351
|
Zhang W, Chen F, Chen R, Xie D, Yang J, Zhao X, Guo R, Zhang Y, Shen Y, Göke J, Liu L, Lu X. Zscan4c activates endogenous retrovirus MERVL and cleavage embryo genes. Nucleic Acids Res 2019; 47:8485-8501. [PMID: 31304534 PMCID: PMC7145578 DOI: 10.1093/nar/gkz594] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 06/24/2019] [Accepted: 06/28/2019] [Indexed: 01/09/2023] Open
Abstract
Endogenous retroviruses (ERVs) contribute to ∼10 percent of the mouse genome. They are often silenced in differentiated somatic cells but differentially expressed at various embryonic developmental stages. A minority of mouse embryonic stem cells (ESCs), like 2-cell cleavage embryos, highly express ERV MERVL. However, the role of ERVs and mechanism of their activation in these cells are still poorly understood. In this study, we investigated the regulation and function of the stage-specific expressed ERVs, with a particular focus on the totipotency marker MT2/MERVL. We show that the transcription factor Zscan4c functions as an activator of MT2/MERVL and 2-cell/4-cell embryo genes. Zinc finger domains of Zscan4c play an important role in this process. In addition, Zscan4c interacts with MT2 and regulates MT2-nearby 2-cell/4-cell genes through promoting enhancer activity of MT2. Furthermore, MT2 activation is accompanied by enhanced H3K4me1, H3K27ac, and H3K14ac deposition on MT2. Zscan4c also interacts with GBAF chromatin remodelling complex through SCAN domain to further activate MT2 enhancer activity. Taken together, we delineate a previously unrecognized regulatory axis that Zscan4c interacts with and activates MT2/MERVL loci and their nearby genes through epigenetic regulation.
Collapse
Affiliation(s)
- Weiyu Zhang
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300350, People's Republic of China.,College of Pharmacy, Nankai University, Tianjin 300350, People's Republic of China
| | - Fuquan Chen
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300350, People's Republic of China.,College of Pharmacy, Nankai University, Tianjin 300350, People's Republic of China
| | - Ruiqing Chen
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300350, People's Republic of China.,College of Pharmacy, Nankai University, Tianjin 300350, People's Republic of China
| | - Dan Xie
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300350, People's Republic of China.,College of Pharmacy, Nankai University, Tianjin 300350, People's Republic of China
| | - Jiao Yang
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300350, People's Republic of China.,College of Life Sciences, Nankai University, Tianjin 300071, People's Republic of China
| | - Xin Zhao
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300350, People's Republic of China.,College of Pharmacy, Nankai University, Tianjin 300350, People's Republic of China
| | - Renpeng Guo
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300350, People's Republic of China.,College of Life Sciences, Nankai University, Tianjin 300071, People's Republic of China
| | - Yongwang Zhang
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300350, People's Republic of China.,College of Pharmacy, Nankai University, Tianjin 300350, People's Republic of China
| | - Yang Shen
- Computational and Systems Biology, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Jonathan Göke
- Computational and Systems Biology, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Lin Liu
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300350, People's Republic of China.,College of Life Sciences, Nankai University, Tianjin 300071, People's Republic of China
| | - Xinyi Lu
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300350, People's Republic of China.,College of Pharmacy, Nankai University, Tianjin 300350, People's Republic of China
| |
Collapse
|
352
|
Chen Z, Yin Q, Inoue A, Zhang C, Zhang Y. Allelic H3K27me3 to allelic DNA methylation switch maintains noncanonical imprinting in extraembryonic cells. SCIENCE ADVANCES 2019; 5:eaay7246. [PMID: 32064321 PMCID: PMC6989337 DOI: 10.1126/sciadv.aay7246] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 11/05/2019] [Indexed: 05/08/2023]
Abstract
Faithful maintenance of genomic imprinting is essential for mammalian development. While germline DNA methylation-dependent (canonical) imprinting is relatively stable during development, the recently found oocyte-derived H3K27me3-mediated noncanonical imprinting is mostly transient in early embryos, with some genes important for placental development maintaining imprinted expression in the extraembryonic lineage. How these noncanonical imprinted genes maintain their extraembryonic-specific imprinting is unknown. Here, we report that maintenance of noncanonical imprinting requires maternal allele-specific de novo DNA methylation [i.e., somatic differentially methylated regions (DMRs)] at implantation. The somatic DMRs are located at the gene promoters, with paternal allele-specific H3K4me3 established during preimplantation development. Genetic manipulation revealed that both maternal EED and zygotic DNMT3A/3B are required for establishing somatic DMRs and maintaining noncanonical imprinting. Thus, our study not only reveals the mechanism underlying noncanonical imprinting maintenance but also sheds light on how histone modifications in oocytes may shape somatic DMRs in postimplantation embryos.
Collapse
Affiliation(s)
- Zhiyuan Chen
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
- Division of Hematology/Oncology, Department of Pediatrics, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Qiangzong Yin
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
- Division of Hematology/Oncology, Department of Pediatrics, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Azusa Inoue
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
- Division of Hematology/Oncology, Department of Pediatrics, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Chunxia Zhang
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
- Division of Hematology/Oncology, Department of Pediatrics, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Yi Zhang
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
- Division of Hematology/Oncology, Department of Pediatrics, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Harvard Stem Cell Institute, Boston, MA 02115, USA
- Corresponding author.
| |
Collapse
|
353
|
Transposable element expression in tumors is associated with immune infiltration and increased antigenicity. Nat Commun 2019; 10:5228. [PMID: 31745090 PMCID: PMC6864081 DOI: 10.1038/s41467-019-13035-2] [Citation(s) in RCA: 162] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 10/15/2019] [Indexed: 12/19/2022] Open
Abstract
Profound global loss of DNA methylation is a hallmark of many cancers. One potential consequence of this is the reactivation of transposable elements (TEs) which could stimulate the immune system via cell-intrinsic antiviral responses. Here, we develop REdiscoverTE, a computational method for quantifying genome-wide TE expression in RNA sequencing data. Using The Cancer Genome Atlas database, we observe increased expression of over 400 TE subfamilies, of which 262 appear to result from a proximal loss of DNA methylation. The most recurrent TEs are among the evolutionarily youngest in the genome, predominantly expressed from intergenic loci, and associated with antiviral or DNA damage responses. Treatment of glioblastoma cells with a demethylation agent results in both increased TE expression and de novo presentation of TE-derived peptides on MHC class I molecules. Therapeutic reactivation of tumor-specific TEs may synergize with immunotherapy by inducing inflammation and the display of potentially immunogenic neoantigens. Treatment with demethylation agents can reactivate transposable elements. Here in glioblastoma, the authors also show that this is accompanied by de novo presentation of TE-derived peptides on MHC class I molecules.
Collapse
|
354
|
Tam OH, Rozhkov NV, Shaw R, Kim D, Hubbard I, Fennessey S, Propp N, Fagegaltier D, Harris BT, Ostrow LW, Phatnani H, Ravits J, Dubnau J, Gale Hammell M. Postmortem Cortex Samples Identify Distinct Molecular Subtypes of ALS: Retrotransposon Activation, Oxidative Stress, and Activated Glia. Cell Rep 2019; 29:1164-1177.e5. [PMID: 31665631 PMCID: PMC6866666 DOI: 10.1016/j.celrep.2019.09.066] [Citation(s) in RCA: 196] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 08/03/2019] [Accepted: 09/20/2019] [Indexed: 12/14/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease characterized by the progressive loss of motor neurons. While several pathogenic mutations have been identified, the vast majority of ALS cases have no family history of disease. Thus, for most ALS cases, the disease may be a product of multiple pathways contributing to varying degrees in each patient. Using machine learning algorithms, we stratify the transcriptomes of 148 ALS postmortem cortex samples into three distinct molecular subtypes. The largest cluster, identified in 61% of patient samples, displays hallmarks of oxidative and proteotoxic stress. Another 19% of the samples shows predominant signatures of glial activation. Finally, a third group (20%) exhibits high levels of retrotransposon expression and signatures of TARDBP/TDP-43 dysfunction. We further demonstrate that TDP-43 (1) directly binds a subset of retrotransposon transcripts and contributes to their silencing in vitro, and (2) pathological TDP-43 aggregation correlates with retrotransposon de-silencing in vivo.
Collapse
Affiliation(s)
- Oliver H Tam
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | | | - Regina Shaw
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Duyang Kim
- Center for Genomics of Neurodegenerative Disease, New York Genome Center, New York, NY 10013, USA
| | - Isabel Hubbard
- Center for Genomics of Neurodegenerative Disease, New York Genome Center, New York, NY 10013, USA
| | - Samantha Fennessey
- Center for Genomics of Neurodegenerative Disease, New York Genome Center, New York, NY 10013, USA
| | - Nadia Propp
- Center for Genomics of Neurodegenerative Disease, New York Genome Center, New York, NY 10013, USA
| | - Delphine Fagegaltier
- Center for Genomics of Neurodegenerative Disease, New York Genome Center, New York, NY 10013, USA
| | - Brent T Harris
- The NYGC ALS Consortium; Department of Neurology, Georgetown University Medical Center, Washington, DC 20007, USA
| | - Lyle W Ostrow
- The NYGC ALS Consortium; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Hemali Phatnani
- Center for Genomics of Neurodegenerative Disease, New York Genome Center, New York, NY 10013, USA; The NYGC ALS Consortium
| | - John Ravits
- The NYGC ALS Consortium; Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Josh Dubnau
- The NYGC ALS Consortium; Department of Anesthesiology, Stony Brook University, Stony Brook, NY 11794, USA; Department of Neurobiology and Behavior, Stony Brook University, Stony Brook, NY 11794, USA
| | - Molly Gale Hammell
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; The NYGC ALS Consortium.
| |
Collapse
|
355
|
Yang WR, Ardeljan D, Pacyna CN, Payer LM, Burns KH. SQuIRE reveals locus-specific regulation of interspersed repeat expression. Nucleic Acids Res 2019; 47:e27. [PMID: 30624635 PMCID: PMC6411935 DOI: 10.1093/nar/gky1301] [Citation(s) in RCA: 115] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 12/18/2018] [Accepted: 01/03/2019] [Indexed: 12/13/2022] Open
Abstract
Transposable elements (TEs) are interspersed repeat sequences that make up much of the human genome. Their expression has been implicated in development and disease. However, TE-derived RNA-seq reads are difficult to quantify. Past approaches have excluded these reads or aggregated RNA expression to subfamilies shared by similar TE copies, sacrificing quantitative accuracy or the genomic context necessary to understand the basis of TE transcription. As a result, the effects of TEs on gene expression and associated phenotypes are not well understood. Here, we present Software for Quantifying Interspersed Repeat Expression (SQuIRE), the first RNA-seq analysis pipeline that provides a quantitative and locus-specific picture of TE expression (https://github.com/wyang17/SQuIRE). SQuIRE is an accurate and user-friendly tool that can be used for a variety of species. We applied SQuIRE to RNA-seq from normal mouse tissues and a Drosophila model of amyotrophic lateral sclerosis. In both model organisms, we recapitulated previously reported TE subfamily expression levels and revealed locus-specific TE expression. We also identified differences in TE transcription patterns relating to transcript type, gene expression and RNA splicing that would be lost with other approaches using subfamily-level analyses. Altogether, our findings illustrate the importance of studying TE transcription with locus-level resolution.
Collapse
Affiliation(s)
- Wan R Yang
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Daniel Ardeljan
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,McKusick-Nathans Institute of Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Clarissa N Pacyna
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA
| | - Lindsay M Payer
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Kathleen H Burns
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,McKusick-Nathans Institute of Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| |
Collapse
|
356
|
Transcriptomic analysis of human endogenous retroviruses in systemic lupus erythematosus. Proc Natl Acad Sci U S A 2019; 116:21350-21351. [PMID: 31594853 PMCID: PMC6815141 DOI: 10.1073/pnas.1907705116] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
|
357
|
McKerrow W, Fenyö D. L1EM: a tool for accurate locus specific LINE-1 RNA quantification. Bioinformatics 2019; 36:1167-1173. [PMID: 31584629 PMCID: PMC8215917 DOI: 10.1093/bioinformatics/btz724] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 05/31/2019] [Accepted: 09/25/2019] [Indexed: 01/31/2023] Open
Abstract
MOTIVATION LINE-1 elements are retrotransposons that are capable of copying their sequence to new genomic loci. LINE-1 derepression is associated with a number of disease states, and has the potential to cause significant cellular damage. Because LINE-1 elements are repetitive, it is difficult to quantify LINE-1 RNA at specific loci and to separate transcripts with protein coding capability from other sources of LINE-1 RNA. RESULTS We provide a tool, L1EM that uses the expectation maximization algorithm to quantify LINE-1 RNA at each genomic locus, separating transcripts that are capable of generating retrotransposition from those that are not. We show the accuracy of L1EM on simulated data and against long read sequencing from HEK cells. AVAILABILITY AND IMPLEMENTATION L1EM is written in python. The source code along with the necessary annotations are available at https://github.com/FenyoLab/L1EM and distributed under GPLv3. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
| | - David Fenyö
- To whom correspondence should be addressed. or
| |
Collapse
|
358
|
|
359
|
Chung N, Jonaid GM, Quinton S, Ross A, Sexton CE, Alberto A, Clymer C, Churchill D, Navarro Leija O, Han MV. Transcriptome analyses of tumor-adjacent somatic tissues reveal genes co-expressed with transposable elements. Mob DNA 2019; 10:39. [PMID: 31497073 PMCID: PMC6720085 DOI: 10.1186/s13100-019-0180-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 08/14/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Despite the long-held assumption that transposons are normally only expressed in the germ-line, recent evidence shows that transcripts of transposable element (TE) sequences are frequently found in the somatic cells. However, the extent of variation in TE transcript levels across different tissues and different individuals are unknown, and the co-expression between TEs and host gene mRNAs have not been examined. RESULTS Here we report the variation in TE derived transcript levels across tissues and between individuals observed in the non-tumorous tissues collected for The Cancer Genome Atlas. We found core TE co-expression modules consisting mainly of transposons, showing correlated expression across broad classes of TEs. Despite this co-expression within tissues, there are individual TE loci that exhibit tissue-specific expression patterns, when compared across tissues. The core TE modules were negatively correlated with other gene modules that consisted of immune response genes in interferon signaling. KRAB Zinc Finger Proteins (KZFPs) were over-represented gene members of the TE modules, showing positive correlation across multiple tissues. But we did not find overlap between TE-KZFP pairs that are co-expressed and TE-KZFP pairs that are bound in published ChIP-seq studies. CONCLUSIONS We find unexpected variation in TE derived transcripts, within and across non-tumorous tissues. We describe a broad view of the RNA state for non-tumorous tissues exhibiting higher level of TE transcripts. Tissues with higher level of TE transcripts have a broad range of TEs co-expressed, with high expression of a large number of KZFPs, and lower RNA levels of immune genes.
