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1.
Cell ; 177(4): 837-851.e28, 2019 05 02.
Artigo em Inglês | MEDLINE | ID: mdl-30955886

RESUMO

L1 retrotransposon-derived sequences comprise approximately 17% of the human genome. Darwinian selective pressures alter L1 genomic distributions during evolution, confounding the ability to determine initial L1 integration preferences. Here, we generated high-confidence datasets of greater than 88,000 engineered L1 insertions in human cell lines that act as proxies for cells that accommodate retrotransposition in vivo. Comparing these insertions to a null model, in which L1 endonuclease activity is the sole determinant dictating L1 integration preferences, demonstrated that L1 insertions are not significantly enriched in genes, transcribed regions, or open chromatin. By comparison, we provide compelling evidence that the L1 endonuclease disproportionately cleaves predominant lagging strand DNA replication templates, while lagging strand 3'-hydroxyl groups may prime endonuclease-independent L1 retrotransposition in a Fanconi anemia cell line. Thus, acquisition of an endonuclease domain, in conjunction with the ability to integrate into replicating DNA, allowed L1 to become an autonomous, interspersed retrotransposon.


Assuntos
Elementos Nucleotídeos Longos e Dispersos/genética , Retroelementos/genética , Linhagem Celular , Endonucleases/genética , Endonucleases/metabolismo , Genoma Humano/genética , Estudo de Associação Genômica Ampla/métodos , Genômica , Células HeLa , Humanos , Mutagênese Insercional/genética
2.
Cell ; 174(6): 1537-1548.e29, 2018 09 06.
Artigo em Inglês | MEDLINE | ID: mdl-30122351

RESUMO

LINE-1 retrotransposition is tightly restricted by layers of regulatory control, with epigenetic pathways being the best characterized. Looking at post-transcriptional regulation, we now show that LINE-1 mRNA 3' ends are pervasively uridylated in various human cellular models and in mouse testes. TUT4 and TUT7 uridyltransferases catalyze the modification and function in cooperation with the helicase/RNPase MOV10 to counteract the RNA chaperone activity of the L1-ORF1p retrotransposon protein. Uridylation potently restricts LINE-1 retrotransposition by a multilayer mechanism depending on differential subcellular localization of the uridyltransferases. We propose that uridine residues added by TUT7 in the cytoplasm inhibit initiation of reverse transcription of LINE-1 mRNAs once they are reimported to the nucleus, whereas uridylation by TUT4, which is enriched in cytoplasmic foci, destabilizes mRNAs. These results provide a model for the post-transcriptional restriction of LINE-1, revealing a key physiological role for TUT4/7-mediated uridylation in maintaining genome stability.


Assuntos
Proteínas de Ligação a DNA/metabolismo , Proteínas Nucleares/metabolismo , RNA Nucleotidiltransferases/metabolismo , Proteínas de Ligação a RNA/metabolismo , Uridina/metabolismo , Animais , Proteínas de Ligação a DNA/antagonistas & inibidores , Proteínas de Ligação a DNA/genética , Células HEK293 , Humanos , Camundongos , Proteínas Nucleares/genética , Ligação Proteica , RNA Helicases/antagonistas & inibidores , RNA Helicases/genética , RNA Helicases/metabolismo , Interferência de RNA , RNA Nucleotidiltransferases/antagonistas & inibidores , RNA Nucleotidiltransferases/genética , Estabilidade de RNA , RNA Mensageiro/metabolismo , RNA Interferente Pequeno/metabolismo , Proteínas de Ligação a RNA/genética , Retroelementos/genética
3.
Mol Cell ; 75(3): 590-604.e12, 2019 08 08.
Artigo em Inglês | MEDLINE | ID: mdl-31230816

RESUMO

Epigenetic silencing defends against LINE-1 (L1) retrotransposition in mammalian cells. However, the mechanisms that repress young L1 families and how L1 escapes to cause somatic genome mosaicism in the brain remain unclear. Here we report that a conserved Yin Yang 1 (YY1) transcription factor binding site mediates L1 promoter DNA methylation in pluripotent and differentiated cells. By analyzing 24 hippocampal neurons with three distinct single-cell genomic approaches, we characterized and validated a somatic L1 insertion bearing a 3' transduction. The source (donor) L1 for this insertion was slightly 5' truncated, lacked the YY1 binding site, and was highly mobile when tested in vitro. Locus-specific bisulfite sequencing revealed that the donor L1 and other young L1s with mutated YY1 binding sites were hypomethylated in embryonic stem cells, during neurodifferentiation, and in liver and brain tissue. These results explain how L1 can evade repression and retrotranspose in the human body.


