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
|
Al-Jawabreh R, Lastik D, McKenzie D, Reynolds K, Suleiman M, Mousley A, Atkinson L, Hunt V. Advancing Strongyloides omics data: bridging the gap with Caenorhabditis elegans. Philos Trans R Soc Lond B Biol Sci 2024; 379:20220437. [PMID: 38008117 PMCID: PMC10676819 DOI: 10.1098/rstb.2022.0437] [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: 06/27/2023] [Accepted: 08/31/2023] [Indexed: 11/28/2023] Open
Abstract
Among nematodes, the free-living model organism Caenorhabditis elegans boasts the most advanced portfolio of high-quality omics data. The resources available for parasitic nematodes, including Strongyloides spp., however, are lagging behind. While C. elegans remains the most tractable nematode and has significantly advanced our understanding of many facets of nematode biology, C. elegans is not suitable as a surrogate system for the study of parasitism and it is important that we improve the omics resources available for parasitic nematode species. Here, we review the omics data available for Strongyloides spp. and compare the available resources to those for C. elegans and other parasitic nematodes. The advancements in C. elegans omics offer a blueprint for improving omics-led research in Strongyloides. We suggest areas of priority for future research that will pave the way for expansions in omics resources and technologies. This article is part of the Theo Murphy meeting issue 'Strongyloides: omics to worm-free populations'.
Collapse
Affiliation(s)
- Reem Al-Jawabreh
- Department of Life Sciences, University of Bath, Bath, BA2 7AY, UK
| | - Dominika Lastik
- Department of Life Sciences, University of Bath, Bath, BA2 7AY, UK
| | | | - Kieran Reynolds
- Department of Life Sciences, University of Bath, Bath, BA2 7AY, UK
| | - Mona Suleiman
- Department of Life Sciences, University of Bath, Bath, BA2 7AY, UK
| | | | | | - Vicky Hunt
- Department of Life Sciences, University of Bath, Bath, BA2 7AY, UK
| |
Collapse
|
3
|
Mangoni D, Simi A, Lau P, Armaos A, Ansaloni F, Codino A, Damiani D, Floreani L, Di Carlo V, Vozzi D, Persichetti F, Santoro C, Pandolfini L, Tartaglia GG, Sanges R, Gustincich S. LINE-1 regulates cortical development by acting as long non-coding RNAs. Nat Commun 2023; 14:4974. [PMID: 37591988 PMCID: PMC10435495 DOI: 10.1038/s41467-023-40743-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 08/07/2023] [Indexed: 08/19/2023] Open
Abstract
Long Interspersed Nuclear Elements-1s (L1s) are transposable elements that constitute most of the genome's transcriptional output yet have still largely unknown functions. Here we show that L1s are required for proper mouse brain corticogenesis operating as regulatory long non-coding RNAs. They contribute to the regulation of the balance between neuronal progenitors and differentiation, the migration of post-mitotic neurons and the proportions of different cell types. In cortical cultured neurons, L1 RNAs are mainly associated to chromatin and interact with the Polycomb Repressive Complex 2 (PRC2) protein subunits enhancer of Zeste homolog 2 (Ezh2) and suppressor of zeste 12 (Suz12). L1 RNA silencing influences PRC2's ability to bind a portion of its targets and the deposition of tri-methylated histone H3 (H3K27me3) marks. Our results position L1 RNAs as crucial signalling hubs for genome-wide chromatin remodelling, enabling the fine-tuning of gene expression during brain development and evolution.
Collapse
Affiliation(s)
- Damiano Mangoni
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genova, Italy
| | - Alessandro Simi
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genova, Italy
| | - Pierre Lau
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genova, Italy
| | - Alexandros Armaos
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genova, Italy
| | - Federico Ansaloni
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genova, Italy
| | - Azzurra Codino
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genova, Italy
| | - Devid Damiani
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genova, Italy
| | - Lavinia Floreani
- Area of Neuroscience, International School for Advanced Studies (SISSA), Trieste, Italy
| | - Valerio Di Carlo
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genova, Italy
| | - Diego Vozzi
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genova, Italy
| | - Francesca Persichetti
- Department of Health Sciences and Research Center on Autoimmune and Allergic Diseases (CAAD), University of Piemonte Orientale (UPO), Novara, Italy
| | - Claudio Santoro
- Department of Health Sciences and Research Center on Autoimmune and Allergic Diseases (CAAD), University of Piemonte Orientale (UPO), Novara, Italy
| | - Luca Pandolfini
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genova, Italy
| | | | - Remo Sanges
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genova, Italy.
