1
|
Skalon EK, Panyushev NV, Podgornaya OI, Smolyaninova AR, Solovyeva AI. Expression of Transposable Elements throughout the Fasciola hepatica Trematode Life Cycle. Noncoding RNA 2024; 10:39. [PMID: 39051373 PMCID: PMC11270206 DOI: 10.3390/ncrna10040039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 06/30/2024] [Accepted: 07/02/2024] [Indexed: 07/27/2024] Open
Abstract
BACKGROUND Transposable elements (TEs) are major components of eukaryotic genomes. The extensive body of evidence suggests that although they were once considered "genomic parasites", transposons and their transcripts perform specific functions, such as regulation of early embryo development. Understanding the role of TEs in such parasites as trematodes is becoming critically important. Fasciola hepatica, a parasite affecting humans and livestock, undergoes a complex life cycle in diverse environments and hosts, and knowledge about its life cycle regulation is scarce so far. METHODS We summarized the data regarding the repetitive elements in F. hepatica and conducted bulk RNA-seq analysis across its life cycle stages. TE expression profiles were analyzed, focusing on differential expression and potential homology with previously described long non-coding RNAs (lncRNAs). RESULTS Differential expression analysis revealed stage-specific TE transcription patterns, notably peaking during egg and metacercariae stages. Some TEs showed homology with known lncRNAs and contained putative transcription factor binding sites. Interestingly, TE transcription levels were highest in eggs and metacercariae compared to adults, suggesting regulatory roles in trematode life cycle transitions. CONCLUSIONS These findings suggest that TEs may play roles in regulating trematode life cycle transitions. Moreover, TE homology with lncRNAs underscores their significance in gene regulation.
Collapse
Affiliation(s)
- Elizaveta K. Skalon
- Zoological Institute, Russian Academy of Sciences, 199034 St. Petersburg, Russia;
| | | | - Olga I. Podgornaya
- Institute of Cytology, Russian Academy of Sciences, 194064 St. Petersburg, Russia; (O.I.P.); (A.R.S.)
| | - Anastasia R. Smolyaninova
- Institute of Cytology, Russian Academy of Sciences, 194064 St. Petersburg, Russia; (O.I.P.); (A.R.S.)
| | - Anna I. Solovyeva
- Zoological Institute, Russian Academy of Sciences, 199034 St. Petersburg, Russia;
- Institute of Cytology, Russian Academy of Sciences, 194064 St. Petersburg, Russia; (O.I.P.); (A.R.S.)
| |
Collapse
|
2
|
Deaville LA, Berrens RV. Technology to the rescue: how to uncover the role of transposable elements in preimplantation development. Biochem Soc Trans 2024; 52:1349-1362. [PMID: 38752836 DOI: 10.1042/bst20231262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 04/23/2024] [Accepted: 04/24/2024] [Indexed: 06/27/2024]
Abstract
Transposable elements (TEs) are highly expressed in preimplantation development. Preimplantation development is the phase when the cells of the early embryo undergo the first cell fate choice and change from being totipotent to pluripotent. A range of studies have advanced our understanding of TEs in preimplantation, as well as their epigenetic regulation and functional roles. However, many questions remain about the implications of TE expression during early development. Challenges originate first due to the abundance of TEs in the genome, and second because of the limited cell numbers in preimplantation. Here we review the most recent technological advancements promising to shed light onto the role of TEs in preimplantation development. We explore novel avenues to identify genomic TE insertions and improve our understanding of the regulatory mechanisms and roles of TEs and their RNA and protein products during early development.
Collapse
Affiliation(s)
- Lauryn A Deaville
- Institute for Developmental and Regenerative Medicine, Oxford University, IMS-Tetsuya Nakamura Building, Old Road Campus, Roosevelt Dr, Oxford OX3 7TY, U.K
- Department of Paediatrics, Oxford University, Level 2, Children's Hospital, John Radcliffe Headington, Oxford OX3 9DU, U.K
- MRC Weatherall Institute of Molecular Medicine, Oxford University, John Radcliffe Hospital, Oxford OX3 9DS, U.K
| | - Rebecca V Berrens
- Institute for Developmental and Regenerative Medicine, Oxford University, IMS-Tetsuya Nakamura Building, Old Road Campus, Roosevelt Dr, Oxford OX3 7TY, U.K
- Department of Paediatrics, Oxford University, Level 2, Children's Hospital, John Radcliffe Headington, Oxford OX3 9DU, U.K
| |
Collapse
|
3
|
Takahashi Ueda M. Retrotransposon-derived transcripts and their functions in immunity and disease. Genes Genet Syst 2024; 98:305-319. [PMID: 38199240 DOI: 10.1266/ggs.23-00187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2024] Open
Abstract
Retrotransposons, which account for approximately 42% of the human genome, have been increasingly recognized as "non-self" pathogen-associated molecular patterns (PAMPs) due to their virus-like sequences. In abnormal conditions such as cancer and viral infections, retrotransposons that are aberrantly expressed due to impaired epigenetic suppression display PAMPs, leading to their recognition by pattern recognition receptors (PRRs) of the innate immune system and triggering inflammation. This viral mimicry mechanism has been observed in various human diseases, including aging and autoimmune disorders. However, recent evidence suggests that retrotransposons possess highly regulated immune reactivity and play important roles in the development and function of the immune system. In this review, I discuss a wide range of retrotransposon-derived transcripts, their role as targets in immune recognition, and the diseases associated with retrotransposon activity. Furthermore, I explore the implications of chimeric transcripts formed between retrotransposons and known gene mRNAs, which have been previously underestimated, for the increase of immune-related gene isoforms and their influence on immune function. Retrotransposon-derived transcripts have profound and multifaceted effects on immune system function. The aim of this comprehensive review is to provide a better understanding of the complex relationship between retrotransposon transcripts and immune defense.
Collapse
Affiliation(s)
- Mahoko Takahashi Ueda
- Department of Genomic Function and Diversity, Medical Research Institute, Tokyo Medical and Dental University
| |
Collapse
|
4
|
He T, Peng J, Yang S, Liu D, Gao S, Zhu Y, Chai Z, Lee BC, Wei R, Wang J, Liu Z, Jin JX. SINE-Associated LncRNA SAWPA Regulates Porcine Zygotic Genome Activation. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2307505. [PMID: 37984872 PMCID: PMC10787077 DOI: 10.1002/advs.202307505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 10/28/2023] [Indexed: 11/22/2023]
Abstract
In mice, retrotransposon-associated long noncoding RNAs (lncRNA) play important regulatory roles in pre-implantation development; however, it is largely unknown whether they function in the pre-implantation development in pigs. The current study aims to screen for retrotransposon-associated lncRNA in porcine early embryos and identifies a porcine 8-cell embryo-specific SINE-associated nuclear long noncoding RNA named SAWPA. SAWPA is essential for porcine embryonic development as depletion of SAWPA results in a developmental arrest at the 8-cell stage, accompanied by the inhibition of the JNK-MAPK signaling pathway. Mechanistically, SAWPA works in trans as a transcription factor for JNK through the formation of an RNA-protein complex with HNRNPA1 and MED8 binding the SINE elements upstream of JNK. Therefore, as the first functional SINE-associated long noncoding RNAs in pigs, SAWPA provides novel insights for the mechanism research on retrotransposons in mammalian pre-implantation development.
Collapse
Affiliation(s)
- Tianyao He
- Key Laboratory of Animal Cellular and Genetics Engineering of Heilongjiang Province, College of Life Science, Northeast Agricultural University, Harbin, 150030, P. R. China
| | - Jinyu Peng
- Key Laboratory of Animal Cellular and Genetics Engineering of Heilongjiang Province, College of Life Science, Northeast Agricultural University, Harbin, 150030, P. R. China
| | - Shu Yang
- Key Laboratory of Animal Cellular and Genetics Engineering of Heilongjiang Province, College of Life Science, Northeast Agricultural University, Harbin, 150030, P. R. China
| | - Dongsong Liu
- Key Laboratory of Animal Cellular and Genetics Engineering of Heilongjiang Province, College of Life Science, Northeast Agricultural University, Harbin, 150030, P. R. China
| | - Shuang Gao
- Key Laboratory of Animal Cellular and Genetics Engineering of Heilongjiang Province, College of Life Science, Northeast Agricultural University, Harbin, 150030, P. R. China
| | - Yanlong Zhu
- Key Laboratory of Animal Cellular and Genetics Engineering of Heilongjiang Province, College of Life Science, Northeast Agricultural University, Harbin, 150030, P. R. China
| | - Zhuang Chai
- Key Laboratory of Animal Cellular and Genetics Engineering of Heilongjiang Province, College of Life Science, Northeast Agricultural University, Harbin, 150030, P. R. China
| | - Byeong Chun Lee
- Department of Theriogenology and Biotechnology, College of Veterinary Medicine, Seoul National University, Seoul, 08826, South Korea
| | - Renyue Wei
- Key Laboratory of Animal Cellular and Genetics Engineering of Heilongjiang Province, College of Life Science, Northeast Agricultural University, Harbin, 150030, P. R. China
| | - Jiaqiang Wang
- Key Laboratory of Animal Cellular and Genetics Engineering of Heilongjiang Province, College of Life Science, Northeast Agricultural University, Harbin, 150030, P. R. China
| | - Zhonghua Liu
- Key Laboratory of Animal Cellular and Genetics Engineering of Heilongjiang Province, College of Life Science, Northeast Agricultural University, Harbin, 150030, P. R. China
| | - Jun-Xue Jin
- Key Laboratory of Animal Cellular and Genetics Engineering of Heilongjiang Province, College of Life Science, Northeast Agricultural University, Harbin, 150030, P. R. China
| |
Collapse
|
5
|
Zhang S, Wang R, Zhu X, Zhang L, Liu X, Sun L. Characteristics and expression of lncRNA and transposable elements in Drosophila aneuploidy. iScience 2023; 26:108494. [PMID: 38125016 PMCID: PMC10730892 DOI: 10.1016/j.isci.2023.108494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 09/28/2023] [Accepted: 11/16/2023] [Indexed: 12/23/2023] Open
Abstract
Aneuploidy can globally affect the expression of the whole genome, which is detrimental to organisms. Dosage-sensitive regulators usually have multiple intermolecular interactions, and changes in their stoichiometry are responsible for the dysregulation of the regulatory network. Currently, studies on noncoding genes in aneuploidy are relatively rare. We studied the characteristics and expression profiles of long noncoding RNAs (lncRNAs) and transposable elements (TEs) in aneuploid Drosophila. It is found that lncRNAs and TEs are affected by genomic imbalance and appear to be more sensitive to an inverse dosage effect than mRNAs. Several dosage-sensitive lncRNAs and TEs were detected for their expression patterns during embryogenesis, and their biological functions in the ovary and testes were investigated using tissue-specific RNAi. This study advances our understanding of the noncoding sequences in imbalanced genomes and provides a novel perspective for the study of aneuploidy-related human diseases such as cancer.
Collapse
Affiliation(s)
- Shuai Zhang
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Ruixue Wang
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Xilin Zhu
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Ludan Zhang
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Xinyu Liu
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Lin Sun
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
- Key Laboratory of Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Science, Beijing Normal University, Beijing 100875, China
| |
Collapse
|
6
|
Yoth M, Maupetit-Méhouas S, Akkouche A, Gueguen N, Bertin B, Jensen S, Brasset E. Reactivation of a somatic errantivirus and germline invasion in Drosophila ovaries. Nat Commun 2023; 14:6096. [PMID: 37773253 PMCID: PMC10541861 DOI: 10.1038/s41467-023-41733-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 09/15/2023] [Indexed: 10/01/2023] Open
Abstract
Most Drosophila transposable elements are LTR retrotransposons, some of which belong to the genus Errantivirus and share structural and functional characteristics with vertebrate endogenous retroviruses. Like endogenous retroviruses, it is unclear whether errantiviruses retain some infectivity and transposition capacity. We created conditions where control of the Drosophila ZAM errantivirus through the piRNA pathway was abolished leading to its de novo reactivation in somatic gonadal cells. After reactivation, ZAM invaded the oocytes and severe fertility defects were observed. While ZAM expression persists in the somatic gonadal cells, the germline then set up its own adaptive genomic immune response by producing piRNAs against the constantly invading errantivirus, restricting invasion. Our results suggest that although errantiviruses are continuously repressed by the piRNA pathway, they may retain their ability to infect the germline and transpose, thus allowing them to efficiently invade the germline if they are expressed.