Assuntos
Repressão Epigenética/genética , Elementos Nucleotídeos Longos e Dispersos/genética , Retroelementos/genética , Fator de Transcrição YY1/genética , Sítios de Ligação/genética , Metilação de DNA/genética , Proteínas de Ligação a DNA/genética , Genoma Humano/genética , Hipocampo/metabolismo , Humanos , Fígado/metabolismo , Neurônios/metabolismo , Análise de Célula Única
4.
PLoS Biol ; 21(6): e3002162, 2023 06.
Artigo em Inglês | MEDLINE | ID: mdl-37339119

RESUMO

There remains much that we do not understand about the earliest stages of human development. On a gross level, there is evidence for apoptosis, but the nature of the affected cell types is unknown. Perhaps most importantly, the inner cell mass (ICM), from which the foetus is derived and hence of interest in reproductive health and regenerative medicine, has proven hard to define. Here, we provide a multi-method analysis of the early human embryo to resolve these issues. Single-cell analysis (on multiple independent datasets), supported by embryo visualisation, uncovers a common previously uncharacterised class of cells lacking commitment markers that segregates after embryonic gene activation (EGA) and shortly after undergo apoptosis. The discovery of this cell type allows us to clearly define their viable ontogenetic sisters, these being the cells of the ICM. While ICM is characterised by the activity of an Old non-transposing endogenous retrovirus (HERVH) that acts to suppress Young transposable elements, the new cell type, by contrast, expresses transpositionally competent Young elements and DNA-damage response genes. As the Young elements are RetroElements and the cells are excluded from the developmental process, we dub these REject cells. With these and ICM being characterised by differential mobile element activities, the human embryo may be a "selection arena" in which one group of cells selectively die, while other less damaged cells persist.


Assuntos
Blastocisto , Elementos de DNA Transponíveis , Humanos , Elementos de DNA Transponíveis/genética , Blastocisto/metabolismo , Embrião de Mamíferos
5.
Genome Res ; 32(7): 1298-1314, 2022 07.
Artigo em Inglês | MEDLINE | ID: mdl-35728967

RESUMO

The retrotransposon LINE-1 (L1) is central to the recent evolutionary history of the human genome and continues to drive genetic diversity and germline pathogenesis. However, the spatiotemporal extent and biological significance of somatic L1 activity are poorly defined and are virtually unexplored in other primates. From a single L1 lineage active at the divergence of apes and Old World monkeys, successive L1 subfamilies have emerged in each descendant primate germline. As revealed by case studies, the presently active human L1 subfamily can also mobilize during embryonic and brain development in vivo. It is unknown whether nonhuman primate L1s can similarly generate somatic insertions in the brain. Here we applied approximately 40× single-cell whole-genome sequencing (scWGS), as well as retrotransposon capture sequencing (RC-seq), to 20 hippocampal neurons from two rhesus macaques (Macaca mulatta). In one animal, we detected and PCR-validated a somatic L1 insertion that generated target site duplications, carried a short 5' transduction, and was present in ∼7% of hippocampal neurons but absent from cerebellum and nonbrain tissues. The corresponding donor L1 allele was exceptionally mobile in vitro and was embedded in PRDM4, a gene expressed throughout development and in neural stem cells. Nanopore long-read methylome and RNA-seq transcriptome analyses indicated young retrotransposon subfamily activation in the early embryo, followed by repression in adult tissues. These data highlight endogenous macaque L1 retrotransposition potential, provide prototypical evidence of L1-mediated somatic mosaicism in a nonhuman primate, and allude to L1 mobility in the brain over the past 30 million years of human evolution.


Assuntos
Encéfalo , Elementos Nucleotídeos Longos e Dispersos , Retroelementos , Animais , Proteínas de Ligação a DNA/genética , Macaca mulatta/genética , Neurônios , Retroelementos/genética , Fatores de Transcrição/genética
6.
EMBO J ; 37(15)2018 08 01.
Artigo em Inglês | MEDLINE | ID: mdl-29959219

