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Liuzzi G, Artimagnella O, Frisari S, Mallamaci A. Foxg1 bimodally tunes L1-mRNA and -DNA dynamics in the developing murine neocortex. Development 2024; 151:dev202292. [PMID: 38655654 PMCID: PMC11190451 DOI: 10.1242/dev.202292] [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: 08/23/2023] [Accepted: 04/16/2024] [Indexed: 04/26/2024]
Abstract
Foxg1 masters telencephalic development via a pleiotropic control over its progression. Expressed within the central nervous system (CNS), L1 retrotransposons are implicated in progression of its histogenesis and tuning of its genomic plasticity. Foxg1 represses gene transcription, and L1 elements share putative Foxg1-binding motifs, suggesting the former might limit telencephalic expression (and activity) of the latter. We tested such a prediction, in vivo as well as in engineered primary neural cultures, using loss- and gain-of-function approaches. We found that Foxg1-dependent, transcriptional L1 repression specifically occurs in neopallial neuronogenic progenitors and post-mitotic neurons, where it is supported by specific changes in the L1 epigenetic landscape. Unexpectedly, we discovered that Foxg1 physically interacts with L1-mRNA and positively regulates neonatal neopallium L1-DNA content, antagonizing the retrotranscription-suppressing activity exerted by Mov10 and Ddx39a helicases. To the best of our knowledge, Foxg1 represents the first CNS patterning gene acting as a bimodal retrotransposon modulator, limiting transcription of L1 elements and promoting their amplification, within a specific domain of the developing mouse brain.
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Affiliation(s)
- Gabriele Liuzzi
- Laboratory of Cerebral Cortex Development, SISSA, Trieste 34136, Italy
| | | | - Simone Frisari
- Laboratory of Cerebral Cortex Development, SISSA, Trieste 34136, Italy
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2
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Meng FW, Murphy KE, Makowski CE, Delatte B, Murphy PJ. Competition for H2A.Z underlies the developmental impacts of repetitive element de-repression. Development 2023; 150:dev202338. [PMID: 37938830 PMCID: PMC10651094 DOI: 10.1242/dev.202338] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 10/10/2023] [Indexed: 11/10/2023]
Abstract
The histone variant H2A.Z is central to early embryonic development, determining transcriptional competency through chromatin regulation of gene promoters and enhancers. In addition to genic loci, we find that H2A.Z resides at a subset of evolutionarily young repetitive elements, including DNA transposons, long interspersed nuclear elements and long terminal repeats, during early zebrafish development. Moreover, increases in H2A.Z occur when repetitive elements become transcriptionally active. Acquisition of H2A.Z corresponds with a reduction in the levels of the repressive histone modification H3K9me3 and a moderate increase in chromatin accessibility. Notably, however, de-repression of repetitive elements also leads to a significant reduction in H2A.Z over non-repetitive genic loci. Genic loss of H2A.Z is accompanied by transcriptional silencing at adjacent coding sequences, but remarkably, these impacts are mitigated by augmentation of total H2A.Z protein via transgenic overexpression. Our study reveals that levels of H2A.Z protein determine embryonic sensitivity to de-repression of repetitive elements, that repetitive elements can function as a nuclear sink for epigenetic factors and that competition for H2A.Z greatly influences overall transcriptional output during development. These findings uncover general mechanisms in which counteractive biological processes underlie phenotypic outcomes.
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Affiliation(s)
- Fanju W. Meng
- University of Rochester Medical Center, Rochester, NY 14642, USA
| | | | | | - Benjamin Delatte
- Advanced Research Laboratory, Active Motif, 1914 Palomar Oaks Way STE 150, Carlsbad, CA 92008, USA
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3
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Hara Y, Kuraku S. The impact of local genomic properties on the evolutionary fate of genes. eLife 2023; 12:82290. [PMID: 37223962 DOI: 10.7554/elife.82290] [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: 07/29/2022] [Accepted: 04/25/2023] [Indexed: 05/25/2023] Open
Abstract
Functionally indispensable genes are likely to be retained and otherwise to be lost during evolution. This evolutionary fate of a gene can also be affected by factors independent of gene dispensability, including the mutability of genomic positions, but such features have not been examined well. To uncover the genomic features associated with gene loss, we investigated the characteristics of genomic regions where genes have been independently lost in multiple lineages. With a comprehensive scan of gene phylogenies of vertebrates with a careful inspection of evolutionary gene losses, we identified 813 human genes whose orthologs were lost in multiple mammalian lineages: designated 'elusive genes.' These elusive genes were located in genomic regions with rapid nucleotide substitution, high GC content, and high gene density. A comparison of the orthologous regions of such elusive genes across vertebrates revealed that these features had been established before the radiation of the extant vertebrates approximately 500 million years ago. The association of human elusive genes with transcriptomic and epigenomic characteristics illuminated that the genomic regions containing such genes were subject to repressive transcriptional regulation. Thus, the heterogeneous genomic features driving gene fates toward loss have been in place and may sometimes have relaxed the functional indispensability of such genes. This study sheds light on the complex interplay between gene function and local genomic properties in shaping gene evolution that has persisted since the vertebrate ancestor.