Collapse
Affiliation(s)
- Marianne Yoth
- iGReD, Université Clermont Auvergne, CNRS, INSERM, Faculté de Médecine, 63000, Clermont-Ferrand, France
| | | | - Abdou Akkouche
- iGReD, Université Clermont Auvergne, CNRS, INSERM, Faculté de Médecine, 63000, Clermont-Ferrand, France
| | - Nathalie Gueguen
- iGReD, Université Clermont Auvergne, CNRS, INSERM, Faculté de Médecine, 63000, Clermont-Ferrand, France
| | - Benjamin Bertin
- LIMAGRAIN EUROPE, Centre de recherche, 63720, Chappes, France
| | - Silke Jensen
- iGReD, Université Clermont Auvergne, CNRS, INSERM, Faculté de Médecine, 63000, Clermont-Ferrand, France.
| | - Emilie Brasset
- iGReD, Université Clermont Auvergne, CNRS, INSERM, Faculté de Médecine, 63000, Clermont-Ferrand, France.
| |
Collapse
|
7
|
Zhang J, Hou W, Zhao Q, Xiao S, Linghu H, Zhang L, Du J, Cui H, Yang X, Ling S, Su J, Kong Q. Deep annotation of long noncoding RNAs by assembling RNA-seq and small RNA-seq data. J Biol Chem 2023; 299:105130. [PMID: 37543366 PMCID: PMC10498003 DOI: 10.1016/j.jbc.2023.105130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 07/20/2023] [Accepted: 07/31/2023] [Indexed: 08/07/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) are increasingly being recognized as modulators in various biological processes. However, due to their low expression, their systematic characterization is difficult to determine. Here, we performed transcript annotation by a newly developed computational pipeline, termed RNA-seq and small RNA-seq combined strategy (RSCS), in a wide variety of cellular contexts. Thousands of high-confidence potential novel transcripts were identified by the RSCS, and the reliability of the transcriptome was verified by analysis of transcript structure, base composition, and sequence complexity. Evidenced by the length comparison, the frequency of the core promoter and the polyadenylation signal motifs, and the locations of transcription start and end sites, the transcripts appear to be full length. Furthermore, taking advantage of our strategy, we identified a large number of endogenous retrovirus-associated lncRNAs, and a novel endogenous retrovirus-lncRNA that was functionally involved in control of Yap1 expression and essential for early embryogenesis was identified. In summary, the RSCS can generate a more complete and precise transcriptome, and our findings greatly expanded the transcriptome annotation for the mammalian community.
Collapse
Affiliation(s)
- Jiaming Zhang
- Oujiang Laboratory, Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang Province, China; Oujiang Laboratory, Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Weibo Hou
- Oujiang Laboratory, Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Qi Zhao
- Oujiang Laboratory, Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Songling Xiao
- Oujiang Laboratory, Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Hongye Linghu
- Oujiang Laboratory, Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Lixin Zhang
- Oujiang Laboratory, Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Jiawei Du
- Oujiang Laboratory, Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Hongdi Cui
- Oujiang Laboratory, Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Xu Yang
- Oujiang Laboratory, Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Shukuan Ling
- Oujiang Laboratory, Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Wenzhou Medical University, Wenzhou, Zhejiang Province, China.
| | - Jianzhong Su
- Oujiang Laboratory, Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Wenzhou Medical University, Wenzhou, Zhejiang Province, China.
| | - Qingran Kong
- Oujiang Laboratory, Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang Province, China.
| |
Collapse
|
8
|
Le Franc L, Petton B, Favrel P, Rivière G. m 6A Profile Dynamics Indicates Regulation of Oyster Development by m 6A-RNA Epitranscriptomes. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:742-755. [PMID: 36496129 PMCID: PMC10787124 DOI: 10.1016/j.gpb.2022.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 11/23/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022]
Abstract
The N6-methylation of RNA adenosines (N6-methyladenosine, m6A) is an important regulator of gene expression with critical implications in vertebrate and insect development. However, the developmental significance of epitranscriptomes in lophotrochozoan organisms remains unknown. Using methylated RNA immunoprecipitation sequencing (MeRIP-seq), we generated transcriptome-wide m6A-RNA methylomes covering the entire development of the oyster from oocytes to juveniles. Oyster RNA classes display specific m6A signatures, with messenger RNAs (mRNAs) and long non-coding RNAs (lncRNAs) exhibiting distinct profiles and being highly methylated compared to transposable element (TE) transcripts. Epitranscriptomes are dynamic and correspond to the chronological steps of development (cleavage, gastrulation, organogenesis, and metamorphosis), with minimal mRNA and lncRNA methylation at the morula stage followed by a global increase. mRNA m6A levels are correlated with transcript levels, and shifts in methylation profiles correspond to expression kinetics. Differentially methylated transcripts cluster according to embryo-larval stages and bear the corresponding developmental functions (cell division, signal transduction, morphogenesis, and cell differentiation). The m6A level of TE transcripts is also regulated and peaks during the gastrulation. We demonstrate that m6A-RNA methylomes are dynamic and associated with gene expression regulation during oyster development. The putative epitranscriptome implication in the cleavage, maternal-to-zygotic transition, and cell differentiation in a lophotrochozoan model brings new insights into the control and evolution of developmental processes.
Collapse
Affiliation(s)
- Lorane Le Franc
- Laboratoire de Biologie des Organismes et des Ecosystèmes Aquatiques (BOREA), Muséum d'Histoire Naturelle, Sorbonne Université, Université de Caen Normandie, Université des Antilles, CNRS UMR 8067, IRD, 14032 Caen, France
| | - Bruno Petton
- Ifremer, Laboratoire des Sciences de l'Environnement Marin, UMR 6539 CNRS/UBO/IRD/Ifremer, Centre Bretagne, 29280 Plouzané, France
| | - Pascal Favrel
- Laboratoire de Biologie des Organismes et des Ecosystèmes Aquatiques (BOREA), Muséum d'Histoire Naturelle, Sorbonne Université, Université de Caen Normandie, Université des Antilles, CNRS UMR 8067, IRD, 14032 Caen, France
| | - Guillaume Rivière
- Laboratoire de Biologie des Organismes et des Ecosystèmes Aquatiques (BOREA), Muséum d'Histoire Naturelle, Sorbonne Université, Université de Caen Normandie, Université des Antilles, CNRS UMR 8067, IRD, 14032 Caen, France.
| |
Collapse
|
9
|
Veschetti L, Treccani M, De Tomi E, Malerba G. Genomic Instability Evolutionary Footprints on Human Health: Driving Forces or Side Effects? Int J Mol Sci 2023; 24:11437. [PMID: 37511197 PMCID: PMC10380557 DOI: 10.3390/ijms241411437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 06/30/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
In this work, we propose a comprehensive perspective on genomic instability comprising not only the accumulation of mutations but also telomeric shortening, epigenetic alterations and other mechanisms that could contribute to genomic information conservation or corruption. First, we present mechanisms playing a role in genomic instability across the kingdoms of life. Then, we explore the impact of genomic instability on the human being across its evolutionary history and on present-day human health, with a particular focus on aging and complex disorders. Finally, we discuss the role of non-coding RNAs, highlighting future approaches for a better living and an expanded healthy lifespan.
Collapse
Affiliation(s)
| | | | | | - Giovanni Malerba
- GM Lab, Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, 37134 Verona, Italy; (L.V.); (M.T.); (E.D.T.)
| |
Collapse
|
10
|
Lynch-Sutherland CF, McDougall LI, Stockwell PA, Almomani SN, Weeks RJ, Ludgate JL, Gamage TKJB, Chatterjee A, James JL, Eccles MR, Macaulay EC. The transposable element-derived transcript of LIN28B has a placental origin and is not specific to tumours. Mol Genet Genomics 2023:10.1007/s00438-023-02033-1. [PMID: 37269361 PMCID: PMC10363060 DOI: 10.1007/s00438-023-02033-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 05/15/2023] [Indexed: 06/05/2023]
Abstract
Transposable elements (TEs) are genetic elements that have evolved as crucial regulators of human development and cancer, functioning as both genes and regulatory elements. When TEs become dysregulated in cancer cells, they can serve as alternate promoters to activate oncogenes, a process known as onco-exaptation. This study aimed to explore the expression and epigenetic regulation of onco-exaptation events in early human developmental tissues. We discovered co-expression of some TEs and oncogenes in human embryonic stem cells and first trimester and term placental tissues. Previous studies identified onco-exaptation events in various cancer types, including an AluJb SINE element-LIN28B interaction in lung cancer cells, and showed that the TE-derived LIN28B transcript is associated with poor patient prognosis in hepatocellular carcinoma. This study further characterized the AluJb-LIN28B transcript and confirmed that its expression is restricted to the placenta. Targeted DNA methylation analysis revealed differential methylation of the two LIN28B promoters between placenta and healthy somatic tissues, indicating that some TE-oncogene interactions are not cancer-specific but arise from the epigenetic reactivation of developmental TE-derived regulatory events. In conclusion, our findings provide evidence that some TE-oncogene interactions are not limited to cancer and may originate from the epigenetic reactivation of TE-derived regulatory events that are involved in early development. These insights broaden our understanding of the role of TEs in gene regulation and suggest the potential importance of targeting TEs in cancer therapy beyond their conventional use as cancer-specific markers.
Collapse
Affiliation(s)
- Chiemi F Lynch-Sutherland
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, 9054, New Zealand.
| | - Lorissa I McDougall
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, 9054, New Zealand
| | - Peter A Stockwell
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, 9054, New Zealand
| | - Suzan N Almomani
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, 9054, New Zealand
| | - Robert J Weeks
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, 9054, New Zealand
| | - Jackie L Ludgate
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, 9054, New Zealand
| | - Teena K J B Gamage
- Department of Physiology, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand
| | - Aniruddha Chatterjee
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, 9054, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Level 2, 3A Symonds Street, Auckland, New Zealand
| | - Joanna L James
- Department of Obstetrics and Gynaecology, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand
| | - Michael R Eccles
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, 9054, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Level 2, 3A Symonds Street, Auckland, New Zealand
| | - Erin C Macaulay
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, 9054, New Zealand
| |
Collapse
|
11
|
Galbraith JD, Hayward A. The influence of transposable elements on animal colouration. Trends Genet 2023:S0168-9525(23)00091-4. [PMID: 37183153 DOI: 10.1016/j.tig.2023.04.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 04/17/2023] [Accepted: 04/19/2023] [Indexed: 05/16/2023]
Abstract
Transposable elements (TEs) are mobile genetic sequences present within host genomes. TEs can contribute to the evolution of host traits, since transposition is mutagenic and TEs often contain host regulatory and protein coding sequences. We review cases where TEs influence animal colouration, reporting major patterns and outstanding questions. TE-induced colouration phenotypes typically arise via introduction of novel regulatory sequences and splice sites, affecting pigment cell development or pigment synthesis. We discuss if particular TE types may be more frequently involved in the evolution of colour variation in animals, given that examples involving long terminal repeat (LTR) elements appear to dominate. Currently, examples of TE-induced colouration phenotypes in animals mainly concern model and domesticated insect and mammal species. However, several influential recent examples, coupled with increases in genome sequencing, suggest cases reported from wild species will increase considerably.
Collapse
Affiliation(s)
- James D Galbraith
- Faculty of Environment, Science and Economy, University of Exeter, Cornwall TR10 9FE, UK.
| | - Alexander Hayward
- Faculty of Environment, Science and Economy, University of Exeter, Cornwall TR10 9FE, UK.
| |
Collapse
|
12
|
Vinuesa CG, Grenov A, Kassiotis G. Innate virus-sensing pathways in B cell systemic autoimmunity. Science 2023; 380:478-484. [PMID: 37141353 DOI: 10.1126/science.adg6427] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Although all multicellular organisms have germ line-encoded innate receptors to sense pathogen-associated molecular patterns, vertebrates also evolved adaptive immunity based on somatically generated antigen receptors on B and T cells. Because randomly generated antigen receptors may also react with self-antigens, tolerance checkpoints operate to limit but not completely prevent autoimmunity. These two systems are intricately linked, with innate immunity playing an instrumental role in the induction of adaptive antiviral immunity. In this work, we review how inborn errors of innate immunity can instigate B cell autoimmunity. Increased nucleic acid sensing, often resulting from defects in metabolizing pathways or retroelement control, can break B cell tolerance and converge into TLR7-, cGAS-STING-, or MAVS-dominant signaling pathways. The resulting syndromes span a spectrum that ranges from chilblain and systemic lupus to severe interferonopathies.
Collapse
Affiliation(s)
- Carola G Vinuesa
- The Francis Crick Institute, London, UK
- China Centre for Personalised Immunology, Renji Hospital, Shanghai, China
| | | | - George Kassiotis
- The Francis Crick Institute, London, UK
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
| |
Collapse
|
13
|
Jin L, He J, Feng H, Li S, Liu H, Dong H, Hu M, Huang J, Wu H, Chen J, Qi L, Wu K. Transposable elements activation triggers necroptosis in mouse embryonic stem cells. Cell Death Dis 2023; 14:184. [PMID: 36882393 PMCID: PMC9992707 DOI: 10.1038/s41419-023-05705-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 02/20/2023] [Accepted: 02/22/2023] [Indexed: 03/09/2023]
Abstract
Deficiency of the histone H3K9 methyltransferase SETDB1 induces RIPK3-dependent necroptosis in mouse embryonic stem cells (mESCs). However, how necroptosis pathway is activated in this process remains elusive. Here we report that the reactivation of transposable elements (TEs) upon SETDB1 knockout is responsible for the RIPK3 regulation through both cis and trans mechanisms. IAPLTR2_Mm and MMERVK10c-int, both of which are suppressed by SETDB1-dependent H3K9me3, act as enhancer-like cis-regulatory elements and their RIPK3 nearby members enhance RIPK3 expression when SETDB1 is knockout. Moreover, reactivated endogenous retroviruses generate excessive viral mimicry, which promotes necroptosis mainly through Z-DNA-binding protein 1 (ZBP1). These results indicate TEs play an important role in regulating necroptosis.
