A, Tang WWC, Pierson Smela M, Dietmann S, Gruhn WH, Brosh R, Surani MA. A critical role of PRDM14 in human primordial germ cell fate revealed by inducible degrons. Nat Commun 2020; 11:1282. [PMID: 32152282 PMCID: PMC7062732 DOI: 10.1038/s41467-020-15042-0] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 12/31/2019] [Indexed: 11/09/2022] Open
Abstract
PRDM14 is a crucial regulator of mouse primordial germ cells (mPGCs), epigenetic reprogramming and pluripotency, but its role in the evolutionarily divergent regulatory network of human PGCs (hPGCs) remains unclear. Besides, a previous knockdown study indicated that PRDM14 might be dispensable for human germ cell fate. Here, we decided to use inducible degrons for a more rapid and comprehensive PRDM14 depletion. We show that PRDM14 loss results in significantly reduced specification efficiency and an aberrant transcriptome of hPGC-like cells (hPGCLCs) obtained in vitro from human embryonic stem cells (hESCs). Chromatin immunoprecipitation and transcriptomic analyses suggest that PRDM14 cooperates with TFAP2C and BLIMP1 to upregulate germ cell and pluripotency genes, while repressing WNT signalling and somatic markers. Notably, PRDM14 targets are not conserved between mouse and human, emphasising the divergent molecular mechanisms of PGC specification. The effectiveness of degrons for acute protein depletion is widely applicable in various developmental contexts.
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Affiliation(s)
- Anastasiya Sybirna
- Wellcome Trust/Cancer Research UK Gurdon Institute, Henry Wellcome Building of Cancer and Developmental Biology, Cambridge, CB2 1QN, UK
- Physiology, Development and Neuroscience Department, University of Cambridge, Cambridge, CB2 3EL, UK
- Wellcome Trust/Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 1QR, UK
| | - Walfred W C Tang
- Wellcome Trust/Cancer Research UK Gurdon Institute, Henry Wellcome Building of Cancer and Developmental Biology, Cambridge, CB2 1QN, UK
- Physiology, Development and Neuroscience Department, University of Cambridge, Cambridge, CB2 3EL, UK
| | - Merrick Pierson Smela
- Wellcome Trust/Cancer Research UK Gurdon Institute, Henry Wellcome Building of Cancer and Developmental Biology, Cambridge, CB2 1QN, UK
- Physiology, Development and Neuroscience Department, University of Cambridge, Cambridge, CB2 3EL, UK
| | - Sabine Dietmann
- Wellcome Trust/Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 1QR, UK
| | - Wolfram H Gruhn
- Wellcome Trust/Cancer Research UK Gurdon Institute, Henry Wellcome Building of Cancer and Developmental Biology, Cambridge, CB2 1QN, UK
- Physiology, Development and Neuroscience Department, University of Cambridge, Cambridge, CB2 3EL, UK
| | - Ran Brosh
- Institute for Systems Genetics, NYU Langone Health, New York, NY, 10016, USA
| | - M Azim Surani
- Wellcome Trust/Cancer Research UK Gurdon Institute, Henry Wellcome Building of Cancer and Developmental Biology, Cambridge, CB2 1QN, UK.
- Physiology, Development and Neuroscience Department, University of Cambridge, Cambridge, CB2 3EL, UK.
- Wellcome Trust/Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 1QR, UK.
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342
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Ovejero T, Sadones O, Sánchez-Fito T, Almenar-Pérez E, Espejo JA, Martín-Martínez E, Nathanson L, Oltra E. Activation of Transposable Elements in Immune Cells of Fibromyalgia Patients. Int J Mol Sci 2020; 21:1366. [PMID: 32085571 PMCID: PMC7072917 DOI: 10.3390/ijms21041366] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 02/06/2020] [Accepted: 02/14/2020] [Indexed: 02/07/2023] Open
Abstract
Advancements in nucleic acid sequencing technology combined with an unprecedented availability of metadata have revealed that 45% of the human genome constituted by transposable elements (TEs) is not only transcriptionally active but also physiologically necessary. Dysregulation of TEs, including human retroviral endogenous sequences (HERVs) has been shown to associate with several neurologic and autoimmune diseases, including Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS). However, no study has yet addressed whether abnormal expression of these sequences correlates with fibromyalgia (FM), a disease frequently comorbid with ME/CFS. The work presented here shows, for the first time, that, in fact, HERVs of the H, K and W types are overexpressed in immune cells of FM patients with or without comorbid ME/CFS. Patients with increased HERV expression (N = 14) presented increased levels of interferon (INF-β and INF-γ) but unchanged levels of TNF-α. The findings reported in this study could explain the flu-like symptoms FM patients present with in clinical practice, in the absence of concomitant infections. Future work aimed at identifying specific genomic loci differentially affected in FM and/or ME/CFS is warranted.