- Area of Neuroscience, International School for Advanced Studies (SISSA), Trieste, Italy.
| | - Stefano Gustincich
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genova, Italy.
| |
Collapse
|
4
|
Wells JN, Chang NC, McCormick J, Coleman C, Ramos N, Jin B, Feschotte C. Transposable elements drive the evolution of metazoan zinc finger genes. Genome Res 2023; 33:1325-1339. [PMID: 37714714 PMCID: PMC10547256 DOI: 10.1101/gr.277966.123] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 06/15/2023] [Indexed: 09/17/2023]
Abstract
Cys2-His2 zinc finger genes (ZNFs) form the largest family of transcription factors in metazoans. ZNF evolution is highly dynamic and characterized by the rapid expansion and contraction of numerous subfamilies across the animal phylogeny. The forces and mechanisms underlying rapid ZNF evolution remain poorly understood, but there is growing evidence that, in tetrapods, the targeting and repression of lineage-specific transposable elements (TEs) plays a critical role in the evolution of the Krüppel-associated box ZNF (KZNF) subfamily. Currently, it is unknown whether this function and coevolutionary relationship is unique to KZNFs or is a broader feature of metazoan ZNFs. Here, we present evidence that genomic conflict with TEs has been a central driver of the diversification of ZNFs in animals. Sampling from 3221 genome assemblies, we show that the copy number of retroelements correlates with that of ZNFs across at least 750 million years of metazoan evolution. Using computational predictions, we show that ZNFs preferentially bind TEs in diverse animal species. We further investigate the largest ZNF subfamily found in cyprinid fish, which is characterized by a conserved sequence we dubbed the fish N-terminal zinc finger-associated (FiNZ) domain. Zebrafish possess approximately 700 FiNZ-ZNFs, many of which are evolving adaptively under positive selection. Like mammalian KZNFs, most zebrafish FiNZ-ZNFs are expressed at the onset of zygotic genome activation, and blocking their translation using morpholinos during early embryogenesis results in derepression of transcriptionally active TEs. Together, these data suggest that ZNF diversification has been intimately connected to TE expansion throughout animal evolution.
Collapse
Affiliation(s)
- Jonathan N Wells
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14850, USA;
| | - Ni-Chen Chang
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14850, USA
| | - John McCormick
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14850, USA
| | - Caitlyn Coleman
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, Florida 33620, USA
| | - Nathalie Ramos
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14850, USA
- Department of Genetics and Genomic Sciences, Center for Transformative Disease Modeling, Tisch Cancer Institute, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Bozhou Jin
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14850, USA
| | - Cédric Feschotte
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14850, USA;
| |
Collapse
|
5
|
Ansaloni F, Gustincich S, Sanges R. In silico characterisation of minor wave genes and LINE-1s transcriptional dynamics at murine zygotic genome activation. Front Cell Dev Biol 2023; 11:1124266. [PMID: 37389353 PMCID: PMC10300423 DOI: 10.3389/fcell.2023.1124266] [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: 12/14/2022] [Accepted: 06/05/2023] [Indexed: 07/01/2023] Open
Abstract
Introduction: In mouse, the zygotic genome activation (ZGA) is coordinated by MERVL elements, a class of LTR retrotransposons. In addition to MERVL, another class of retrotransposons, LINE-1 elements, recently came under the spotlight as key regulators of murine ZGA. In particular, LINE-1 transcripts seem to be required to switch-off the transcriptional program started by MERVL sequences, suggesting an antagonistic interplay between LINE-1 and MERVL pathways. Methods: To better investigate the activities of LINE-1 and MERVL elements at ZGA, we integrated publicly available transcriptomics (RNA-seq), chromatin accessibility (ATAC-seq) and Pol-II binding (Stacc-seq) datasets and characterised the transcriptional and epigenetic dynamics of such elements during murine ZGA. Results: We identified two likely distinct transcriptional activities characterising the murine zygotic genome at ZGA onset. On the one hand, our results confirmed that ZGA minor wave genes are preferentially transcribed from MERVL-rich and gene-dense genomic compartments, such as gene clusters. On the other hand, we identified a set of evolutionary young and likely transcriptionally autonomous LINE-1s located in intergenic and gene-poor regions showing, at the same stage, features such as open chromatin and RNA Pol II binding suggesting them to be, at least, poised for transcription. Discussion: These results suggest that, across evolution, transcription of two different classes of transposable elements, MERVLs and LINE-1s, have likely been confined in genic and intergenic regions respectively in order to maintain and regulate two successive transcriptional programs at ZGA.