Collapse
Affiliation(s)
- Lingmei Jin
- Institute of Digestive Disease, the Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, B24 Yinquan South Road, Qingyuan, 511518, Guang Dong, China.,CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory, Guangzhou Regenerative Medicine and Health GuangDong Laboratory, Guangzhou, China
| | - Jiangping He
- Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory, Guangzhou Regenerative Medicine and Health GuangDong Laboratory, Guangzhou, China.,Guangzhou Laboratory, Guangzhou, 510005, Guangdong Province, China
| | - Huijian Feng
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory, Guangzhou Regenerative Medicine and Health GuangDong Laboratory, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Sa Li
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - He Liu
- Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory, Guangzhou Regenerative Medicine and Health GuangDong Laboratory, Guangzhou, China
| | - Hongzhi Dong
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - MingLi Hu
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Junju Huang
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Haoyu Wu
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Jiekai Chen
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China. .,Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory, Guangzhou Regenerative Medicine and Health GuangDong Laboratory, Guangzhou, China. .,Centre for Regenerative Medicine and Health, Hong Kong Institute of Science & Innovation, Chinese Academy of Sciences, Hong Kong SAR, China.
| | - Ling Qi
- Institute of Digestive Disease, the Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, B24 Yinquan South Road, Qingyuan, 511518, Guang Dong, China.
| | - Kaixin Wu
- Institute of Digestive Disease, the Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, B24 Yinquan South Road, Qingyuan, 511518, Guang Dong, China. .,Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory, Guangzhou Regenerative Medicine and Health GuangDong Laboratory, Guangzhou, China. .,Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.
| |
Collapse
|
14
|
Stamidis N, Żylicz JJ. RNA-mediated heterochromatin formation at repetitive elements in mammals. EMBO J 2023; 42:e111717. [PMID: 36847618 PMCID: PMC10106986 DOI: 10.15252/embj.2022111717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 12/12/2022] [Accepted: 02/07/2023] [Indexed: 03/01/2023] Open
Abstract
The failure to repress transcription of repetitive genomic elements can lead to catastrophic genome instability and is associated with various human diseases. As such, multiple parallel mechanisms cooperate to ensure repression and heterochromatinization of these elements, especially during germline development and early embryogenesis. A vital question in the field is how specificity in establishing heterochromatin at repetitive elements is achieved. Apart from trans-acting protein factors, recent evidence points to a role of different RNA species in targeting repressive histone marks and DNA methylation to these sites in mammals. Here, we review recent discoveries on this topic and predominantly focus on the role of RNA methylation, piRNAs, and other localized satellite RNAs.
Collapse
Affiliation(s)
- Nikolaos Stamidis
- Novo Nordisk Foundation Center for Stem Cell Medicine, reNEW, University of Copenhagen, Copenhagen, Denmark
| | - Jan Jakub Żylicz
- Novo Nordisk Foundation Center for Stem Cell Medicine, reNEW, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
15
|
Gasparotto E, Burattin FV, Di Gioia V, Panepuccia M, Ranzani V, Marasca F, Bodega B. Transposable Elements Co-Option in Genome Evolution and Gene Regulation. Int J Mol Sci 2023; 24:ijms24032610. [PMID: 36768929 PMCID: PMC9917352 DOI: 10.3390/ijms24032610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/26/2023] [Accepted: 01/28/2023] [Indexed: 01/31/2023] Open
Abstract
The genome is no longer deemed as a fixed and inert item but rather as a moldable matter that is continuously evolving and adapting. Within this frame, Transposable Elements (TEs), ubiquitous, mobile, repetitive elements, are considered an alive portion of the genomes to date, whose functions, although long considered "dark", are now coming to light. Here we will review that, besides the detrimental effects that TE mobilization can induce, TEs have shaped genomes in their current form, promoting genome sizing, genomic rearrangements and shuffling of DNA sequences. Although TEs are mostly represented in the genomes by evolutionarily old, short, degenerated, and sedentary fossils, they have been thoroughly co-opted by the hosts as a prolific and original source of regulatory instruments for the control of gene transcription and genome organization in the nuclear space. For these reasons, the deregulation of TE expression and/or activity is implicated in the onset and progression of several diseases. It is likely that we have just revealed the outermost layers of TE functions. Further studies on this portion of the genome are required to unlock novel regulatory functions that could also be exploited for diagnostic and therapeutic approaches.
Collapse
Affiliation(s)
- Erica Gasparotto
- Fondazione INGM, Istituto Nazionale di Genetica Molecolare “Enrica e Romeo Invernizzi”, 20122 Milan, Italy
- SEMM, European School of Molecular Medicine, 20139 Milan, Italy
| | - Filippo Vittorio Burattin
- Fondazione INGM, Istituto Nazionale di Genetica Molecolare “Enrica e Romeo Invernizzi”, 20122 Milan, Italy
- Department of Biosciences, University of Milan, 20133 Milan, Italy
| | - Valeria Di Gioia
- Fondazione INGM, Istituto Nazionale di Genetica Molecolare “Enrica e Romeo Invernizzi”, 20122 Milan, Italy
- SEMM, European School of Molecular Medicine, 20139 Milan, Italy
| | - Michele Panepuccia
- Fondazione INGM, Istituto Nazionale di Genetica Molecolare “Enrica e Romeo Invernizzi”, 20122 Milan, Italy
| | - Valeria Ranzani
- Fondazione INGM, Istituto Nazionale di Genetica Molecolare “Enrica e Romeo Invernizzi”, 20122 Milan, Italy
| | - Federica Marasca
- Fondazione INGM, Istituto Nazionale di Genetica Molecolare “Enrica e Romeo Invernizzi”, 20122 Milan, Italy
- Department of Clinical Sciences and Community Health, University of Milan, 20122 Milan, Italy
| | - Beatrice Bodega
- Fondazione INGM, Istituto Nazionale di Genetica Molecolare “Enrica e Romeo Invernizzi”, 20122 Milan, Italy
- Department of Biosciences, University of Milan, 20133 Milan, Italy
- Correspondence:
| |
Collapse
|
16
|
Gunasekara CJ, MacKay H, Scott CA, Li S, Laritsky E, Baker MS, Grimm SL, Jun G, Li Y, Chen R, Wiemels JL, Coarfa C, Waterland RA. Systemic interindividual epigenetic variation in humans is associated with transposable elements and under strong genetic control. Genome Biol 2023; 24:2. [PMID: 36631879 PMCID: PMC9835319 DOI: 10.1186/s13059-022-02827-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 12/01/2022] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Genetic variants can modulate phenotypic outcomes via epigenetic intermediates, for example at methylation quantitative trait loci (mQTL). We present the first large-scale assessment of mQTL at human genomic regions selected for interindividual variation in CpG methylation, which we call correlated regions of systemic interindividual variation (CoRSIVs). These can be assayed in blood DNA and do not reflect interindividual variation in cellular composition. RESULTS We use target-capture bisulfite sequencing to assess DNA methylation at 4086 CoRSIVs in multiple tissues from each of 188 donors in the NIH Gene-Tissue Expression (GTEx) program. At CoRSIVs, DNA methylation in peripheral blood correlates with methylation and gene expression in internal organs. We also discover unprecedented mQTL at these regions. Genetic influences on CoRSIV methylation are extremely strong (median R2=0.76), cumulatively comprising over 70-fold more human mQTL than detected in the most powerful previous study. Moreover, mQTL beta coefficients at CoRSIVs are highly skewed (i.e., the major allele predicts higher methylation). Both surprising findings are independently validated in a cohort of 47 non-GTEx individuals. Genomic regions flanking CoRSIVs show long-range enrichments for LINE-1 and LTR transposable elements; the skewed beta coefficients may therefore reflect evolutionary selection of genetic variants that promote their methylation and silencing. Analyses of GWAS summary statistics show that mQTL polymorphisms at CoRSIVs are associated with metabolic and other classes of disease. CONCLUSIONS A focus on systemic interindividual epigenetic variants, clearly enhanced in mQTL content, should likewise benefit studies attempting to link human epigenetic variation to the risk of disease.
Collapse
Affiliation(s)
- Chathura J. Gunasekara
- grid.508989.50000 0004 6410 7501USDA/ARS Children’s Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX USA
| | - Harry MacKay
- grid.508989.50000 0004 6410 7501USDA/ARS Children’s Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX USA
| | - C. Anthony Scott
- grid.508989.50000 0004 6410 7501USDA/ARS Children’s Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX USA
| | - Shaobo Li
- grid.42505.360000 0001 2156 6853Keck School of Medicine, University of Southern California, Los Angeles, CA USA
| | - Eleonora Laritsky
- grid.508989.50000 0004 6410 7501USDA/ARS Children’s Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX USA
| | - Maria S. Baker
- grid.508989.50000 0004 6410 7501USDA/ARS Children’s Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX USA
| | - Sandra L. Grimm
- grid.39382.330000 0001 2160 926XDepartment of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX USA
| | - Goo Jun
- grid.267308.80000 0000 9206 2401Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX USA
| | - Yumei Li
- grid.39382.330000 0001 2160 926XDepartment of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - Rui Chen
- grid.39382.330000 0001 2160 926XDepartment of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - Joseph L. Wiemels
- grid.42505.360000 0001 2156 6853Keck School of Medicine, University of Southern California, Los Angeles, CA USA
| | - Cristian Coarfa
- grid.39382.330000 0001 2160 926XDepartment of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX USA ,grid.39382.330000 0001 2160 926XDan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX USA
| | - Robert A. Waterland
- grid.508989.50000 0004 6410 7501USDA/ARS Children’s Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX USA ,grid.39382.330000 0001 2160 926XDepartment of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX USA
| |
Collapse
|
17
|
Jachowicz JW. Epigenetic Manipulation of Transposable and Repetitive Elements. Methods Mol Biol 2023; 2607:355-368. [PMID: 36449170 DOI: 10.1007/978-1-0716-2883-6_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
This protocol describes methods to design, assemble, and validate tools for targeted activation or repression of single-copy and multi-copy genes, including repetitive and transposable elements. It uses transcription activator-like effector (TALE) technology combined with VP64 activator or Kruppel-associated box (KRAB) repressor, both of which are potent transcriptional regulators that modify the epigenetic state of endogenous DNA loci. This protocol has been successfully used to simultaneously modify expression patterns of thousands of LINE-1 transposable elements and satellite repeats, both in cell culture model systems and in preimplantation mouse embryos.
Collapse
Affiliation(s)
- Joanna W Jachowicz
- California Institute of Technology, Pasadena, CA, USA.
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria.
| |
Collapse
|
18
|
Petrzilek J, Pasulka J, Malik R, Horvat F, Kataruka S, Fulka H, Svoboda P. De novo emergence, existence, and demise of a protein-coding gene in murids. BMC Biol 2022; 20:272. [PMID: 36482406 PMCID: PMC9733328 DOI: 10.1186/s12915-022-01470-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 11/15/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Genes, principal units of genetic information, vary in complexity and evolutionary history. Less-complex genes (e.g., long non-coding RNA (lncRNA) expressing genes) readily emerge de novo from non-genic sequences and have high evolutionary turnover. Genesis of a gene may be facilitated by adoption of functional genic sequences from retrotransposon insertions. However, protein-coding sequences in extant genomes rarely lack any connection to an ancestral protein-coding sequence. RESULTS We describe remarkable evolution of the murine gene D6Ertd527e and its orthologs in the rodent Muroidea superfamily. The D6Ertd527e emerged in a common ancestor of mice and hamsters most likely as a lncRNA-expressing gene. A major contributing factor was a long terminal repeat (LTR) retrotransposon insertion carrying an oocyte-specific promoter and a 5' terminal exon of the gene. The gene survived as an oocyte-specific lncRNA in several extant rodents while in some others the gene or its expression were lost. In the ancestral lineage of Mus musculus, the gene acquired protein-coding capacity where the bulk of the coding sequence formed through CAG (AGC) trinucleotide repeat expansion and duplications. These events generated a cytoplasmic serine-rich maternal protein. Knock-out of D6Ertd527e in mice has a small but detectable effect on fertility and the maternal transcriptome. CONCLUSIONS While this evolving gene is not showing a clear function in laboratory mice, its documented evolutionary history in Muroidea during the last ~ 40 million years provides a textbook example of how a several common mutation events can support de novo gene formation, evolution of protein-coding capacity, as well as gene's demise.
Collapse
Affiliation(s)
- Jan Petrzilek
- grid.418827.00000 0004 0620 870XInstitute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague 4, Czech Republic ,grid.22937.3d0000 0000 9259 8492Present address: Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Josef Pasulka
- grid.418827.00000 0004 0620 870XInstitute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague 4, Czech Republic
| | - Radek Malik
- grid.418827.00000 0004 0620 870XInstitute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague 4, Czech Republic
| | - Filip Horvat
- grid.418827.00000 0004 0620 870XInstitute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague 4, Czech Republic ,grid.4808.40000 0001 0657 4636Bioinformatics Group, Division of Biology, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia
| | - Shubhangini Kataruka
- grid.418827.00000 0004 0620 870XInstitute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague 4, Czech Republic ,grid.47100.320000000419368710Present address: Department of Genetics, Yale School of Medicine, New Haven, CT 06510 USA
| | - Helena Fulka
- grid.418827.00000 0004 0620 870XInstitute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague 4, Czech Republic ,grid.418095.10000 0001 1015 3316Current address: Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague 4, Czech Republic
| | - Petr Svoboda
- grid.418827.00000 0004 0620 870XInstitute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague 4, Czech Republic
| |
Collapse
|
19
|
Modenini G, Abondio P, Boattini A. The coevolution between APOBEC3 and retrotransposons in primates. Mob DNA 2022; 13:27. [PMID: 36443831 PMCID: PMC9706992 DOI: 10.1186/s13100-022-00283-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 10/31/2022] [Indexed: 12/02/2022] Open
Abstract
Retrotransposons are genetic elements with the ability to replicate in the genome using reverse transcriptase: they have been associated with the development of different biological structures, such as the Central Nervous System (CNS), and their high mutagenic potential has been linked to various diseases, including cancer and neurological disorders. Throughout evolution and over time, Primates and Homo had to cope with infections from viruses and bacteria, and also with endogenous retroelements. Therefore, host genomes have evolved numerous methods to counteract the activity of endogenous and exogenous pathogens, and the APOBEC3 family of mutators is a prime example of a defensive mechanism in this context.In most Primates, there are seven members of the APOBEC3 family of deaminase proteins: among their functions, there is the ability to inhibit the mobilization of retrotransposons and the functionality of viruses. The evolution of the APOBEC3 proteins found in Primates is correlated with the expansion of two major families of retrotransposons, i.e. ERV and LINE-1.In this review, we will discuss how the rapid expansion of the APOBEC3 family is linked to the evolution of retrotransposons, highlighting the strong evolutionary arms race that characterized the history of APOBEC3s and endogenous retroelements in Primates. Moreover, the possible role of this relationship will be assessed in the context of embryonic development and brain-associated diseases.