Collapse
Affiliation(s)
- Nicky Chung
- School of Life Sciences, University of Nevada, Las Vegas, NV 89154 USA
| | - G. M. Jonaid
- School of Life Sciences, University of Nevada, Las Vegas, NV 89154 USA
| | - Sophia Quinton
- School of Life Sciences, University of Nevada, Las Vegas, NV 89154 USA
| | - Austin Ross
- School of Life Sciences, University of Nevada, Las Vegas, NV 89154 USA
| | - Corinne E. Sexton
- School of Life Sciences, University of Nevada, Las Vegas, NV 89154 USA
| | - Adrian Alberto
- Department of Computer Science, University of Nevada, Las Vegas, NV 89154 USA
| | - Cody Clymer
- Department of Computer Science, University of Nevada, Las Vegas, NV 89154 USA
| | - Daphnie Churchill
- Department of Computer Science, University of Nevada, Las Vegas, NV 89154 USA
| | - Omar Navarro Leija
- Department of Computer Science, University of Nevada, Las Vegas, NV 89154 USA
| | - Mira V. Han
- School of Life Sciences, University of Nevada, Las Vegas, NV 89154 USA
- Nevada Institute of Personalized Medicine, Las Vegas, NV 89154 USA
| |
Collapse
|
360
|
Bendall ML, de Mulder M, Iñiguez LP, Lecanda-Sánchez A, Pérez-Losada M, Ostrowski MA, Jones RB, Mulder LCF, Reyes-Terán G, Crandall KA, Ormsby CE, Nixon DF. Telescope: Characterization of the retrotranscriptome by accurate estimation of transposable element expression. PLoS Comput Biol 2019; 15:e1006453. [PMID: 31568525 PMCID: PMC6786656 DOI: 10.1371/journal.pcbi.1006453] [Citation(s) in RCA: 108] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 10/10/2019] [Accepted: 09/17/2019] [Indexed: 12/20/2022] Open
Abstract
Characterization of Human Endogenous Retrovirus (HERV) expression within the transcriptomic landscape using RNA-seq is complicated by uncertainty in fragment assignment because of sequence similarity. We present Telescope, a computational software tool that provides accurate estimation of transposable element expression (retrotranscriptome) resolved to specific genomic locations. Telescope directly addresses uncertainty in fragment assignment by reassigning ambiguously mapped fragments to the most probable source transcript as determined within a Bayesian statistical model. We demonstrate the utility of our approach through single locus analysis of HERV expression in 13 ENCODE cell types. When examined at this resolution, we find that the magnitude and breadth of the retrotranscriptome can be vastly different among cell types. Furthermore, our approach is robust to differences in sequencing technology and demonstrates that the retrotranscriptome has potential to be used for cell type identification. We compared our tool with other approaches for quantifying transposable element (TE) expression, and found that Telescope has the greatest resolution, as it estimates expression at specific TE insertions rather than at the TE subfamily level. Telescope performs highly accurate quantification of the retrotranscriptomic landscape in RNA-seq experiments, revealing a differential complexity in the transposable element biology of complex systems not previously observed. Telescope is available at https://github.com/mlbendall/telescope.
Collapse
Affiliation(s)
- Matthew L. Bendall
- Computational Biology Institute, Milken Institute School of Public Health, George Washington University, Washington, D.C., United States of America
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, N.Y., United States of America
| | - Miguel de Mulder
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, N.Y., United States of America
| | - Luis Pedro Iñiguez
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, N.Y., United States of America
- Center for Research in Infectious Diseases (CIENI), Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico
| | - Aarón Lecanda-Sánchez
- Center for Research in Infectious Diseases (CIENI), Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico
| | - Marcos Pérez-Losada
- Computational Biology Institute, Milken Institute School of Public Health, George Washington University, Washington, D.C., United States of America
- Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, George Washington University, Washington, D.C., United States of America
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal
| | - Mario A. Ostrowski
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada
- Keenan Research Centre for Biomedical Science of St. Michael's Hospital, Toronto, Ontario, Canada
| | - R. Brad Jones
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, N.Y., United States of America
| | - Lubbertus C. F. Mulder
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- The Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Gustavo Reyes-Terán
- Center for Research in Infectious Diseases (CIENI), Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico
| | - Keith A. Crandall
- Computational Biology Institute, Milken Institute School of Public Health, George Washington University, Washington, D.C., United States of America
- Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, George Washington University, Washington, D.C., United States of America
| | - Christopher E. Ormsby
- Center for Research in Infectious Diseases (CIENI), Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico
| | - Douglas F. Nixon
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, N.Y., United States of America
| |
Collapse
|
361
|
Navarro FCP, Hoops J, Bellfy L, Cerveira E, Zhu Q, Zhang C, Lee C, Gerstein MB. TeXP: Deconvolving the effects of pervasive and autonomous transcription of transposable elements. PLoS Comput Biol 2019; 15:e1007293. [PMID: 31425522 PMCID: PMC6715295 DOI: 10.1371/journal.pcbi.1007293] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 08/29/2019] [Accepted: 07/26/2019] [Indexed: 11/19/2022] Open
Abstract
The Long interspersed nuclear element 1 (LINE-1) is a primary source of genetic variation in humans and other mammals. Despite its importance, LINE-1 activity remains difficult to study because of its highly repetitive nature. Here, we developed and validated a method called TeXP to gauge LINE-1 activity accurately. TeXP builds mappability signatures from LINE-1 subfamilies to deconvolve the effect of pervasive transcription from autonomous LINE-1 activity. In particular, it apportions the multiple reads aligned to the many LINE-1 instances in the genome into these two categories. Using our method, we evaluated well-established cell lines, cell-line compartments and healthy tissues and found that the vast majority (91.7%) of transcriptome reads overlapping LINE-1 derive from pervasive transcription. We validated TeXP by independently estimating the levels of LINE-1 autonomous transcription using ddPCR, finding high concordance. Next, we applied our method to comprehensively measure LINE-1 activity across healthy somatic cells, while backing out the effect of pervasive transcription. Unexpectedly, we found that LINE-1 activity is present in many normal somatic cells. This finding contrasts with earlier studies showing that LINE-1 has limited activity in healthy somatic tissues, except for neuroprogenitor cells. Interestingly, we found that the amount of LINE-1 activity was associated with the with the amount of cell turnover, with tissues with low cell turnover rates (e.g. the adult central nervous system) showing lower LINE-1 activity. Altogether, our results show how accounting for pervasive transcription is critical to accurately quantify the activity of highly repetitive regions of the human genome. Repetitive sequences, such as LINEs, comprise more than half of the human genome. Due to their repetitive nature, LINEs are hard to grasp. In particular, we find that pervasive transcription is a major confounding factor in transcriptome data. We observe that, on average, more than 90% of LINE signal derives from pervasive transcription. To investigate this issue, we developed and validated a new method called TeXP. TeXP accounts and removes the effects of pervasive transcription when quantifying LINE activity. Our method uses the broad distribution of LINEs to estimate the effects of pervasive transcription. Using TeXP, we processed thousands of transcriptome datasets to uniformly, and unbiasedly measure LINE-1 activity across healthy somatic cells. By removing the pervasive transcription component, we find that (1) LINE-1 is broadly expressed in healthy somatic tissues; (2) Adult brain show small levels of LINE transcription and; (3) LINE-1 transcription level is correlated with tissue cell turnover. Our method thus offers insights into how repetitive sequences and influenced by pervasive transcription. Moreover, we uncover the activity of LINE-1 in somatic tissues at an unmatched scale.
Collapse
Affiliation(s)
- Fabio CP Navarro
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
| | - Jacob Hoops
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
| | - Lauren Bellfy
- The Jackson Laboratory for Genomic Medicine, Farmington, Michigan, United States of America
| | - Eliza Cerveira
- The Jackson Laboratory for Genomic Medicine, Farmington, Michigan, United States of America
| | - Qihui Zhu
- The Jackson Laboratory for Genomic Medicine, Farmington, Michigan, United States of America
| | - Chengsheng Zhang
- The Jackson Laboratory for Genomic Medicine, Farmington, Michigan, United States of America
| | - Charles Lee
- The Jackson Laboratory for Genomic Medicine, Farmington, Michigan, United States of America
- Department of Life Sciences, Ewha Womans University, Seoul, Korea
| | - Mark B. Gerstein
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
- Department of Computer Science, Yale University, New Haven, Connecticut, United States of America
- * E-mail:
| |
Collapse
|
362
|
Guffanti G, Bartlett A, Klengel T, Klengel C, Hunter R, Glinsky G, Macciardi F. Novel Bioinformatics Approach Identifies Transcriptional Profiles of Lineage-Specific Transposable Elements at Distinct Loci in the Human Dorsolateral Prefrontal Cortex. Mol Biol Evol 2019; 35:2435-2453. [PMID: 30053206 PMCID: PMC6188555 DOI: 10.1093/molbev/msy143] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Expression of transposable elements (TE) is transiently activated during human preimplantation embryogenesis in a developmental stage- and cell type-specific manner and TE-mediated epigenetic regulation is intrinsically wired in developmental genetic networks in human embryos and embryonic stem cells. However, there are no systematic studies devoted to a comprehensive analysis of the TE transcriptome in human adult organs and tissues, including human neural tissues. To investigate TE expression in the human Dorsolateral Prefrontal Cortex (DLPFC), we developed and validated a straightforward analytical approach to chart quantitative genome-wide expression profiles of all annotated TE loci based on unambiguous mapping of discrete TE-encoded transcripts using a de novo assembly strategy. To initially evaluate the potential regulatory impact of DLPFC-expressed TE, we adopted a comparative evolutionary genomics approach across humans, primates, and rodents to document conservation patterns, lineage-specificity, and colocalizations with transcription factor binding sites mapped within primate- and human-specific TE. We identified 654,665 transcripts expressed from 477,507 distinct loci of different TE classes and families, the majority of which appear to have originated from primate-specific sequences. We discovered 4,687 human-specific and transcriptionally active TEs in DLPFC, of which the prominent majority (80.2%) appears spliced. Our analyses revealed significant associations of DLPFC-expressed TE with primate- and human-specific transcription factor binding sites, suggesting potential cross-talks of concordant regulatory functions. We identified 1,689 TEs differentially expressed in the DLPFC of Schizophrenia patients, a majority of which is located within introns of 1,137 protein-coding genes. Our findings imply that identified DLPFC-expressed TEs may affect human brain structures and functions following different evolutionary trajectories. On one side, hundreds of thousands of TEs maintained a remarkably high conservation for ∼8 My of primates’ evolution, suggesting that they are likely conveying evolutionary-constrained primate-specific regulatory functions. In parallel, thousands of transcriptionally active human-specific TE loci emerged more recently, suggesting that they could be relevant for human-specific behavioral or cognitive functions.
Collapse
Affiliation(s)
- Guia Guffanti
- Department of Psychiatry, Harvard Medical School, Cambridge, MA.,Division of Depression and Anxiety, McLean Hospital, Belmont, MA
| | - Andrew Bartlett
- Department of Psychology, University of Massachusetts, Boston, MA
| | - Torsten Klengel
- Department of Psychiatry, Harvard Medical School, Cambridge, MA.,Division of Depression and Anxiety, McLean Hospital, Belmont, MA.,Department of Psychiatry and Psychotherapy, University Medical Center Göttingen, Georg-August-University, Goettingen, Germany
| | - Claudia Klengel
- Department of Psychiatry, Harvard Medical School, Cambridge, MA.,Division of Depression and Anxiety, McLean Hospital, Belmont, MA
| | - Richard Hunter
- Department of Psychology, University of Massachusetts, Boston, MA
| | - Gennadi Glinsky
- Translational & Functional Genomics, Institute of Engineering in Medicine, University of California San Diego, La Jolla, CA
| | - Fabio Macciardi
- Department of Psychiatry and Human Behavior, University of California Irvine, Irvine, CA
| |
Collapse
|
363
|
Chen Z, Zhang Y. Loss of DUX causes minor defects in zygotic genome activation and is compatible with mouse development. Nat Genet 2019; 51:947-951. [PMID: 31133747 PMCID: PMC6545155 DOI: 10.1038/s41588-019-0418-7] [Citation(s) in RCA: 147] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 04/11/2019] [Indexed: 11/09/2022]
Affiliation(s)
- Zhiyuan Chen
- Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA.,Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA.,Division of Hematology/Oncology, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
| | - Yi Zhang
- Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA. .,Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA. .,Division of Hematology/Oncology, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA. .,Department of Genetics, Harvard Medical School, Boston, MA, USA. .,Harvard Stem Cell Institute, Boston, MA, USA.
| |
Collapse
|
364
|
Kaul T, Morales ME, Smither E, Baddoo M, Belancio VP, Deininger P. RNA Next-Generation Sequencing and a Bioinformatics Pipeline to Identify Expressed LINE-1s at the Locus-Specific Level. J Vis Exp 2019. [PMID: 31157783 DOI: 10.3791/59771] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Long INterspersed Elements-1 (LINEs/L1s) are repetitive elements that can copy and randomly insert in the genome resulting in genomic instability and mutagenesis. Understanding the expression patterns of L1 loci at the individual level will lend to the understanding of the biology of this mutagenic element. This autonomous element makes up a significant portion of the human genome with over 500,000 copies, though 99% are truncated and defective. However, their abundance and dominant number of defective copies make it challenging to identify authentically expressed L1s from L1-related sequences expressed as part of other genes. It is also challenging to identify which specific L1 locus is expressed due to the repetitive nature of the elements. Overcoming these challenges, we present an RNA-Seq bioinformatic approach to identify L1 expression at the locus specific level. In summary, we collect cytoplasmic RNA, select for polyadenylated transcripts, and utilize strand-specific RNA-Seq analyses to uniquely map reads to L1 loci in the human reference genome. We visually curate each L1 locus with uniquely mapped reads to confirm transcription from its own promoter and adjust mapped transcript reads to account for mappability of each individual L1 locus. This approach was applied to a prostate tumor cell line, DU145, to demonstrate the ability of this protocol to detect expression from a small number of the full-length L1 elements.