Collapse
Affiliation(s)
- Federico Ansaloni
- Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy
- Central RNA Laboratory, Istituto Italiano di Tecnologia—IIT, Genova, Italy
| | - Stefano Gustincich
- Central RNA Laboratory, Istituto Italiano di Tecnologia—IIT, Genova, Italy
| | - Remo Sanges
- Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy
- Central RNA Laboratory, Istituto Italiano di Tecnologia—IIT, Genova, Italy
| |
Collapse
|
6
|
Ansaloni F, Gualandi N, Esposito M, Gustincich S, Sanges R. TEspeX: consensus-specific quantification of transposable element expression preventing biases from exonized fragments. Bioinformatics 2022; 38:4430-4433. [PMID: 35876845 PMCID: PMC9477521 DOI: 10.1093/bioinformatics/btac526] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 07/08/2022] [Accepted: 07/12/2022] [Indexed: 12/24/2022] Open
Abstract
SUMMARY Transposable elements (TEs) play key roles in crucial biological pathways. Therefore, several tools enabling the quantification of their expression were recently developed. However, many of the existing tools lack the capability to distinguish between the transcription of autonomously expressed TEs and TE fragments embedded in canonical coding/non-coding non-TE transcripts. Consequently, an apparent change in the expression of a given TE may simply reflect the variation in the expression of the transcripts containing TE-derived sequences. To overcome this issue, we have developed TEspeX, a pipeline for the quantification of TE expression at the consensus level. TEspeX uses Illumina RNA-seq short reads to quantify TE expression avoiding counting reads deriving from inactive TE fragments embedded in canonical transcripts. AVAILABILITY AND IMPLEMENTATION The tool is implemented in python3, distributed under the GNU General Public License (GPL) and available on Github at https://github.com/fansalon/TEspeX (Zenodo URL: https://doi.org/10.5281/zenodo.6800331). SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Federico Ansaloni
- Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste 34136, Italy,Central RNA Laboratory, Istituto Italiano di Tecnologia, Genova 16163, Italy
| | - Nicolò Gualandi
- Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste 34136, Italy
| | - Mauro Esposito
- Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste 34136, Italy
| | | | - Remo Sanges
- To whom correspondence should be addressed. or
| |
Collapse
|
7
|
Athanasouli M, Rödelsperger C. Analysis of repeat elements in the Pristionchus pacificus genome reveals an ancient invasion by horizontally transferred transposons. BMC Genomics 2022; 23:523. [PMID: 35854227 PMCID: PMC9297572 DOI: 10.1186/s12864-022-08731-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 07/01/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Repetitive sequences and mobile elements make up considerable fractions of individual genomes. While transposition events can be detrimental for organismal fitness, repetitive sequences form an enormous reservoir for molecular innovation. In this study, we aim to add repetitive elements to the annotation of the Pristionchus pacificus genome and assess their impact on novel gene formation. RESULTS Different computational approaches define up to 24% of the P. pacificus genome as repetitive sequences. While retroelements are more frequently found at the chromosome arms, DNA transposons are distributed more evenly. We found multiple DNA transposons, as well as LTR and LINE elements with abundant evidence of expression as single-exon transcripts. When testing whether transposons disproportionately contribute towards new gene formation, we found that roughly 10-20% of genes across all age classes overlap transposable elements with the strongest trend being an enrichment of low complexity regions among the oldest genes. Finally, we characterized a horizontal gene transfer of Zisupton elements into diplogastrid nematodes. These DNA transposons invaded nematodes from eukaryotic donor species and experienced a recent burst of activity in the P. pacificus lineage. CONCLUSIONS The comprehensive annotation of repetitive elements in the P. pacificus genome builds a resource for future functional genomic analyses as well as for more detailed investigations of molecular innovations.
Collapse
Affiliation(s)
- Marina Athanasouli
- Max Planck Institute for Biology, Department for Integrative Evolutionary Biology, Max-Planck-Ring 9, 72076, Tübingen, Germany
| | - Christian Rödelsperger
- Max Planck Institute for Biology, Department for Integrative Evolutionary Biology, Max-Planck-Ring 9, 72076, Tübingen, Germany.