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Affiliation(s)
- Tamara Ovejero
- School of Medicine, Universidad Católica de Valencia San Vicente Mártir, 46001 Valencia, Spain;
| | | | - Teresa Sánchez-Fito
- Escuela de Doctorado, Universidad Católica de Valencia San Vicente Mártir, 46008 Valencia, Spain; (T.S.-F.); (E.A.-P.)
| | - Eloy Almenar-Pérez
- Escuela de Doctorado, Universidad Católica de Valencia San Vicente Mártir, 46008 Valencia, Spain; (T.S.-F.); (E.A.-P.)
| | - José Andrés Espejo
- School of Biotechnology, Universidad Católica de Valencia San Vicente Mártir, 46001 Valencia, Spain;
| | | | - Lubov Nathanson
- Institute for Neuro Immune Medicine, Nova Southeastern University, Ft Lauderdale, FL 33314, USA;
| | - Elisa Oltra
- School of Medicine, Universidad Católica de Valencia San Vicente Mártir, 46001 Valencia, Spain;
- Centro de Investigación Traslacional San Alberto Magno, Universidad Católica de Valencia San Vicente Mártir, 46001 Valencia, Spain
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343
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A role for the rare endogenous retrovirus β4 in development of Japanese fancy mice. Commun Biol 2020; 3:53. [PMID: 32020010 PMCID: PMC7000388 DOI: 10.1038/s42003-020-0781-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 01/14/2020] [Indexed: 11/18/2022] Open
Abstract
Two coat-color mutations, nonagouti, which changes coat color from wild-type agouti to black, and piebald, which induces irregular white spotting, are the characteristics of Japanese fancy mouse strain JF1/Ms. In our Communications Biology article, we reported that insertion of a rare type of endogenous retrovirus β4 has caused both coat color mutations. Although there are some reports on the roles of β4 in the mouse genome, further studies on β4 will uncover new features of endogenous retrovirus sequences. In light of their recent finding that insertion of a rare endogenous retrovirus, β4, is the cause of the characteristic coat coloring in agouti and piebald mice, Akira Tanave and Tsuyoshi Koide now discuss the origin and expansion of this element as well as potential roles of β4 in the mouse genome.
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344
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Fouché S, Badet T, Oggenfuss U, Plissonneau C, Francisco CS, Croll D. Stress-Driven Transposable Element De-repression Dynamics and Virulence Evolution in a Fungal Pathogen. Mol Biol Evol 2020; 37:221-239. [PMID: 31553475 DOI: 10.1093/molbev/msz216] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Transposable elements (TEs) are drivers of genome evolution and affect the expression landscape of the host genome. Stress is a major factor inducing TE activity; however, the regulatory mechanisms underlying de-repression are poorly understood. Plant pathogens are excellent models to dissect the impact of stress on TEs. The process of plant infection induces stress for the pathogen, and virulence factors (i.e., effectors) located in TE-rich regions become expressed. To dissect TE de-repression dynamics and contributions to virulence, we analyzed the TE expression landscape of four strains of the major wheat pathogen Zymoseptoria tritici. We experimentally exposed strains to nutrient starvation and host infection stress. Contrary to expectations, we show that the two distinct conditions induce the expression of different sets of TEs. In particular, the most highly expressed TEs, including miniature inverted-repeat transposable element and long terminal repeat-Gypsy element, show highly distinct de-repression across stress conditions. Both the genomic context of TEs and the genetic background stress (i.e., different strains harboring the same TEs) were major predictors of de-repression under stress. Gene expression profiles under stress varied significantly depending on the proximity to the closest TEs and genomic defenses against TEs were largely ineffective to prevent de-repression. Next, we analyzed the locus encoding the Avr3D1 effector. We show that the insertion and subsequent silencing of TEs in close proximity likely contributed to reduced expression and virulence on a specific wheat cultivar. The complexity of TE responsiveness to stress across genetic backgrounds and genomic locations demonstrates substantial intraspecific genetic variation to control TEs with consequences for virulence.