RESUMO

Long INterspersed Element class 1 (LINE-1) elements are a type of abundant retrotransposons active in mammalian genomes. An average human genome contains ~100 retrotransposition-competent LINE-1s, whose activity is influenced by the combined action of cellular repressors and activators. TREX1, SAMHD1 and ADAR1 are known LINE-1 repressors and when mutated cause the autoinflammatory disorder Aicardi-Goutières syndrome (AGS). Mutations in RNase H2 are the most common cause of AGS, and its activity was proposed to similarly control LINE-1 retrotransposition. It has therefore been suggested that increased LINE-1 activity may be the cause of aberrant innate immune activation in AGS Here, we establish that, contrary to expectations, RNase H2 is required for efficient LINE-1 retrotransposition. As RNase H1 overexpression partially rescues the defect in RNase H2 null cells, we propose a model in which RNase H2 degrades the LINE-1 RNA after reverse transcription, allowing retrotransposition to be completed. This also explains how LINE-1 elements can retrotranspose efficiently without their own RNase H activity. Our findings appear to be at odds with LINE-1-derived nucleic acids driving autoinflammation in AGS.


Assuntos
Doenças Autoimunes do Sistema Nervoso/genética , Elementos Nucleotídeos Longos e Dispersos/genética , Malformações do Sistema Nervoso/genética , Ribonuclease H/genética , Linhagem Celular Tumoral , Técnicas de Inativação de Genes , Células HCT116 , Células HeLa , Humanos , Transcrição Reversa/genética , Ribonuclease H/biossíntese
7.
Trends Genet ; 33(11): 802-816, 2017 11.
Artigo em Inglês | MEDLINE | ID: mdl-28797643

RESUMO

The retrotransposon LINE-1 (long interspersed element 1, L1) is a transposable element that has extensively colonized the mammalian germline. L1 retrotransposition can also occur in somatic cells, causing genomic mosaicism, as well as in cancer. However, the extent of L1-driven mosaicism arising during ontogenesis is unclear. We discuss here recent experimental data which, at a minimum, fully substantiate L1 mosaicism in early embryonic development and neural cells, including post-mitotic neurons. We also consider the possible biological impact of somatic L1 insertions in neurons, the existence of donor L1s that are highly active ('hot') in specific spatiotemporal niches, and the evolutionary selection of donor L1s driving neuronal mosaicism.


Assuntos
Mamíferos/genética , Mosaicismo , Animais , Desenvolvimento Embrionário/genética , Humanos , Elementos Nucleotídeos Longos e Dispersos , Neurônios/metabolismo , Retroelementos
8.
Genome Res ; 27(3): 335-348, 2017 03.
Artigo em Inglês | MEDLINE | ID: mdl-27965292

RESUMO

Half the human genome is made of transposable elements (TEs), whose ongoing activity continues to impact our genome. LINE-1 (or L1) is an autonomous non-LTR retrotransposon in the human genome, comprising 17% of its genomic mass and containing an average of 80-100 active L1s per average genome that provide a source of inter-individual variation. New LINE-1 insertions are thought to accumulate mostly during human embryogenesis. Surprisingly, the activity of L1s can further impact the somatic human brain genome. However, it is currently unknown whether L1 can retrotranspose in other somatic healthy tissues or if L1 mobilization is restricted to neuronal precursor cells (NPCs) in the human brain. Here, we took advantage of an engineered L1 retrotransposition assay to analyze L1 mobilization rates in human mesenchymal (MSCs) and hematopoietic (HSCs) somatic stem cells. Notably, we have observed that L1 expression and engineered retrotransposition is much lower in both MSCs and HSCs when compared to NPCs. Remarkably, we have further demonstrated for the first time that engineered L1s can retrotranspose efficiently in mature nondividing neuronal cells. Thus, these findings suggest that the degree of somatic mosaicism and the impact of L1 retrotransposition in the human brain is likely much higher than previously thought.


Assuntos
Elementos de DNA Transponíveis , Elementos Nucleotídeos Longos e Dispersos , Células-Tronco Neurais/metabolismo , Divisão Celular , Células Cultivadas , Células HeLa , Células-Tronco Hematopoéticas/metabolismo , Humanos , Células-Tronco Mesenquimais/metabolismo , Mosaicismo , Células-Tronco Neurais/citologia
9.
Genome Res ; 27(8): 1395-1405, 2017 08.
Artigo em Inglês | MEDLINE | ID: mdl-28483779