Collapse
Affiliation(s)
| | | | | | - Melody Baddoo
- Tulane Cancer Center, Tulane University; Department of Pathology, Tulane University
| | - Victoria P Belancio
- Tulane Cancer Center, Tulane University; Department of Structural and Cellular Biology, Tulane University
| | - Prescott Deininger
- Tulane Cancer Center, Tulane University; Department of Epidemiology, Tulane University;
| |
Collapse
|
365
|
Babarinde IA, Li Y, Hutchins AP. Computational Methods for Mapping, Assembly and Quantification for Coding and Non-coding Transcripts. Comput Struct Biotechnol J 2019; 17:628-637. [PMID: 31193391 PMCID: PMC6526290 DOI: 10.1016/j.csbj.2019.04.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 04/24/2019] [Accepted: 04/29/2019] [Indexed: 12/17/2022] Open
Abstract
The measurement of gene expression has long provided significant insight into biological functions. The development of high-throughput short-read sequencing technology has revealed transcriptional complexity at an unprecedented scale, and informed almost all areas of biology. However, as researchers have sought to gather more insights from the data, these new technologies have also increased the computational analysis burden. In this review, we describe typical computational pipelines for RNA-Seq analysis and discuss their strengths and weaknesses for the assembly, quantification and analysis of coding and non-coding RNAs. We also discuss the assembly of transposable elements into transcripts, and the difficulty these repetitive elements pose. In summary, RNA-Seq is a powerful technology that is likely to remain a key asset in the biologist's toolkit.
Collapse
Affiliation(s)
| | | | - Andrew P. Hutchins
- Department of Biology, Southern University of Science and Technology, 1088 Xueyuan Lu, Shenzhen, China
| |
Collapse
|
366
|
Choi J, Strickler SR, Richards EJ. Loss of CRWN Nuclear Proteins Induces Cell Death and Salicylic Acid Defense Signaling. PLANT PHYSIOLOGY 2019; 179:1315-1329. [PMID: 30696746 PMCID: PMC6446779 DOI: 10.1104/pp.18.01020] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 01/18/2019] [Indexed: 05/09/2023]
Abstract
Defects in the nuclear lamina of animal cell nuclei have dramatic effects on nuclear structure and gene expression as well as diverse physiological manifestations. We report that deficiencies in CROWDED NUCLEI (CRWN), which are candidate nuclear lamina proteins in Arabidopsis (Arabidopsis thaliana), trigger widespread changes in transcript levels and whole-plant phenotypes, including dwarfing and spontaneous cell death lesions. These phenotypes are caused in part by ectopic induction of plant defense responses via the salicylic acid pathway. Loss of CRWN proteins induces the expression of the salicylic acid biosynthetic gene ISOCHORISMATE SYNTHASE1, which leads to spontaneous defense responses in crwn1 crwn2 and crwn1 crwn4 mutants, which are deficient in two of the four CRWN paralogs. The symptoms of ectopic defense response, including pathogenesis marker gene expression and cell death, increase in older crwn double mutants. These age-dependent effects are postulated to reflect an increase in nuclear dysfunction or damage over time, a phenomenon reminiscent of aging effects seen in animal nuclei and in some human laminopathy patients.
Collapse
Affiliation(s)
- Junsik Choi
- Section of Plant Biology, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853
- Boyce Thompson Institute, Ithaca, New York 14853
| | | | | |
Collapse
|
367
|
Benayoun BA, Pollina EA, Singh PP, Mahmoudi S, Harel I, Casey KM, Dulken BW, Kundaje A, Brunet A. Remodeling of epigenome and transcriptome landscapes with aging in mice reveals widespread induction of inflammatory responses. Genome Res 2019; 29:697-709. [PMID: 30858345 PMCID: PMC6442391 DOI: 10.1101/gr.240093.118] [Citation(s) in RCA: 225] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 01/25/2019] [Indexed: 12/20/2022]
Abstract
Aging is accompanied by the functional decline of tissues. However, a systematic study of epigenomic and transcriptomic changes across tissues during aging is missing. Here, we generated chromatin maps and transcriptomes from four tissues and one cell type from young, middle-aged, and old mice—yielding 143 high-quality data sets. We focused on chromatin marks linked to gene expression regulation and cell identity: histone H3 trimethylation at lysine 4 (H3K4me3), a mark enriched at promoters, and histone H3 acetylation at lysine 27 (H3K27ac), a mark enriched at active enhancers. Epigenomic and transcriptomic landscapes could easily distinguish between ages, and machine-learning analysis showed that specific epigenomic states could predict transcriptional changes during aging. Analysis of data sets from all tissues identified recurrent age-related chromatin and transcriptional changes in key processes, including the up-regulation of immune system response pathways such as the interferon response. The up-regulation of the interferon response pathway with age was accompanied by increased transcription and chromatin remodeling at specific endogenous retroviral sequences. Pathways misregulated during mouse aging across tissues, notably innate immune pathways, were also misregulated with aging in other vertebrate species—African turquoise killifish, rat, and humans—indicating common signatures of age across species. To date, our data set represents the largest multitissue epigenomic and transcriptomic data set for vertebrate aging. This resource identifies chromatin and transcriptional states that are characteristic of young tissues, which could be leveraged to restore aspects of youthful functionality to old tissues.
Collapse
Affiliation(s)
- Bérénice A Benayoun
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Elizabeth A Pollina
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Param Priya Singh
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Salah Mahmoudi
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Itamar Harel
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Kerriann M Casey
- Department of Comparative Medicine, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Ben W Dulken
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Anshul Kundaje
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA.,Department of Computer Science, Stanford University, Stanford, California 94305, USA
| | - Anne Brunet
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA.,Paul F. Glenn Laboratories for the Biology of Aging, Stanford University, Stanford, California 94305, USA
| |
Collapse
|
368
|
Stein CB, Genzor P, Mitra S, Elchert AR, Ipsaro JJ, Benner L, Sobti S, Su Y, Hammell M, Joshua-Tor L, Haase AD. Decoding the 5' nucleotide bias of PIWI-interacting RNAs. Nat Commun 2019; 10:828. [PMID: 30783109 PMCID: PMC6381166 DOI: 10.1038/s41467-019-08803-z] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 01/30/2019] [Indexed: 12/26/2022] Open
Abstract
PIWI-interacting RNAs (piRNAs) are at the center of a small RNA-based immune system that defends genomes against the deleterious action of mobile genetic elements (transposons). PiRNAs are highly variable in sequence with extensive targeting potential. Their diversity is restricted by their preference to start with a Uridine (U) at the 5' most position (1U-bias), a bias that remains poorly understood. Here we uncover that the 1U-bias of Piwi-piRNAs is established by consecutive discrimination against all nucleotides but U, first during piRNA biogenesis and then upon interaction with Piwi's specificity loop. Sequence preferences during piRNA processing also restrict U across the piRNA body with the potential to directly impact target recognition. Overall, the uncovered signatures could modulate specificity and efficacy of piRNA-mediated transposon restriction, and provide a substrate for purifying selection in the ongoing arms race between genomes and their mobile parasites.
Collapse
Affiliation(s)
- Chad B Stein
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.,PhD Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA 02115, USA
| | - Pavol Genzor
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Sanga Mitra
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Alexandra R Elchert
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Jonathan J Ipsaro
- W.M. Keck Structural Biology Laboratory, Howard Hughes Medical Institute, Cold Spring Harbor, 11724, USA.,Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Leif Benner
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.,Department of Biology, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Sushil Sobti
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Yijun Su
- National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Molly Hammell
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Leemor Joshua-Tor
- W.M. Keck Structural Biology Laboratory, Howard Hughes Medical Institute, Cold Spring Harbor, 11724, USA.,Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Astrid D Haase
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.
| |
Collapse
|
369
|
Transposable elements are regulated by context-specific patterns of chromatin marks in mouse embryonic stem cells. Nat Commun 2019; 10:34. [PMID: 30604769 PMCID: PMC6318327 DOI: 10.1038/s41467-018-08006-y] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 12/11/2018] [Indexed: 01/18/2023] Open
Abstract
The majority of mammalian genomes are devoted to transposable elements (TEs). Whilst TEs are increasingly recognized for their important biological functions, they are a potential danger to genomic stability and are carefully regulated by the epigenetic system. However, the full complexity of this regulatory system is not understood. Here, using mouse embryonic stem cells, we show that TEs are suppressed by heterochromatic marks like H3K9me3, and are also labelled by all major types of chromatin modification in complex patterns, including bivalent activatory and repressive marks. We identified 29 epigenetic modifiers that significantly deregulated at least one type of TE. The loss of Setdb1, Ncor2, Rnf2, Kat5, Prmt5, Uhrf1, and Rrp8 caused widespread changes in TE expression and chromatin accessibility. These effects were context-specific, with different chromatin modifiers regulating the expression and chromatin accessibility of specific subsets of TEs. Our work reveals the complex patterns of epigenetic regulation of TEs. Transposable elements (TEs) fulfill essential but poorly understood roles in genome organization and gene expression control. Here the authors show that the regulation of TEs occurs through overlapping epigenetic mechanisms that control the expression and chromatin signatures at TEs.
Collapse
|
370
|
Panzade G, Gangwar I, Awasthi S, Sharma N, Shankar R. Plant Regulomics Portal (PRP): a comprehensive integrated regulatory information and analysis portal for plant genomes. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2019; 2019:5650983. [PMID: 31796964 PMCID: PMC6891001 DOI: 10.1093/database/baz130] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 10/16/2019] [Accepted: 10/17/2019] [Indexed: 12/20/2022]
Abstract
Gene regulation is a highly complex and networked phenomenon where multiple tiers of control determine the cell state in a spatio-temporal manner. Among these, the transcription factors, DNA and histone modifications, and post-transcriptional control by small RNAs like miRNAs serve as major regulators. An understanding of the integrative and spatio-temporal impact of these regulatory factors can provide better insights into the state of a ‘cell system’. Yet, there are limited resources available to this effect. Therefore, we hereby report an integrative information portal (Plant Regulomics Portal; PRP) for plants for the first time. The portal has been developed by integrating a huge amount of curated data from published sources, RNA-, methylome- and sRNA/miRNA sequencing, histone modifications and repeats, gene ontology, digital gene expression and characterized pathways. The key features of the portal include a regulatory search engine for fetching numerous analytical outputs and tracks of the abovementioned regulators and also a genome browser for integrated visualization of the search results. It also has numerous analytical features for analyses of transcription factors (TFs) and sRNA/miRNA, spot-specific methylation, gene expression and interactions and details of pathways for any given genomic element. It can also provide information on potential RdDM regulation, while facilitating enrichment analysis, generation of visually rich plots and downloading of data in a selective manner. Visualization of intricate biological networks is an important feature which utilizes the Neo4j Graph database making analysis of relationships and long-range system viewing possible. Till date, PRP hosts 571-GB processed data for four plant species namely Arabidopsis thaliana, Oryza sativa subsp. japonica, Zea mays and Glycine max. Database URL: https://scbb.ihbt.res.in/PRP
Collapse
Affiliation(s)
- Ganesh Panzade
- Studio of Computational Biology & Bioinformatics, Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Kangra, Himachal Pradesh 176061, India.,Academy of Scientific & Innovative Research (AcSIR), CSIR-HRDC Campus, Postal Staff College Area, Sector 19, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh 201002, India.,Division of Biology, Kansas State University, Zinovyeva Lab, 28 Ackert Hall, Manhattan, KS, USA, 66506
| | - Indu Gangwar
- Studio of Computational Biology & Bioinformatics, Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Kangra, Himachal Pradesh 176061, India.,Academy of Scientific & Innovative Research (AcSIR), CSIR-HRDC Campus, Postal Staff College Area, Sector 19, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh 201002, India
| | - Supriya Awasthi
- Studio of Computational Biology & Bioinformatics, Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Kangra, Himachal Pradesh 176061, India
| | - Nitesh Sharma
- Studio of Computational Biology & Bioinformatics, Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Kangra, Himachal Pradesh 176061, India.,Academy of Scientific & Innovative Research (AcSIR), CSIR-HRDC Campus, Postal Staff College Area, Sector 19, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh 201002, India
| | - Ravi Shankar
- Studio of Computational Biology & Bioinformatics, Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Kangra, Himachal Pradesh 176061, India.,Academy of Scientific & Innovative Research (AcSIR), CSIR-HRDC Campus, Postal Staff College Area, Sector 19, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh 201002, India
| |
Collapse
|
371
|
Pereira GC, Sanchez L, Schaughency PM, Rubio-Roldán A, Choi JA, Planet E, Batra R, Turelli P, Trono D, Ostrow LW, Ravits J, Kazazian HH, Wheelan SJ, Heras SR, Mayer J, García-Pérez JL, Goodier JL. Properties of LINE-1 proteins and repeat element expression in the context of amyotrophic lateral sclerosis. Mob DNA 2018; 9:35. [PMID: 30564290 PMCID: PMC6295051 DOI: 10.1186/s13100-018-0138-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 11/15/2018] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease involving loss of motor neurons and having no known cure and uncertain etiology. Several studies have drawn connections between altered retrotransposon expression and ALS. Certain features of the LINE-1 (L1) retrotransposon-encoded ORF1 protein (ORF1p) are analogous to those of neurodegeneration-associated RNA-binding proteins, including formation of cytoplasmic aggregates. In this study we explore these features and consider possible links between L1 expression and ALS. RESULTS We first considered factors that modulate aggregation and subcellular distribution of LINE-1 ORF1p, including nuclear localization. Changes to some ORF1p amino acid residues alter both retrotransposition efficiency and protein aggregation dynamics, and we found that one such polymorphism is present in endogenous L1s abundant in the human genome. We failed, however, to identify CRM1-mediated nuclear export signals in ORF1p nor strict involvement of cell cycle in endogenous ORF1p nuclear localization in human 2102Ep germline teratocarcinoma cells. Some proteins linked with ALS bind and colocalize with L1 ORF1p ribonucleoprotein particles in cytoplasmic RNA granules. Increased expression of several ALS-associated proteins, including TAR DNA Binding Protein (TDP-43), strongly limits cell culture retrotransposition, while some disease-related mutations modify these effects. Using quantitative reverse transcription PCR (RT-qPCR) of ALS tissues and reanalysis of publicly available RNA-Seq datasets, we asked if changes in expression of retrotransposons are associated with ALS. We found minimal altered expression in sporadic ALS tissues but confirmed a previous report of differential expression of many repeat subfamilies in C9orf72 gene-mutated ALS patients. CONCLUSIONS Here we extended understanding of the subcellular localization dynamics of the aggregation-prone LINE-1 ORF1p RNA-binding protein. However, we failed to find compelling evidence for misregulation of LINE-1 retrotransposons in sporadic ALS nor a clear effect of ALS-associated TDP-43 protein on L1 expression. In sum, our study reveals that the interplay of active retrotransposons and the molecular features of ALS are more complex than anticipated. Thus, the potential consequences of altered retrotransposon activity for ALS and other neurodegenerative disorders are worthy of continued investigation.