| |
Collapse
|
8
|
Meta-Analysis Suggests That Intron Retention Can Affect Quantification of Transposable Elements from RNA-Seq Data. BIOLOGY 2022; 11:biology11060826. [PMID: 35741347 PMCID: PMC9220773 DOI: 10.3390/biology11060826] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/20/2022] [Accepted: 05/26/2022] [Indexed: 02/08/2023]
Abstract
Simple Summary Transposable elements (TEs) are repetitive sequences comprising more than one third of the human genome with the original ability to change their location within the genome. Owing to their repetitive nature, the quantification of TEs results often challenging. RNA-seq is a useful tool for genome-wide TEs quantification, nevertheless it also presents technical issues, including low reads mappability and erroneous quantification derived from the transcription of TEs fragments embedded in canonical transcripts. Fragments derived from TEs are found within the introns of most genes, which led to the hypothesis that intron retention (IR) can affect the unbiased quantification of TEs expression. Performing meta-analysis of public RNA-seq datasets, here we observe that IR can indeed impact the quantification of TEs by increasing the number of reads mapped on intronic TE copies. Our work highlights a correlation between IR and TEs expression measurement by RNA-seq that should be taken into account to achieve reliable TEs quantification, especially in samples characterized by extensive IR, because differential IR might be confused with differential TEs expression. Abstract Transposable elements (TEs), also known as “jumping genes”, are repetitive sequences with the capability of changing their location within the genome. They are key players in many different biological processes in health and disease. Therefore, a reliable quantification of their expression as transcriptional units is crucial to distinguish between their independent expression and the transcription of their sequences as part of canonical transcripts. TEs quantification faces difficulties of different types, the most important one being low reads mappability due to their repetitive nature preventing an unambiguous mapping of reads originating from their sequences. A large fraction of TEs fragments localizes within introns, which led to the hypothesis that intron retention (IR) can be an additional source of bias, potentially affecting accurate TEs quantification. IR occurs when introns, normally removed from the mature transcript by the splicing machinery, are maintained in mature transcripts. IR is a widespread mechanism affecting many different genes with cell type-specific patterns. We hypothesized that, in an RNA-seq experiment, reads derived from retained introns can introduce a bias in the detection of overlapping, independent TEs RNA expression. In this study we performed meta-analysis using public RNA-seq data from lymphoblastoid cell lines and show that IR can impact TEs quantification using established tools with default parameters. Reads mapped on intronic TEs were indeed associated to the expression of TEs and influence their correct quantification as independent transcriptional units. We confirmed these results using additional independent datasets, demonstrating that this bias does not appear in samples where IR is not present and that differential TEs expression does not impact on IR quantification. We concluded that IR causes the over-quantification of intronic TEs and differential IR might be confused with differential TEs expression. Our results should be taken into account for a correct quantification of TEs expression from RNA-seq data, especially in samples in which IR is abundant.
Collapse
|
9
|
Floreani L, Ansaloni F, Mangoni D, Agostoni E, Sanges R, Persichetti F, Gustincich S. Analysis of LINE1 Retrotransposons in Huntington’s Disease. Front Cell Neurosci 2022; 15:743797. [PMID: 35095420 PMCID: PMC8795916 DOI: 10.3389/fncel.2021.743797] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 12/27/2021] [Indexed: 12/27/2022] Open
Abstract
Transposable elements (TEs) are mobile genetic elements that made up about half the human genome. Among them, the autonomous non-LTR retrotransposon long interspersed nuclear element-1 (L1) is the only currently active TE in mammals and covers about 17% of the mammalian genome. L1s exert their function as structural elements in the genome, as transcribed RNAs to influence chromatin structure and as retrotransposed elements to shape genomic variation in somatic cells. L1s activity has been shown altered in several diseases of the nervous system. Huntington disease (HD) is a dominantly inherited neurodegenerative disorder caused by an expansion of a CAG repeat in the HTT gene which leads to a gradual loss of neurons most prominently in the striatum and, to a lesser extent, in cortical brain regions. The length of the expanded CAG tract is related to age at disease onset, with longer repeats leading to earlier onset. Here we carried out bioinformatic analysis of public RNA-seq data of a panel of HD mouse models showing that a decrease of L1 RNA expression recapitulates two hallmarks of the disease: it correlates to CAG repeat length and it occurs in the striatum, the site of neurodegeneration. Results were then experimentally validated in HttQ111 knock-in mice. The expression of L1-encoded proteins was independent from L1 RNA levels and differentially regulated in time and tissues. The pattern of expression L1 RNAs in human HD post-mortem brains showed similarity to mouse models of the disease. This work suggests the need for further study of L1s in HD and adds support to the current hypothesis that dysregulation of TEs may be involved in neurodegenerative diseases.