Collapse
Affiliation(s)
- Giorgia Modenini
- grid.6292.f0000 0004 1757 1758Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Paolo Abondio
- grid.6292.f0000 0004 1757 1758Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy ,grid.6292.f0000 0004 1757 1758Department of Cultural Heritage, University of Bologna, Ravenna, Italy
| | - Alessio Boattini
- grid.6292.f0000 0004 1757 1758Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| |
Collapse
|
20
|
Paloviita P, Vuoristo S. The non-coding genome in early human development - Recent advancements. Semin Cell Dev Biol 2022; 131:4-13. [PMID: 35177347 DOI: 10.1016/j.semcdb.2022.02.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 02/08/2022] [Accepted: 02/08/2022] [Indexed: 12/14/2022]
Abstract
Not that long ago, the human genome was discovered to be mainly non-coding, that is comprised of DNA sequences that do not code for proteins. The initial paradigm that non-coding is also non-functional was soon overturned and today the work to uncover the functions of non-coding DNA and RNA in human early embryogenesis has commenced. Early human development is characterized by large-scale changes in genomic activity and the transcriptome that are partly driven by the coordinated activation and repression of repetitive DNA elements scattered across the genome. Here we provide examples of recent novel discoveries of non-coding DNA and RNA interactions and mechanisms that ensure accurate non-coding activity during human maternal-to-zygotic transition and lineage segregation. These include studies on small and long non-coding RNAs, transposable element regulation, and RNA tailing in human oocytes and early embryos. High-throughput approaches to dissect the non-coding regulatory networks governing early human development are a foundation for functional studies of specific genomic elements and molecules that has only begun and will provide a wider understanding of early human embryogenesis and causes of infertility.
Collapse
Affiliation(s)
- Pauliina Paloviita
- Department of Obstetrics and Gynaecology, University of Helsinki, 00014 Helsinki, Finland
| | - Sanna Vuoristo
- Department of Obstetrics and Gynaecology, University of Helsinki, 00014 Helsinki, Finland.
| |
Collapse
|
21
|
SoloTE for improved analysis of transposable elements in single-cell RNA-Seq data using locus-specific expression. Commun Biol 2022; 5:1063. [PMID: 36202992 PMCID: PMC9537157 DOI: 10.1038/s42003-022-04020-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 09/21/2022] [Indexed: 11/08/2022] Open
Abstract
Transposable Elements (TEs) contribute to the repetitive fraction in almost every eukaryotic genome known to date, and their transcriptional activation can influence the expression of neighboring genes in healthy and disease states. Single cell RNA-Seq (scRNA-Seq) is a technical advance that allows the study of gene expression on a cell-by-cell basis. Although a current computational approach is available for the single cell analysis of TE expression, it omits their genomic location. Here we show SoloTE, a pipeline that outperforms the previous approach in terms of computational resources and by allowing the inclusion of locus-specific TE activity in scRNA-Seq expression matrixes. We then apply SoloTE to several datasets to reveal the repertoire of TEs that become transcriptionally active in different cell groups, and based on their genomic location, we predict their potential impact on gene expression. As our tool takes as input the resulting files from standard scRNA-Seq processing pipelines, we expect it to be widely adopted in single cell studies to help researchers discover patterns of cellular diversity associated with TE expression.
Collapse
|
22
|
Dynamic Transcriptional Landscape of Grass Carp (Ctenopharyngodon idella) Reveals Key Transcriptional Features Involved in Fish Development. Int J Mol Sci 2022; 23:ijms231911547. [PMID: 36232849 PMCID: PMC9569805 DOI: 10.3390/ijms231911547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/23/2022] [Accepted: 09/23/2022] [Indexed: 11/17/2022] Open
Abstract
A high-quality baseline transcriptome is a valuable resource for developmental research as well as a useful reference for other studies. We gathered 41 samples representing 11 tissues/organs from 22 important developmental time points within 197 days of fertilization of grass carp eggs in order to systematically examine the role of lncRNAs and alternative splicing in fish development. We created a high-quality grass carp baseline transcriptome with a completeness of up to 93.98 percent by combining strand-specific RNA sequencing and single-molecule real-time RNA sequencing technologies, and we obtained temporal expression profiles of 33,055 genes and 77,582 transcripts during development and tissue differentiation. A family of short interspersed elements was preferentially expressed at the early stage of zygotic activation in grass carp, and its possible regulatory components were discovered through analysis. Additionally, after thoroughly analyzing alternative splicing events, we discovered that retained intron (RI) alternative splicing events change significantly in both zygotic activation and tissue differentiation. During zygotic activation, we also revealed the precise regulatory characteristics of the underlying functional RI events.
Collapse
|
23
|
Paulat NS, McGuire E, Subramanian K, Osmanski AB, Moreno-Santillán DD, Ray DA, Xing J. Transposable Elements in Bats Show Differential Accumulation Patterns Determined by Class and Functionality. LIFE (BASEL, SWITZERLAND) 2022; 12:life12081190. [PMID: 36013369 PMCID: PMC9409754 DOI: 10.3390/life12081190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/01/2022] [Accepted: 08/02/2022] [Indexed: 11/16/2022]
Abstract
Bat genomes are characterized by a diverse transposable element (TE) repertoire. In particular, the genomes of members of the family Vespertilionidae contain both active retrotransposons and active DNA transposons. Each TE type is characterized by a distinct pattern of accumulation over the past ~40 million years. Each also exhibits its own target site preferences (sometimes shared with other TEs) that impact where they are likely to insert when mobilizing. Therefore, bats provide a great resource for understanding the diversity of TE insertion patterns. To gain insight into how these diverse TEs impact genome structure, we performed comparative spatial analyses between different TE classes and genomic features, including genic regions and CpG islands. Our results showed a depletion of all TEs in the coding sequence and revealed patterns of species- and element-specific attraction in the transcript. Trends of attraction in the distance tests also suggested significant TE activity in regions adjacent to genes. In particular, the enrichment of small, non-autonomous TE insertions in introns and near coding regions supports the hypothesis that the genomic distribution of TEs is the product of a balance of the TE insertion preference in open chromatin regions and the purifying selection against TEs within genes.
Collapse
Affiliation(s)
- Nicole S. Paulat
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA
| | - Erin McGuire
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Krishnamurthy Subramanian
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Austin B. Osmanski
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA
| | | | - David A. Ray
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA
- Correspondence: (D.A.R.); (J.X.)
| | - Jinchuan Xing
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Correspondence: (D.A.R.); (J.X.)
| |
Collapse
|
24
|
Yu C, Lei X, Chen F, Mao S, Lv L, Liu H, Hu X, Wang R, Shen L, Zhang N, Meng Y, Shen Y, Chen J, Li P, Huang S, Lin C, Zhang Z, Yuan K. ARID1A loss derepresses a group of human endogenous retrovirus-H loci to modulate BRD4-dependent transcription. Nat Commun 2022; 13:3501. [PMID: 35715442 PMCID: PMC9205910 DOI: 10.1038/s41467-022-31197-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 06/07/2022] [Indexed: 11/25/2022] Open
Abstract
Transposable elements (TEs) through evolutionary exaptation have become an integral part of the human genome, offering ample regulatory sequences and shaping chromatin 3D architecture. While the functional impacts of TE-derived sequences on early embryogenesis have been recognized, their roles in malignancy are only starting to emerge. Here we show that many TEs, especially the pluripotency-related human endogenous retrovirus H (HERVH), are abnormally activated in colorectal cancer (CRC) samples. Transcriptional upregulation of HERVH is associated with mutations of several tumor suppressors, particularly ARID1A. Knockout of ARID1A in CRC cells leads to increased transcription at several HERVH loci, which involves compensatory contribution by ARID1B. Suppression of HERVH in CRC cells and patient-derived organoids impairs tumor growth. Mechanistically, HERVH transcripts colocalize with nuclear BRD4 foci, modulating their dynamics and co-regulating many target genes. Altogether, we uncover a critical role for ARID1A in restraining HERVH, whose abnormal activation can promote tumorigenesis by stimulating BRD4-dependent transcription. Here the authors show mutation of the BAF chromatin remodeler subunit ARID1A results in an ARID1B-dependent upregulation of HERVH, an ERV required for the pluripotency regulatory network. These HERVH RNAs can partition into BRD4 foci, affecting BRD4-dependent transcription. Suppression of HERVH in colorectal cancer cells and patient-derived organoids impairs tumor growth.
Collapse
Affiliation(s)
- Chunhong Yu
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xiaoyun Lei
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Fang Chen
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Song Mao
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Lu Lv
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Honglu Liu
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xueying Hu
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Runhan Wang
- Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Licong Shen
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Department of Gynecology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Na Zhang
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yang Meng
- Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Yunfan Shen
- Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Jiale Chen
- Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Pishun Li
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Shi Huang
- Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Changwei Lin
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Department of Gastrointestinal Surgery, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Zhuohua Zhang
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Kai Yuan
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, China. .,Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China. .,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China. .,The Biobank of Xiangya Hospital, Central South University, Changsha, Hunan, China.
| |
Collapse
|
25
|
Abstract
Dramatic nuclear reorganization occurs during early development to convert terminally differentiated gametes to a totipotent zygote, which then gives rise to an embryo. Aberrant epigenome resetting severely impairs embryo development and even leads to lethality. How the epigenomes are inherited, reprogrammed, and reestablished in this critical developmental period has gradually been unveiled through the rapid development of technologies including ultrasensitive chromatin analysis methods. In this review, we summarize the latest findings on epigenetic reprogramming in gametogenesis and embryogenesis, and how it contributes to gamete maturation and parental-to-zygotic transition. Finally, we highlight the key questions that remain to be answered to fully understand chromatin regulation and nuclear reprogramming in early development.
Collapse
Affiliation(s)
- Zhenhai Du
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Ke Zhang
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Wei Xie
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| |
Collapse
|
26
|
Ma G, Babarinde IA, Zhou X, Hutchins AP. Transposable Elements in Pluripotent Stem Cells and Human Disease. Front Genet 2022; 13:902541. [PMID: 35719395 PMCID: PMC9201960 DOI: 10.3389/fgene.2022.902541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 05/20/2022] [Indexed: 11/18/2022] Open
Abstract
Transposable elements (TEs) are mobile genetic elements that can randomly integrate into other genomic sites. They have successfully replicated and now occupy around 40% of the total DNA sequence in humans. TEs in the genome have a complex relationship with the host cell, being both potentially deleterious and advantageous at the same time. Only a tiny minority of TEs are still capable of transposition, yet their fossilized sequence fragments are thought to be involved in various molecular processes, such as gene transcriptional activity, RNA stability and subcellular localization, and chromosomal architecture. TEs have also been implicated in biological processes, although it is often hard to reveal cause from correlation due to formidable technical issues in analyzing TEs. In this review, we compare and contrast two views of TE activity: one in the pluripotent state, where TEs are broadly beneficial, or at least mechanistically useful, and a second state in human disease, where TEs are uniformly considered harmful.
Collapse
|
27
|
Shridharan RV, Kalakuntla N, Chirmule N, Tiwari B. The Happy Hopping of Transposons: The Origins of V(D)J Recombination in Adaptive Immunity. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.836066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Nearly 50% of the human genome is derived from transposable elements (TEs). Though dysregulated transposons are deleterious to humans and can lead to diseases, co-opted transposons play an important role in generating alternative or new DNA sequence combinations to perform novel cellular functions. The appearance of an adaptive immune system in jawed vertebrates, wherein the somatic rearrangement of T and B cells generates a repertoire of antibodies and receptors, is underpinned by Class II TEs. This review follows the evolution of recombination activation genes (RAGs), components of adaptive immunity, from TEs, focusing on the structural and mechanistic similarities between RAG recombinases and DNA transposases. As evolution occurred from a transposon precursor, DNA transposases developed a more targeted and constrained mechanism of mobilization. As DNA repair is integral to transposition and recombination, we note key similarities and differences in the choice of DNA repair pathways following these processes. Understanding the regulation of V(D)J recombination from its evolutionary origins may help future research to specifically target RAG proteins to rectify diseases associated with immune dysregulation.