Collapse
Affiliation(s)
- Gavin C. Pereira
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland USA
| | - Laura Sanchez
- GENYO. Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, Granada, Spain
| | - Paul M. Schaughency
- Oncology Center-Cancer Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland USA
| | - Alejandro Rubio-Roldán
- GENYO. Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, Granada, Spain
| | - Jungbin A. Choi
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland USA
| | - Evarist Planet
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Ranjan Batra
- Department of Neurosciences, School of Medicine, University of California at San Diego, San Diego, California USA
| | - Priscilla Turelli
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Didier Trono
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Lyle W. Ostrow
- Neuromuscular Division, Johns Hopkins University School of Medicine, Baltimore, Maryland USA
| | - John Ravits
- Department of Neurosciences, School of Medicine, University of California at San Diego, San Diego, California USA
| | - Haig H. Kazazian
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland USA
| | - Sarah J. Wheelan
- Oncology Center-Cancer Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland USA
| | - Sara R. Heras
- GENYO. Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, Granada, Spain
- Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, Granada, Spain
| | - Jens Mayer
- Department of Human Genetics, Medical Faculty, University of Saarland, Homburg/Saar, Germany
| | - 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
| | - John L. Goodier
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland USA
| |
Collapse
|
372
|
Lai YS, Zhang W, Zhang X, Shen D, Wang H, Qiu Y, Song J, Li X. Integrative Analysis of Transcriptomic and Methylomic Data in Photoperiod-Dependent Regulation of Cucumber Sex Expression. G3 (BETHESDA, MD.) 2018; 8:3981-3991. [PMID: 30377155 PMCID: PMC6288824 DOI: 10.1534/g3.118.200755] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 10/29/2018] [Indexed: 12/31/2022]
Abstract
The cucumber (Cucumis sativus) is characterized by its diversity and seasonal plasticity in sexual type. A long day length condition significantly decreased the cucumber female flower ratio by 17.7-52.9%, and the effect of photoperiod treatment is more significant under low temperature than under high temperature. Transcriptome analysis indicates that the photoperiod treatment preferentially significantly influenced flower development processes, particularly MADS-box genes in shoot apices. The long-day treatment resulted in predominantly transposable element (TE)- and gene-associated CHH-types of DNA methylation changes. Nevertheless, there was significant enrichment of CG- and CHG-types of DNA methylation changes nearing transcription start sites (TSSs)/transcription end sites (TESs) and gene bodies, respectively. Predominantly negative association between differentially methylated regions (DMRs) and differentially expressed genes (DEGs) were observed which implied epiregulation of DEGs. Two MADS-box genes that were significantly downregulated by long photoperiod showed significant hypermethylation in promoter regions that is essentially TE-rich. This study indicates MADS-box genes which are partially regulated by promoter methylation state may mediate photoperiod-dependent regulation of cucumber sex expression.
Collapse
Affiliation(s)
- Yun-Song Lai
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Institute of Pomology & Olericulture, Sichuan Agricultural University, Chengdu 611180, China
| | - Wei Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiaohui Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Di Shen
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Haiping Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yang Qiu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jiangping Song
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xixiang Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| |
Collapse
|
373
|
Lai YS, Shen D, Zhang W, Zhang X, Qiu Y, Wang H, Dou X, Li S, Wu Y, Song J, Ji G, Li X. Temperature and photoperiod changes affect cucumber sex expression by different epigenetic regulations. BMC PLANT BIOLOGY 2018; 18:268. [PMID: 30400867 PMCID: PMC6220452 DOI: 10.1186/s12870-018-1490-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Accepted: 10/19/2018] [Indexed: 05/25/2023]
Abstract
BACKGROUND Cucumbers (Cucumis sativus) are known for their plasticity in sex expression. DNA methylation status determines gene activity but is susceptible to environmental condition changes. Thus, DNA methylation-based epigenetic regulation may at least partially account for the instability of cucumber sex expression. Do temperature and photoperiod that are the two most important environmental factors have equal effect on cucumber sex expression by similar epigenetic regulation mechanism? To answer this question, we did a two-factor experiment of temperature and photoperiod and generated methylome and transcriptome data from cucumber shoot apices. RESULTS The seasonal change in the femaleness of a cucumber core germplasm collection was investigated over five consecutive years. As a result, 71.3% of the 359 cucumber accessions significantly decreased their femaleness in early autumn when compared with spring. High temperature and long-day photoperiod treatments, which mimic early autumn conditions, are both unfavorable for female flower formation, and temperature is the predominant factor. High temperatures and long-day treatments both predominantly resulted in hypermethylation compared to demethylation, and temperature effect was decisive. The targeted cytosines shared in high-temperature and long-day photoperiod treatment showed the same change in DNA methylation level. Moreover, differentially expressed TEs (DETs) and the predicted epiregulation sites were clustered across chromosomes, and importantly, these sites were reproducible among different treatments. Essentially, the photoperiod treatment preferentially and significantly influenced flower development processes, while temperature treatment produced stronger responses from phytohormone-pathway-related genes. Cucumber AGAMOUS was likely epicontrolled exclusively by photoperiod while CAULIFLOWER A and CsACO3 were likely epicontrolled by both photoperiod and temperature. CONCLUSIONS Seasonal change of sex expression is a germplasm-wide phenomenon in cucumbers. High temperature and long-day photoperiod might have the same effect on the methylome via the same mechanism of gene-TE interaction but resulted in different epicontrol sites that account for different mechanisms between temperature- and photoperiod-dependent sex expression changes.
Collapse
Affiliation(s)
- Yun-Song Lai
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Institute of Pomology & Olericulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Di Shen
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Wei Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiaohui Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yang Qiu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Haiping Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xinxin Dou
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Sigeng Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yuanqi Wu
- Institute of Pomology & Olericulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jiangping Song
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Guanyu Ji
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xixiang Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| |
Collapse
|
374
|
Göbel U, Arce AL, He F, Rico A, Schmitz G, de Meaux J. Robustness of Transposable Element Regulation but No Genomic Shock Observed in Interspecific Arabidopsis Hybrids. Genome Biol Evol 2018; 10:1403-1415. [PMID: 29788048 PMCID: PMC6007786 DOI: 10.1093/gbe/evy095] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/16/2018] [Indexed: 12/23/2022] Open
Abstract
The merging of two divergent genomes in a hybrid is believed to trigger a “genomic shock”, disrupting gene regulation and transposable element (TE) silencing. Here, we tested this expectation by comparing the pattern of expression of transposable elements in their native and hybrid genomic context. For this, we sequenced the transcriptome of the Arabidopsis thaliana genotype Col-0, the A. lyrata genotype MN47 and their F1 hybrid. Contrary to expectations, we observe that the level of TE expression in the hybrid is strongly correlated to levels in the parental species. We detect that at most 1.1% of expressed transposable elements belonging to two specific subfamilies change their expression level upon hybridization. Most of these changes, however, are of small magnitude. We observe that the few hybrid-specific modifications in TE expression are more likely to occur when TE insertions are close to genes. In addition, changes in epigenetic histone marks H3K9me2 and H3K27me3 following hybridization do not coincide with TEs with changed expression. Finally, we further examined TE expression in parents and hybrids exposed to severe dehydration stress. Despite the major reorganization of gene and TE expression by stress, we observe that hybridization does not lead to increased disorganization of TE expression in the hybrid. Although our study did not examine TE transposition activity in hybrids, the examination of the transcriptome shows that TE expression is globally robust to hybridization. The term “genomic shock” is perhaps not appropriate to describe transcriptional modification in a viable hybrid merging divergent genomes.
Collapse
Affiliation(s)
- Ulrike Göbel
- Botanical Institute, University of Cologne, Germany
| | - Agustin L Arce
- Laboratorio de Biología del ARN, Instituto de Agrobiotecnología del Litoral (CONICET-UNL), 3000 Santa Fe, Argentina
| | - Fei He
- Botanical Institute, University of Cologne, Germany
| | - Alain Rico
- Thermo Fisher Scientific, Villebon-sur-Yvette, France
| | | | | |
Collapse
|
375
|
Guo J, Grow EJ, Mlcochova H, Maher GJ, Lindskog C, Nie X, Guo Y, Takei Y, Yun J, Cai L, Kim R, Carrell DT, Goriely A, Hotaling JM, Cairns BR. The adult human testis transcriptional cell atlas. Cell Res 2018; 28:1141-1157. [PMID: 30315278 PMCID: PMC6274646 DOI: 10.1038/s41422-018-0099-2] [Citation(s) in RCA: 437] [Impact Index Per Article: 62.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 09/07/2018] [Accepted: 09/19/2018] [Indexed: 11/09/2022] Open
Abstract
Human adult spermatogenesis balances spermatogonial stem cell (SSC) self-renewal and differentiation, alongside complex germ cell-niche interactions, to ensure long-term fertility and faithful genome propagation. Here, we performed single-cell RNA sequencing of ~6500 testicular cells from young adults. We found five niche/somatic cell types (Leydig, myoid, Sertoli, endothelial, macrophage), and observed germline-niche interactions and key human-mouse differences. Spermatogenesis, including meiosis, was reconstructed computationally, revealing sequential coding, non-coding, and repeat-element transcriptional signatures. Interestingly, we identified five discrete transcriptional/developmental spermatogonial states, including a novel early SSC state, termed State 0. Epigenetic features and nascent transcription analyses suggested developmental plasticity within spermatogonial States. To understand the origin of State 0, we profiled testicular cells from infants, and identified distinct similarities between adult State 0 and infant SSCs. Overall, our datasets describe key transcriptional and epigenetic signatures of the normal adult human testis, and provide new insights into germ cell developmental transitions and plasticity.
Collapse
Affiliation(s)
- Jingtao Guo
- Department of Oncological Sciences and Huntsman Cancer Institute, Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, UT, 84112, USA.,Department of Surgery (Andrology/Urology), Center for Reconstructive Urology and Men's Health, University of Utah Health Sciences Center, Salt Lake City, UT, 84122, USA
| | - Edward J Grow
- Department of Oncological Sciences and Huntsman Cancer Institute, Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, UT, 84112, USA
| | - Hana Mlcochova
- Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX39DS, UK
| | - Geoffrey J Maher
- Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX39DS, UK
| | - Cecilia Lindskog
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, SE-751 85, Uppsala, Sweden
| | - Xichen Nie
- Department of Oncological Sciences and Huntsman Cancer Institute, Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, UT, 84112, USA
| | - Yixuan Guo
- Department of Oncological Sciences and Huntsman Cancer Institute, Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, UT, 84112, USA
| | - Yodai Takei
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Jina Yun
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Long Cai
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Robin Kim
- Section of Transplantation, Department of Surgery, University of Utah School of Medicine, Salt Lake City, UT, 84132, USA
| | - Douglas T Carrell
- Department of Surgery (Andrology/Urology), Center for Reconstructive Urology and Men's Health, University of Utah Health Sciences Center, Salt Lake City, UT, 84122, USA
| | - Anne Goriely
- Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX39DS, UK
| | - James M Hotaling
- Department of Surgery (Andrology/Urology), Center for Reconstructive Urology and Men's Health, University of Utah Health Sciences Center, Salt Lake City, UT, 84122, USA
| | - Bradley R Cairns
- Department of Oncological Sciences and Huntsman Cancer Institute, Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, UT, 84112, USA.
| |
Collapse
|
376
|
|
377
|
Attig J, Agostini F, Gooding C, Chakrabarti AM, Singh A, Haberman N, Zagalak JA, Emmett W, Smith CWJ, Luscombe NM, Ule J. Heteromeric RNP Assembly at LINEs Controls Lineage-Specific RNA Processing. Cell 2018; 174:1067-1081.e17. [PMID: 30078707 PMCID: PMC6108849 DOI: 10.1016/j.cell.2018.07.001] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Revised: 04/23/2018] [Accepted: 07/01/2018] [Indexed: 12/30/2022]
Abstract
Long mammalian introns make it challenging for the RNA processing machinery to identify exons accurately. We find that LINE-derived sequences (LINEs) contribute to this selection by recruiting dozens of RNA-binding proteins (RBPs) to introns. This includes MATR3, which promotes binding of PTBP1 to multivalent binding sites within LINEs. Both RBPs repress splicing and 3' end processing within and around LINEs. Notably, repressive RBPs preferentially bind to evolutionarily young LINEs, which are located far from exons. These RBPs insulate the LINEs and the surrounding intronic regions from RNA processing. Upon evolutionary divergence, changes in RNA motifs within LINEs lead to gradual loss of their insulation. Hence, older LINEs are located closer to exons, are a common source of tissue-specific exons, and increasingly bind to RBPs that enhance RNA processing. Thus, LINEs are hubs for the assembly of repressive RBPs and also contribute to the evolution of new, lineage-specific transcripts in mammals. VIDEO ABSTRACT.