Collapse
Affiliation(s)
- Lavinia Floreani
- Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy
| | - Federico Ansaloni
- Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy
- Central RNA Laboratory, Istituto Italiano di Tecnologia—IIT, Genova, Italy
| | - Damiano Mangoni
- Central RNA Laboratory, Istituto Italiano di Tecnologia—IIT, Genova, Italy
| | - Elena Agostoni
- Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy
| | - Remo Sanges
- Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy
- Central RNA Laboratory, Istituto Italiano di Tecnologia—IIT, Genova, Italy
- *Correspondence: Remo Sanges,
| | - Francesca Persichetti
- Department of Health Sciences, University of Piemonte Orientale “ A. Avogadro,”Novara, Italy
- Francesca Persichetti,
| | - Stefano Gustincich
- Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy
- Central RNA Laboratory, Istituto Italiano di Tecnologia—IIT, Genova, Italy
- Stefano Gustincich,
| |
Collapse
|
10
|
Panyushev N, Okorokova L, Danilov L, Adonin L. Pattern of Repetitive Element Transcription Segregate Cell Lineages during the Embryogenesis of Sea Urchin Strongylocentrotus purpuratus. Biomedicines 2021; 9:1736. [PMID: 34829966 PMCID: PMC8615465 DOI: 10.3390/biomedicines9111736] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 11/12/2021] [Accepted: 11/17/2021] [Indexed: 11/17/2022] Open
Abstract
Repetitive elements (REs) occupy a significant part of eukaryotic genomes and are shown to play diverse roles in genome regulation. During embryogenesis of the sea urchin, a large number of REs are expressed, but the role of these elements in the regulation of biological processes remains unknown. The aim of this study was to identify the RE expression at different stages of embryogenesis. REs occupied 44% of genomic DNA of Strongylocentrotus purpuratus. The most prevalent among these elements were the unknown elements-in total, they contributed 78.5% of REs (35% in total genome occupancy). It was revealed that the transcription pattern of genes and REs changes significantly during gastrulation. Using the de novo transcriptome assembly, we showed that the expression of RE is independent of its copy number in the genome. We also identified copies that are expressed. Only active RE copies were used for mapping and quantification of RE expression in the single-cell RNA sequencing data. REs expression was observed in all cell lineages and they were detected as population markers. Moreover, the primary mesenchyme cell (PMC) line had the greatest diversity of REs among the markers. Our data suggest a role for RE in the organization of developmental domains during the sea urchin embryogenesis at the single-cell resolution level.
Collapse
Affiliation(s)
- Nick Panyushev
- Bioinformatics Institute, 197342 St. Petersburg, Russia; (N.P.); (L.O.)
| | - Larisa Okorokova
- Bioinformatics Institute, 197342 St. Petersburg, Russia; (N.P.); (L.O.)
| | - Lavrentii Danilov
- St. Petersburg State University, Department of Genetics and Biotechnology, 199034 St. Petersburg, Russia;
| | - Leonid Adonin
- Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
- Institute of Biomedical Chemistry, Group of Mechanisms for Nanosystems Targeted Delivery, 119121 Moscow, Russia
- Institute of Environmental and Agricultural Biology (X-BIO), Tyumen State University, 625003 Tyumen, Russia
| |
Collapse
|
11
|
Napoletano F, Ferrari Bravo G, Voto IAP, Santin A, Celora L, Campaner E, Dezi C, Bertossi A, Valentino E, Santorsola M, Rustighi A, Fajner V, Maspero E, Ansaloni F, Cancila V, Valenti CF, Santo M, Artimagnella OB, Finaurini S, Gioia U, Polo S, Sanges R, Tripodo C, Mallamaci A, Gustincich S, d'Adda di Fagagna F, Mantovani F, Specchia V, Del Sal G. The prolyl-isomerase PIN1 is essential for nuclear Lamin-B structure and function and protects heterochromatin under mechanical stress. Cell Rep 2021; 36:109694. [PMID: 34525372 DOI: 10.1016/j.celrep.2021.109694] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 06/29/2021] [Accepted: 08/19/2021] [Indexed: 01/24/2023] Open
Abstract
Chromatin organization plays a crucial role in tissue homeostasis. Heterochromatin relaxation and consequent unscheduled mobilization of transposable elements (TEs) are emerging as key contributors of aging and aging-related pathologies, including Alzheimer's disease (AD) and cancer. However, the mechanisms governing heterochromatin maintenance or its relaxation in pathological conditions remain poorly understood. Here we show that PIN1, the only phosphorylation-specific cis/trans prolyl isomerase, whose loss is associated with premature aging and AD, is essential to preserve heterochromatin. We demonstrate that this PIN1 function is conserved from Drosophila to humans and prevents TE mobilization-dependent neurodegeneration and cognitive defects. Mechanistically, PIN1 maintains nuclear type-B Lamin structure and anchoring function for heterochromatin protein 1α (HP1α). This mechanism prevents nuclear envelope alterations and heterochromatin relaxation under mechanical stress, which is a key contributor to aging-related pathologies.