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Affiliation(s)
- Yuichiro Hara
- Research Center for Genome & Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Shigehiro Kuraku
- Molecular Life History Laboratory, Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Japan
- Department of Genetics, Sokendai (Graduate University for Advanced Studies), Mishima, Japan
- RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
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4
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Freeman B, White T, Kaul T, Stow EC, Baddoo M, Ungerleider N, Morales M, Yang H, Deharo D, Deininger P, Belancio V. Analysis of epigenetic features characteristic of L1 loci expressed in human cells. Nucleic Acids Res 2022; 50:1888-1907. [PMID: 35100410 PMCID: PMC8887483 DOI: 10.1093/nar/gkac013] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 12/27/2021] [Accepted: 01/24/2022] [Indexed: 12/26/2022] Open
Abstract
Only a select few L1 loci in the human genome are expressed in any given cell line or organ, likely to minimize damage done to the genome. The epigenetic features and requirements of expressed L1 loci are currently unknown. Using human cells and comprehensive epigenetic analysis of individual expressed and unexpressed L1 loci, we determined that endogenous L1 transcription depends on a combination of epigenetic factors, including open chromatin, activating histone modifications, and hypomethylation at the L1 promoter. We demonstrate that the L1 promoter seems to require interaction with enhancer elements for optimal function. We utilize epigenetic context to predict the expression status of L1Hs loci that are poorly mappable with RNA-Seq. Our analysis identified a population of ‘transitional’ L1 loci that likely have greater potential to be activated during the epigenetic dysregulation seen in tumors and during aging because they are the most responsive to targeted CRISPR-mediated delivery of trans-activating domains. We demonstrate that an engineered increase in endogenous L1 mRNA expression increases Alu mobilization. Overall, our findings present the first global and comprehensive analysis of epigenetic status of individual L1 loci based on their expression status and demonstrate the importance of epigenetic context for L1 expression heterogeneity.
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Affiliation(s)
- Benjamin Freeman
- Department of Structural and Cellular Biology, Tulane University School of Medicine, Tulane Cancer Center, Tulane Center for Aging, New Orleans, LA 70112, USA
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA
| | - Travis White
- Sloan Kettering Institute for Cancer Research, NY, NY 10065, USA
| | - Tiffany Kaul
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA
| | - Emily C Stow
- Department of Structural and Cellular Biology, Tulane University School of Medicine, Tulane Cancer Center, Tulane Center for Aging, New Orleans, LA 70112, USA
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA
| | - Melody Baddoo
- Department of Pathology, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, LA 70112, USA
| | - Nathan Ungerleider
- Department of Pathology, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, LA 70112, USA
| | - Maria Morales
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA
| | - Hanlin Yang
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA
| | - Dawn Deharo
- Department of Structural and Cellular Biology, Tulane University School of Medicine, Tulane Cancer Center, Tulane Center for Aging, New Orleans, LA 70112, USA
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA
| | - Prescott Deininger
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA
- Department of Epidemiology, Tulane School of Public Health and Tropical Medicine, New Orleans, LA 70112, USA
| | - Victoria P Belancio
- To whom correspondence should be addressed. Tel: +1 504 988 4506; Fax: +1 504 988 1687;
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Pappalardo AM, Ferrito V, Biscotti MA, Canapa A, Capriglione T. Transposable Elements and Stress in Vertebrates: An Overview. Int J Mol Sci 2021; 22:1970. [PMID: 33671215 PMCID: PMC7922186 DOI: 10.3390/ijms22041970] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/13/2021] [Accepted: 02/14/2021] [Indexed: 12/17/2022] Open
Abstract
Since their identification as genomic regulatory elements, Transposable Elements (TEs) were considered, at first, molecular parasites and later as an important source of genetic diversity and regulatory innovations. In vertebrates in particular, TEs have been recognized as playing an important role in major evolutionary transitions and biodiversity. Moreover, in the last decade, a significant number of papers has been published highlighting a correlation between TE activity and exposition to environmental stresses and dietary factors. In this review we present an overview of the impact of TEs in vertebrate genomes, report the silencing mechanisms adopted by host genomes to regulate TE activity, and finally we explore the effects of environmental and dietary factor exposures on TE activity in mammals, which is the most studied group among vertebrates. The studies here reported evidence that several factors can induce changes in the epigenetic status of TEs and silencing mechanisms leading to their activation with consequent effects on the host genome. The study of TE can represent a future challenge for research for developing effective markers able to detect precocious epigenetic changes and prevent human diseases.