RESUMO

LINE-1 (L1) retrotransposons are a noted source of genetic diversity and disease in mammals. To expand its genomic footprint, L1 must mobilize in cells that will contribute their genetic material to subsequent generations. Heritable L1 insertions may therefore arise in germ cells and in pluripotent embryonic cells, prior to germline specification, yet the frequency and predominant developmental timing of such events remain unclear. Here, we applied mouse retrotransposon capture sequencing (mRC-seq) and whole-genome sequencing (WGS) to pedigrees of C57BL/6J animals, and uncovered an L1 insertion rate of ≥1 event per eight births. We traced heritable L1 insertions to pluripotent embryonic cells and, strikingly, to early primordial germ cells (PGCs). New L1 insertions bore structural hallmarks of target-site primed reverse transcription (TPRT) and mobilized efficiently in a cultured cell retrotransposition assay. Together, our results highlight the rate and evolutionary impact of heritable L1 retrotransposition and reveal retrotransposition-mediated genomic diversification as a fundamental property of pluripotent embryonic cells in vivo.


Assuntos
Embrião de Mamíferos/metabolismo , Elementos Nucleotídeos Longos e Dispersos , Animais , Embrião de Mamíferos/citologia , Feminino , Genômica/métodos , Células Germinativas , Células HeLa , Humanos , Masculino , Camundongos , Camundongos Endogâmicos C57BL , Mosaicismo , Sequenciamento Completo do Genoma/métodos
10.
Development ; 143(22): 4101-4114, 2016 11 15.
Artigo em Inglês | MEDLINE | ID: mdl-27875251

RESUMO

Despite often being classified as selfish or junk DNA, transposable elements (TEs) are a group of abundant genetic sequences that have a significant impact on mammalian development and genome regulation. In recent years, our understanding of how pre-existing TEs affect genome architecture, gene regulatory networks and protein function during mammalian embryogenesis has dramatically expanded. In addition, the mobilization of active TEs in selected cell types has been shown to generate genetic variation during development and in fully differentiated tissues. Importantly, the ongoing domestication and evolution of TEs appears to provide a rich source of regulatory elements, functional modules and genetic variation that fuels the evolution of mammalian developmental processes. Here, we review the functional impact that TEs exert on mammalian developmental processes and discuss how the somatic activity of TEs can influence gene regulatory networks.


Assuntos
Elementos de DNA Transponíveis/fisiologia , Crescimento e Desenvolvimento/genética , Mamíferos/crescimento & desenvolvimento , Animais , Evolução Molecular , Redes Reguladoras de Genes , Variação Genética , Humanos , Mamíferos/embriologia
11.
Nucleic Acids Res ; 44(10): 4665-83, 2016 06 02.
Artigo em Inglês | MEDLINE | ID: mdl-26883630

RESUMO

Cell differentiation is a central process in development and in cancer growth and dissemination. OCT4 (POU5F1) and NANOG are essential for cell stemness and pluripotency; yet, the mechanisms that regulate their expression remain largely unknown. Repetitive elements account for almost half of the Human Genome; still, their role in gene regulation is poorly understood. Here, we show that the dioxin receptor (AHR) leads to differentiation of human carcinoma cells through the transcriptional upregulation of Alu retrotransposons, whose RNA transcripts can repress pluripotency genes. Despite the genome-wide presence of Alu elements, we provide evidences that those located at the NANOG and OCT4 promoters bind AHR, are transcribed by RNA polymerase-III and repress NANOG and OCT4 in differentiated cells. OCT4 and NANOG repression likely involves processing of Alu-derived transcripts through the miRNA machinery involving the Microprocessor and RISC. Consistently, stable AHR knockdown led to basal undifferentiation, impaired Alus transcription and blockade of OCT4 and NANOG repression. We suggest that transcripts produced from AHR-regulated Alu retrotransposons may control the expression of stemness genes OCT4 and NANOG during differentiation of carcinoma cells. The control of discrete Alu elements by specific transcription factors may have a dynamic role in genome regulation under physiological and diseased conditions.


Assuntos
Elementos Alu , Fatores de Transcrição Hélice-Alça-Hélice Básicos/fisiologia , Diferenciação Celular/genética , Regulação Neoplásica da Expressão Gênica , Receptores de Hidrocarboneto Arílico/fisiologia , Teratocarcinoma/genética , Animais , Fatores de Transcrição Hélice-Alça-Hélice Básicos/metabolismo , Carcinoma/patologia , Diferenciação Celular/efeitos dos fármacos , Linhagem Celular Tumoral , Núcleo Celular/metabolismo , Humanos , Camundongos , MicroRNAs/metabolismo , Proteína Homeobox Nanog/genética , Fator 3 de Transcrição de Octâmero/genética , Regiões Promotoras Genéticas , RNA Polimerase III/metabolismo , Receptores de Hidrocarboneto Arílico/metabolismo , Teratocarcinoma/enzimologia , Teratocarcinoma/metabolismo , Teratocarcinoma/patologia , Teratoma/genética , Teratoma/metabolismo , Transcrição Gênica , Tretinoína/farmacologia
12.
Biochim Biophys Acta ; 1849(4): 417-26, 2015 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-25042909