Collapse
Affiliation(s)
- Francesco Napoletano
- Laboratorio Nazionale CIB (LNCIB), Area Science Park, Padriciano 99, 34149 Trieste, Italy; Department of Life Sciences (DSV), University of Trieste, 34127 Trieste, Italy.
| | - Gloria Ferrari Bravo
- Laboratorio Nazionale CIB (LNCIB), Area Science Park, Padriciano 99, 34149 Trieste, Italy; Department of Life Sciences (DSV), University of Trieste, 34127 Trieste, Italy
| | - Ilaria Anna Pia Voto
- Laboratorio Nazionale CIB (LNCIB), Area Science Park, Padriciano 99, 34149 Trieste, Italy
| | - Aurora Santin
- Laboratorio Nazionale CIB (LNCIB), Area Science Park, Padriciano 99, 34149 Trieste, Italy
| | - Lucia Celora
- Laboratorio Nazionale CIB (LNCIB), Area Science Park, Padriciano 99, 34149 Trieste, Italy
| | - Elena Campaner
- Laboratorio Nazionale CIB (LNCIB), Area Science Park, Padriciano 99, 34149 Trieste, Italy; Department of Life Sciences (DSV), University of Trieste, 34127 Trieste, Italy
| | - Clara Dezi
- Department of Life Sciences (DSV), University of Trieste, 34127 Trieste, Italy
| | - Arianna Bertossi
- Laboratorio Nazionale CIB (LNCIB), Area Science Park, Padriciano 99, 34149 Trieste, Italy; Department of Life Sciences (DSV), University of Trieste, 34127 Trieste, Italy
| | - Elena Valentino
- Laboratorio Nazionale CIB (LNCIB), Area Science Park, Padriciano 99, 34149 Trieste, Italy
| | - Mariangela Santorsola
- Laboratorio Nazionale CIB (LNCIB), Area Science Park, Padriciano 99, 34149 Trieste, Italy; Department of Life Sciences (DSV), University of Trieste, 34127 Trieste, Italy
| | - Alessandra Rustighi
- Laboratorio Nazionale CIB (LNCIB), Area Science Park, Padriciano 99, 34149 Trieste, Italy; Department of Life Sciences (DSV), University of Trieste, 34127 Trieste, Italy
| | | | - Elena Maspero
- FIRC Institute of Molecular Oncology (IFOM), 20139 Milan, Italy
| | - Federico Ansaloni
- Area of Neuroscience, International School for Advanced Studies (SISSA), 34146 Trieste, Italy
| | - Valeria Cancila
- Tumor Immunology Unit, Department of Health Science, Human Pathology Section, School of Medicine, University of Palermo, 90133 Palermo, Italy
| | - Cesare Fabio Valenti
- Tumor Immunology Unit, Department of Health Science, Human Pathology Section, School of Medicine, University of Palermo, 90133 Palermo, Italy
| | - Manuela Santo
- Area of Neuroscience, International School for Advanced Studies (SISSA), 34146 Trieste, Italy
| | | | - Sara Finaurini
- Area of Neuroscience, International School for Advanced Studies (SISSA), 34146 Trieste, Italy
| | - Ubaldo Gioia
- FIRC Institute of Molecular Oncology (IFOM), 20139 Milan, Italy
| | - Simona Polo
- FIRC Institute of Molecular Oncology (IFOM), 20139 Milan, Italy
| | - Remo Sanges
- Area of Neuroscience, International School for Advanced Studies (SISSA), 34146 Trieste, Italy
| | - Claudio Tripodo
- FIRC Institute of Molecular Oncology (IFOM), 20139 Milan, Italy; Tumor Immunology Unit, Department of Health Science, Human Pathology Section, School of Medicine, University of Palermo, 90133 Palermo, Italy
| | - Antonello Mallamaci
- Area of Neuroscience, International School for Advanced Studies (SISSA), 34146 Trieste, Italy
| | - Stefano Gustincich
- Area of Neuroscience, International School for Advanced Studies (SISSA), 34146 Trieste, Italy; Central RNA Laboratory, Italian Institute of Technology, 16163 Genova, Italy
| | - Fabrizio d'Adda di Fagagna
- FIRC Institute of Molecular Oncology (IFOM), 20139 Milan, Italy; Institute of Molecular Genetics, National Research Institute (CNR), Pavia, Italy
| | - Fiamma Mantovani
- Laboratorio Nazionale CIB (LNCIB), Area Science Park, Padriciano 99, 34149 Trieste, Italy; Department of Life Sciences (DSV), University of Trieste, 34127 Trieste, Italy
| | - Valeria Specchia
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, 73100 Lecce, Italy
| | - Giannino Del Sal
- Laboratorio Nazionale CIB (LNCIB), Area Science Park, Padriciano 99, 34149 Trieste, Italy; Department of Life Sciences (DSV), University of Trieste, 34127 Trieste, Italy; FIRC Institute of Molecular Oncology (IFOM), 20139 Milan, Italy.