Collapse
|
28
|
Somatic Mobilization: High Somatic Insertion Rate of mariner Transposable Element in Drosophila simulans. INSECTS 2022; 13:insects13050454. [PMID: 35621789 PMCID: PMC9144738 DOI: 10.3390/insects13050454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 05/09/2022] [Accepted: 05/10/2022] [Indexed: 11/17/2022]
Abstract
Although transposable elements (TEs) are usually silent in somatic tissues, they are sometimes mobilized in the soma and can potentially have biological consequences. The mariner element is one of the TEs involved in somatic mobilization (SM) in Drosophila and has a high rate of somatic excision. It is also known that temperature is an important factor in the increase of the mariner element SM in the fly. However, it is important to emphasize that excision is only one step of TE transposition, and the final step in this process is insertion. In the present study, we used an assay based on sequencing of the mariner flanking region and developed a pipeline to identify novel mariner insertions in Drosophila simulans at 20 and 28 °C. We found that flies carrying two mariner copies (one autonomous and one non-autonomous) had an average of 236.4 (±99.3) to 279 (±107.7) new somatic insertions at 20 °C and an average of 172.7 (±95.3) to 252.6 (±67.3) at 28 °C. In addition, we detected fragments containing mariner and others without mariner in the same regions with low-coverage long-read sequencing, indicating the process of excision and insertion. In conclusion, a low number of autonomous copies of the mariner transposon can promote a high rate of new somatic insertions during the developmental stages of Drosophila. Additionally, the developed method seems to be sensitive and adequate for the verification and estimation of somatic insertion.
Collapse
|
29
|
Vuoristo S, Bhagat S, Hydén-Granskog C, Yoshihara M, Gawriyski L, Jouhilahti EM, Ranga V, Tamirat M, Huhtala M, Kirjanov I, Nykänen S, Krjutškov K, Damdimopoulos A, Weltner J, Hashimoto K, Recher G, Ezer S, Paluoja P, Paloviita P, Takegami Y, Kanemaru A, Lundin K, Airenne TT, Otonkoski T, Tapanainen JS, Kawaji H, Murakawa Y, Bürglin TR, Varjosalo M, Johnson MS, Tuuri T, Katayama S, Kere J. DUX4 is a multifunctional factor priming human embryonic genome activation. iScience 2022; 25:104137. [PMID: 35402882 PMCID: PMC8990217 DOI: 10.1016/j.isci.2022.104137] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 02/04/2022] [Accepted: 03/18/2022] [Indexed: 12/13/2022] Open
Abstract
Double homeobox 4 (DUX4) is expressed at the early pre-implantation stage in human embryos. Here we show that induced human DUX4 expression substantially alters the chromatin accessibility of non-coding DNA and activates thousands of newly identified transcribed enhancer-like regions, preferentially located within ERVL-MaLR repeat elements. CRISPR activation of transcribed enhancers by C-terminal DUX4 motifs results in the increased expression of target embryonic genome activation (EGA) genes ZSCAN4 and KHDC1P1. We show that DUX4 is markedly enriched in human zygotes, followed by intense nuclear DUX4 localization preceding and coinciding with minor EGA. DUX4 knockdown in human zygotes led to changes in the EGA transcriptome but did not terminate the embryos. We also show that the DUX4 protein interacts with the Mediator complex via the C-terminal KIX binding motif. Our findings contribute to the understanding of DUX4 as a regulator of the non-coding genome.
Collapse
Affiliation(s)
- Sanna Vuoristo
- Department of Biosciences and Nutrition, Karolinska Institutet, 17177 Huddinge, Sweden.,Department of Obstetrics and Gynecology, 00014, University of Helsinki and Helsinki University Hospital, 00290 Helsinki, Finland
| | - Shruti Bhagat
- Department of Biosciences and Nutrition, Karolinska Institutet, 17177 Huddinge, Sweden.,RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan.,Instutute for the Advanced Study of Human Biology, Kyoto University, Kyoto 606-8501, Japan
| | | | - Masahito Yoshihara
- Department of Biosciences and Nutrition, Karolinska Institutet, 17177 Huddinge, Sweden
| | - Lisa Gawriyski
- Institute of Biotechnology, University of Helsinki, 00790 Helsinki, Finland
| | - Eeva-Mari Jouhilahti
- Stem Cells and Metabolism Research Program, University of Helsinki, 00014 Helsinki, Finland
| | - Vipin Ranga
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland
| | - Mahlet Tamirat
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland
| | - Mikko Huhtala
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland
| | - Ida Kirjanov
- Department of Obstetrics and Gynecology, 00014, University of Helsinki and Helsinki University Hospital, 00290 Helsinki, Finland
| | - Sonja Nykänen
- Department of Obstetrics and Gynecology, 00014, University of Helsinki and Helsinki University Hospital, 00290 Helsinki, Finland
| | - Kaarel Krjutškov
- Department of Biosciences and Nutrition, Karolinska Institutet, 17177 Huddinge, Sweden.,Stem Cells and Metabolism Research Program, University of Helsinki, 00014 Helsinki, Finland.,Competence Centre for Health Technologies, 51010 Tartu, Estonia.,University of Tartu, Department of Obstetrics and Gynecology, Institute of Clinical Medicine, 50406 Tartu, Estonia
| | | | - Jere Weltner
- Stem Cells and Metabolism Research Program, University of Helsinki, 00014 Helsinki, Finland
| | - Kosuke Hashimoto
- RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Gaëlle Recher
- Laboratoire Photonique Numérique et Nanosciences, CNRS, Institut d'Optique Graduate School, University of Bordeaux, UMR 5298, 33400 Bordeaux, France
| | - Sini Ezer
- Stem Cells and Metabolism Research Program, University of Helsinki, 00014 Helsinki, Finland.,Folkhälsan Research Center, 00290 Helsinki, Finland
| | - Priit Paluoja
- Competence Centre for Health Technologies, 51010 Tartu, Estonia.,Institute of Clinical Medicine, University of Tartu, 50090 Tartu, Estonia.,University of Helsinki, Doctoral Program in Population Health, 00014 Helsinki, Finland
| | - Pauliina Paloviita
- Department of Obstetrics and Gynecology, 00014, University of Helsinki and Helsinki University Hospital, 00290 Helsinki, Finland
| | | | | | - Karolina Lundin
- Department of Obstetrics and Gynecology, 00014, University of Helsinki and Helsinki University Hospital, 00290 Helsinki, Finland
| | - Tomi T Airenne
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland
| | - Timo Otonkoski
- Stem Cells and Metabolism Research Program, University of Helsinki, 00014 Helsinki, Finland.,Children's Hospital, Helsinki University Central Hospital, 00290
| | - Juha S Tapanainen
- Department of Obstetrics and Gynecology, 00014, University of Helsinki and Helsinki University Hospital, 00290 Helsinki, Finland.,Reproductive Medicine Unit, Helsinki University Hospital, 00290 Helsinki, Finland.,Oulu University Hospital, 90220 Oulu, Finland
| | - Hideya Kawaji
- RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan.,RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako 351-0198, Japan.,Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan
| | - Yasuhiro Murakawa
- RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan.,Instutute for the Advanced Study of Human Biology, Kyoto University, Kyoto 606-8501, Japan.,IFOM, The FIRC Institute of Molecular Oncology, 20139 Milan, Italy.,Department of Medical Systems Genomics, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Thomas R Bürglin
- Department of Biomedicine, University of Basel, 4031 Basel, Switzerland
| | - Markku Varjosalo
- Institute of Biotechnology, University of Helsinki, 00790 Helsinki, Finland
| | - Mark S Johnson
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland
| | - Timo Tuuri
- Department of Obstetrics and Gynecology, 00014, University of Helsinki and Helsinki University Hospital, 00290 Helsinki, Finland.,Reproductive Medicine Unit, Helsinki University Hospital, 00290 Helsinki, Finland
| | - Shintaro Katayama
- Department of Biosciences and Nutrition, Karolinska Institutet, 17177 Huddinge, Sweden.,Stem Cells and Metabolism Research Program, University of Helsinki, 00014 Helsinki, Finland.,Folkhälsan Research Center, 00290 Helsinki, Finland
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, 17177 Huddinge, Sweden.,Stem Cells and Metabolism Research Program, University of Helsinki, 00014 Helsinki, Finland.,Folkhälsan Research Center, 00290 Helsinki, Finland
| |
Collapse
|
30
|
A hypothesis: Retrotransposons as a relay of epigenetic marks in intergenerational epigenetic inheritance. Gene 2022; 817:146229. [PMID: 35063571 DOI: 10.1016/j.gene.2022.146229] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 12/13/2021] [Accepted: 01/13/2022] [Indexed: 12/19/2022]
Abstract
Epigenetic marks in gametes, which both respond to the parental environmental factors and shape offspring phenotypes, are usually positioned to mediate intergenerational or transgenerational epigenetic inheritance. Nonetheless, the mechanisms through which gametic epigenetic signatures encode parental acquired phenotypes, and further initiate a cascade of molecular events to affect offspring phenotypes during early embryonic development, remain unclear. Retrotransposons are mobile DNA elements that could resist to genomic epigenetic reprogramming at specific loci and rewire the core regulatory networks of embryogenesis. Increasing evidences show that retrotransposons in the embryonic genome could interact with gametic epigenetic marks, which provides a tentative possibility that retrotransposons may serve as a relay of gametic epigenetic marks to transmit parental acquired traits. Here, we summarize the recent progress in exploring the crosstalk between gametic epigenetic marks and retrotransposons, and the regulation of gene expression and early embryonic development by retrotransposons. Accordingly, deciphering the mystery of interactions between gametic epigenetic marks and retrotransposons during early embryonic development will provide valuable insights into the intergenerational or transgenerational transmission of acquired traits.
Collapse
|
31
|
Almeida MV, Vernaz G, Putman AL, Miska EA. Taming transposable elements in vertebrates: from epigenetic silencing to domestication. Trends Genet 2022; 38:529-553. [DOI: 10.1016/j.tig.2022.02.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 02/14/2022] [Accepted: 02/15/2022] [Indexed: 12/20/2022]
|
32
|
Sperm Histone H3 Lysine 4 tri-methylation serves as a metabolic sensor of paternal obesity and is associated with the inheritance of metabolic dysfunction. Mol Metab 2022; 59:101463. [PMID: 35183795 PMCID: PMC8931445 DOI: 10.1016/j.molmet.2022.101463] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 02/12/2022] [Accepted: 02/14/2022] [Indexed: 11/28/2022] Open
Abstract
Objective Parental environmental exposures can strongly influence descendant risks for adult disease. How paternal obesity changes the sperm chromatin leading to the acquisition of metabolic disease in offspring remains controversial and ill-defined. The objective of this study was to assess (1) whether obesity induced by a high-fat diet alters sperm histone methylation; (2) whether paternal obesity can induce metabolic disturbances across generations; (3) whether there could be cumulative damage to the sperm epigenome leading to enhanced metabolic dysfunction in descendants; and (4) whether obesity-sensitive regions associate with embryonic epigenetic and transcriptomic profiles. Using a genetic mouse model of epigenetic inheritance, we investigated the role of histone H3 lysine 4 methylation (H3K4me3) in the paternal transmission of metabolic dysfunction. This transgenic mouse overexpresses the histone demethylase enzyme KDM1A in the developing germline and has an altered sperm epigenome at the level of histone H3K4 methylation. We hypothesized that challenging transgenic sires with a high-fat diet would further erode the sperm epigenome and lead to enhanced metabolic disturbances in the next generations. Methods To assess whether paternal obesity can have inter- or transgenerational impacts, and if so to identify potential mechanisms of this non-genetic inheritance, we used wild-type C57BL/6NCrl and transgenic males with a pre-existing altered sperm epigenome. To induce obesity, sires were fed either a control or high-fat diet (10% or 60% kcal fat, respectively) for 10–12 weeks, then bred to wild-type C57BL/6NCrl females fed a regular diet. F1 and F2 descendants were characterized for metabolic phenotypes by examining the effects of paternal obesity by sex, on body weight, fat mass distribution, the liver transcriptome, intraperitoneal glucose, and insulin tolerance tests. To determine whether obesity altered the F0 sperm chromatin, native chromatin immunoprecipitation-sequencing targeting H3K4me3 was performed. To gain insight into mechanisms of paternal transmission, we compared our sperm H3K4me3 profiles with embryonic and placental chromatin states, histone modification, and gene expression profiles. Results Obesity-induced alterations in H3K4me3 occurred in genes implicated in metabolic, inflammatory, and developmental processes. These processes were associated with offspring metabolic dysfunction and corresponded to genes enriched for H3K4me3 in embryos and overlapped embryonic and placenta gene expression profiles. Transgenerational susceptibility to metabolic disease was only observed when obese F0 had a pre-existing modified sperm epigenome. This coincided with increased H3K4me3 alterations in sperm and more severe phenotypes affecting their offspring. Conclusions Our data suggest sperm H3K4me3 might serve as a metabolic sensor that connects paternal diet with offspring phenotypes via the placenta. This non-DNA-based knowledge of inheritance has the potential to improve our understanding of how environment shapes heritability and may lead to novel routes for the prevention of disease. This study highlights the need to further study the connection between the sperm epigenome, placental development, and children's health. Summary sentence Paternal obesity impacts sperm H3K4me3 and is associated with placenta, embryonic and metabolic outcomes in descendants. Sperm H3K4me3 serves as a metabolic sensor of HFD-induced obesity. Obesity-altered sperm H3K4me3 corresponds to embryonic transcription and chromatin profiles. HFD- and KDM1A-induced cumulative sperm epimutations enhanced F1 metabolic dysfunction. Sperm epimutations may influence placenta function inducing F1 metabolic phenotypes.