RESUMO

Transposable Elements are pieces of DNA able to mobilize from one location to another within genomes. Although they constitute more than 50% of the human genome, they have been classified as selfish DNA, with the only mission to spread within genomes and generate more copies of themselves that will ensure their presence over generations. Despite their remarkable prevalence, only a minor group of transposable elements remain active in the human genome and can sporadically be associated with the generation of a genetic disorder due to their ongoing mobility. Most of the transposable elements identified in the human genome corresponded to fixed insertions that no longer move in genomes. As selfish DNA, transposable element insertions accumulate in cell types where genetic information can be passed to the next generation. Indeed, work from different laboratories has demonstrated that the main heritable load of TE accumulation in humans occurs during early embryogenesis. Thus, active transposable elements have a clear impact on our pluripotent genome. However, recent findings suggest that the main proportion of fixed non-mobile transposable elements might also have emerging roles in cellular plasticity. In this concise review, we provide an overview of the impact of currently active transposable elements in our pluripotent genome and further discuss new roles of transposable elements (active or not) in regulating pluripotency. This article is part of a Special Issue entitled: Stress as a fundamental theme in cell plasticity.


Assuntos
Desdiferenciação Celular/genética , Células-Tronco Pluripotentes/fisiologia , Retroelementos/fisiologia , Animais , Epigênese Genética/fisiologia , Evolução Molecular , Genoma Humano , Humanos
13.
Nature ; 466(7307): 769-73, 2010 Aug 05.
Artigo em Inglês | MEDLINE | ID: mdl-20686575

RESUMO

Long interspersed element-1 (LINE-1 or L1) retrotransposition continues to affect human genome evolution. L1s can retrotranspose in the germline, during early development and in select somatic cells; however, the host response to L1 retrotransposition remains largely unexplored. Here we show that reporter genes introduced into the genome of various human embryonic carcinoma-derived cell lines (ECs) by L1 retrotransposition are rapidly and efficiently silenced either during or immediately after their integration. Treating ECs with histone deacetylase inhibitors rapidly reverses this silencing, and chromatin immunoprecipitation experiments revealed that reactivation of the reporter gene was correlated with changes in chromatin status at the L1 integration site. Under our assay conditions, rapid silencing was also observed when reporter genes were delivered into ECs by mouse L1s and a zebrafish LINE-2 element, but not when similar reporter genes were delivered into ECs by Moloney murine leukaemia virus or human immunodeficiency virus, suggesting that these integration events are silenced by distinct mechanisms. Finally, we demonstrate that subjecting ECs to culture conditions that promote differentiation attenuates the silencing of reporter genes delivered by L1 retrotransposition, but that differentiation, in itself, is not sufficient to reactivate previously silenced reporter genes. Thus, our data indicate that ECs differ from many differentiated cells in their ability to silence reporter genes delivered by L1 retrotransposition.


Assuntos
Células-Tronco de Carcinoma Embrionário/metabolismo , Epigênese Genética/genética , Inativação Gênica , Retroelementos/genética , Animais , Diferenciação Celular/genética , Diferenciação Celular/fisiologia , Linhagem Celular Tumoral , Cromatina/efeitos dos fármacos , Cromatina/genética , Cromatina/metabolismo , Imunoprecipitação da Cromatina , Células-Tronco de Carcinoma Embrionário/patologia , Epigênese Genética/efeitos dos fármacos , Feminino , Regulação Neoplásica da Expressão Gênica/efeitos dos fármacos , Inativação Gênica/efeitos dos fármacos , Genes Reporter/genética , Engenharia Genética , Vetores Genéticos/genética , Genoma Humano/genética , HIV/genética , Inibidores de Histona Desacetilases/farmacologia , Humanos , Elementos Nucleotídeos Longos e Dispersos/genética , Masculino , Camundongos , Modelos Genéticos , Vírus da Leucemia Murina de Moloney/genética , Peixe-Zebra/genética
14.
Nature ; 460(7259): 1127-31, 2009 Aug 27.
Artigo em Inglês | MEDLINE | ID: mdl-19657334