| |
Collapse
|
12
|
Li CL, Pu M, Wang W, Chaturbedi A, Emerson FJ, Lee SS. Region-specific H3K9me3 gain in aged somatic tissues in Caenorhabditis elegans. PLoS Genet 2021; 17:e1009432. [PMID: 34506495 PMCID: PMC8457455 DOI: 10.1371/journal.pgen.1009432] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 09/22/2021] [Accepted: 08/17/2021] [Indexed: 12/13/2022] Open
Abstract
Epigenetic alterations occur as organisms age, and lead to chromatin deterioration, loss of transcriptional silencing and genomic instability. Dysregulation of the epigenome has been associated with increased susceptibility to age-related disorders. In this study, we aimed to characterize the age-dependent changes of the epigenome and, in turn, to understand epigenetic processes that drive aging phenotypes. We focused on the aging-associated changes in the repressive histone marks H3K9me3 and H3K27me3 in C. elegans. We observed region-specific gain and loss of both histone marks, but the changes are more evident for H3K9me3. We further found alteration of heterochromatic boundaries in aged somatic tissues. Interestingly, we discovered that the most statistically significant changes reflected H3K9me3-marked regions that are formed during aging, and are absent in developing worms, which we termed "aging-specific repressive regions" (ASRRs). These ASRRs preferentially occur in genic regions that are marked by high levels of H3K9me2 and H3K36me2 in larval stages. Maintenance of high H3K9me2 levels in these regions have been shown to correlate with a longer lifespan. Next, we examined whether the changes in repressive histone marks lead to de-silencing of repetitive DNA elements, as reported for several other organisms. We observed increased expression of active repetitive DNA elements but not global re-activation of silent repeats in old worms, likely due to the distributed nature of repetitive elements in the C. elegans genome. Intriguingly, CELE45, a putative short interspersed nuclear element (SINE), was greatly overexpressed at old age and upon heat stress. SINEs have been suggested to regulate transcription in response to various cellular stresses in mammals. It is likely that CELE45 RNAs also play roles in stress response and aging in C. elegans. Taken together, our study revealed significant and specific age-dependent changes in repressive histone modifications and repetitive elements, providing important insights into aging biology.
Collapse
Affiliation(s)
- Cheng-Lin Li
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Mintie Pu
- State Key Laboratory for Conservation and Utilization of Bio-Resources and Center for Life Science, School of Life Sciences, Yunnan University, Kunming, Yunnan, China
| | - Wenke Wang
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Amaresh Chaturbedi
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Felicity J Emerson
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Siu Sylvia Lee
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| |
Collapse
|
13
|
Kozlowski DKL, Hassanaly‐Goulamhoussen R, Da Rocha M, Koutsovoulos GD, Bailly‐Bechet M, Danchin EGJ. Movements of transposable elements contribute to the genomic plasticity and species diversification in an asexually reproducing nematode pest. Evol Appl 2021; 14:1844-1866. [PMID: 34295368 PMCID: PMC8288018 DOI: 10.1111/eva.13246] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 04/12/2021] [Accepted: 04/15/2021] [Indexed: 12/14/2022] Open
Abstract
Despite reproducing without sexual recombination, Meloidogyne incognita is an adaptive and versatile phytoparasitic nematode. This species displays a global distribution, can parasitize a large range of plants, and can overcome plant resistance in a few generations. The mechanisms underlying this adaptability remain poorly known. At the whole-genome level, only a few single nucleotide variations have been observed across different geographical isolates with distinct ranges of compatible hosts. Exploring other factors possibly involved in genomic plasticity is thus important. Transposable elements (TEs), by their repetitive nature and mobility, can passively and actively impact the genome dynamics. This is particularly expected in polyploid hybrid genomes such as the one of M. incognita. Here, we have annotated the TE content of M. incognita, analyzed the statistical properties of this TE landscape, and used whole-genome pool-seq data to estimate the mobility of these TEs across twelve geographical isolates, presenting variations in ranges of compatible host plants. DNA transposons are more abundant than retrotransposons, and the high similarity of TE copies to their consensus sequences suggests they have been at least recently active. We have identified loci in the genome where the frequencies of presence of a TE showed substantial variations across the different isolates. Overall, variations in TE frequencies across isolates followed their phylogenetic divergence, suggesting TEs participate in the species diversification. Compared with the M. incognita reference genome, we detected isolate and lineage-specific de novo insertion of some TEs, including within genic regions or in the upstream regulatory regions. We validated by PCR the insertion of some of these TEs inside genic regions, confirming TE movements have possible functional impacts. Overall, we show DNA transposons can drive genomic plasticity in M. incognita and their role in genome evolution of other parthenogenetic animal deserves further investigation.