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Affiliation(s)
- Simone Fouché
- Plant Pathology, Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland.,Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Thomas Badet
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Ursula Oggenfuss
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Clémence Plissonneau
- Plant Pathology, Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
| | | | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
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345
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Macchietto MG, Langlois RA, Shen SS. Virus-induced transposable element expression up-regulation in human and mouse host cells. Life Sci Alliance 2020; 3:3/2/e201900536. [PMID: 31964680 PMCID: PMC6977392 DOI: 10.26508/lsa.201900536] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 01/09/2020] [Accepted: 01/10/2020] [Indexed: 12/18/2022] Open
Abstract
Genome-wide transposon expression up-regulation in host cells regardless of virus, species, and host cell tissue types occurs early during viral infection and likely contributes to promoting the host innate immune response. Virus–host cell interactions initiate a host cell–defensive response during virus infection. How transposable elements in the host cell respond to viral stress at the molecular level remains largely unclear. By reanalyzing next generation sequencing data sets from dozens of virus infection studies from the Gene Expression Omnibus database, we found that genome-wide transposon expression up-regulation in host cells occurs near antiviral response genes and exists in all studies regardless of virus, species, and host cell tissue types. Some transposons were found to be up-regulated almost immediately upon infection and before increases in virus replication and significant increases in interferon β expression. These findings indicate that transposon up-regulation is a common phenomenon during virus infection in human and mouse and that early up-regulated transposons are part of the first wave response during virus infection.
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Affiliation(s)
| | - Ryan A Langlois
- Biochemistry, Molecular Biology and Biophysics Graduate Program, University of Minnesota, Minneapolis, MN, USA
| | - Steven S Shen
- Institute for Health Informatics, University of Minnesota, Minneapolis, MN, USA .,Clinical Translational Science Institute, University of Minnesota, Minneapolis, MN, USA
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346
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Neou M, Villa C, Armignacco R, Jouinot A, Raffin-Sanson ML, Septier A, Letourneur F, Diry S, Diedisheim M, Izac B, Gaspar C, Perlemoine K, Verjus V, Bernier M, Boulin A, Emile JF, Bertagna X, Jaffrezic F, Laloe D, Baussart B, Bertherat J, Gaillard S, Assié G. Pangenomic Classification of Pituitary Neuroendocrine Tumors. Cancer Cell 2020; 37:123-134.e5. [PMID: 31883967 DOI: 10.1016/j.ccell.2019.11.002] [Citation(s) in RCA: 205] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 10/07/2019] [Accepted: 11/21/2019] [Indexed: 12/14/2022]
Abstract
Pituitary neuroendocrine tumors (PitNETs) are common, with five main histological subtypes: lactotroph, somatotroph, and thyrotroph (POU1F1/PIT1 lineage); corticotroph (TBX19/TPIT lineage); and gonadotroph (NR5A1/SF1 lineage). We report a comprehensive pangenomic classification of PitNETs. PitNETs from POU1F1/PIT1 lineage showed an epigenetic signature of diffuse DNA hypomethylation, with transposable elements expression and chromosomal instability (except for GNAS-mutated somatotrophs). In TPIT lineage, corticotrophs were divided into three classes: the USP8-mutated with overt secretion, the USP8-wild-type with increased invasiveness and increased epithelial-mesenchymal transition, and the large silent tumors with gonadotroph transdifferentiation. Unexpected expression of gonadotroph markers was also found in GNAS-wild-type somatotrophs (SF1 expression), challenging the current definition of SF1/gonadotroph lineage. This classification improves our understanding and affects the clinical stratification of patients with PitNETs.