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Affiliation(s)
- Anna Maria Pappalardo
- Department of Biological, Geological and Environmental Sciences-Section of Animal Biology "M. La Greca", University of Catania, Via Androne 81, 95124 Catania, Italy
| | - Venera Ferrito
- Department of Biological, Geological and Environmental Sciences-Section of Animal Biology "M. La Greca", University of Catania, Via Androne 81, 95124 Catania, Italy
| | - Maria Assunta Biscotti
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Adriana Canapa
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Teresa Capriglione
- Department of Biology, University of Naples "Federico II", Via Cinthia 21-Ed7, 80126 Naples, Italy
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Barberet J, Barry F, Choux C, Guilleman M, Karoui S, Simonot R, Bruno C, Fauque P. What impact does oocyte vitrification have on epigenetics and gene expression? Clin Epigenetics 2020; 12:121. [PMID: 32778156 PMCID: PMC7418205 DOI: 10.1186/s13148-020-00911-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 07/21/2020] [Indexed: 02/07/2023] Open
Abstract
Children conceived by assisted reproductive technologies (ART) have a moderate risk for a number of adverse events and conditions. The question whether this additional risk is associated with specific procedures used in ART or whether it is related to the intrinsic biological factors associated with infertility remains unresolved. One of the main hypotheses is that laboratory procedures could have an effect on the epigenome of gametes and embryos. This suspicion is linked to the fact that ART procedures occur precisely during the period when there are major changes in the organization of the epigenome. Oocyte freezing protocols are generally considered safe; however, some evidence suggests that vitrification may be associated with modifications of the epigenetic marks. In this manuscript, after describing the main changes that occur during epigenetic reprogramming, we will provide current information regarding the impact of oocyte vitrification on epigenetic regulation and the consequences on gene expression, both in animals and humans. Overall, the literature suggests that epigenetic and transcriptomic profiles are sensitive to the stress induced by oocyte vitrification, and it also underlines the need to improve our knowledge in this field.
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Affiliation(s)
- Julie Barberet
- CHU Dijon Bourgogne, Laboratoire de Biologie de la Reproduction, CECOS, 14 rue Gaffarel, 21079 Dijon Cedex, France
| | - Fatima Barry
- CHU Dijon Bourgogne, Laboratoire de Biologie de la Reproduction, CECOS, 14 rue Gaffarel, 21079 Dijon Cedex, France
| | - Cécile Choux
- Gynécologie-Obstétrique, CHU Dijon Bourgogne, 14 rue Gaffarel, 21079 Dijon Cedex, France
| | - Magali Guilleman
- CHU Dijon Bourgogne, Laboratoire de Biologie de la Reproduction, CECOS, 14 rue Gaffarel, 21079 Dijon Cedex, France
| | - Sara Karoui
- CHU Dijon Bourgogne, Laboratoire de Biologie de la Reproduction, CECOS, 14 rue Gaffarel, 21079 Dijon Cedex, France
| | - Raymond Simonot
- CHU Dijon Bourgogne, Laboratoire de Biologie de la Reproduction, CECOS, 14 rue Gaffarel, 21079 Dijon Cedex, France
| | - Céline Bruno
- CHU Dijon Bourgogne, Laboratoire de Biologie de la Reproduction, CECOS, 14 rue Gaffarel, 21079 Dijon Cedex, France
| | - Patricia Fauque
- CHU Dijon Bourgogne, Laboratoire de Biologie de la Reproduction, CECOS, 14 rue Gaffarel, 21079 Dijon Cedex, France
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7
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LINE-1 specific nuclear organization in mice olfactory sensory neurons. Mol Cell Neurosci 2020; 105:103494. [PMID: 32387751 DOI: 10.1016/j.mcn.2020.103494] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 03/31/2020] [Accepted: 04/05/2020] [Indexed: 12/21/2022] Open
Abstract
Long interspersed nuclear elements-1 (LINE-1) are mobile DNA elements that comprise the majority of interspersed repeats in the mammalian genome. During the last decade, these transposable sequences have been described as controlling elements involved in transcriptional regulation and genome plasticity. Recently, LINE-1 have been implicated in neurogenesis, but to date little is known about their nuclear organization in neurons. The olfactory epithelium is a site of continuous neurogenesis, and loci of olfactory receptor genes are enriched in LINE-1 copies. Olfactory neurons have a unique inverted nuclear architecture and constitutive heterochromatin forms a block in the center of the nuclei. Our DNA FISH images show that, even though LINE-1 copies are dispersed throughout the mice genome, they are clustered forming a cap around the central heterochromatin block and frequently occupy the same position as facultative heterochromatin in olfactory neurons nuclei. This specific LINE-1 organization could not be observed in other olfactory epithelium cell types. Analyses of H3K27me3 and H3K9me3 ChIP-seq data from olfactory epithelium revealed that LINE-1 copies located at OR gene loci show different enrichment for these heterochromatin marks. We also found that LINE-1 are transcribed in mouse olfactory epithelium. These results suggest that LINE-1 play a role in the olfactory neurons' nuclear architecture. SIGNIFICANCE STATEMENT: LINE-1 are mobile DNA elements and comprise almost 20% of mice and human genomes. These retrotransposons have been implicated in neurogenesis. We show for the first time that LINE-1 retrotransposons have a specific nuclear organization in olfactory neurons, forming aggregates concentric to the heterochromatin block and frequently occupying the same region as facultative heterochromatin. We found that LINE-1 at olfactory receptor gene loci are differently enriched for H3K9me3 and H3K27me3, but LINE-1 transcripts could be detected in the olfactory epithelium. We speculate that these retrotransposons play an active role in olfactory neurons' nuclear architecture.