RESUMO

Long interspersed element 1 (LINE-1 or L1) retrotransposons have markedly affected the human genome. L1s must retrotranspose in the germ line or during early development to ensure their evolutionary success, yet the extent to which this process affects somatic cells is poorly understood. We previously demonstrated that engineered human L1s can retrotranspose in adult rat hippocampus progenitor cells in vitro and in the mouse brain in vivo. Here we demonstrate that neural progenitor cells isolated from human fetal brain and derived from human embryonic stem cells support the retrotransposition of engineered human L1s in vitro. Furthermore, we developed a quantitative multiplex polymerase chain reaction that detected an increase in the copy number of endogenous L1s in the hippocampus, and in several regions of adult human brains, when compared to the copy number of endogenous L1s in heart or liver genomic DNAs from the same donor. These data suggest that de novo L1 retrotransposition events may occur in the human brain and, in principle, have the potential to contribute to individual somatic mosaicism.


Assuntos
Células-Tronco Embrionárias/citologia , Células-Tronco Embrionárias/metabolismo , Neurônios/citologia , Neurônios/metabolismo , Retroelementos/genética , Regiões 5' não Traduzidas/genética , Encéfalo/citologia , Linhagem Celular , Imunoprecipitação da Cromatina , Metilação de DNA , Feto/citologia , Dosagem de Genes , Humanos , Reação em Cadeia da Polimerase
15.
Epigenetics Chromatin ; 16(1): 39, 2023 10 16.
Artigo em Inglês | MEDLINE | ID: mdl-37845773

RESUMO

BACKGROUND: Vitamin C (vitC) enhances the activity of 2-oxoglutarate-dependent dioxygenases, including TET enzymes, which catalyse DNA demethylation, and Jumonji-domain histone demethylases. The epigenetic remodelling promoted by vitC improves the efficiency of induced pluripotent stem cell derivation, and is required to attain a ground-state of pluripotency in embryonic stem cells (ESCs) that closely mimics the inner cell mass of the early blastocyst. However, genome-wide DNA and histone demethylation can lead to upregulation of transposable elements (TEs), and it is not known how vitC addition in culture media affects TE expression in pluripotent stem cells. RESULTS: Here we show that vitC increases the expression of several TE families, including evolutionarily young LINE-1 (L1) elements, in mouse ESCs. We find that TET activity is dispensable for L1 upregulation, and that instead it occurs largely as a result of H3K9me3 loss mediated by KDM4A/C histone demethylases. Despite increased L1 levels, we did not detect increased somatic insertion rates in vitC-treated cells. Notably, treatment of human ESCs with vitC also increases L1 protein levels, albeit through a distinct, post-transcriptional mechanism. CONCLUSION: VitC directly modulates the expression of mouse L1s and other TEs through epigenetic mechanisms, with potential for downstream effects related to the multiple emerging roles of L1s in cellular function.


Assuntos
Ácido Ascórbico , Células-Tronco Embrionárias Murinas , Humanos , Animais , Camundongos , Ácido Ascórbico/farmacologia , Células-Tronco Embrionárias Murinas/metabolismo , Elementos Nucleotídeos Longos e Dispersos , Metilação de DNA , Histona Desmetilases/metabolismo , DNA/metabolismo , Desmetilação , Histona Desmetilases com o Domínio Jumonji/genética , Histona Desmetilases com o Domínio Jumonji/metabolismo
16.
Methods Mol Biol ; 2607: 257-309, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-36449167

RESUMO

The ongoing mobilization of active non-long terminal repeat (LTR) retrotransposons continues to impact the genomes of most mammals, including humans and rodents. Non-LTR retrotransposons mobilize using an intermediary RNA and a copy-and-paste mechanism termed retrotransposition. Non-LTR retrotransposons are subdivided into long and short interspersed elements (LINEs and SINEs, respectively), depending on their size and autonomy; while active class 1 LINEs (LINE-1s or L1s) encode the enzymatic machinery required to mobilize in cis, active SINEs use the enzymatic machinery of active LINE-1s to mobilize in trans. The mobilization mechanism used by LINE-1s/SINEs was exploited to develop ingenious plasmid-based retrotransposition assays in cultured cells, which typically exploit a reporter gene that can only be activated after a round of retrotransposition. Retrotransposition assays, in cis or in trans, are instrumental tools to study the biology of mammalian LINE-1s and SINEs. In fact, these and other biochemical/genetic assays were used to uncover that endogenous mammalian LINE-1s/SINEs naturally retrotranspose during early embryonic development. However, embryonic stem cells (ESCs) are typically used as a cellular model in these and other studies interrogating LINE-1/SINE expression/regulation during early embryogenesis. Thus, human and mouse ESCs represent an excellent model to understand how active retrotransposons are regulated and how their activity impacts the germline. Here, we describe robust and quantitative protocols to study human/mouse LINE-1 (in cis) and SINE (in trans) retrotransposition using (human and mice) ESCs. These protocols are designed to study the mobilization of active non-LTR retrotransposons in a cellular physiologically relevant context.