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Affiliation(s)
- Mario Neou
- INSERM U1016, Institut Cochin, 75014 Paris, France; CNRS UMR 8104, 75014 Paris, France; Université Paris Descartes-Université de Paris, 75006 Paris, France
| | - Chiara Villa
- INSERM U1016, Institut Cochin, 75014 Paris, France; CNRS UMR 8104, 75014 Paris, France; Université Paris Descartes-Université de Paris, 75006 Paris, France; Department of Pathological Cytology and Anatomy, Foch Hospital, 92151 Suresnes, France; Department of Endocrinology, Sart Tilman B35, 4000 Liège, Belgium
| | - Roberta Armignacco
- INSERM U1016, Institut Cochin, 75014 Paris, France; CNRS UMR 8104, 75014 Paris, France; Université Paris Descartes-Université de Paris, 75006 Paris, France
| | - Anne Jouinot
- INSERM U1016, Institut Cochin, 75014 Paris, France; CNRS UMR 8104, 75014 Paris, France; Université Paris Descartes-Université de Paris, 75006 Paris, France
| | - Marie-Laure Raffin-Sanson
- Department of Endocrinology, Hôpital Ambroise Paré, Assistance Publique-Hôpitaux de Paris, 92100 Boulogne Billancourt, France; UE4340, Université de Versailles Saint-Quentin-en-Yvelines Montigny-le-Bretonneux, 78000 Versailles, France
| | - Amandine Septier
- INSERM U1016, Institut Cochin, 75014 Paris, France; CNRS UMR 8104, 75014 Paris, France; Université Paris Descartes-Université de Paris, 75006 Paris, France
| | - Franck Letourneur
- INSERM U1016, Institut Cochin, 75014 Paris, France; CNRS UMR 8104, 75014 Paris, France; Université Paris Descartes-Université de Paris, 75006 Paris, France; Plate-Forme Séquençage et Génomique (Genom'IC), INSERM U1016, Institut Cochin, 75014 Paris, France
| | - Ségolène Diry
- INSERM U1016, Institut Cochin, 75014 Paris, France; CNRS UMR 8104, 75014 Paris, France; Université Paris Descartes-Université de Paris, 75006 Paris, France
| | - Marc Diedisheim
- Department of Diabetology, Assistance Publique-Hôpitaux de Paris, Hôpital Cochin, 75014 Paris, France
| | - Brigitte Izac
- INSERM U1016, Institut Cochin, 75014 Paris, France; CNRS UMR 8104, 75014 Paris, France; Université Paris Descartes-Université de Paris, 75006 Paris, France; Plate-Forme Séquençage et Génomique (Genom'IC), INSERM U1016, Institut Cochin, 75014 Paris, France
| | - Cassandra Gaspar
- INSERM U1016, Institut Cochin, 75014 Paris, France; CNRS UMR 8104, 75014 Paris, France; Université Paris Descartes-Université de Paris, 75006 Paris, France; Sorbonne Université, Inserm, UMS PASS, Plateforme Post-génomique de la Pitié-Salpêtrière, P3S, 75013 Paris, France
| | - Karine Perlemoine
- INSERM U1016, Institut Cochin, 75014 Paris, France; CNRS UMR 8104, 75014 Paris, France; Université Paris Descartes-Université de Paris, 75006 Paris, France
| | - Victoria Verjus
- INSERM U1016, Institut Cochin, 75014 Paris, France; CNRS UMR 8104, 75014 Paris, France; Université Paris Descartes-Université de Paris, 75006 Paris, France
| | - Michèle Bernier
- Department of Pathological Cytology and Anatomy, Foch Hospital, 92151 Suresnes, France
| | - Anne Boulin
- Department of Diagnostic and Interventional Neuroradiology, Foch Hospital, 92151 Suresnes, France
| | - Jean-François Emile
- Department of Pathology, Ambroise Paré, Assistance Publique-Hôpitaux de Paris, 92100 Boulogne Billancourt, France
| | - Xavier Bertagna