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8
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Bertozzi TM, Ferguson-Smith AC. Metastable epialleles and their contribution to epigenetic inheritance in mammals. Semin Cell Dev Biol 2020; 97:93-105. [PMID: 31551132 DOI: 10.1016/j.semcdb.2019.08.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 08/15/2019] [Accepted: 08/20/2019] [Indexed: 02/02/2023]
Abstract
Many epigenetic differences between individuals are driven by genetic variation. Mammalian metastable epialleles are unusual in that they show variable DNA methylation states between genetically identical individuals. The occurrence of such states across generations has resulted in their consideration by many as strong evidence for epigenetic inheritance in mammals, with the classic Avy and AxinFu mouse models - each products of repeat element insertions - being the most widely accepted examples. Equally, there has been interest in exploring their use as epigenetic biosensors given their susceptibility to environmental compromise. Here we review the classic murine metastable epialleles as well as more recently identified candidates, with the aim of providing a more holistic understanding of their biology. We consider the extent to which epigenetic inheritance occurs at metastable epialleles and explore the limited mechanistic insights into the establishment of their variable epigenetic states. We discuss their environmental modulation and their potential relevance in genome regulation. In light of recent whole-genome screens for novel metastable epialleles, we point out the need to reassess their biological relevance in multi-generational studies and we highlight their value as a model to study repeat element silencing as well as the mechanisms and consequences of mammalian epigenetic stochasticity.
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Affiliation(s)
- Tessa M Bertozzi
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
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9
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Transcription factor profiling reveals molecular choreography and key regulators of human retrotransposon expression. Proc Natl Acad Sci U S A 2018; 115:E5526-E5535. [PMID: 29802231 PMCID: PMC6004460 DOI: 10.1073/pnas.1722565115] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Transposable elements (TEs) represent a substantial fraction of many eukaryotic genomes, and transcriptional regulation of these factors is important to determine TE activities in human cells. However, due to the repetitive nature of TEs, identifying transcription factor (TF)-binding sites from ChIP-sequencing (ChIP-seq) datasets is challenging. Current algorithms are focused on subtle differences between TE copies and thus bias the analysis to relatively old and inactive TEs. Here we describe an approach termed "MapRRCon" (mapping repeat reads to a consensus) which allows us to identify proteins binding to TE DNA sequences by mapping ChIP-seq reads to the TE consensus sequence after whole-genome alignment. Although this method does not assign binding sites to individual insertions in the genome, it provides a landscape of interacting TFs by capturing factors that bind to TEs under various conditions. We applied this method to screen TFs' interaction with L1 in human cells/tissues using ENCODE ChIP-seq datasets and identified 178 of the 512 TFs tested as bound to L1 in at least one biological condition with most of them (138) localized to the promoter. Among these L1-binding factors, we focused on Myc and CTCF, as they play important roles in cancer progression and 3D chromatin structure formation. Furthermore, we explored the transcriptomes of The Cancer Genome Atlas breast and ovarian tumor samples in which a consistent anti-/correlation between L1 and Myc/CTCF expression was observed, suggesting that these two factors may play roles in regulating L1 transcription during the development of such tumors.
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10
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Rhyu MG, Oh JH, Hong SJ. Species-specific role of gene-adjacent retroelements in human and mouse gastric carcinogenesis. Int J Cancer 2017; 142:1520-1527. [PMID: 29055047 DOI: 10.1002/ijc.31120] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 09/22/2017] [Accepted: 10/09/2017] [Indexed: 12/15/2022]
Abstract
Helicobacter pylori (HP) infection promotes the recruitment of bone marrow stem cells into chronic gastritis lesions. Some of these marrow stem cells can differentiate into gastric epithelial cells and neoplastic cells. We propose that HP-associated methylation could stabilize trans-differentiation of marrow-derived stem cells and that an unstable methylation status is associated with a risk of gastric cancer. Pathobiologic behavior of experimental mouse gastric cancer is mild compared to invasive and metastatic human gastric cancer. Differences in epigenetic stabilization of adult cell phenotypes between humans and mice could provide a foundation to explore the development of invasive and metastatic gastric cancer. Retroelements are highly repetitive sequences that play an essential role in the generation of species diversity. In this review, we analyzed retroelements adjacent to human and mouse housekeeping genes and proposed a possible epigenetic mechanism for HP-associated carcinogenesis.
