Ontology highlight
ABSTRACT:
PROVIDER: PRJNA525338 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Genome sequencing of desiccating bdelloid rotifers
| PRJEB30117 | ENA
Project description:Population genomics of bdelloid rotifers
| PRJEB30091 | ENA
Project description:Bdelloid rotifers are part of the restricted circle of multicellular animals that can withstand a wide range of genotoxic stresses at any stage of their life cycle. In this study, bdelloid rotifer Adineta vaga was used as a model to decipher the molecular basis of their extreme tolerance. Proteomic analysis showed that a specific DNA ligase, different from those usually involved in DNA repair in eukaryotes, is strongly over-represented upon ionizing radiation. A phylogenetic analysis revealed its orthology to prokaryotic DNA ligase E, and its horizontal acquisition by bdelloid rotifers and plausibly other eukaryotes. The fungus Mortierella verticillata, having a single copy of this DNA Ligase E homolog, also exhibits an increased radiation tolerance with an over-expression of this DNA ligase E following X-ray exposure. We also provide evidence that A. vaga ligase E is a major contributor of DNA breaks ligation activity, which is a common step of all important DNA repair pathways. Consistently, its heterologous expression in human cell lines significantly improved their radio-tolerance. Overall, this study highlights the potential of horizontal gene transfers in eukaryotes, and their contribution to the adaptation to extreme conditions.
2024-01-24 | PXD043051 | Pride
Project description:Evolutionary dynamics of transposable elements in bdelloid rotifers
| PRJEB39843 | ENA
Project description:Methylation of cytosines at the 5th carbon position of the aromatic ring has long been regarded as the predominant type of DNA base modification in eukaryotes. Often called “the fifth base”, C5-methylcytosine (5mC) plays an important role in genome defense against mobile genetic elements, and is mostly associated with transcriptional silencing, establishment of the closed chromatin configuration, and repressive histone modifications. Recently, another type of DNA modification, N6-methyladenine (6mA), has been added to the repertoire of modified bases in eukaryotic DNA, and was mostly linked to elevated transcription levels. In prokaryotes, 5mC and 6mA typically constitute components of restriction-modification (R-M) systems, along with N4-methylcytosine (4mC), which so far has been confined to bacteria. Here we report the first case of 4mC occurrence in eukaryotic DNA. We find that bdelloid rotifers, small freshwater invertebrates known for their ability to reproduce clonally and to acquire genes from non-metazoan sources, lack the canonical eukaryotic C5-methyltransferases but instead encode an amino-methyltransferase of bacterial origin, N4CMT, which is present in all bdelloid families separated by tens of millions of years of evolution. The recombinant N4CMT introduces 4mC into genomic DNA in vivo and in vitro. Using SMRT-seq (PRJNA558051), MeDIP-seq, ChIP-seq, and RNA-seq, we examined genome-wide distribution of non-canonical base modifications over annotated genomic features and observed an excess of 4mC in silenced transposable elements and certain tandem repeats, while 6mA tends to associate with transcribed genes and active chromatin. The presence of the chromodomain in N4CMT explains its affinity for repressive histone marks, H3K9me3 and especially H3K27me3. Our results expand the known repertoire of eukaryotic base modifications, shed light on the process of recruitment of methyl groups as epigenetic marks in DNA, and highlight the role of horizontal gene transfer as an important driver of evolutionary innovation in eukaryotes.
2022-01-07 | GSE140049 | GEO
Project description:Methylation of cytosines at the 5th carbon position of the aromatic ring has long been regarded as the predominant type of DNA base modification in eukaryotes. Often called “the fifth base”, C5-methylcytosine (5mC) plays an important role in genome defense against mobile genetic elements, and is mostly associated with transcriptional silencing, establishment of the closed chromatin configuration, and repressive histone modifications. Recently, another type of DNA modification, N6-methyladenine (6mA), has been added to the repertoire of modified bases in eukaryotic DNA, and was mostly linked to elevated transcription levels. In prokaryotes, 5mC and 6mA typically constitute components of restriction-modification (R-M) systems, along with N4-methylcytosine (4mC), which so far has been confined to bacteria. Here we report the first case of 4mC occurrence in eukaryotic DNA. We find that bdelloid rotifers, small freshwater invertebrates known for their ability to reproduce clonally and to acquire genes from non-metazoan sources, lack the canonical eukaryotic C5-methyltransferases but instead encode an amino-methyltransferase of bacterial origin, N4CMT, which is present in all bdelloid families separated by tens of millions of years of evolution. The recombinant N4CMT introduces 4mC into genomic DNA in vivo and in vitro. Using SMRT-seq (PRJNA558051), MeDIP-seq, ChIP-seq, and RNA-seq, we examined genome-wide distribution of non-canonical base modifications over annotated genomic features and observed an excess of 4mC in silenced transposable elements and certain tandem repeats, while 6mA tends to associate with transcribed genes and active chromatin. The presence of the chromodomain in N4CMT explains its affinity for repressive histone marks, H3K9me3 and especially H3K27me3. Our results expand the known repertoire of eukaryotic base modifications, shed light on the process of recruitment of methyl groups as epigenetic marks in DNA, and highlight the role of horizontal gene transfer as an important driver of evolutionary innovation in eukaryotes.
2022-01-07 | GSE140051 | GEO
Project description:Methylation of cytosines at the 5th carbon position of the aromatic ring has long been regarded as the predominant type of DNA base modification in eukaryotes. Often called “the fifth base”, C5-methylcytosine (5mC) plays an important role in genome defense against mobile genetic elements, and is mostly associated with transcriptional silencing, establishment of the closed chromatin configuration, and repressive histone modifications. Recently, another type of DNA modification, N6-methyladenine (6mA), has been added to the repertoire of modified bases in eukaryotic DNA, and was mostly linked to elevated transcription levels. In prokaryotes, 5mC and 6mA typically constitute components of restriction-modification (R-M) systems, along with N4-methylcytosine (4mC), which so far has been confined to bacteria. Here we report the first case of 4mC occurrence in eukaryotic DNA. We find that bdelloid rotifers, small freshwater invertebrates known for their ability to reproduce clonally and to acquire genes from non-metazoan sources, lack the canonical eukaryotic C5-methyltransferases but instead encode an amino-methyltransferase of bacterial origin, N4CMT, which is present in all bdelloid families separated by tens of millions of years of evolution. The recombinant N4CMT introduces 4mC into genomic DNA in vivo and in vitro. Using SMRT-seq (PRJNA558051), MeDIP-seq, ChIP-seq, and RNA-seq, we examined genome-wide distribution of non-canonical base modifications over annotated genomic features and observed an excess of 4mC in silenced transposable elements and certain tandem repeats, while 6mA tends to associate with transcribed genes and active chromatin. The presence of the chromodomain in N4CMT explains its affinity for repressive histone marks, H3K9me3 and especially H3K27me3. Our results expand the known repertoire of eukaryotic base modifications, shed light on the process of recruitment of methyl groups as epigenetic marks in DNA, and highlight the role of horizontal gene transfer as an important driver of evolutionary innovation in eukaryotes.
2022-01-07 | GSE140050 | GEO
Project description:Comparative genomics of bdelloid rotifers: evaluating the effects of asexuality and desiccation tolerance on genome evolution
| PRJEB22744 | ENA