- INSERM U1016, Institut Cochin, 75014 Paris, France; CNRS UMR 8104, 75014 Paris, France; Université Paris Descartes-Université de Paris, 75006 Paris, France; Department of Endocrinology, Center for Rare Adrenal Diseases, Assistance Publique-Hôpitaux de Paris, Hôpital Cochin, 75014 Paris, France
| | - Florence Jaffrezic
- INRA, UMR 1313 GABI, Université Paris Saclay, AgroParisTech, 78352 Jouy-en-Josas, France
| | - Denis Laloe
- INRA, UMR 1313 GABI, Université Paris Saclay, AgroParisTech, 78352 Jouy-en-Josas, France
| | | | - Jérôme Bertherat
- INSERM U1016, Institut Cochin, 75014 Paris, France; CNRS UMR 8104, 75014 Paris, France; Université Paris Descartes-Université de Paris, 75006 Paris, France; Department of Endocrinology, Center for Rare Adrenal Diseases, Assistance Publique-Hôpitaux de Paris, Hôpital Cochin, 75014 Paris, France
| | - Stephan Gaillard
- Department of Neurosurgery, Foch Hospital, 92151 Suresnes, France
| | - Guillaume Assié
- INSERM U1016, Institut Cochin, 75014 Paris, France; CNRS UMR 8104, 75014 Paris, France; Université Paris Descartes-Université de Paris, 75006 Paris, France; Department of Endocrinology, Center for Rare Adrenal Diseases, Assistance Publique-Hôpitaux de Paris, Hôpital Cochin, 75014 Paris, France.
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347
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Kaul T, Morales ME, Sartor AO, Belancio VP, Deininger P. Comparative analysis on the expression of L1 loci using various RNA-Seq preparations. Mob DNA 2020; 11:2. [PMID: 31921361 PMCID: PMC6945437 DOI: 10.1186/s13100-019-0194-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 12/05/2019] [Indexed: 01/08/2023] Open
Abstract
Background Retrotransposons are one of the oldest evolutionary forces shaping mammalian genomes, with the ability to mobilize from one genomic location to another. This mobilization is also a significant factor in human disease. The only autonomous human retroelement, L1, has propagated to make up 17% of the human genome, accumulating over 500,000 copies. The majority of these loci are truncated or defective with only a few reported to remain capable of retrotransposition. We have previously published a strand-specific RNA-Seq bioinformatics approach to stringently identify at the locus-specific level the few expressed full-length L1s using cytoplasmic RNA. With growing repositories of RNA-Seq data, there is potential to mine these datasets to identify and study expressed L1s at single-locus resolution, although many datasets are not strand-specific or not generated from cytoplasmic RNA. Results We developed whole-cell, cytoplasmic and nuclear RNA-Seq datasets from 22Rv1 prostate cancer cells to test the influence of different preparations on the quality and effort needed to measure L1 expression. We found that there was minimal data loss in the identification of full-length expressed L1 s using whole cell, strand-specific RNA-Seq data compared to cytoplasmic, strand-specific RNA-Seq data. However, this was only possible with an increased amount of manual curation of the bioinformatics output to eliminate increased background. About half of the data was lost when the sequenced datasets were non-strand specific. Conclusions The results of these studies demonstrate that with rigorous manual curation the utilization of stranded RNA-Seq datasets allow identification of expressed L1 loci from either cytoplasmic or whole-cell RNA-Seq datasets.