Collapse
|
33
|
Valdebenito-Maturana B, Guatimosim C, Carrasco MA, Tapia JC. Spatially Resolved Expression of Transposable Elements in Disease and Somatic Tissue with SpatialTE. Int J Mol Sci 2021; 22:ijms222413623. [PMID: 34948421 PMCID: PMC8708317 DOI: 10.3390/ijms222413623] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 12/10/2021] [Accepted: 12/13/2021] [Indexed: 11/23/2022] Open
Abstract
Spatial transcriptomics (ST) is transforming the way we can study gene expression and its regulation through position-specific resolution within tissues. However, as in bulk RNA-Seq, transposable elements (TEs) are not being studied due to their highly repetitive nature. In recent years, TEs have been recognized as important regulators of gene expression, and thus, TE expression analysis in a spatially resolved manner could further help to understand their role in gene regulation within tissues. We present SpatialTE, a tool to analyze TE expression from ST datasets and show its application in somatic and diseased tissues. The results indicate that TEs have spatially regulated expression patterns and that their expression profiles are spatially altered in ALS disease, indicating that TEs might perform differential regulatory functions within tissue organs. We have made SpatialTE publicly available as open-source software under an MIT license.
Collapse
Affiliation(s)
- Braulio Valdebenito-Maturana
- Núcleo Científico Multidisciplinario, School of Medicine, Universidad de Talca, Campus Talca, Talca 3460000, Chile;
| | - Cristina Guatimosim
- Departamento de Morfologia, ICB, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil;
| | - Mónica Alejandra Carrasco
- School of Medicine, Universidad de Talca, Campus Talca, Talca 3460000, Chile
- Correspondence: (M.A.C.); (J.C.T.)
| | - Juan Carlos Tapia
- School of Medicine, Universidad de Talca, Campus Talca, Talca 3460000, Chile
- Correspondence: (M.A.C.); (J.C.T.)
| |
Collapse
|
34
|
Yeh CY, Huang WH, Chen HC, Meir YJJ. Capturing Pluripotency and Beyond. Cells 2021; 10:cells10123558. [PMID: 34944066 PMCID: PMC8700150 DOI: 10.3390/cells10123558] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 11/16/2022] Open
Abstract
During the development of a multicellular organism, the specification of different cell lineages originates in a small group of pluripotent cells, the epiblasts, formed in the preimplantation embryo. The pluripotent epiblast is protected from premature differentiation until exposure to inductive cues in strictly controlled spatially and temporally organized patterns guiding fetus formation. Epiblasts cultured in vitro are embryonic stem cells (ESCs), which recapitulate the self-renewal and lineage specification properties of their endogenous counterparts. The characteristics of totipotency, although less understood than pluripotency, are becoming clearer. Recent studies have shown that a minor ESC subpopulation exhibits expanded developmental potential beyond pluripotency, displaying a characteristic reminiscent of two-cell embryo blastomeres (2CLCs). In addition, reprogramming both mouse and human ESCs in defined media can produce expanded/extended pluripotent stem cells (EPSCs) similar to but different from 2CLCs. Further, the molecular roadmaps driving the transition of various potency states have been clarified. These recent key findings will allow us to understand eutherian mammalian development by comparing the underlying differences between potency network components during development. Using the mouse as a paradigm and recent progress in human PSCs, we review the epiblast's identity acquisition during embryogenesis and their ESC counterparts regarding their pluripotent fates and beyond.
Collapse
Affiliation(s)
- Chih-Yu Yeh
- Department of Medicine, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan; (C.-Y.Y.); (W.-H.H.)
| | - Wei-Han Huang
- Department of Medicine, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan; (C.-Y.Y.); (W.-H.H.)
| | - Hung-Chi Chen
- Department of Medicine, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan; (C.-Y.Y.); (W.-H.H.)
- Limbal Stem Cell Laboratory, Department of Ophthalmology, Chang Gung Memorial Hospital, Linkou 333, Taiwan
- Correspondence: (H.-C.C.); (Y.-J.J.M.)
| | - Yaa-Jyuhn James Meir
- Limbal Stem Cell Laboratory, Department of Ophthalmology, Chang Gung Memorial Hospital, Linkou 333, Taiwan
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan
- Correspondence: (H.-C.C.); (Y.-J.J.M.)
| |
Collapse
|
35
|
Mustafin RN. Relationship of Peptides and Long Non-Coding RNAs with Aging. ADVANCES IN GERONTOLOGY 2021. [DOI: 10.1134/s2079057021040081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
36
|
Ball HC, Ansari MY, Ahmad N, Novak K, Haqqi TM. A retrotransposon gag-like-3 gene RTL3 and SOX-9 co-regulate the expression of COL2A1 in chondrocytes. Connect Tissue Res 2021; 62:615-628. [PMID: 33043724 PMCID: PMC8404968 DOI: 10.1080/03008207.2020.1828380] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
PURPOSE Transposable elements are known to remodel gene structure and provide a known source of genetic variation. Retrotransposon gag-like-3 (RTL3) is a mammalian retrotransposon-derived transcript (MART) whose function in the skeletal tissue is unknown. This study aimed to elucidate the biological significance of RTL3 in chondrogenesis and type-II collagen (COL2A1) gene expression in chondrocytes. MATERIALS AND METHODS Expression of RTL3, SOX-9 and COL2A1 mRNAs was determined by TaqMan assays and the protein expression by immunoblotting. RTL3 and Sox-9 depletion in human chondrocytes was achieved using validated siRNAs. An RTL3 mutant (∆RTL3) lacking the zinc finger domain was created using in vitro mutagenesis. Forced expression of RTL3, ∆RTL3, and SOX-9 was achieved using CMV promoter containing expression plasmids. CRISPR-Cas9 was utilized to delete Rtl3 and create a stable ATDC5Rlt3-/- cell line. Matrix deposition and Col2a1 quantification during chondrogenesis were determined by Alcian blue staining and Sircol™ Soluble Collagen Assay, respectively. RESULTS RTL3 is not ubiquitously expressed but showed strong expression in cartilage, chondrocytes and synoviocytes but not in muscle, brain, or other tissues analyzed. Loss-of-function and gain-of-function studies demonstrated a critical role of RTL3 in the regulation of SOX-9 and COL2A1 expression and matrix synthesis during chondrogenesis. Both RTL3 and SOX-9 displayed co-regulated expression in chondrocytes. Gene regulatory activity of RTL3 requires the c-terminal CCHC zinc-finger binding domain. CONCLUSIONS Our results identify a novel regulatory mechanism of COL2A1 expression in chondrocytes that may help to further understand the skeletal development and the pathogenesis of diseases with altered COL2A1 expression.
Collapse
Affiliation(s)
- Hope. C. Ball
- Department of Anatomy and Neurobiology, Northeast Ohio Medical University, Rootstown, USA
| | - Mohammad Y. Ansari
- Department of Anatomy and Neurobiology, Northeast Ohio Medical University, Rootstown, USA
| | - Nashrah Ahmad
- Department of Anatomy and Neurobiology, Northeast Ohio Medical University, Rootstown, USA.,Department of Biomedical Science, Kent State University, Kent, USA
| | - Kimberly Novak
- Department of Anatomy and Neurobiology, Northeast Ohio Medical University, Rootstown, USA
| | - Tariq M. Haqqi
- Department of Anatomy and Neurobiology, Northeast Ohio Medical University, Rootstown, USA.,To whom correspondence should be addressed: Prof. Tariq M. Haqqi: Department of Anatomy and Neurobiology, Northeast Ohio Medical University, Rootstown OH 44272; ; Tel (330) 325-6704
| |
Collapse
|
37
|
Modzelewski AJ, Shao W, Chen J, Lee A, Qi X, Noon M, Tjokro K, Sales G, Biton A, Anand A, Speed TP, Xuan Z, Wang T, Risso D, He L. A mouse-specific retrotransposon drives a conserved Cdk2ap1 isoform essential for development. Cell 2021; 184:5541-5558.e22. [PMID: 34644528 PMCID: PMC8787082 DOI: 10.1016/j.cell.2021.09.021] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 07/26/2021] [Accepted: 09/14/2021] [Indexed: 12/13/2022]
Abstract
Retrotransposons mediate gene regulation in important developmental and pathological processes. Here, we characterized the transient retrotransposon induction during preimplantation development of eight mammals. Induced retrotransposons exhibit similar preimplantation profiles across species, conferring gene regulatory activities, particularly through long terminal repeat (LTR) retrotransposon promoters. A mouse-specific MT2B2 retrotransposon promoter generates an N-terminally truncated Cdk2ap1ΔN that peaks in preimplantation embryos and promotes proliferation. In contrast, the canonical Cdk2ap1 peaks in mid-gestation and represses cell proliferation. This MT2B2 promoter, whose deletion abolishes Cdk2ap1ΔN production, reduces cell proliferation and impairs embryo implantation, is developmentally essential. Intriguingly, Cdk2ap1ΔN is evolutionarily conserved in sequence and function yet is driven by different promoters across mammals. The distinct preimplantation Cdk2ap1ΔN expression in each mammalian species correlates with the duration of its preimplantation development. Hence, species-specific transposon promoters can yield evolutionarily conserved, alternative protein isoforms, bestowing them with new functions and species-specific expression to govern essential biological divergence.
Collapse
Affiliation(s)
- Andrew J Modzelewski
- Division of Cellular and Developmental Biology, MCB Department, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Wanqing Shao
- Department of Genetics, Edison Family Center for Genome Science and System Biology, McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jingqi Chen
- Division of Cellular and Developmental Biology, MCB Department, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Angus Lee
- Division of Cellular and Developmental Biology, MCB Department, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Xin Qi
- Division of Cellular and Developmental Biology, MCB Department, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Mackenzie Noon
- Division of Cellular and Developmental Biology, MCB Department, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Kristy Tjokro
- Division of Cellular and Developmental Biology, MCB Department, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Gabriele Sales
- Department of Biology, University of Padova, Padova 35122, Italy
| | - Anne Biton
- Department of Statistics, University of California, Berkeley, Berkeley, CA 94720, USA; Bioinformatics and Biostatistics, Department of Computational Biology, USR 3756 CNRS, Institut Pasteur, Paris 75015, France
| | - Aparna Anand
- Department of Genetics, Edison Family Center for Genome Science and System Biology, McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Terence P Speed
- Bioinformatics Division, WEHI, Parkville, VIC 3052, Australia
| | - Zhenyu Xuan
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, TX 75080, USA
| | - Ting Wang
- Department of Genetics, Edison Family Center for Genome Science and System Biology, McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63110, USA.
| | - Davide Risso
- Department of Statistical Sciences, University of Padova, Padova 35122, Italy.
| | - Lin He
- Division of Cellular and Developmental Biology, MCB Department, University of California, Berkeley, Berkeley, CA 94720, USA.
| |
Collapse
|
38
|
Stockwell PA, Lynch-Sutherland CF, Chatterjee A, Macaulay EC, Eccles MR. RepExpress: A Novel Pipeline for the Quantification and Characterization of Transposable Element Expression from RNA-seq Data. Curr Protoc 2021; 1:e206. [PMID: 34387946 DOI: 10.1002/cpz1.206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Transposable elements (TEs) are key regulators of both development and disease; however, their repetitive nature presents substantial computational challenges to their analysis. Due to a lack of computational tools and suitable analysis frameworks, TE expression is often not quantified at the locus level. Therefore, we have developed RepExpress, a novel pipeline that enables locus-level TE quantification and characterization. RepExpress enables the characterization of TE expression in a genomic context, and is the first tool focusing on the identification of tissue-specific TE-derived and TE-regulated genes. RepExpress identifies expressed TEs overlapping with annotated genomic features and enables tissue-specific profiles of TE-derived genes. TEs that are expressed with no overlap with any known genomic features are characterized by the closest downstream genomic feature enabling identification of novel TE-gene regulatory relationships. RepExpress takes standard RNA-seq data as input and performs genomic alignment optimized for TEs. Our novel pipeline quantifies expression of both TEs and genes using featureCounts and Stringtie, respectively. RepExpress then filters expressed repeats and characterizes their genomic context, enabling the identification of TEs that overlap with genes, or that may be influencing gene expression. Here, we describe RepExpress, and provide a step-by-step protocol detailing its workflow. We also discuss other TE analysis tools and their applicability to addressing different biological questions. © 2021 Wiley Periodicals LLC. Basic Protocol: RepExpress workflow.
Collapse
Affiliation(s)
- Peter A Stockwell
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | | | - Aniruddha Chatterjee
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand
| | - Erin C Macaulay
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Michael R Eccles
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand
| |
Collapse
|
39
|
Anvar Z, Chakchouk I, Demond H, Sharif M, Kelsey G, Van den Veyver IB. DNA Methylation Dynamics in the Female Germline and Maternal-Effect Mutations That Disrupt Genomic Imprinting. Genes (Basel) 2021; 12:genes12081214. [PMID: 34440388 PMCID: PMC8394515 DOI: 10.3390/genes12081214] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/30/2021] [Accepted: 08/03/2021] [Indexed: 11/16/2022] Open
Abstract
Genomic imprinting is an epigenetic marking process that results in the monoallelic expression of a subset of genes. Many of these ‘imprinted’ genes in mice and humans are involved in embryonic and extraembryonic growth and development, and some have life-long impacts on metabolism. During mammalian development, the genome undergoes waves of (re)programming of DNA methylation and other epigenetic marks. Disturbances in these events can cause imprinting disorders and compromise development. Multi-locus imprinting disturbance (MLID) is a condition by which imprinting defects touch more than one locus. Although most cases with MLID present with clinical features characteristic of one imprinting disorder. Imprinting defects also occur in ‘molar’ pregnancies-which are characterized by highly compromised embryonic development-and in other forms of reproductive compromise presenting clinically as infertility or early pregnancy loss. Pathogenic variants in some of the genes encoding proteins of the subcortical maternal complex (SCMC), a multi-protein complex in the mammalian oocyte, are responsible for a rare subgroup of moles, biparental complete hydatidiform mole (BiCHM), and other adverse reproductive outcomes which have been associated with altered imprinting status of the oocyte, embryo and/or placenta. The finding that defects in a cytoplasmic protein complex could have severe impacts on genomic methylation at critical times in gamete or early embryo development has wider implications beyond these relatively rare disorders. It signifies a potential for adverse maternal physiology, nutrition, or assisted reproduction to cause epigenetic defects at imprinted or other genes. Here, we review key milestones in DNA methylation patterning in the female germline and the embryo focusing on humans. We provide an overview of recent findings regarding DNA methylation deficits causing BiCHM, MLID, and early embryonic arrest. We also summarize identified SCMC mutations with regard to early embryonic arrest, BiCHM, and MLID.