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Affiliation(s)
- Mun-Gan Rhyu
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Jung-Hwan Oh
- Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Seung-Jin Hong
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Korea
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11
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Genetic and epigenetic features direct differential efficiency of Xist-mediated silencing at X-chromosomal and autosomal locations. Nat Commun 2017; 8:690. [PMID: 28947736 PMCID: PMC5612955 DOI: 10.1038/s41467-017-00528-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 07/06/2017] [Indexed: 02/02/2023] Open
Abstract
Xist is indispensable for X chromosome inactivation. However, how Xist RNA directs chromosome-wide silencing and why some regions are more efficiently silenced than others remains unknown. Here, we explore the function of Xist by inducing ectopic Xist expression from multiple different X-linked and autosomal loci in mouse aneuploid and female diploid embryonic stem cells in which Xist-mediated silencing does not lead to lethal functional monosomy. We show that ectopic Xist expression faithfully recapitulates endogenous X chromosome inactivation from any location on the X chromosome, whereas long-range silencing of autosomal genes is less efficient. Long interspersed elements facilitate inactivation of genes located far away from the Xist transcription locus, and genes escaping X chromosome inactivation show enrichment of CTCF on X chromosomal but not autosomal loci. Our findings highlight important genomic and epigenetic features acquired during sex chromosome evolution to facilitate an efficient X chromosome inactivation process.Xist RNA is required for X chromosome inactivation but it is not well understood how Xist silences some regions more efficiently than others. Here, the authors induce ectopic Xist expression from multiple different X-linked and autosomal loci in cells to explore Xist function.
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12
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Ornithine decarboxylase regulates M1 macrophage activation and mucosal inflammation via histone modifications. Proc Natl Acad Sci U S A 2017; 114:E751-E760. [PMID: 28096401 DOI: 10.1073/pnas.1614958114] [Citation(s) in RCA: 132] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Macrophage activation is a critical step in host responses during bacterial infections. Ornithine decarboxylase (ODC), the rate-limiting enzyme in polyamine metabolism, has been well studied in epithelial cells and is known to have essential roles in many different cellular functions. However, its role in regulating macrophage function during bacterial infections is not well characterized. We demonstrate that macrophage-derived ODC is a critical regulator of M1 macrophage activation during both Helicobacter pylori and Citrobacter rodentium infection. Myeloid-specific Odc deletion significantly increased gastric and colonic inflammation, respectively, and enhanced M1 activation. Add-back of putrescine, the product of ODC, reversed the increased macrophage activation, indicating that ODC and putrescine are regulators of macrophage function. Odc-deficient macrophages had increased histone 3, lysine 4 (H3K4) monomethylation, and H3K9 acetylation, accompanied by decreased H3K9 di/trimethylation both in vivo and ex vivo in primary macrophages. These alterations in chromatin structure directly resulted in up-regulated gene transcription, especially M1 gene expression. Thus, ODC in macrophages tempers antimicrobial, M1 macrophage responses during bacterial infections through histone modifications and altered euchromatin formation, leading to the persistence and pathogenesis of these organisms.
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13
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Identification of recurrent combinatorial patterns of chromatin modifications at promoters across various tissue types. BMC Bioinformatics 2016; 17:534. [PMID: 28155643 PMCID: PMC5259941 DOI: 10.1186/s12859-016-1346-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Background Identification and analysis of recurrent combinatorial patterns of multiple chromatin modifications provide invaluable information for understanding epigenetic regulations. Furthermore, as more data becomes available, it is computationally expensive and unnecessary to study combinatorial patterns of all modifications. Methods A novel framework is proposed to investigate recurrent combinatorial patterns of a subset of quantitatively selected chromatin modifications. The framework is based on heirarchical clustering and selects subsets of chromatin modifications that form distinct recurrent patterns at regulatory regions. The identified recurrent combinatorial patterns can be further utilized to discover novel regulatory regions. Data is in the form of genome wide maps of histone acetylations, methylations, and histone variant of human skeletal muscular and B-lymphocyte cells both derived from the ENCODE project. Results A case study conducted at promoter regions is presented: four out of twelve chromatin modifications were selected, eight different promoter states were identified and the identified patterns of active promoters were further utilized to discover novel promoter regions. Several previously un-annotated promoters were discovered, further investigations confirm their promoter functions. Conclusions This framework is approproiately general and could lead to better understanding of epigenetic regulations by discovering previously unknown regulatory regions. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-1346-5) contains supplementary material, which is available to authorized users.