Collapse
Affiliation(s)
- Jan Attig
- The Francis Crick Institute, Midland Road 1, Kings Cross, London NW1 1AT, UK; Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK.
| | - Federico Agostini
- The Francis Crick Institute, Midland Road 1, Kings Cross, London NW1 1AT, UK
| | - Clare Gooding
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, UK
| | - Anob M Chakrabarti
- The Francis Crick Institute, Midland Road 1, Kings Cross, London NW1 1AT, UK; Department of Genetics, Environment and Evolution, UCL Genetics Institute, Gower Street, London WC1E 6BT, UK
| | - Aarti Singh
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK; Department of Comparative Biomedical Sciences, The Royal Veterinary College, Royal College Street, London NW1 0TU, UK
| | - Nejc Haberman
- The Francis Crick Institute, Midland Road 1, Kings Cross, London NW1 1AT, UK; Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - Julian A Zagalak
- The Francis Crick Institute, Midland Road 1, Kings Cross, London NW1 1AT, UK; Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - Warren Emmett
- The Francis Crick Institute, Midland Road 1, Kings Cross, London NW1 1AT, UK; Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK; Department of Genetics, Environment and Evolution, UCL Genetics Institute, Gower Street, London WC1E 6BT, UK
| | - Christopher W J Smith
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, UK
| | - Nicholas M Luscombe
- The Francis Crick Institute, Midland Road 1, Kings Cross, London NW1 1AT, UK; Department of Genetics, Environment and Evolution, UCL Genetics Institute, Gower Street, London WC1E 6BT, UK; Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa 904-0495, Japan
| | - Jernej Ule
- The Francis Crick Institute, Midland Road 1, Kings Cross, London NW1 1AT, UK; Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK.
| |
Collapse
|
378
|
Warkocki Z, Krawczyk PS, Adamska D, Bijata K, Garcia-Perez JL, Dziembowski A. Uridylation by TUT4/7 Restricts Retrotransposition of Human LINE-1s. Cell 2018; 174:1537-1548.e29. [PMID: 30122351 PMCID: PMC6191937 DOI: 10.1016/j.cell.2018.07.022] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 05/27/2018] [Accepted: 07/18/2018] [Indexed: 12/19/2022]
Abstract
LINE-1 retrotransposition is tightly restricted by layers of regulatory control, with epigenetic pathways being the best characterized. Looking at post-transcriptional regulation, we now show that LINE-1 mRNA 3' ends are pervasively uridylated in various human cellular models and in mouse testes. TUT4 and TUT7 uridyltransferases catalyze the modification and function in cooperation with the helicase/RNPase MOV10 to counteract the RNA chaperone activity of the L1-ORF1p retrotransposon protein. Uridylation potently restricts LINE-1 retrotransposition by a multilayer mechanism depending on differential subcellular localization of the uridyltransferases. We propose that uridine residues added by TUT7 in the cytoplasm inhibit initiation of reverse transcription of LINE-1 mRNAs once they are reimported to the nucleus, whereas uridylation by TUT4, which is enriched in cytoplasmic foci, destabilizes mRNAs. These results provide a model for the post-transcriptional restriction of LINE-1, revealing a key physiological role for TUT4/7-mediated uridylation in maintaining genome stability.
Collapse
Affiliation(s)
- Zbigniew Warkocki
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland.
| | - Paweł S Krawczyk
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland; Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Dorota Adamska
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland; Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Krystian Bijata
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland; Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Jose L Garcia-Perez
- Department of Genomic Medicine, Centre for Genomics and Oncology (Pfizer-University of Granada and Andalusian Regional Government), PTS Granada, Granada 18016, Spain; Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Andrzej Dziembowski
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland; Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland.
| |
Collapse
|
379
|
Yao B, Li Y, Wang Z, Chen L, Poidevin M, Zhang C, Lin L, Wang F, Bao H, Jiao B, Lim J, Cheng Y, Huang L, Phillips BL, Xu T, Duan R, Moberg KH, Wu H, Jin P. Active N 6-Methyladenine Demethylation by DMAD Regulates Gene Expression by Coordinating with Polycomb Protein in Neurons. Mol Cell 2018; 71:848-857.e6. [PMID: 30078725 DOI: 10.1016/j.molcel.2018.07.005] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 06/05/2018] [Accepted: 07/03/2018] [Indexed: 12/22/2022]
Abstract
A ten-eleven translocation (TET) ortholog exists as a DNA N6-methyladenine (6mA) demethylase (DMAD) in Drosophila. However, the molecular roles of 6mA and DMAD remain unexplored. Through genome-wide 6mA and transcriptome profiling in Drosophila brains and neuronal cells, we found that 6mA may epigenetically regulate a group of genes involved in neurodevelopment and neuronal functions. Mechanistically, DMAD interacts with the Trithorax-related complex protein Wds to maintain active transcription by dynamically demethylating intragenic 6mA. Accumulation of 6mA by depleting DMAD coordinates with Polycomb proteins and contributes to transcriptional repression of these genes. Our findings suggest that active 6mA demethylation by DMAD plays essential roles in fly CNS by orchestrating through added epigenetic mechanisms.
Collapse
Affiliation(s)
- Bing Yao
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA.
| | - Yujing Li
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Zhiqin Wang
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Li Chen
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA; Department of Biostatistics and Bioinformatics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Mickael Poidevin
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Can Zhang
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Li Lin
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Feng Wang
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Han Bao
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Bin Jiao
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Junghwa Lim
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Ying Cheng
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Luoxiu Huang
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | | | - Tianlei Xu
- Department of Biostatistics and Bioinformatics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Ranhui Duan
- State Key Laboratory of Medical Genetics, School of Life Science, Central South University, Changsha, Hunan 410078, China
| | - Kenneth H Moberg
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Hao Wu
- Department of Biostatistics and Bioinformatics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Peng Jin
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA.
| |
Collapse
|
380
|
Kenchanmane Raju SK, Shao M, Wamboldt Y, Mackenzie S. Epigenomic plasticity of Arabidopsis msh1 mutants under prolonged cold stress. PLANT DIRECT 2018; 2:e00079. [PMID: 31245744 PMCID: PMC6508824 DOI: 10.1002/pld3.79] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 06/20/2018] [Accepted: 07/05/2018] [Indexed: 05/05/2023]
Abstract
Dynamic transcriptional and epigenetic changes enable rapid adaptive benefit to environmental fluctuations. However, the underlying mechanisms and the extent to which this occurs are not well known. MutS Homolog 1 (MSH1) mutants cause heritable developmental phenotypes accompanied by modulation of defense, phytohormone, stress-response, and circadian rhythm genes, as well as heritable changes in DNA methylation patterns. Consistent with gene expression changes, msh1 mutants display enhanced tolerance for abiotic stress including drought and salt stress, while showing increased susceptibility to freezing temperatures. Despite changes in defense and biotic stress-response genes, msh1 mutants showed increasing susceptibility to the bacterial pathogen Pseudomonas syringae. Our results suggest that chronic cold and low light stress (10°C, 150 μmol m-2 s-1) influences non-CG methylation to a greater degree in msh1 mutants compared to wild-type Col-0. Furthermore, CHG changes are more closely pericentromeric, whereas CHH changes are generally more dispersed. This increased variation in non-CG methylation pattern does not significantly affect the msh1-derived enhanced growth behavior after mutants are crossed with isogenic wild type, reiterating the importance of CG methylation changes in msh1-derived enhanced vigor. These results indicate that msh1methylome is hyper-responsive to environmental stress in a manner distinct from the wild-type response, but CG methylation changes are potentially responsible for growth vigor changes in the crossed progeny.
Collapse
Affiliation(s)
| | - Mon‐Ray Shao
- Department of Agronomy and HorticultureUniversity of Nebraska‐LincolnLincolnNebraska
| | - Yashitola Wamboldt
- Department of Agronomy and HorticultureUniversity of Nebraska‐LincolnLincolnNebraska
| | - Sally Mackenzie
- Department of Agronomy and HorticultureUniversity of Nebraska‐LincolnLincolnNebraska
- Present address:
Departments of Biology and Plant SciencePennsylvania State UniversityUniversity ParkPennsylvania
| |
Collapse
|
381
|
Jung H, Choi JK, Lee EA. Immune signatures correlate with L1 retrotransposition in gastrointestinal cancers. Genome Res 2018; 28:1136-1146. [PMID: 29970450 PMCID: PMC6071633 DOI: 10.1101/gr.231837.117] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 06/29/2018] [Indexed: 12/15/2022]
Abstract
Long interspersed nuclear element-1 (LINE-1 or L1) retrotransposons are normally suppressed in somatic tissues mainly due to DNA methylation and antiviral defense. However, the mechanism to suppress L1s may be disrupted in cancers, thus allowing L1s to act as insertional mutagens and cause genomic rearrangement and instability. Whereas the frequency of somatic L1 insertions varies greatly among individual tumors, much remains to be learned about underlying genetic, cellular, or environmental factors. Here, we report multiple correlates of L1 activity in stomach, colorectal, and esophageal tumors through an integrative analysis of cancer whole-genome and matched RNA-sequencing profiles. Clinical indicators of tumor progression, such as tumor grade and patient age, showed positive association. A potential L1 expression suppressor, TP53, was mutated in tumors with frequent L1 insertions. We characterized the effects of somatic L1 insertions on mRNA splicing and expression, and demonstrated an increased risk of gene disruption in retrotransposition-prone cancers. In particular, we found that a cancer-specific L1 insertion in an exon of MOV10, a key L1 suppressor, caused exon skipping and decreased expression of the affected allele due to nonsense-mediated decay in a tumor with a high L1 insertion load. Importantly, tumors with high immune activity, for example, those associated with Epstein–Barr virus infection or microsatellite instability, tended to carry a low number of L1 insertions in genomes with high expression levels of L1 suppressors such as APOBEC3s and SAMHD1. Our results indicate that cancer immunity may contribute to genome stability by suppressing L1 retrotransposition in gastrointestinal cancers.
Collapse
Affiliation(s)
- Hyunchul Jung
- Department of Bio and Brain Engineering, KAIST, Daejeon 34141, South Korea
| | - Jung Kyoon Choi
- Department of Bio and Brain Engineering, KAIST, Daejeon 34141, South Korea
| | - Eunjung Alice Lee
- Division of Genetics and Genomics, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| |
Collapse
|
382
|
Abstract
In the course of analyzing whole-genome data, it is common practice to mask or filter out repetitive regions of a genome, such as transposable elements and endogenous retroviruses, in order to focus only on genes and thus simplify the results. This Commentary is a plea from one member of the Mobile DNA community to all gene-centric researchers: please do not ignore the repetitive fraction of the genome. Please stop narrowing your findings by only analyzing a minority of the genome, and instead broaden your analyses to include the rich biology of repetitive and mobile DNA. In this article, I present four arguments supporting a case for retaining repetitive DNA in your genome-wide analysis.
Collapse
Affiliation(s)
- R Keith Slotkin
- Department of Molecular Genetics and Center for Applied Plant Sciences, The Ohio State University, 500 Aronoff Laboratory, 318 West 12th Ave, Columbus, Ohio 43210 USA
| |
Collapse
|
383
|
Jiao W, Yuan J, Jiang S, Liu Y, Wang L, Liu M, Zheng D, Ye W, Wang X, Chen ZJ. Asymmetrical changes of gene expression, small RNAs and chromatin in two resynthesized wheat allotetraploids. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 93:828-842. [PMID: 29265531 DOI: 10.1111/tpj.13805] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 12/04/2017] [Indexed: 05/26/2023]
Abstract
Polyploidy occurs in some animals and all flowering plants, including important crops such as wheat. The consequences of polyploidy in crops remain elusive, partly because their progenitors are unknown. Using two resynthesized wheat allotetraploids Sl Sl AA and AADD with known diploid progenitors, we analyzed mRNA and small RNA transcriptomes in the endosperm, compared transcriptomes between endosperm and root in AADD, and examined chromatin changes in the allotetraploids. In the endosperm, there were more non-additively expressed genes in Sl Sl AA than in AADD. In AADD, non-additively expressed genes were developmentally regulated, and the majority (62-70%) were repressed. The repressed genes in AADD included a group of histone methyltransferase gene homologs, which correlated with reduced histone H3K9me2 levels and activation of various transposable elements in AADD. In Sl Sl AA, there was a tendency for expression dominance of Sl over A homoeologs, but the histone methyltransferase gene homologs were additively expressed, correlating with insignificant changes in histone H3K9me2 levels. Moreover, more 24-nucleotide small inferring RNAs (siRNAs) in the A subgenome were disrupted in AADD than in Sl Sl AA, which were associated with expression changes of siRNA-associated genes. Our results indicate that asymmetrical changes in siRNAs, chromatin modifications, transposons and gene expression coincide with unstable AADD genomes and stable Sl Sl AA genomes, which could help explain the evolutionary trajectories of wheat allotetraploids formed by different progenitors.