Collapse
Affiliation(s)
- Zahra Anvar
- Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX 77030, USA; (Z.A.); (I.C.); (M.S.)
- Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Imen Chakchouk
- Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX 77030, USA; (Z.A.); (I.C.); (M.S.)
- Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Hannah Demond
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK;
| | - Momal Sharif
- Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX 77030, USA; (Z.A.); (I.C.); (M.S.)
- Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Gavin Kelsey
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK;
- Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, UK
- Correspondence: (G.K.); (I.B.V.d.V.); Tel.: +44-1223-496332 (G.K.); +832-824-8125 (I.B.V.d.V.)
| | - Ignatia B. Van den Veyver
- Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX 77030, USA; (Z.A.); (I.C.); (M.S.)
- Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Correspondence: (G.K.); (I.B.V.d.V.); Tel.: +44-1223-496332 (G.K.); +832-824-8125 (I.B.V.d.V.)
| |
Collapse
|
40
|
Almojil D, Bourgeois Y, Falis M, Hariyani I, Wilcox J, Boissinot S. The Structural, Functional and Evolutionary Impact of Transposable Elements in Eukaryotes. Genes (Basel) 2021; 12:genes12060918. [PMID: 34203645 PMCID: PMC8232201 DOI: 10.3390/genes12060918] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 06/04/2021] [Accepted: 06/07/2021] [Indexed: 12/22/2022] Open
Abstract
Transposable elements (TEs) are nearly ubiquitous in eukaryotes. The increase in genomic data, as well as progress in genome annotation and molecular biology techniques, have revealed the vast number of ways mobile elements have impacted the evolution of eukaryotes. In addition to being the main cause of difference in haploid genome size, TEs have affected the overall organization of genomes by accumulating preferentially in some genomic regions, by causing structural rearrangements or by modifying the recombination rate. Although the vast majority of insertions is neutral or deleterious, TEs have been an important source of evolutionary novelties and have played a determinant role in the evolution of fundamental biological processes. TEs have been recruited in the regulation of host genes and are implicated in the evolution of regulatory networks. They have also served as a source of protein-coding sequences or even entire genes. The impact of TEs on eukaryotic evolution is only now being fully appreciated and the role they may play in a number of biological processes, such as speciation and adaptation, remains to be deciphered.
Collapse
Affiliation(s)
- Dareen Almojil
- New York University Abu Dhabi, Saadiyat Island, Abu Dhabi P.O. Box 129188, United Arab Emirates; (D.A.); (M.F.); (I.H.); (J.W.)
| | - Yann Bourgeois
- School of Biological Sciences, University of Portsmouth, Portsmouth, UK;
| | - Marcin Falis
- New York University Abu Dhabi, Saadiyat Island, Abu Dhabi P.O. Box 129188, United Arab Emirates; (D.A.); (M.F.); (I.H.); (J.W.)
| | - Imtiyaz Hariyani
- New York University Abu Dhabi, Saadiyat Island, Abu Dhabi P.O. Box 129188, United Arab Emirates; (D.A.); (M.F.); (I.H.); (J.W.)
| | - Justin Wilcox
- New York University Abu Dhabi, Saadiyat Island, Abu Dhabi P.O. Box 129188, United Arab Emirates; (D.A.); (M.F.); (I.H.); (J.W.)
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Saadiyat Island, Abu Dhabi P.O. Box 129188, United Arab Emirates
| | - Stéphane Boissinot
- New York University Abu Dhabi, Saadiyat Island, Abu Dhabi P.O. Box 129188, United Arab Emirates; (D.A.); (M.F.); (I.H.); (J.W.)
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Saadiyat Island, Abu Dhabi P.O. Box 129188, United Arab Emirates
- Correspondence:
| |
Collapse
|
41
|
DNA methylation profile of liver of mice conceived by in vitro fertilization. J Dev Orig Health Dis 2021; 13:358-366. [PMID: 34121654 DOI: 10.1017/s2040174421000313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Offspring generated by in vitro fertilization (IVF) are believed to be healthy but display a possible predisposition to chronic diseases, like hypertension and glucose intolerance. Since epigenetic changes are believed to underlie such phenotype, this study aimed at describing global DNA methylation changes in the liver of adult mice generated by natural mating (FB group) or by IVF. Embryos were generated by IVF or natural mating. At 30 weeks of age, mice were sacrificed. The liver was removed, and global DNA methylation was assessed using whole-genome bisulfite sequencing (WGBS). Genomic Regions for Enrichment Analysis Tool (GREAT) and G:Profilerβ were used to identify differentially methylated regions (DMRs) and for functional enrichment analysis. Overrepresented gene ontology terms were summarized with REVIGO, while canonical pathways (CPs) were identified with Ingenuity® Pathway Analysis. Overall, 2692 DMRs (4.91%) were different between the groups. The majority of DMRs (84.92%) were hypomethylated in the IVF group. Surprisingly, only 0.16% of CpG islands were differentially methylated and only a few DMRs were located on known gene promoters (n = 283) or enhancers (n = 190). Notably, the long-interspersed element (LINE), short-interspersed element (SINE), and long terminal repeat (LTR1) transposable elements showed reduced methylation (P < 0.05) in IVF livers. Cellular metabolic process, hepatic fibrosis, and insulin receptor signaling were some of the principal biological processes and CPs modified by IVF. In summary, IVF modifies the DNA methylation signature in the adult liver, resulting in hypomethylation of genes involved in metabolism and gene transcription regulation. These findings may shed light on the mechanisms underlying the developmental origin of health and disease.
Collapse
|
42
|
Liu J. Giant cells: Linking McClintock's heredity to early embryogenesis and tumor origin throughout millennia of evolution on Earth. Semin Cancer Biol 2021; 81:176-192. [PMID: 34116161 DOI: 10.1016/j.semcancer.2021.06.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/12/2021] [Accepted: 06/06/2021] [Indexed: 02/08/2023]
Abstract
The "life code" theory postulates that egg cells, which are giant, are the first cells in reproduction and that damaged or aged giant somatic cells are the first cells in tumorigenesis. However, the hereditary basis for giant cells remains undefined. Here I propose that stress-induced genomic reorganization proposed by Nobel Laureate Barbara McClintock may represent the underlying heredity for giant cells, referred to as McClintock's heredity. Increase in cell size may serve as a response to environmental stress via switching proliferative mitosis to intranuclear replication for reproduction. Intranuclear replication activates McClintock's heredity to reset the genome following fertilization for reproduction or restructures the somatic genome for neoplastic transformation via formation of polyploid giant cancer cells (PGCCs). The genome-based McClintock heredity functions together with gene-based Mendel's heredity to regulate the genomic stability at two different stages of life cycle or tumorigenesis. Thus, giant cells link McClintock's heredity to both early embryogenesis and tumor origin. Cycling change in cell size together with ploidy number switch may represent the most fundamental mechanism on how both germ and soma for coping with environmental stresses for the survival across the tree of life which evolved over millions of years on Earth.
Collapse
Affiliation(s)
- Jinsong Liu
- Department of Anatomical Pathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, United States.
| |
Collapse
|
43
|
Bansal P, Ahern DT, Kondaveeti Y, Qiu CW, Pinter SF. Contiguous erosion of the inactive X in human pluripotency concludes with global DNA hypomethylation. Cell Rep 2021; 35:109215. [PMID: 34107261 PMCID: PMC8267460 DOI: 10.1016/j.celrep.2021.109215] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 08/18/2020] [Accepted: 05/13/2021] [Indexed: 01/21/2023] Open
Abstract
Female human pluripotent stem cells (hPSCs) routinely undergo inactive X (Xi) erosion. This progressive loss of key repressive features follows the loss of XIST expression, the long non-coding RNA driving X inactivation, and causes reactivation of silenced genes across the eroding X (Xe). To date, the sporadic and progressive nature of erosion has obscured its scale, dynamics, and key transition events. To address this problem, we perform an integrated analysis of DNA methylation (DNAme), chromatin accessibility, and gene expression across hundreds of hPSC samples. Differential DNAme orders female hPSCs across a trajectory from initiation to terminal Xi erosion. Our results identify a cis-regulatory element crucial for XIST expression, trace contiguously growing reactivated domains to a few euchromatic origins, and indicate that the late-stage Xe impairs DNAme genome-wide. Surprisingly, from this altered regulatory landscape emerge select features of naive pluripotency, suggesting that its link to X dosage may be partially conserved in human embryonic development. Reactivation of the silenced X in human female iPSC/ESCs compromises their utility. Bansal et al. perform an integrated genomics analysis to reveal a prevalent X erosion trajectory that they validate in long-term culture. Starting with XIST loss, this trajectory indicates that reactivation may spread contiguously from escapees to silenced genes.
Collapse
Affiliation(s)
- Prakhar Bansal
- Graduate Program in Genetics and Developmental Biology, UCONN Health, University of Connecticut, Farmington, CT, USA; Department of Genetics and Genome Sciences, UCONN Health, University of Connecticut, Farmington, CT, USA
| | - Darcy T Ahern
- Graduate Program in Genetics and Developmental Biology, UCONN Health, University of Connecticut, Farmington, CT, USA; Department of Genetics and Genome Sciences, UCONN Health, University of Connecticut, Farmington, CT, USA
| | - Yuvabharath Kondaveeti
- Department of Genetics and Genome Sciences, UCONN Health, University of Connecticut, Farmington, CT, USA
| | - Catherine W Qiu
- Department of Genetics and Genome Sciences, UCONN Health, University of Connecticut, Farmington, CT, USA
| | - Stefan F Pinter
- Graduate Program in Genetics and Developmental Biology, UCONN Health, University of Connecticut, Farmington, CT, USA; Department of Genetics and Genome Sciences, UCONN Health, University of Connecticut, Farmington, CT, USA; Institute for Systems Genomics, University of Connecticut, Farmington, CT, USA.
| |
Collapse
|
44
|
Jansz N, Faulkner GJ. Endogenous retroviruses in the origins and treatment of cancer. Genome Biol 2021; 22:147. [PMID: 33971937 PMCID: PMC8108463 DOI: 10.1186/s13059-021-02357-4] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 04/21/2021] [Indexed: 02/07/2023] Open
Abstract
Endogenous retroviruses (ERVs) are emerging as promising therapeutic targets in cancer. As remnants of ancient retroviral infections, ERV-derived regulatory elements coordinate expression from gene networks, including those underpinning embryogenesis and immune cell function. ERV activation can promote an interferon response, a phenomenon termed viral mimicry. Although ERV expression is associated with cancer, and provisionally with autoimmune and neurodegenerative diseases, ERV-mediated inflammation is being explored as a way to sensitize tumors to immunotherapy. Here we review ERV co-option in development and innate immunity, the aberrant contribution of ERVs to tumorigenesis, and the wider biomedical potential of therapies directed at ERVs.
Collapse
Affiliation(s)
- Natasha Jansz
- Mater Research Institute - University of Queensland, TRI Building, Woolloongabba, QLD, 4102, Australia.
| | - Geoffrey J Faulkner
- Mater Research Institute - University of Queensland, TRI Building, Woolloongabba, QLD, 4102, Australia. .,Queensland Brain Institute, University of Queensland, Brisbane, QLD, 4072, Australia.
| |
Collapse
|
45
|
Gazquez-Gutierrez A, Witteveldt J, R Heras S, Macias S. Sensing of transposable elements by the antiviral innate immune system. RNA (NEW YORK, N.Y.) 2021; 27:rna.078721.121. [PMID: 33888553 PMCID: PMC8208052 DOI: 10.1261/rna.078721.121] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 04/17/2021] [Indexed: 05/15/2023]
Abstract
Around half of the genome in mammals is composed of transposable elements (TEs) such as DNA transposons and retrotransposons. Several mechanisms have evolved to prevent their activity and the detrimental impact of their insertional mutagenesis. Despite these potentially negative effects, TEs are essential drivers of evolution, and in certain settings, beneficial to their hosts. For instance, TEs have rewired the antiviral gene regulatory network and are required for early embryonic development. However, due to structural similarities between TE-derived and viral nucleic acids, cells can misidentify TEs as invading viruses and trigger the major antiviral innate immune pathway, the type I interferon (IFN) response. This review will focus on the different settings in which the role of TE-mediated IFN activation has been documented, including cancer and senescence. Importantly, TEs may also play a causative role in the development of complex autoimmune diseases characterised by constitutive type I IFN activation. All these observations suggest the presence of strong but opposing forces driving the coevolution of TEs and antiviral defence. A better biological understanding of the TE replicative cycle as well as of the antiviral nucleic acid sensing mechanisms will provide insights into how these two biological processes interact and will help to design better strategies to treat human diseases characterised by aberrant TE expression and/or type I IFN activation.