Assuntos
Elementos Nucleotídeos Longos e Dispersos , Retroelementos , Feminino , Gravidez , Humanos , Camundongos , Animais , Retroelementos/genética , Elementos Nucleotídeos Longos e Dispersos/genética , Células-Tronco Embrionárias , Elementos Nucleotídeos Curtos e Dispersos , Bioensaio , Mamíferos
17.
Stem Cells ; 29(2): 251-62, 2011 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-21732483

RESUMO

Human ESCs provide access to the earliest stages of human development and may serve as an unlimited source of functional cells for future cell therapies. The optimization of methods directing the differentiation of human embryonic stem cells (hESCs) into tissue-specific precursors becomes crucial. We report an efficient enrichment of mesenchymal stem cells (MSCs) from hESCs through specific inhibition of SMAD-2/3 signaling. Human ESC-derived MSCs (hESC-MSCs) emerged as a population of fibroblastoid cells expressing a MSC phenotype: CD73+ CD90+ CD105+ CD44+ CD166+ CD45- CD34- CD14- CD19- human leucocyte antigen-DR (HLA-DR)-. After 28 days of SMAD-2/3 inhibition, hESC cultures were enriched (>42%) in multipotent MSCs. CD73+CD90+ hESC-MSCs were fluorescence activated cell sorting (FACS)-isolated and long-term cultures were established and maintained for many passages displaying a faster growth than somatic tissue-derived MSCs while maintaining MSC morphology and phenotype. They displayed osteogenic, adipogenic, and chondrocytic differentiation potential and exhibited potent immunosuppressive and anti-inflammatory properties in vitro and in vivo, where hESC-MSCs were capable of protecting against an experimental model of inflammatory bowel disease. Interestingly, the efficient enrichment of hESCs into MSCs through inhibition of SMAD-2/3 signaling was not reproducible with distinct induced pluripotent stem cell lines. Our findings provide mechanistic insights into the differentiation of hESCs into immunosuppressive and anti-inflammatory multipotent MSCs with potential future clinical applications.


Assuntos
Células-Tronco Embrionárias/imunologia , Células-Tronco Embrionárias/metabolismo , Doenças Inflamatórias Intestinais/prevenção & controle , Células-Tronco Multipotentes/imunologia , Células-Tronco Multipotentes/metabolismo , Proteína Smad2/antagonistas & inibidores , Proteína Smad3/antagonistas & inibidores , Antígenos CD , Benzamidas/farmacologia , Diferenciação Celular/fisiologia , Linhagem Celular , Terapia Baseada em Transplante de Células e Tecidos , Dioxóis/farmacologia , Células-Tronco Embrionárias/citologia , Citometria de Fluxo , Humanos , Terapia de Imunossupressão , Doenças Inflamatórias Intestinais/imunologia , Células-Tronco Mesenquimais/citologia , Células-Tronco Mesenquimais/imunologia , Células-Tronco Mesenquimais/metabolismo , Células-Tronco Multipotentes/citologia , Transdução de Sinais
18.
Am J Med Genet A ; 158A(4): 839-49, 2012 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-22407726