Collapse
Affiliation(s)
- Wu Jiao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 1 Weigang Road, Nanjing, 210095, China
| | - Jingya Yuan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 1 Weigang Road, Nanjing, 210095, China
| | - Shan Jiang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 1 Weigang Road, Nanjing, 210095, China
| | - Yanfeng Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 1 Weigang Road, Nanjing, 210095, China
| | - Lili Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 1 Weigang Road, Nanjing, 210095, China
| | - Mingming Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 1 Weigang Road, Nanjing, 210095, China
| | - Dewei Zheng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 1 Weigang Road, Nanjing, 210095, China
| | - Wenxue Ye
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 1 Weigang Road, Nanjing, 210095, China
| | - Xiue Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 1 Weigang Road, Nanjing, 210095, China
| | - Z Jeffrey Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 1 Weigang Road, Nanjing, 210095, China
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, and Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, TX, 78712, USA
| |
Collapse
|
384
|
Mangul S, Yang HT, Strauli N, Gruhl F, Porath HT, Hsieh K, Chen L, Daley T, Christenson S, Wesolowska-Andersen A, Spreafico R, Rios C, Eng C, Smith AD, Hernandez RD, Ophoff RA, Santana JR, Levanon EY, Woodruff PG, Burchard E, Seibold MA, Shifman S, Eskin E, Zaitlen N. ROP: dumpster diving in RNA-sequencing to find the source of 1 trillion reads across diverse adult human tissues. Genome Biol 2018; 19:36. [PMID: 29548336 PMCID: PMC5857127 DOI: 10.1186/s13059-018-1403-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 02/02/2018] [Indexed: 11/22/2022] Open
Abstract
High-throughput RNA-sequencing (RNA-seq) technologies provide an unprecedented opportunity to explore the individual transcriptome. Unmapped reads are a large and often overlooked output of standard RNA-seq analyses. Here, we present Read Origin Protocol (ROP), a tool for discovering the source of all reads originating from complex RNA molecules. We apply ROP to samples across 2630 individuals from 54 diverse human tissues. Our approach can account for 99.9% of 1 trillion reads of various read length. Additionally, we use ROP to investigate the functional mechanisms underlying connections between the immune system, microbiome, and disease. ROP is freely available at https://github.com/smangul1/rop/wiki.
Collapse
Affiliation(s)
- Serghei Mangul
- Department of Computer Science, University of California, Los Angeles, CA, USA. .,Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, CA, USA.
| | - Harry Taegyun Yang
- Department of Computer Science, University of California, Los Angeles, CA, USA
| | - Nicolas Strauli
- Biomedical Sciences Graduate Program, University of California, San Francisco, CA, USA
| | - Franziska Gruhl
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland.,SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Hagit T Porath
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Kevin Hsieh
- Department of Computer Science, University of California, Los Angeles, CA, USA
| | - Linus Chen
- Department of Bioengineering, University of California, Los Angeles, CA, USA
| | - Timothy Daley
- Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Stephanie Christenson
- Division of Pulmonary, Critical Care, Sleep and Allergy, Department of Medicine, and Cardiovascular Research Institute, University of California, San Francisco, CA, USA
| | | | - Roberto Spreafico
- Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, CA, USA
| | - Cydney Rios
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
| | - Celeste Eng
- Department of Medicine, University of California, San Francisco, CA, USA
| | - Andrew D Smith
- Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Ryan D Hernandez
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA.,Institute for Quantitative Biosciences, University of California, San Francisco, CA, USA.,Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Roel A Ophoff
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University California, Los Angeles, CA, USA.,Department of Human Genetics, University of California, Los Angeles, CA, USA.,Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Erez Y Levanon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Prescott G Woodruff
- Division of Pulmonary, Critical Care, Sleep and Allergy, Department of Medicine, and Cardiovascular Research Institute, University of California, San Francisco, CA, USA
| | - Esteban Burchard
- Schools of Pharmacy and Medicine, Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
| | - Max A Seibold
- Department of Pediatrics, National Jewish Health, Denver, CO, USA.,University of Colorado School of Medicine, Denver, CO, USA
| | - Sagiv Shifman
- Department of Genetics, The Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Eleazar Eskin
- Department of Computer Science, University of California, Los Angeles, CA, USA.,Department of Human Genetics, University of California, Los Angeles, CA, USA
| | - Noah Zaitlen
- Division of Pulmonary, Critical Care, Sleep and Allergy, Department of Medicine, and Cardiovascular Research Institute, University of California, San Francisco, CA, USA.
| |
Collapse
|
385
|
Jankovics F, Bence M, Sinka R, Faragó A, Bodai L, Pettkó-Szandtner A, Ibrahim K, Takács Z, Szarka-Kovács AB, Erdélyi M. Drosophila small ovary gene is required for transposon silencing and heterochromatin organisation and ensures germline stem cell maintenance and differentiation. Development 2018; 145:dev.170639. [DOI: 10.1242/dev.170639] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 10/29/2018] [Indexed: 12/17/2022]
Abstract
Self-renewal and differentiation of stem cells is one of the fundamental biological phenomena relying on proper chromatin organisation. In our study, we describe a novel chromatin regulator encoded by the Drosophila small ovary (sov) gene. We demonstrate that sov is required in both the germline stem cells (GSCs) and the surrounding somatic niche cells to ensure GSC survival and differentiation. Sov maintains niche integrity and function by repressing transposon mobility, not only in the germline, but also in the soma. Protein interactome analysis of Sov revealed an interaction between Sov and HP1a. In the germ cell nuclei, Sov co-localises with HP1a, suggesting that Sov affects transposon repression as a component of the heterochromatin. In a position effect variegation assay, we found a dominant genetic interaction between sov and HP1a, indicating their functional cooperation in promoting the spread of heterochromatin. An in vivo tethering assay and FRAP analysis revealed that Sov enhances heterochromatin formation by supporting the recruitment of HP1a to the chromatin. We propose a model in which sov maintains GSC niche integrity by regulating transposon silencing and heterochromatin formation.
Collapse
Affiliation(s)
- Ferenc Jankovics
- Institute of Genetics, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Melinda Bence
- Institute of Genetics, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Rita Sinka
- Department of Genetics, University of Szeged, Szeged, Hungary
| | - Anikó Faragó
- Department of Biochemistry and Molecular Biology, University of Szeged, Szeged, Hungary
| | - László Bodai
- Department of Biochemistry and Molecular Biology, University of Szeged, Szeged, Hungary
| | - Aladár Pettkó-Szandtner
- Institute of Plant Biology, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Karam Ibrahim
- Institute of Genetics, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Zsanett Takács
- Institute of Genetics, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
| | | | - Miklós Erdélyi
- Institute of Genetics, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
| |
Collapse
|
386
|
Abstract
Transposable elements (TE) are mobile genetic elements that can readily change their genomic position. When not properly silenced, TEs can contribute a substantial portion to the cell's transcriptome, but are typically ignored in most RNA-seq data analyses. One reason for leaving TE-derived reads out of RNA-seq analyses is the complexities involved in properly aligning short sequencing reads to these highly repetitive regions. Here we describe a method for including TE-derived reads in RNA-seq differential expression analysis using an open source software package called TEtranscripts. TEtranscripts is designed to assign both uniquely and ambiguously mapped reads to all possible gene and TE-derived transcripts in order to statistically infer the correct gene/TE abundances. Here, we provide a detailed tutorial of TEtranscripts using a published qPCR validated dataset.Barbara McClintock laid the foundation for TE research with her discoveries in maize of mobile genetic elements capable of inserting into novel locations in the genome, altering the expression of nearby genes [1]. Since then, our appreciation of the contribution of repetitive TE-derived sequences to eukaryotic genomes has vastly increased. With the publication of the first human genome draft by the Human Genome Project, it was determined that nearly half of the human genome is derived from TE sequences [2, 3], with varying levels of repetitive DNA present in most plant and animal species. More recent studies looking at distantly related TE-like sequences have estimated that up to two thirds of the human genome might be repeat-derived [4], with the vast majority of these sequences attributed to retrotransposons that require transcription as part of the mobilization process, as discussed below.
Collapse
|
387
|
Yao B, Cheng Y, Wang Z, Li Y, Chen L, Huang L, Zhang W, Chen D, Wu H, Tang B, Jin P. DNA N6-methyladenine is dynamically regulated in the mouse brain following environmental stress. Nat Commun 2017; 8:1122. [PMID: 29066820 PMCID: PMC5654764 DOI: 10.1038/s41467-017-01195-y] [Citation(s) in RCA: 162] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 08/25/2017] [Indexed: 12/13/2022] Open
Abstract
Chemical modifications on DNA molecules, such as 5-methylcytosine and 5-hydroxymethylcytosine, play important roles in the mammalian brain. A novel DNA adenine modification, N(6)-methyladenine (6mA), has recently been found in mammalian cells. However, the presence and function(s) of 6mA in the mammalian brain remain unclear. Here we demonstrate 6mA dynamics in the mouse brain in response to environmental stress. We find that overall 6mA levels are significantly elevated upon stress. Genome-wide 6mA and transcriptome profiling reveal an inverse association between 6mA dynamic changes and a set of upregulated neuronal genes or downregulated LINE transposon expression. Genes bearing stress-induced 6mA changes significantly overlap with loci associated with neuropsychiatric disorders. These results suggest an epigenetic role for 6mA in the mammalian brain as well as its potential involvement in neuropsychiatric disorders. N6-methyladenine is a covalent epigenetic modification of the genome. Here, Yao and colleagues show that N6-methyladenine level in the mouse brain is dynamic following environmental stress, and the subsequent differential gene expression is correlated with LINE transposon expression.
Collapse
Affiliation(s)
- Bing Yao
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Ying Cheng
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Zhiqin Wang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Yujing Li
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Li Chen
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA.,Department of Health Outcomes Research and Policy, Harrison School of Pharmacy, Auburn University, Auburn, AL, 36849, USA
| | - Luoxiu Huang
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Wenxin Zhang
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Dahua Chen
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Hao Wu
- Department of Biostatistics and Bioinformatics, Emory University School of Public Health, Atlanta, GA, 30322, USA
| | - Beisha Tang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Peng Jin
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA.
| |
Collapse
|
388
|
Fast I, Hewel C, Wester L, Schumacher J, Gebert D, Zischler H, Berger C, Rosenkranz D. Temperature-responsive miRNAs in Drosophila orchestrate adaptation to different ambient temperatures. RNA (NEW YORK, N.Y.) 2017; 23:1352-1364. [PMID: 28630141 PMCID: PMC5558905 DOI: 10.1261/rna.061119.117] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 06/06/2017] [Indexed: 06/14/2023]
Abstract
The majority of Drosophila genes are expressed in a temperature-dependent manner, but the way in which small RNAs may contribute to this effect is completely unknown as we currently lack an idea of how small RNA transcriptomes change as a function of temperature. Applying high-throughput sequencing techniques complemented by quantitative real-time PCR experiments, we demonstrate that altered ambient temperature induces drastic but reversible changes in sequence composition and total abundance of both miRNA and piRNA populations. Further, mRNA sequencing reveals that the expression of miRNAs and their predicted target transcripts correlates inversely, suggesting that temperature-responsive miRNAs drive adaptation to different ambient temperatures on the transcriptome level. Finally, we demonstrate that shifts in temperature affect both primary and secondary piRNA pools, and the observed aberrations are consistent with altered expression levels of the involved Piwi-pathway factors. We further reason that enhanced ping-pong processing at 29°C is driven by dissolved RNA secondary structures at higher temperatures, uncovering target sites that are not accessible at low temperatures. Together, our results show that small RNAs are an important part of epigenetic regulatory mechanisms that ensure homeostasis and adaptation under fluctuating environmental conditions.
Collapse
Affiliation(s)
- Isabel Fast
- Institute of Organismic and Molecular Evolutionary Biology, Anthropology, Johannes Gutenberg University, 55099 Mainz, Germany
| | - Charlotte Hewel
- Institute of Organismic and Molecular Evolutionary Biology, Anthropology, Johannes Gutenberg University, 55099 Mainz, Germany
| | - Laura Wester
- Institute of Organismic and Molecular Evolutionary Biology, Anthropology, Johannes Gutenberg University, 55099 Mainz, Germany
| | - Julia Schumacher
- Institute of Organismic and Molecular Evolutionary Biology, Anthropology, Johannes Gutenberg University, 55099 Mainz, Germany
| | - Daniel Gebert
- Institute of Organismic and Molecular Evolutionary Biology, Anthropology, Johannes Gutenberg University, 55099 Mainz, Germany
| | - Hans Zischler
- Institute of Organismic and Molecular Evolutionary Biology, Anthropology, Johannes Gutenberg University, 55099 Mainz, Germany
| | - Christian Berger
- Institute of Developmental Biology and Neurobiology, Johannes Gutenberg University, 55099 Mainz, Germany
| | - David Rosenkranz
- Institute of Organismic and Molecular Evolutionary Biology, Anthropology, Johannes Gutenberg University, 55099 Mainz, Germany
| |
Collapse
|
389
|
Jakšić AM, Kofler R, Schlötterer C. Regulation of transposable elements: Interplay between TE-encoded regulatory sequences and host-specific trans-acting factors in Drosophila melanogaster. Mol Ecol 2017; 26:5149-5159. [PMID: 28742942 DOI: 10.1111/mec.14259] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 07/14/2017] [Accepted: 07/17/2017] [Indexed: 12/18/2022]
Abstract
Transposable elements (TEs) are mobile genetic elements that can move around the genome, and their expression is one precondition for this mobility. Because the insertion of TEs in new genomic positions is largely deleterious, the molecular mechanisms for transcriptional suppression have been extensively studied. In contrast, very little is known about their primary transcriptional regulation. Here, we characterize the expression dynamics of TE families in Drosophila melanogaster across a broad temperature range (13-29°C). In 71% of the expressed TE families, the expression is modulated by temperature. We show that this temperature-dependent regulation is specific for TE families and strongly affected by the genetic background. We deduce that TEs carry family-specific regulatory sequences, which are targeted by host-specific trans-acting factors, such as transcription factors. Consistent with the widespread dominant inheritance of gene expression, we also find the prevailing dominance of TE family expression. We conclude that TE family expression across a range of temperatures is regulated by an interaction between TE family-specific regulatory elements and trans-acting factors of the host.