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Affiliation(s)
- Tiffany Kaul
- 1Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112 USA
| | - Maria E Morales
- 1Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112 USA
| | - Alton O Sartor
- 1Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112 USA.,2Section of Hematology and Oncology, Department of Medicine, Tulane School of Medicine, 1430 Tulane Ave, New Orleans, LA 70112 USA
| | - Victoria P Belancio
- 1Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112 USA.,3Department of Structural and Cellular Biology, Tulane School of Medicine, 1430 Tulane Ave, New Orleans, 70112 USA
| | - Prescott Deininger
- 1Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112 USA.,4Department of Epidemiology, Tulane School of Public Health and Tropical Medicine, New Orleans, LA 70112 USA
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348
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Vendrell-Mir P, López-Obando M, Nogué F, Casacuberta JM. Different Families of Retrotransposons and DNA Transposons Are Actively Transcribed and May Have Transposed Recently in Physcomitrium ( Physcomitrella) patens. FRONTIERS IN PLANT SCIENCE 2020; 11:1274. [PMID: 32973835 PMCID: PMC7466625 DOI: 10.3389/fpls.2020.01274] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 08/05/2020] [Indexed: 05/07/2023]
Abstract
Similarly to other plant genomes of similar size, more than half of the genome of P. patens is covered by Transposable Elements (TEs). However, the composition and distribution of P. patens TEs is quite peculiar, with Long Terminal Repeat (LTR)-retrotransposons, which form patches of TE-rich regions interleaved with gene-rich regions, accounting for the vast majority of the TE space. We have already shown that RLG1, the most abundant TE in P. patens, is expressed in non-stressed protonema tissue. Here we present a non-targeted analysis of the TE expression based on RNA-Seq data and confirmed by qRT-PCR analyses that shows that, at least four LTR-RTs (RLG1, RLG2, RLC4 and tRLC5) and one DNA transposon (PpTc2) are expressed in P. patens. These TEs are expressed during development or under stresses that P. patens frequently faces, such as dehydratation/rehydratation stresses, suggesting that TEs have ample possibilities to transpose during P. patens life cycle. Indeed, an analysis of the TE polymorphisms among four different P. patens accessions shows that different TE families have recently transposed in this species and have generated genetic variability that may have phenotypic consequences, as a fraction of the TE polymorphisms are within or close to genes. Among the transcribed and mobile TEs, tRLC5 is particularly interesting as it concentrates in a single position per chromosome that could coincide with the centromere, and its expression is specifically induced in young sporophyte, where meiosis takes place.
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Affiliation(s)
- Pol Vendrell-Mir
- Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Barcelona, Spain
| | - Mauricio López-Obando
- Department of Plant Biology, Swedish University of Agricultural Sciences, The Linnean Centre of Plant Biology in Uppsala, Uppsala, Sweden
| | - Fabien Nogué
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, France
- *Correspondence: Fabien Nogué, ; Josep M. Casacuberta,
| | - Josep M. Casacuberta
- Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Barcelona, Spain
- *Correspondence: Fabien Nogué, ; Josep M. Casacuberta,
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349
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Teissandier A, Servant N, Barillot E, Bourc'his D. Tools and best practices for retrotransposon analysis using high-throughput sequencing data. Mob DNA 2019; 10:52. [PMID: 31890048 PMCID: PMC6935493 DOI: 10.1186/s13100-019-0192-1] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 12/04/2019] [Indexed: 12/26/2022] Open
Abstract
Background Sequencing technologies give access to a precise picture of the molecular mechanisms acting upon genome regulation. One of the biggest technical challenges with sequencing data is to map millions of reads to a reference genome. This problem is exacerbated when dealing with repetitive sequences such as transposable elements that occupy half of the mammalian genome mass. Sequenced reads coming from these regions introduce ambiguities in the mapping step. Therefore, applying dedicated parameters and algorithms has to be taken into consideration when transposable elements regulation is investigated with sequencing datasets. Results Here, we used simulated reads on the mouse and human genomes to define the best parameters for aligning transposable element-derived reads on a reference genome. The efficiency of the most commonly used aligners was compared and we further evaluated how transposable element representation should be estimated using available methods. The mappability of the different transposon families in the mouse and the human genomes was calculated giving an overview into their evolution. Conclusions Based on simulated data, we provided recommendations on the alignment and the quantification steps to be performed when transposon expression or regulation is studied, and identified the limits in detecting specific young transposon families of the mouse and human genomes. These principles may help the community to adopt standard procedures and raise awareness of the difficulties encountered in the study of transposable elements.