Collapse
|
14
|
Siudeja K, van den Beek M, Riddiford N, Boumard B, Wurmser A, Stefanutti M, Lameiras S, Bardin AJ. Unraveling the features of somatic transposition in the Drosophila intestine. EMBO J 2021; 40:e106388. [PMID: 33634906 PMCID: PMC8090852 DOI: 10.15252/embj.2020106388] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 01/20/2021] [Accepted: 01/27/2021] [Indexed: 12/22/2022] Open
Abstract
Transposable elements (TEs) play a significant role in evolution, contributing to genetic variation. However, TE mobilization in somatic cells is not well understood. Here, we address the prevalence of transposition in a somatic tissue, exploiting the Drosophila midgut as a model. Using whole-genome sequencing of in vivo clonally expanded gut tissue, we have mapped hundreds of high-confidence somatic TE integration sites genome-wide. We show that somatic retrotransposon insertions are associated with inactivation of the tumor suppressor Notch, likely contributing to neoplasia formation. Moreover, applying Oxford Nanopore long-read sequencing technology we provide evidence for tissue-specific differences in retrotransposition. Comparing somatic TE insertional activity with transcriptomic and small RNA sequencing data, we demonstrate that transposon mobility cannot be simply predicted by whole tissue TE expression levels or by small RNA pathway activity. Finally, we reveal that somatic TE insertions in the adult fly intestine are enriched in genic regions and in transcriptionally active chromatin. Together, our findings provide clear evidence of ongoing somatic transposition in Drosophila and delineate previously unknown features underlying somatic TE mobility in vivo.
Collapse
Affiliation(s)
- Katarzyna Siudeja
- Institut CurieCNRSUMR 3215INSERM U934Stem Cells and Tissue Homeostasis GroupPSL Research UniversityParisFrance
- Sorbonne UniversitésUPMC Univ Paris 6ParisFrance
| | - Marius van den Beek
- Institut CurieCNRSUMR 3215INSERM U934Stem Cells and Tissue Homeostasis GroupPSL Research UniversityParisFrance
- Sorbonne UniversitésUPMC Univ Paris 6ParisFrance
| | - Nick Riddiford
- Institut CurieCNRSUMR 3215INSERM U934Stem Cells and Tissue Homeostasis GroupPSL Research UniversityParisFrance
- Sorbonne UniversitésUPMC Univ Paris 6ParisFrance
| | - Benjamin Boumard
- Institut CurieCNRSUMR 3215INSERM U934Stem Cells and Tissue Homeostasis GroupPSL Research UniversityParisFrance
- Sorbonne UniversitésUPMC Univ Paris 6ParisFrance
| | - Annabelle Wurmser
- Institut CurieCNRSUMR 3215INSERM U934Stem Cells and Tissue Homeostasis GroupPSL Research UniversityParisFrance
- Sorbonne UniversitésUPMC Univ Paris 6ParisFrance
| | - Marine Stefanutti
- Institut CurieCNRSUMR 3215INSERM U934Stem Cells and Tissue Homeostasis GroupPSL Research UniversityParisFrance
- Sorbonne UniversitésUPMC Univ Paris 6ParisFrance
| | - Sonia Lameiras
- ICGex Next‐Generation Sequencing PlatformInstitut CuriePSL Research UniversityParisFrance
| | - Allison J Bardin
- Institut CurieCNRSUMR 3215INSERM U934Stem Cells and Tissue Homeostasis GroupPSL Research UniversityParisFrance
- Sorbonne UniversitésUPMC Univ Paris 6ParisFrance
| |
Collapse
|
15
|
Lanciano S, Cristofari G. Measuring and interpreting transposable element expression. Nat Rev Genet 2020; 21:721-736. [PMID: 32576954 DOI: 10.1038/s41576-020-0251-y] [Citation(s) in RCA: 168] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/19/2020] [Indexed: 12/21/2022]
Abstract
Transposable elements (TEs) are insertional mutagens that contribute greatly to the plasticity of eukaryotic genomes, influencing the evolution and adaptation of species as well as physiology or disease in individuals. Measuring TE expression helps to understand not only when and where TE mobilization can occur but also how this process alters gene expression, chromatin accessibility or cellular signalling pathways. Although genome-wide gene expression assays such as RNA sequencing include transposon-derived transcripts, most computational analytical tools discard or misinterpret TE-derived reads. Emerging approaches are improving the identification of expressed TE loci and helping to discriminate TE transcripts that permit TE mobilization from chimeric gene-TE transcripts or pervasive transcription. Here we review the main challenges associated with the detection of TE expression, including mappability, insertional and internal sequence polymorphisms, and the diversity of the TE transcriptional landscape, as well as the different experimental and computational strategies to solve them.
Collapse
|