Collapse
Affiliation(s)
- Ana Marija Jakšić
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria.,Vienna Graduate School of Population Genetics, Vetmeduni Vienna, Vienna, Austria
| | - Robert Kofler
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
| | | |
Collapse
|
390
|
Ludwig AK, Zhang P, Hastert FD, Meyer S, Rausch C, Herce HD, Müller U, Lehmkuhl A, Hellmann I, Trummer C, Storm C, Leonhardt H, Cardoso MC. Binding of MBD proteins to DNA blocks Tet1 function thereby modulating transcriptional noise. Nucleic Acids Res 2017; 45:2438-2457. [PMID: 27923996 PMCID: PMC5389475 DOI: 10.1093/nar/gkw1197] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 11/20/2016] [Indexed: 12/18/2022] Open
Abstract
Aberrant DNA methylation is a hallmark of various human disorders, indicating that the spatial and temporal regulation of methylation readers and modifiers is imperative for development and differentiation. In particular, the cross-regulation between 5-methylcytosine binders (MBD) and modifiers (Tet) has not been investigated. Here, we show that binding of Mecp2 and Mbd2 to DNA protects 5-methylcytosine from Tet1-mediated oxidation. The mechanism is not based on competition for 5-methylcytosine binding but on Mecp2 and Mbd2 directly restricting Tet1 access to DNA. We demonstrate that the efficiency of this process depends on the number of bound MBDs per DNA molecule. Accordingly, we find 5-hydroxymethylcytosine enriched at heterochromatin of Mecp2-deficient neurons of a mouse model for Rett syndrome and Tet1-induced reexpression of silenced major satellite repeats. These data unveil fundamental regulatory mechanisms of Tet enzymes and their potential pathophysiological role in Rett syndrome. Importantly, it suggests that Mecp2 and Mbd2 have an essential physiological role as guardians of the epigenome.
Collapse
Affiliation(s)
- Anne K Ludwig
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Peng Zhang
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Florian D Hastert
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Stephanie Meyer
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Cathia Rausch
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Henry D Herce
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Udo Müller
- Human Biology and BioImaging, Department of Biology II, LMU Munich, 82152 Martinsried, Germany
| | - Anne Lehmkuhl
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Ines Hellmann
- Anthropology and Human Genomics, Department Biology II, LMU Munich, 82152 Martinsried, Germany
| | - Carina Trummer
- Human Biology and BioImaging, Department of Biology II, LMU Munich, 82152 Martinsried, Germany
| | - Christian Storm
- Chemical Plant Ecology, Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Heinrich Leonhardt
- Human Biology and BioImaging, Department of Biology II, LMU Munich, 82152 Martinsried, Germany
| | - M Cristina Cardoso
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| |
Collapse
|
391
|
Jain D, Meydan C, Lange J, Claeys Bouuaert C, Lailler N, Mason CE, Anderson KV, Keeney S. rahu is a mutant allele of Dnmt3c, encoding a DNA methyltransferase homolog required for meiosis and transposon repression in the mouse male germline. PLoS Genet 2017; 13:e1006964. [PMID: 28854222 PMCID: PMC5607212 DOI: 10.1371/journal.pgen.1006964] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 09/20/2017] [Accepted: 08/07/2017] [Indexed: 12/30/2022] Open
Abstract
Transcriptional silencing by heritable cytosine-5 methylation is an ancient strategy to repress transposable elements. It was previously thought that mammals possess four DNA methyltransferase paralogs-Dnmt1, Dnmt3a, Dnmt3b and Dnmt3l-that establish and maintain cytosine-5 methylation. Here we identify a fifth paralog, Dnmt3c, that is essential for retrotransposon methylation and repression in the mouse male germline. From a phenotype-based forward genetics screen, we isolated a mutant mouse called 'rahu', which displays severe defects in double-strand-break repair and homologous chromosome synapsis during male meiosis, resulting in sterility. rahu is an allele of a transcription unit (Gm14490, renamed Dnmt3c) that was previously mis-annotated as a Dnmt3-family pseudogene. Dnmt3c encodes a cytosine methyltransferase homolog, and Dnmt3crahu mutants harbor a non-synonymous mutation of a conserved residue within one of its cytosine methyltransferase motifs, similar to a mutation in human DNMT3B observed in patients with immunodeficiency, centromeric instability and facial anomalies syndrome. The rahu mutation lies at a potential dimerization interface and near the potential DNA binding interface, suggesting that it compromises protein-protein and/or protein-DNA interactions required for normal DNMT3C function. Dnmt3crahu mutant males fail to establish normal methylation within LINE and LTR retrotransposon sequences in the germline and accumulate higher levels of transposon-derived transcripts and proteins, particularly from distinct L1 and ERVK retrotransposon families. Phylogenetic analysis indicates that Dnmt3c arose during rodent evolution by tandem duplication of Dnmt3b, after the divergence of the Dipodoidea and Muroidea superfamilies. These findings provide insight into the evolutionary dynamics and functional specialization of the transposon suppression machinery critical for mammalian sexual reproduction and epigenetic regulation.
Collapse
Affiliation(s)
- Devanshi Jain
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States of America
| | - Cem Meydan
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, United States of America
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, United States of America
| | - Julian Lange
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States of America
- Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, United States of America
| | - Corentin Claeys Bouuaert
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States of America
- Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, United States of America
| | - Nathalie Lailler
- Integrated Genomics Operation, Memorial Sloan Kettering Cancer Center, New York, United States of America
| | - Christopher E. Mason
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, United States of America
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, United States of America
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medical College, New York, United States of America
| | - Kathryn V. Anderson
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States of America
| | - Scott Keeney
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States of America
- Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, United States of America
| |
Collapse
|
392
|
Systematic identification and characterization of regulatory elements derived from human endogenous retroviruses. PLoS Genet 2017; 13:e1006883. [PMID: 28700586 PMCID: PMC5529029 DOI: 10.1371/journal.pgen.1006883] [Citation(s) in RCA: 106] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 07/26/2017] [Accepted: 06/21/2017] [Indexed: 12/26/2022] Open
Abstract
Human endogenous retroviruses (HERVs) and other long terminal repeat (LTR)-type retrotransposons (HERV/LTRs) have regulatory elements that possibly influence the transcription of host genes. We systematically identified and characterized these regulatory elements based on publicly available datasets of ChIP-Seq of 97 transcription factors (TFs) provided by ENCODE and Roadmap Epigenomics projects. We determined transcription factor-binding sites (TFBSs) using the ChIP-Seq datasets and identified TFBSs observed on HERV/LTR sequences (HERV-TFBSs). Overall, 794,972 HERV-TFBSs were identified. Subsequently, we identified "HERV/LTR-shared regulatory element (HSRE)," defined as a TF-binding motif in HERV-TFBSs, shared within a substantial fraction of a HERV/LTR type. HSREs could be an indication that the regulatory elements of HERV/LTRs are present before their insertions. We identified 2,201 HSREs, comprising specific associations of 354 HERV/LTRs and 84 TFs. Clustering analysis showed that HERV/LTRs can be grouped according to the TF binding patterns; HERV/LTR groups bounded to pluripotent TFs (e.g., SOX2, POU5F1, and NANOG), embryonic endoderm/mesendoderm TFs (e.g., GATA4/6, SOX17, and FOXA1/2), hematopoietic TFs (e.g., SPI1 (PU1), GATA1/2, and TAL1), and CTCF were identified. Regulatory elements of HERV/LTRs tended to locate nearby and/or interact three-dimensionally with the genes involved in immune responses, indicating that the regulatory elements play an important role in controlling the immune regulatory network. Further, we demonstrated subgroup-specific TF binding within LTR7, LTR5B, and LTR5_Hs, indicating that gains or losses of the regulatory elements occurred during genomic invasions of the HERV/LTRs. Finally, we constructed dbHERV-REs, an interactive database of HERV/LTR regulatory elements (http://herv-tfbs.com/). This study provides fundamental information in understanding the impact of HERV/LTRs on host transcription, and offers insights into the transcriptional modulation systems of HERV/LTRs and ancestral HERVs.
Collapse
|
393
|
McKerrow WH, Savva YA, Rezaei A, Reenan RA, Lawrence CE. Predicting RNA hyper-editing with a novel tool when unambiguous alignment is impossible. BMC Genomics 2017; 18:522. [PMID: 28693467 PMCID: PMC5502491 DOI: 10.1186/s12864-017-3898-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 06/22/2017] [Indexed: 12/13/2022] Open
Abstract
Background Repetitive elements are now known to have relevant cellular functions, including self-complementary sequences that form double stranded (ds) RNA. There are numerous pathways that determine the fate of endogenous dsRNA, and misregulation of endogenous dsRNA is a driver of autoimmune disease, particularly in the brain. Unfortunately, the alignment of high-throughput, short-read sequences to repeat elements poses a dilemma: Such sequences may align equally well to multiple genomic locations. In order to differentiate repeat elements, current alignment methods depend on sequence variation in the reference genome. Reads are discarded when no such variations are present. However, RNA hyper-editing, a possible fate for dsRNA, introduces enough variation to distinguish between repeats that are otherwise identical. Results To take advantage of this variation, we developed a new algorithm, RepProfile, that simultaneously aligns reads and predicts novel variations. RepProfile accurately aligns hyper-edited reads that other methods discard. In particular we predict hyper-editing of Drosophila melanogaster repeat elements in vivo at levels previously described only in vitro, and provide validation by Sanger sequencing sixty-two individual cloned sequences. We find that hyper-editing is concentrated in genes involved in cell-cell communication at the synapse, including some that are associated with neurodegeneration. We also find that hyper-editing tends to occur in short runs. Conclusions Previous studies of RNA hyper-editing discarded ambiguously aligned reads, ignoring hyper-editing in long, perfect dsRNA – the perfect substrate for hyper-editing. We provide a method that simulation and Sanger validation show accurately predicts such RNA editing, yielding a superior picture of hyper-editing. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3898-9) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Wilson H McKerrow
- Division of Applied Mathematics, Brown University, Providence, 02912, RI, USA.
| | - Yiannis A Savva
- Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, 02912, RI, USA
| | - Ali Rezaei
- Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, 02912, RI, USA
| | - Robert A Reenan
- Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, 02912, RI, USA
| | - Charles E Lawrence
- Division of Applied Mathematics, Brown University, Providence, 02912, RI, USA
| |
Collapse
|
394
|
Zhang P, Ludwig AK, Hastert FD, Rausch C, Lehmkuhl A, Hellmann I, Smets M, Leonhardt H, Cardoso MC. L1 retrotransposition is activated by Ten-eleven-translocation protein 1 and repressed by methyl-CpG binding proteins. Nucleus 2017; 8:548-562. [PMID: 28524723 PMCID: PMC5703239 DOI: 10.1080/19491034.2017.1330238] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
One of the major functions of DNA methylation is the repression of transposable elements, such as the long-interspersed nuclear element 1 (L1). The underlying mechanism(s), however, are unclear. Here, we addressed how retrotransposon activation and mobilization are regulated by methyl-cytosine modifying ten-eleven-translocation (Tet) proteins and how this is modulated by methyl-CpG binding domain (MBD) proteins. We show that Tet1 activates both, endogenous and engineered L1 retrotransposons. Furthermore, we found that Mecp2 and Mbd2 repress Tet1-mediated activation of L1 by preventing 5hmC formation at the L1 promoter. Finally, we demonstrate that the methyl-CpG binding domain, as well as the adjacent non-sequence specific DNA binding domain of Mecp2 are each sufficient to mediate repression of Tet1-induced L1 mobilization. Our study reveals a mechanism how L1 elements get activated in the absence of Mecp2 and suggests that Tet1 may contribute to Mecp2/Mbd2-deficiency phenotypes, such as the Rett syndrome. We propose that the balance between methylation "reader" and "eraser/writer" controls L1 retrotransposition.