Collapse
Affiliation(s)
| | - Jeroen Witteveldt
- University of Edinburgh - Institute of Immunology and Infection Research
| | - Sara R Heras
- GENYO. Centre for Genomics and Oncological Research, Pfizer University of Granada
| | - Sara Macias
- Institute of Immunology and Infection Research
| |
Collapse
|
46
|
Glinsky GV. Genomics-Guided Drawing of Molecular and Pathophysiological Components of Malignant Regulatory Signatures Reveals a Pivotal Role in Human Diseases of Stem Cell-Associated Retroviral Sequences and Functionally-Active hESC Enhancers. Front Oncol 2021; 11:638363. [PMID: 33869024 PMCID: PMC8044830 DOI: 10.3389/fonc.2021.638363] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 03/10/2021] [Indexed: 12/31/2022] Open
Abstract
Repetitive DNA sequences (repeats) colonized two-third of human genome and a majority of repeats comprised of transposable genetic elements (TE). Evolutionary distinct categories of TE represent nucleic acid sequences that are repeatedly copied from and pasted into chromosomes at multiple genomic locations and acquired a multitude of regulatory functions. Here, genomics-guided maps of stemness regulatory signatures were drawn to dissect the contribution of TE to clinical manifestations of malignant phenotypes of human cancers. From patients’ and physicians’ perspectives, the clinical definition of a tumor’s malignant phenotype could be restricted to the early diagnosis of sub-types of malignancies with the increased risk of existing therapy failure and high likelihood of death from cancer. It is the viewpoint from which the understanding of stemness and malignant regulatory signatures is considered in this contribution. Genomics-guided analyses of experimental and clinical observations revealed the pivotal role of human stem cell-associated retroviral sequences (SCARS) in the origin and pathophysiology of clinically-lethal malignancies. SCARS were defined as the evolutionary- and biologically-related family of genomic regulatory sequences, the principal physiological function of which is to create and maintain the stemness phenotype during human preimplantation embryogenesis. For cell differentiation to occur, SCARS expression must be silenced and SCARS activity remains repressed in most terminally-differentiated human cells which are destined to perform specialized functions in the human body. Epigenetic reprogramming, de-repression, and sustained activity of SCARS results in various differentiation-defective phenotypes. One of the most prominent tissue- and organ-specific clinical manifestations of sustained SCARS activities is diagnosed as a pathological condition defined by a consensus of morphological, molecular, and genetic examinations as the malignant growth. Here, contemporary evidence are acquired, analyzed, and reported defining both novel diagnostic tools and druggable molecular targets readily amenable for diagnosis and efficient therapeutic management of clinically-lethal malignancies. These diagnostic and therapeutic approaches are based on monitoring of high-fidelity molecular signals of continuing SCARS activities in conjunction with genomic regulatory networks of thousands’ functionally-active embryonic enhancers affecting down-stream phenotype-altering genetic loci. Collectively, reported herein observations support a model of SCARS-activation triggered singular source code facilitating the intracellular propagation and intercellular (systemic) dissemination of disease states in the human body.
Collapse
Affiliation(s)
- Gennadi V Glinsky
- Institute of Engineering in Medicine, University of California, San Diego, CA, United States.,Department of Functional & Translational Genomics, OncoSCAR, Inc., Portland, OR, United States
| |
Collapse
|
47
|
Telonis AG, Rigoutsos I. The transcriptional trajectories of pluripotency and differentiation comprise genes with antithetical architecture and repetitive-element content. BMC Biol 2021; 19:60. [PMID: 33765992 PMCID: PMC7995781 DOI: 10.1186/s12915-020-00928-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 11/18/2020] [Indexed: 12/12/2022] Open
Abstract
Background Extensive molecular differences exist between proliferative and differentiated cells. Here, we conduct a meta-analysis of publicly available transcriptomic datasets from preimplantation and differentiation stages examining the architectural properties and content of genes whose abundance changes significantly across developmental time points. Results Analysis of preimplantation embryos from human and mouse showed that short genes whose introns are enriched in Alu (human) and B (mouse) elements, respectively, have higher abundance in the blastocyst compared to the zygote. These highly expressed genes encode ribosomal proteins or metabolic enzymes. On the other hand, long genes whose introns are depleted in repetitive elements have lower abundance in the blastocyst and include genes from signaling pathways. Additionally, the sequences of the genes that are differentially expressed between the blastocyst and the zygote contain distinct collections of pyknon motifs that differ between up- and down-regulated genes. Further examination of the genes that participate in the stem cell-specific protein interaction network shows that their introns are short and enriched in Alu (human) and B (mouse) elements. As organogenesis progresses, in both human and mouse, we find that the primarily short and repeat-rich expressed genes make way for primarily longer, repeat-poor genes. With that in mind, we used a machine learning-based approach to identify gene signatures able to classify human adult tissues: we find that the most discriminatory genes comprising these signatures have long introns that are repeat-poor and include transcription factors and signaling-cascade genes. The introns of widely expressed genes across human tissues, on the other hand, are short and repeat-rich, and coincide with those with the highest expression at the blastocyst stage. Conclusions Protein-coding genes that are characteristic of each trajectory, i.e., proliferation/pluripotency or differentiation, exhibit antithetical biases in their intronic and exonic lengths and in their repetitive-element content. While the respective human and mouse gene signatures are functionally and evolutionarily conserved, their introns and exons are enriched or depleted in organism-specific repetitive elements. We posit that these organism-specific repetitive sequences found in exons and introns are used to effect the corresponding genes’ regulation. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-020-00928-8.
Collapse
Affiliation(s)
- Aristeidis G Telonis
- Computational Medicine Center, Sidney Kimmel College of Medicine, Thomas Jefferson University, 1020 Locust Street, Suite M81, Philadelphia, PA, 19107, USA. .,Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA.
| | - Isidore Rigoutsos
- Computational Medicine Center, Sidney Kimmel College of Medicine, Thomas Jefferson University, 1020 Locust Street, Suite M81, Philadelphia, PA, 19107, USA.
| |
Collapse
|
48
|
Mustafin RN, Kazantseva AV, Enikeeva RF, Malykh SB, Khusnutdinova EK. Longitudinal genetic studies of cognitive characteristics. Vavilovskii Zhurnal Genet Selektsii 2021; 24:87-95. [PMID: 33659785 PMCID: PMC7716536 DOI: 10.18699/vj20.599] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The present review describes longitudinal studies of cognitive traits and functions determining the causes of their variations and their possible correction to prevent cognitive impairment. The present study reviews the involvement of such environmental factors as nutrition, prenatal maternal stress, social isolation and others in cognitive functioning. The role of epigenetic factors in the implementation of environmental effects in cognitive characteristics is revealed. Considering the epigenome significance, several studies were focused on the design of substances affecting methylation and histone modification, which can be used for the treatment of cognitive disorders. The appropriate correction of epigenetic factors related to environmental differences in cognitive abilities requires to determine the mechanisms of chromatin modifications and variations in DNA methylation. Transposons representing stress-sensitive DNA elements appeared to mediate the environmental influence on epigenetic modifications. They can explain the mechanism of transgenerational transfer of information on cognitive abilities. Recently, large-scale meta-analyses based on the results of studies, which identified genetic associations with various cognitive traits, were carried out. As a result, the role of genes actively expressed in the brain, such as BDNF, COMT, CADM2, CYP2D6, APBA1, CHRNA7, PDE1C, PDE4B, and PDE4D in cognitive abilities was revealed. The association between cognitive functioning and genes, which have been previously involved in developing psychiatric disorders (MEF2C, CYP2D6, FAM109B, SEPT3, NAGA, TCF20, NDUFA6 genes), was revealed, thus indicating the role of the similar mechanisms of genetic and neural networks in both normal cognition and cognitive impairment. An important role in both processes belongs to common epigenetic factors. The genes involved in DNA methylation (DNMT1, DNMT3B, and FTO), histone modifications (CREBBP, CUL4B, EHMT1, EP300, EZH2, HLCS, HUWE1, KAT6B, KMT2A, KMT2D, KMT2C, NSD1, WHSC1, and UBE2A) and chromatin remodeling (ACTB, ARID1A, ARID1B, ATRX, CHD2, CHD7, CHD8, SMARCA2, SMARCA4, SMARCB1, SMARCE1, SRCAP, and SS18L1) are associated with increased risk of psychiatric diseases with cognitive deficiency together with normal cognitive functioning. The data on the correlation between transgenerational epigenetic inheritance of cognitive abilities and the insert of transposable elements in intergenic regions is discussed. Transposons regulate genes functioning in the brain due to the processing of their transcripts into non-coding RNAs. The content, quantity and arrangement of transposable elements in human genome, which do not affect changes in nucleotide sequences of protein encoding genes, but affect their expression, can be transmitted to the next generation.
Collapse
Affiliation(s)
| | - A V Kazantseva
- Institute of Biochemistry and Genetics - Subdivision of the Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa, Russia
| | - R F Enikeeva
- Institute of Biochemistry and Genetics - Subdivision of the Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa, Russia
| | - S B Malykh
- Psychological Institute of the Russian Academy of Education, Moscow, Russia M.V. Lomonosov Moscow State University, Laboratory of psychology of professions and conflicts, Moscow, Russia
| | - E K Khusnutdinova
- Institute of Biochemistry and Genetics - Subdivision of the Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa, Russia M.V. Lomonosov Moscow State University, Laboratory of psychology of professions and conflicts, Moscow, Russia
| |
Collapse
|
49
|
Kohlrausch FB, Berteli TS, Wang F, Navarro PA, Keefe DL. Control of LINE-1 Expression Maintains Genome Integrity in Germline and Early Embryo Development. Reprod Sci 2021; 29:328-340. [PMID: 33481218 DOI: 10.1007/s43032-021-00461-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 01/06/2021] [Indexed: 11/28/2022]
Abstract
Maintenance of genome integrity in the germline and in preimplantation embryos is crucial for mammalian development. Epigenetic remodeling during primordial germ cell (PGC) and preimplantation embryo development may contribute to genomic instability in these cells, since DNA methylation is an important mechanism to silence retrotransposons. Long interspersed elements 1 (LINE-1 or L1) are the most common autonomous retrotransposons in mammals, corresponding to approximately 17% of the human genome. Retrotransposition events are more frequent in germ cells and in early stages of embryo development compared with somatic cells. It has been shown that L1 activation and expression occurs in germline and is essential for preimplantation development. In this review, we focus on the role of L1 retrotransposon in mouse and human germline and early embryo development and discuss the possible relationship between L1 expression and genomic instability during these stages. Although several studies have addressed L1 expression at different stages of development, the developmental consequences of this expression remain poorly understood. Future research is still needed to highlight the relationship between L1 retrotransposition events and genomic instability during germline and early embryo development.
Collapse
Affiliation(s)
- Fabiana B Kohlrausch
- Department of Obstetrics and Gynecology, New York University Langone Medical Center, 462 1st Avenue, New York, NY, 10016, USA.,Departamento de Biologia Geral, Instituto de Biologia, Universidade Federal Fluminense, Niterói, RJ, Brazil
| | - Thalita S Berteli
- Department of Obstetrics and Gynecology, New York University Langone Medical Center, 462 1st Avenue, New York, NY, 10016, USA.,Departamento de Ginecologia e Obstetrícia, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Fang Wang
- Department of Obstetrics and Gynecology, New York University Langone Medical Center, 462 1st Avenue, New York, NY, 10016, USA
| | - Paula A Navarro
- Departamento de Ginecologia e Obstetrícia, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - David L Keefe
- Department of Obstetrics and Gynecology, New York University Langone Medical Center, 462 1st Avenue, New York, NY, 10016, USA.
| |
Collapse
|
50
|
Shao W, Wang T. Transcript assembly improves expression quantification of transposable elements in single-cell RNA-seq data. Genome Res 2021; 31:88-100. [PMID: 33355230 PMCID: PMC7849386 DOI: 10.1101/gr.265173.120] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 11/24/2020] [Indexed: 12/28/2022]
Abstract
Transposable elements (TEs) are an integral part of the host transcriptome. TE-containing noncoding RNAs (ncRNAs) show considerable tissue specificity and play important roles during development, including stem cell maintenance and cell differentiation. Recent advances in single-cell RNA-seq (scRNA-seq) revolutionized cell type-specific gene expression analysis. However, effective scRNA-seq quantification tools tailored for TEs are lacking, limiting our ability to dissect TE expression dynamics at single-cell resolution. To address this issue, we established a TE expression quantification pipeline that is compatible with scRNA-seq data generated across multiple technology platforms. We constructed TE-containing ncRNA references using bulk RNA-seq data and showed that quantifying TE expression at the transcript level effectively reduces noise. As proof of principle, we applied this strategy to mouse embryonic stem cells and successfully captured the expression profile of endogenous retroviruses in single cells. We further expanded our analysis to scRNA-seq data from early stages of mouse embryogenesis. Our results illustrated the dynamic TE expression at preimplantation stages and revealed 146 TE-containing ncRNA transcripts with substantial tissue specificity during gastrulation and early organogenesis.
Collapse
Affiliation(s)
- Wanqing Shao
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Ting Wang
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| |
Collapse
|