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14
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Prior S, Miousse IR, Nzabarushimana E, Pathak R, Skinner C, Kutanzi KR, Allen AR, Raber J, Tackett AJ, Hauer-Jensen M, Nelson GA, Koturbash I. Densely ionizing radiation affects DNA methylation of selective LINE-1 elements. ENVIRONMENTAL RESEARCH 2016; 150:470-481. [PMID: 27419368 PMCID: PMC5003736 DOI: 10.1016/j.envres.2016.06.043] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 06/15/2016] [Accepted: 06/27/2016] [Indexed: 05/26/2023]
Abstract
Long Interspersed Nucleotide Element 1 (LINE-1) retrotransposons are heavily methylated and are the most abundant transposable elements in mammalian genomes. Here, we investigated the differential DNA methylation within the LINE-1 under normal conditions and in response to environmentally relevant doses of sparsely and densely ionizing radiation. We demonstrate that DNA methylation of LINE-1 elements in the lungs of C57BL6 mice is dependent on their evolutionary age, where the elder age of the element is associated with the lower extent of DNA methylation. Exposure to 5-aza-2'-deoxycytidine and methionine-deficient diet affected DNA methylation of selective LINE-1 elements in an age- and promoter type-dependent manner. Exposure to densely IR, but not sparsely IR, resulted in DNA hypermethylation of older LINE-1 elements, while the DNA methylation of evolutionary younger elements remained mostly unchanged. We also demonstrate that exposure to densely IR increased mRNA and protein levels of LINE-1 via the loss of the histone H3K9 dimethylation and an increase in the H3K4 trimethylation at the LINE-1 5'-untranslated region, independently of DNA methylation. Our findings suggest that DNA methylation is important for regulation of LINE-1 expression under normal conditions, but histone modifications may dictate the transcriptional activity of LINE-1 in response to exposure to densely IR.
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Affiliation(s)
- Sara Prior
- Department of Environmental and Occupational Health, Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Isabelle R Miousse
- Department of Environmental and Occupational Health, Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Etienne Nzabarushimana
- Department of Environmental and Occupational Health, Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; Department of Bioinformatics, School of Informatics and Computing, Indiana University, Bloomington, IN 47405, USA
| | - Rupak Pathak
- Division of Radiation Health, Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Charles Skinner
- Department of Environmental and Occupational Health, Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Kristy R Kutanzi
- Department of Environmental and Occupational Health, Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Antiño R Allen
- Division of Radiation Health, Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Jacob Raber
- Departments of Behavioral Neuroscience, Neurology, and Radiation Medicine, Division of Neuroscience, ONPRC, Oregon Health & Science University, Portland, OR 97239, USA
| | - Alan J Tackett
- Department of Biochemistry, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Martin Hauer-Jensen
- Division of Radiation Health, Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Gregory A Nelson
- Department of Basic Sciences, Division of Radiation Research, Loma Linda University, Loma Linda, CA 92350, USA
| | - Igor Koturbash
- Department of Environmental and Occupational Health, Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA.
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15
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Abstract
Retrotransposons have generated about 40 % of the human genome. This review examines the strategies the cell has evolved to coexist with these genomic "parasites", focussing on the non-long terminal repeat retrotransposons of humans and mice. Some of the restriction factors for retrotransposition, including the APOBECs, MOV10, RNASEL, SAMHD1, TREX1, and ZAP, also limit replication of retroviruses, including HIV, and are part of the intrinsic immune system of the cell. Many of these proteins act in the cytoplasm to degrade retroelement RNA or inhibit its translation. Some factors act in the nucleus and involve DNA repair enzymes or epigenetic processes of DNA methylation and histone modification. RISC and piRNA pathway proteins protect the germline. Retrotransposon control is relaxed in some cell types, such as neurons in the brain, stem cells, and in certain types of disease and cancer, with implications for human health and disease. This review also considers potential pitfalls in interpreting retrotransposon-related data, as well as issues to consider for future research.
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Affiliation(s)
- John L. Goodier
- McKusick-Nathans Institute for Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD USA 212051
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16
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Grégoire L, Haudry A, Lerat E. The transposable element environment of human genes is associated with histone and expression changes in cancer. BMC Genomics 2016; 17:588. [PMID: 27506777 PMCID: PMC4979156 DOI: 10.1186/s12864-016-2970-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 07/27/2016] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Only 2 % of the human genome code for proteins. Among the remaining 98 %, transposable elements (TEs) represent millions of sequences. TEs have an impact on genome evolution by promoting mutations. Especially, TEs possess their own regulatory sequences and can alter the expression pattern of neighboring genes. Since they can potentially be harmful, TE activity is regulated by epigenetic mechanisms. These mechanisms participate in the modulation of gene expression and can be associated with some human diseases resulting from gene expression deregulation. The fact that the TE silencing can be removed in cancer could explain a part of the changes in gene expression. Indeed, epigenetic modifications associated locally with TE sequences could impact neighboring genes since these modifications can spread to adjacent sequences. RESULTS We compared the histone enrichment, TE neighborhood, and expression divergence of human genes between a normal and a cancer conditions. We show that the presence of TEs near genes is associated with greater changes in histone enrichment and that differentially expressed genes harbor larger histone enrichment variation related to the presence of particular TEs. CONCLUSIONS Taken together, these results suggest that the presence of TEs near genes could favor important variation in gene expression when the cell environment is modified.