Collapse
Affiliation(s)
- Peng Zhang
- a Department of Biology , Technical University Darmstadt , Darmstadt , Germany
| | - Anne K Ludwig
- a Department of Biology , Technical University Darmstadt , Darmstadt , Germany
| | - Florian D Hastert
- a Department of Biology , Technical University Darmstadt , Darmstadt , Germany
| | - Cathia Rausch
- a Department of Biology , Technical University Darmstadt , Darmstadt , Germany
| | - Anne Lehmkuhl
- a Department of Biology , Technical University Darmstadt , Darmstadt , Germany
| | - Ines Hellmann
- b Anthropology and Human Genomics, Department Biology II , LMU Munich , Germany
| | - Martha Smets
- c Human Biology and BioImaging, Department of Biology II , LMU Munich , Germany
| | - Heinrich Leonhardt
- c Human Biology and BioImaging, Department of Biology II , LMU Munich , Germany
| | - M Cristina Cardoso
- a Department of Biology , Technical University Darmstadt , Darmstadt , Germany
| |
Collapse
|
395
|
Krug L, Chatterjee N, Borges-Monroy R, Hearn S, Liao WW, Morrill K, Prazak L, Rozhkov N, Theodorou D, Hammell M, Dubnau J. Retrotransposon activation contributes to neurodegeneration in a Drosophila TDP-43 model of ALS. PLoS Genet 2017; 13:e1006635. [PMID: 28301478 PMCID: PMC5354250 DOI: 10.1371/journal.pgen.1006635] [Citation(s) in RCA: 142] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 02/14/2017] [Indexed: 12/11/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are two incurable neurodegenerative disorders that exist on a symptomological spectrum and share both genetic underpinnings and pathophysiological hallmarks. Functional abnormality of TAR DNA-binding protein 43 (TDP-43), an aggregation-prone RNA and DNA binding protein, is observed in the vast majority of both familial and sporadic ALS cases and in ~40% of FTLD cases, but the cascade of events leading to cell death are not understood. We have expressed human TDP-43 (hTDP-43) in Drosophila neurons and glia, a model that recapitulates many of the characteristics of TDP-43-linked human disease including protein aggregation pathology, locomotor impairment, and premature death. We report that such expression of hTDP-43 impairs small interfering RNA (siRNA) silencing, which is the major post-transcriptional mechanism of retrotransposable element (RTE) control in somatic tissue. This is accompanied by de-repression of a panel of both LINE and LTR families of RTEs, with somewhat different elements being active in response to hTDP-43 expression in glia versus neurons. hTDP-43 expression in glia causes an early and severe loss of control of a specific RTE, the endogenous retrovirus (ERV) gypsy. We demonstrate that gypsy causes the degenerative phenotypes in these flies because we are able to rescue the toxicity of glial hTDP-43 either by genetically blocking expression of this RTE or by pharmacologically inhibiting RTE reverse transcriptase activity. Moreover, we provide evidence that activation of DNA damage-mediated programmed cell death underlies both neuronal and glial hTDP-43 toxicity, consistent with RTE-mediated effects in both cell types. Our findings suggest a novel mechanism in which RTE activity contributes to neurodegeneration in TDP-43-mediated diseases such as ALS and FTLD.
Collapse
Affiliation(s)
- Lisa Krug
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States of America
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States of America
| | - Nabanita Chatterjee
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States of America
| | | | - Stephen Hearn
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States of America
| | - Wen-Wei Liao
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States of America
| | - Kathleen Morrill
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States of America
| | - Lisa Prazak
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States of America
- Department of Biology, Farmingdale State College, Farmingdale, NY United States of America
| | - Nikolay Rozhkov
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States of America
| | - Delphine Theodorou
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States of America
| | - Molly Hammell
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States of America
| | - Josh Dubnau
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States of America
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States of America
- Department of Anesthesiology, Stony Brook School of Medicine, Stony Brook, New York, United States of America
- Department of Neurobiology and Behavior, Stony Brook School of Medicine, Stony Brook, New York, United States of America
| |
Collapse
|
396
|
Ge SX. Exploratory bioinformatics investigation reveals importance of "junk" DNA in early embryo development. BMC Genomics 2017; 18:200. [PMID: 28231763 PMCID: PMC5324221 DOI: 10.1186/s12864-017-3566-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 02/07/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Instead of testing predefined hypotheses, the goal of exploratory data analysis (EDA) is to find what data can tell us. Following this strategy, we re-analyzed a large body of genomic data to study the complex gene regulation in mouse pre-implantation development (PD). RESULTS Starting with a single-cell RNA-seq dataset consisting of 259 mouse embryonic cells derived from zygote to blastocyst stages, we reconstructed the temporal and spatial gene expression pattern during PD. The dynamics of gene expression can be partially explained by the enrichment of transposable elements in gene promoters and the similarity of expression profiles with those of corresponding transposons. Long Terminal Repeats (LTRs) are associated with transient, strong induction of many nearby genes at the 2-4 cell stages, probably by providing binding sites for Obox and other homeobox factors. B1 and B2 SINEs (Short Interspersed Nuclear Elements) are correlated with the upregulation of thousands of nearby genes during zygotic genome activation. Such enhancer-like effects are also found for human Alu and bovine tRNA SINEs. SINEs also seem to be predictive of gene expression in embryonic stem cells (ESCs), raising the possibility that they may also be involved in regulating pluripotency. We also identified many potential transcription factors underlying PD and discussed the evolutionary necessity of transposons in enhancing genetic diversity, especially for species with longer generation time. CONCLUSIONS Together with other recent studies, our results provide further evidence that many transposable elements may play a role in establishing the expression landscape in early embryos. It also demonstrates that exploratory bioinformatics investigation can pinpoint developmental pathways for further study, and serve as a strategy to generate novel insights from big genomic data.
Collapse
Affiliation(s)
- Steven Xijin Ge
- Department of Mathematics and Statistics, South Dakota State University, Box 2225, Brookings, SD, 57110, USA.
| |
Collapse
|
397
|
Shao MR, Kumar Kenchanmane Raju S, Laurie JD, Sanchez R, Mackenzie SA. Stress-responsive pathways and small RNA changes distinguish variable developmental phenotypes caused by MSH1 loss. BMC PLANT BIOLOGY 2017; 17:47. [PMID: 28219335 PMCID: PMC5319189 DOI: 10.1186/s12870-017-0996-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 02/08/2017] [Indexed: 05/03/2023]
Abstract
BACKGROUND Proper regulation of nuclear-encoded, organelle-targeted genes is crucial for plastid and mitochondrial function. Among these genes, MutS Homolog 1 (MSH1) is notable for generating an assortment of mutant phenotypes with varying degrees of penetrance and pleiotropy. Stronger phenotypes have been connected to stress tolerance and epigenetic changes, and in Arabidopsis T-DNA mutants, two generations of homozygosity with the msh1 insertion are required before severe phenotypes begin to emerge. These observations prompted us to examine how msh1 mutants contrast according to generation and phenotype by profiling their respective transcriptomes and small RNA populations. RESULTS Using RNA-seq, we analyze pathways that are associated with MSH1 loss, including abiotic stresses such as cold response, pathogen defense and immune response, salicylic acid, MAPK signaling, and circadian rhythm. Subtle redox and environment-responsive changes also begin in the first generation, in the absence of strong phenotypes. Using small RNA-seq we further identify miRNA changes, and uncover siRNA trends that indicate modifications at the chromatin organization level. In all cases, the magnitude of changes among protein-coding genes, transposable elements, and small RNAs increases according to generation and phenotypic severity. CONCLUSION Loss of MSH1 is sufficient to cause large-scale regulatory changes in pathways that have been individually linked to one another, but rarely described all together within a single mutant background. This study enforces the recognition of organelles as critical integrators of both internal and external cues, and highlights the relationship between organelle and nuclear regulation in fundamental aspects of plant development and stress signaling. Our findings also encourage further investigation into potential connections between organelle state and genome regulation vis-á-vis small RNA feedback.
Collapse
Affiliation(s)
- Mon-Ray Shao
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE USA
| | | | - John D. Laurie
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE USA
- Sainsbury Laboratory, University of Cambridge, Cambridge, UK
| | - Robersy Sanchez
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE USA
| | - Sally A. Mackenzie
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE USA
| |
Collapse
|
398
|
Bodak M, Cirera-Salinas D, Yu J, Ngondo RP, Ciaudo C. Dicer, a new regulator of pluripotency exit and LINE-1 elements in mouse embryonic stem cells. FEBS Open Bio 2017; 7:204-220. [PMID: 28174687 PMCID: PMC5292673 DOI: 10.1002/2211-5463.12174] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 11/18/2016] [Accepted: 12/05/2016] [Indexed: 12/18/2022] Open
Abstract
A gene regulation network orchestrates processes ensuring the maintenance of cellular identity and genome integrity. Small RNAs generated by the RNAse III DICER have emerged as central players in this network. Moreover, deletion of Dicer in mice leads to early embryonic lethality. To better understand the underlying mechanisms leading to this phenotype, we generated Dicer‐deficient mouse embryonic stem cells (mESCs). Their detailed characterization revealed an impaired differentiation potential, and incapacity to exit from the pluripotency state. We also observed a strong accumulation of LINE‐1 (L1s) transcripts, which was translated at protein level and led to an increased L1s retrotransposition. Our findings reveal Dicer as a new essential player that sustains mESCs self‐renewal and genome integrity by controlling L1s regulation.
Collapse
Affiliation(s)
- Maxime Bodak
- Department of Biology RNAi and Genome Integrity IMHS Swiss Federal Institute of Technology Zurich Zurich Switzerland; Life Science Zurich Graduate School Molecular Life Science Program University of Zurich Switzerland
| | - Daniel Cirera-Salinas
- Department of Biology RNAi and Genome Integrity IMHS Swiss Federal Institute of Technology Zurich Zurich Switzerland
| | - Jian Yu
- Department of Biology RNAi and Genome Integrity IMHS Swiss Federal Institute of Technology Zurich Zurich Switzerland; Life Science Zurich Graduate School Molecular and Translational Biomedicine Program University of Zurich Switzerland
| | - Richard P Ngondo
- Department of Biology RNAi and Genome Integrity IMHS Swiss Federal Institute of Technology Zurich Zurich Switzerland
| | - Constance Ciaudo
- Department of Biology RNAi and Genome Integrity IMHS Swiss Federal Institute of Technology Zurich Zurich Switzerland
| |
Collapse
|
399
|
De S, Gorospe M. Bioinformatic tools for analysis of CLIP ribonucleoprotein data. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 8. [PMID: 28008714 DOI: 10.1002/wrna.1404] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 09/26/2016] [Accepted: 10/07/2016] [Indexed: 12/15/2022]
Abstract
Investigating the interactions of RNA-binding proteins (RBPs) with RNAs is a complex task for molecular and computational biologists. The molecular biology techniques and the computational approaches to understand RBP-RNA (or ribonucleoprotein, RNP) interactions have advanced considerably over the past few years and numerous and diverse software tools have been developed to analyze these data. Accordingly, laboratories interested in RNP biology face the challenge of choosing adequately among the available software tools those that best address the biological problem they are studying. Here, we focus on state-of-the-art molecular biology techniques that employ crosslinking and immunoprecipitation (CLIP) of an RBP to study and map RNP interactions. We review the different software tools and databases available to analyze the most widely used CLIP methods, HITS-CLIP, PAR-CLIP, and iCLIP. WIREs RNA 2017, 8:e1404. doi: 10.1002/wrna.1404 For further resources related to this article, please visit the WIREs website.
Collapse
Affiliation(s)
- Supriyo De
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Myriam Gorospe
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| |
Collapse
|
400
|
Clayton EA, Wang L, Rishishwar L, Wang J, McDonald JF, Jordan IK. Patterns of Transposable Element Expression and Insertion in Cancer. Front Mol Biosci 2016; 3:76. [PMID: 27900322 PMCID: PMC5110550 DOI: 10.3389/fmolb.2016.00076] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 10/31/2016] [Indexed: 11/20/2022] Open
Abstract
Human transposable element (TE) activity in somatic tissues causes mutations that can contribute to tumorigenesis. Indeed, TE insertion mutations have been implicated in the etiology of a number of different cancer types. Nevertheless, the full extent of somatic TE activity, along with its relationship to tumorigenesis, have yet to be fully explored. Recent developments in bioinformatics software make it possible to analyze TE expression levels and TE insertional activity directly from transcriptome (RNA-seq) and whole genome (DNA-seq) next-generation sequence data. We applied these new sequence analysis techniques to matched normal and primary tumor patient samples from the Cancer Genome Atlas (TCGA) in order to analyze the patterns of TE expression and insertion for three cancer types: breast invasive carcinoma, head and neck squamous cell carcinoma, and lung adenocarcinoma. Our analysis focused on the three most abundant families of active human TEs: Alu, SVA, and L1. We found evidence for high levels of somatic TE activity for these three families in normal and cancer samples across diverse tissue types. Abundant transcripts for all three TE families were detected in both normal and cancer tissues along with an average of ~80 unique TE insertions per individual patient/tissue. We observed an increase in L1 transcript expression and L1 insertional activity in primary tumor samples for all three cancer types. Tumor-specific TE insertions are enriched for private mutations, consistent with a potentially causal role in tumorigenesis. We used genome feature analysis to investigate two specific cases of putative cancer-causing TE mutations in further detail. An Alu insertion in an upstream enhancer of the CBL tumor suppressor gene is associated with down-regulation of the gene in a single breast cancer patient, and an L1 insertion in the first exon of the BAALC gene also disrupts its expression in head and neck squamous cell carcinoma. Our results are consistent with widespread somatic activity of human TEs leading to numerous insertion mutations that can contribute to tumorigenesis in a variety of tissues.
Collapse
Affiliation(s)
- Evan A Clayton
- Integrated Cancer Research Center, School of Biology, Georgia Institute of TechnologyAtlanta, GA, USA; Ovarian Cancer InstituteAtlanta, GA, USA
| | - Lu Wang
- School of Biology, Georgia Institute of TechnologyAtlanta, GA, USA; PanAmerican Bioinformatics InstituteCali, Colombia
| | - Lavanya Rishishwar
- School of Biology, Georgia Institute of TechnologyAtlanta, GA, USA; PanAmerican Bioinformatics InstituteCali, Colombia; Applied Bioinformatics LaboratoryAtlanta, GA, USA
| | - Jianrong Wang
- Department of Computational Mathematics, Science and Engineering, Michigan State University East Lansing, MI, USA
| | - John F McDonald
- Integrated Cancer Research Center, School of Biology, Georgia Institute of TechnologyAtlanta, GA, USA; Ovarian Cancer InstituteAtlanta, GA, USA
| | - I King Jordan
- School of Biology, Georgia Institute of TechnologyAtlanta, GA, USA; PanAmerican Bioinformatics InstituteCali, Colombia; Applied Bioinformatics LaboratoryAtlanta, GA, USA
| |
Collapse
|