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Affiliation(s)
- Aurélie Teissandier
- 1Institut Curie, PSL Research University, 75005 Paris, France.,2INSERM U900, 75005 Paris, France.,3MINES ParisTech, PSL Research University, 75005 Paris, France.,4INSERM U934, CNRS UMR 3215, 75005 Paris, France
| | - Nicolas Servant
- 1Institut Curie, PSL Research University, 75005 Paris, France.,2INSERM U900, 75005 Paris, France.,3MINES ParisTech, PSL Research University, 75005 Paris, France
| | - Emmanuel Barillot
- 1Institut Curie, PSL Research University, 75005 Paris, France.,2INSERM U900, 75005 Paris, France.,3MINES ParisTech, PSL Research University, 75005 Paris, France
| | - Deborah Bourc'his
- 1Institut Curie, PSL Research University, 75005 Paris, France.,4INSERM U934, CNRS UMR 3215, 75005 Paris, France
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350
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Bhargava V, Goldstein CD, Russell L, Xu L, Ahmed M, Li W, Casey A, Servage K, Kollipara R, Picciarelli Z, Kittler R, Yatsenko A, Carmell M, Orth K, Amatruda JF, Yanowitz JL, Buszczak M. GCNA Preserves Genome Integrity and Fertility Across Species. Dev Cell 2019; 52:38-52.e10. [PMID: 31839537 DOI: 10.1016/j.devcel.2019.11.007] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 08/07/2019] [Accepted: 11/13/2019] [Indexed: 12/20/2022]
Abstract
The propagation of species depends on the ability of germ cells to protect their genome from numerous exogenous and endogenous threats. While these cells employ ubiquitous repair pathways, specialized mechanisms that ensure high-fidelity replication, chromosome segregation, and repair of germ cell genomes remain incompletely understood. We identified Germ Cell Nuclear Acidic Peptidase (GCNA) as a conserved regulator of genome stability in flies, worms, zebrafish, and human germ cell tumors. GCNA contains an acidic intrinsically disordered region (IDR) and a protease-like SprT domain. In addition to chromosomal instability and replication stress, Gcna mutants accumulate DNA-protein crosslinks (DPCs). GCNA acts in parallel with the SprT domain protein Spartan. Structural analysis reveals that while the SprT domain is needed to limit DNA damage, the IDR imparts significant function. This work shows that GCNA protects germ cells from various sources of damage, providing insights into conserved mechanisms that promote genome integrity across generations.
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Affiliation(s)
- Varsha Bhargava
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Courtney D Goldstein
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Logan Russell
- Magee-Womens Research Institute, Department of Obstetrics, Gynecology, and Reproductive Sciences, University of Pittsburgh School of Medicine, PA 15213, USA
| | - Lin Xu
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Murtaza Ahmed
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Wei Li
- Magee-Womens Research Institute, Department of Obstetrics, Gynecology, and Reproductive Sciences, University of Pittsburgh School of Medicine, PA 15213, USA; Tsinghua University MD Program, School of Medicine, Tsinghua University, Haidian District, Beijing 100084, PR China
| | - Amanda Casey
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Kelly Servage
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Howard Hughes Medical Institute, 6000 Harry Hines Boulevard NA5.120F, Dallas, TX 75235, USA
| | - Rahul Kollipara
- McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Zachary Picciarelli
- Magee-Womens Research Institute, Department of Obstetrics, Gynecology, and Reproductive Sciences, University of Pittsburgh School of Medicine, PA 15213, USA
| | - Ralf Kittler
- McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Alexander Yatsenko
- Magee-Womens Research Institute, Department of Obstetrics, Gynecology, and Reproductive Sciences, University of Pittsburgh School of Medicine, PA 15213, USA
| | - Michelle Carmell
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA; RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA; Department of Biological Sciences, Wellesley College, Wellesley, MA 02481, USA
| | - Kim Orth
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Howard Hughes Medical Institute, 6000 Harry Hines Boulevard NA5.120F, Dallas, TX 75235, USA
| | - James F Amatruda
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| | - Judith L Yanowitz
- Magee-Womens Research Institute, Department of Obstetrics, Gynecology, and Reproductive Sciences, University of Pittsburgh School of Medicine, PA 15213, USA.
| | - Michael Buszczak
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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