RESUMO

Two hereditary syndromes, lymphedema-distichiasis (LD) syndrome and blepharo-chelio-dontic (BCD) syndrome include the aberrant growth of eyelashes from the meibomian glands, known as distichiasis. LD is an autosomal dominant syndrome primarily characterized by distichiasis and the onset of lymphedema usually during puberty. Mutations in the forkhead transcription factor FOXC2 are the only known cause of LD. BCD syndrome consists of autosomal dominant abnormalities of the eyelid, lip, and teeth, and the etiology remains unknown. In this report, we describe a proband that presented with distichiasis, microcephaly, bilateral grade IV vesicoureteral reflux requiring ureteral re-implantation, mild intellectual impairment and apparent glomuvenous malformations (GVM). Distichiasis was present in three generations of the proband's maternal side of the family. The GVMs were severe in the proband, and maternal family members exhibited lower extremity varicosities of variable degree. A GLMN (glomulin) gene mutation was identified in the proband that accounts for the observed GVMs; no other family member could be tested. TIE2 sequencing revealed no mutations. In the proband, an additional submicroscopic 265 kb contiguous gene deletion was identified in 16q24.3, located 609 kb distal to the FOXC2 locus, which was inherited from the proband's mother. The deletion includes the C16ORF95, FBXO31, MAP1LC3B, and ZCCHC14 loci and 115 kb of a gene desert distal to FOXC2 and FOXL1. Thus, it is likely that the microcephaly, distichiasis, vesicoureteral, and intellectual impairment in this family may be caused by the deletion of one or more of these genes and/or deletion of distant cis-regulatory elements of FOXC2 expression.


Assuntos
Proteínas Adaptadoras de Transdução de Sinal/genética , Cromossomos Humanos Par 16/genética , Linfedema/genética , Criança , Mapeamento Cromossômico , Variações do Número de Cópias de DNA , Pestanas/anormalidades , Feminino , Fatores de Transcrição Forkhead/genética , Deleção de Genes , Genótipo , Tumor Glômico/genética , Humanos , Deficiência Intelectual/genética , Imageamento por Ressonância Magnética , Microcefalia/genética , Paraganglioma Extrassuprarrenal/genética , Receptor TIE-2/genética , Refluxo Vesicoureteral/genética
19.
Gene ; 843: 146799, 2022 Nov 15.
Artigo em Inglês | MEDLINE | ID: mdl-35963498

RESUMO

The genetics of an individual is a crucial factor in understanding the risk of developing the neurodegenerative disease amyotrophic lateral sclerosis (ALS). There is still a large proportion of the heritability of ALS, particularly in sporadic cases, to be understood. Among others, active transposable elements drive inter-individual variability, and in humans long interspersed element 1 (LINE1, L1), Alu and SINE-VNTR-Alu (SVA) retrotransposons are a source of polymorphic insertions in the population. We undertook a pilot study to characterise the landscape of non-reference retrotransposon insertion polymorphisms (non-ref RIPs) in 15 control and 15 ALS individuals' whole genomes from Project MinE, an international project to identify potential genetic causes of ALS. The combination of two bioinformatics tools (mobile element locator tool (MELT) and TEBreak) identified on average 1250 Alu, 232 L1 and 77 SVA non-ref RIPs per genome across the 30 analysed. Further PCR validation of individual polymorphic retrotransposon insertions showed a similar level of accuracy for MELT and TEBreak. Our preliminary study did not identify a specific RIP or a significant difference in the total number of non-ref RIPs in ALS compared to control genomes. The use of multiple bioinformatic tools improved the accuracy of non-ref RIP detection and our study highlights the potential importance of studying these elements further in ALS.


Assuntos
Esclerose Lateral Amiotrófica , Doenças Neurodegenerativas , Esclerose Lateral Amiotrófica/genética , Humanos , Elementos Nucleotídeos Longos e Dispersos/genética , Doenças Neurodegenerativas/genética , Projetos Piloto , Retroelementos/genética , Sequenciamento Completo do Genoma
20.
Commun Biol ; 4(1): 691, 2021 06 07.
Artigo em Inglês | MEDLINE | ID: mdl-34099857

RESUMO

Chromatin of male and female gametes undergoes a number of reprogramming events during the transition from germ cell to embryonic developmental programs. Although the rearrangement of DNA methylation patterns occurring in the zygote has been extensively characterized, little is known about the dynamics of DNA modifications during spermatid maturation. Here, we demonstrate that the dynamics of 5-carboxylcytosine (5caC) correlate with active transcription of LINE-1 retroelements during murine spermiogenesis. We show that the open reading frames of active and evolutionary young LINE-1s are 5caC-enriched in round spermatids and 5caC is eliminated from LINE-1s and spermiogenesis-specific genes during spermatid maturation, being simultaneously retained at promoters and introns of developmental genes. Our results reveal an association of 5caC with activity of LINE-1 retrotransposons suggesting a potential direct role for this DNA modification in fine regulation of their transcription.


Assuntos
Citosina/análogos & derivados , Elementos Nucleotídeos Longos e Dispersos , Fases de Leitura Aberta , Espermátides/metabolismo , Animais , Citosina/metabolismo , Masculino , Camundongos , Espermátides/citologia , Espermatogênese , Transcrição Gênica
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