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Affiliation(s)
- Laura Grégoire
- Université de Lyon; F-69000, France; Université Lyon 1, CNRS, UMR 5558, Laboratoire Biométrie et Biologie Evolutive, F-69622, Villeurbanne, France
| | - Annabelle Haudry
- Université de Lyon; F-69000, France; Université Lyon 1, CNRS, UMR 5558, Laboratoire Biométrie et Biologie Evolutive, F-69622, Villeurbanne, France
| | - Emmanuelle Lerat
- Université de Lyon; F-69000, France; Université Lyon 1, CNRS, UMR 5558, Laboratoire Biométrie et Biologie Evolutive, F-69622, Villeurbanne, France.
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17
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Miousse IR, Chalbot MCG, Lumen A, Ferguson A, Kavouras IG, Koturbash I. Response of transposable elements to environmental stressors. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2015; 765:19-39. [PMID: 26281766 PMCID: PMC4544780 DOI: 10.1016/j.mrrev.2015.05.003] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Revised: 05/27/2015] [Accepted: 05/28/2015] [Indexed: 12/21/2022]
Abstract
Transposable elements (TEs) comprise a group of repetitive sequences that bring positive, negative, as well as neutral effects to the host organism. Earlier considered as "junk DNA," TEs are now well-accepted driving forces of evolution and critical regulators of the expression of genetic information. Their activity is regulated by epigenetic mechanisms, including methylation of DNA and histone modifications. The loss of epigenetic control over TEs, exhibited as loss of DNA methylation and decondensation of the chromatin structure, may result in TEs reactivation, initiation of their insertional mutagenesis (retrotransposition) and has been reported in numerous human diseases, including cancer. Accumulating evidence suggests that these alterations are not the simple consequences of the disease, but often may drive the pathogenesis, as they can be detected early during disease development. Knowledge derived from the in vitro, in vivo, and epidemiological studies, clearly demonstrates that exposure to ubiquitous environmental stressors, many of which are carcinogens or suspected carcinogens, are capable of causing alterations in methylation and expression of TEs and initiate retrotransposition events. Evidence summarized in this review suggests that TEs are the sensitive endpoints for detection of effects caused by such environmental stressors, as ionizing radiation (terrestrial, space, and UV-radiation), air pollution (including particulate matter [PM]-derived and gaseous), persistent organic pollutants, and metals. Furthermore, the significance of these effects is characterized by their early appearance, persistence and presence in both, target organs and peripheral blood. Altogether, these findings suggest that TEs may potentially be introduced into safety and risk assessment and serve as biomarkers of exposure to environmental stressors. Furthermore, TEs also show significant potential to become invaluable surrogate biomarkers in clinic and possible targets for therapeutic modalities for disease treatment and prevention.
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Affiliation(s)
- Isabelle R Miousse
- Department of Environmental and Occupational Health, Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA.
| | - Marie-Cecile G Chalbot
- Department of Environmental and Occupational Health, Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA.
| | - Annie Lumen
- Division of Biochemical Toxicology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA.
| | - Alesia Ferguson
- Department of Environmental and Occupational Health, Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA.
| | - Ilias G Kavouras
- Department of Environmental and Occupational Health, Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA.
| | - Igor Koturbash
- Department of Environmental and Occupational Health, Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA.
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18
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Exploiting the power of LINE-1 retrotransposon mutagenesis for identification of genes involved in embryonic stem cell differentiation. Stem Cell Rev Rep 2014; 10:408-16. [PMID: 24610122 PMCID: PMC4008784 DOI: 10.1007/s12015-014-9500-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Identifying the genes or epigenetic factors that control the self-renewal and differentiation of stem cells is critical to understanding the molecular basis of cell commitment. Although a number of insertional mutagenesis vectors have been developed for identifying gene functions in animal models, the L1 retrotransposition system offers additional advantages as a tool to disrupt genes in embryonic stem cells in order to identify their functions and the phenotypes associated with them. Recent advances in producing synthetic versions of L1 retrotransposon vector system and the optimization of techniques to accurately identify retrotransposon integration sites have increased their utility for gene discovery applications. We have developed a novel episomal, nonviral L1 retrotransposon vector using scaffold/matrix attachment regions that provides stable, sustained levels of retrotransposition in cell cultures without being affected by epigenetic silencing or from some of the common problems of vector integration. This modified vector contains a GFP marker whose expression occurs only after successful gene disruption events and thus the cells with disrupted genes can be easily picked for functional analysis. Here we present a method to disrupt gene function in embryonic stem cells that aid in the identification of genes involved in stem cell differentiation processes. The methods presented here can be easily adapted to the study of other types of cancer stem cells or induced pluripotent stem cells using the L1 retrotransposon as an insertional mutagen.
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19
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Ohms S, Lee SH, Rangasamy D. LINE-1 retrotransposons and let-7 miRNA: partners in the pathogenesis of cancer? Front Genet 2014; 5:338. [PMID: 25339972 PMCID: PMC4188135 DOI: 10.3389/fgene.2014.00338] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2014] [Accepted: 09/09/2014] [Indexed: 11/13/2022] Open
Abstract
Long interspersed nuclear element-1 (LINE-1 or L1) retrotransposons are insertional mutagens capable of altering the genomic landscape in many ways. Activation of the normally silent LINE-1 retrotransposon is associated with a high level of cancer-associated DNA damage and genomic instability. Studies of LINE-1 have so far focused mainly on changes in gene expression, and our knowledge of its impact on functional non-coding RNAs is in its infancy. However, current evidence suggests that a significant number of human miRNAs originate from retrotransposon sequences. Furthermore, LINE-1 is generally not expressed in normal tissues while its expression is widespread in epithelial cancers. Based on our recent studies, we demonstrate a functional link between aberrant LINE-1 expression and deregulation of let-7 miRNA expression. Since the expression of let-7 is modulated by LINE-1 activity, we discuss possible mechanisms for this effect and how the silencing of LINE-1 activation could provide new therapeutic options for cancer treatment. Based on the deep sequencing of small RNAs in parallel with gene expression profiling in breast cancer cells, we have identified potential pathways linking L1 activity to let-7 processing and maturation and ultimately to the control of stemness in human cancer cells.
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Affiliation(s)
- Stephen Ohms
- Department of Molecular Bioscience, John Curtin School of Medical Research, The Australian National University Canberra, ACT, Australia
| | - Sung-Hun Lee
- Department of Molecular Bioscience, John Curtin School of Medical Research, The Australian National University Canberra, ACT, Australia ; Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center Houston, TX, USA
| | - Danny Rangasamy
- Department of Molecular Bioscience, John Curtin School of Medical Research, The Australian National University Canberra, ACT, Australia
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20
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Benard A, Goossens-Beumer IJ, van Hoesel AQ, de Graaf W, Horati H, Putter H, Zeestraten ECM, van de Velde CJH, Kuppen PJK. Histone trimethylation at H3K4, H3K9 and H4K20 correlates with patient survival and tumor recurrence in early-stage colon cancer. BMC Cancer 2014; 14:531. [PMID: 25047223 PMCID: PMC4223547 DOI: 10.1186/1471-2407-14-531] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 07/17/2014] [Indexed: 01/09/2023] Open
Abstract
Background Post-translational modification of histone tails by methylation plays an important role in tumorigenesis. In this study, we investigated the nuclear expression of H3K4me3, H3K9me3 and H4K20me3 in early-stage colon cancer in relation to clinical outcome. Methods Tumor tissue cores of 254 TNM stage I-III colorectal cancer patients were immunohistochemically stained for H3K4me3, H3K9me3 and H4K20me3 and scored using the semi-automated Ariol system. Cox proportional hazard trend analyses were performed to assess the prognostic value of the combined markers with respect to patient survival and tumor recurrence. Results The histone methylation markers only showed prognostic value in early-stage (TNM stage I and II) colon cancer. Therefore, only this patient set (n = 121) was used for further statistical analyses. Low nuclear expression of H3K4me3, and high expression of H3K9me3 and H4K20me3 were associated with good prognosis. In combined marker analyses, the patient group showing most favorable expression (low H3K4me3, high H3K9me3 and high H4K20me3) was associated with the best prognosis. Multivariate trend analyses showed significantly increased hazard ratios (HR) for each additional marker showing unfavorable expression, as compared to the “all favorable” reference group. The HR for disease-free survival was 3.81 (1.72-8.45; p = 0.001), for locoregional recurrence-free survival 2.86 (1.59-5.13; p < 0.001) and for distant recurrence-free survival 2.94 (1.66-5.22; p < 0.001). Conclusions Combined nuclear expression of histone modifications H3K4me3, H3K9me3 and H4K20me3 is prognostic in early-stage colon cancer. The combination of expression of the three histone modifications provides better stratification of patient groups as compared to the individual markers and provides a good risk assessment for each patient group.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Peter J K Kuppen
- Department of Surgery, K6-R, Leiden University Medical Center, P,O, Box 9600, 2300 RC Leiden, The Netherlands.
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