TET-catalyzed 5-carboxylcytosine promotes CTCF binding to suboptimal sequences genome-wide
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA507546 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8260200.fastq.gz | Fastqsanger.gz | |||
| SRR8260210_1.fastq.gz | Fastqsanger.gz | |||
| SRR8260210_2.fastq.gz | Fastqsanger.gz | |||
| SRR8260201.fastq.gz | Fastqsanger.gz | |||
| SRR8260211_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 24 |
Similar Datasets
Project description:The mechanisms supporting dynamic regulation of CTCF binding sites remain poorly understood. Here we describe the TET-catalyzed 5-methylcytosine derivative, 5-carboxylcytosine (5caC) as a factor driving new CTCF binding within genomic DNA. Through a combination of in vivo and in vitro approaches, we reveal that 5caC generally strengthens CTCF association with DNA and facilitates binding to suboptimal sequences. Dramatically, profiling of CTCF binding in a cellular model that accumulates genomic 5caC identified ∼13,000 new CTCF sites. The new sites were enriched for overlapping 5caC and were marked by an overall reduction in CTCF motif strength. As CTCF has multiple roles in gene expression, these findings have wide-reaching implications and point to induced 5caC as a potential mechanism to achieve differential CTCF binding in cells.
2019-08-08 | GSE123101 | GEO
Project description:The mechanisms supporting dynamic regulation of CTCF-binding sites remain poorly understood. Here we describe the TET-catalyzed 5-methylcytosine derivative, 5-carboxylcytosine (5caC), as a factor driving new CTCF binding within genomic DNA. Through a combination of in vivo and in vitro approaches, we reveal that 5caC generally strengthens CTCF association with DNA and facilitates binding to suboptimal sequences. Dramatically, profiling of CTCF binding in a cellular model that accumulates genomic 5caC identified ~13,000 new CTCF sites. The new sites were enriched for overlapping 5caC and were marked by an overall reduction in CTCF motif strength. As CTCF has multiple roles in gene expression, these findings have wide-reaching implications and point to induced 5caC as a potential mechanism to achieve differential CTCF binding in cells.
| S-EPMC6699469 | biostudies-literature
Project description:DNA methylation at 5-position of cytosine (5mC) is one of the best studied epigenetic modifications that plays important roles in diverse biological processes. Iterative oxidation of 5mC by the Ten-eleven translocation (Tet) family of proteins generates 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC), which can be further processed by DNA repair proteins leading to DNA demethylation. Functional characterization of the Tet proteins has been complicated by the redundancy between the three Tet proteins. Using the CRISPR/Cas9 technology, we have generated mouse embryonic stem cells (ESCs) deficient for all three Tet proteins (TKO). Whole genome bisulphite sequencing (WGBS) analysis revealed that Tet-mediated DNA demethylation mainly occurs distal enhancers as well as promoters that significantly overlap with 5hmC, 5fC and 5caC. Characterization of the Tet TKO ESCs revealed a function for Tet proteins in cell fate restriction as Tet TKO ESCs tend to adopt both primed pluripotent stem cell-like state and 2-cell embryo-like state. In addition, Tet TKO ESCs exhibit elongated telomeres. Thus, our study reveals a role of Tet proteins not only in DNA demethylation, but also in cell fate restriction and telomere maintenance. 2 samples for WGBS and 2 samples for RNA-seq
2014-09-22 | E-GEOD-56986 | biostudies-arrayexpress
Project description:Intragenic 5-methylcytosine and CTCF mediate opposing effects on pre-mRNA splicing: CTCF promotes inclusion of weak upstream exons through RNA polymerase II pausing, whereas 5-methylcytosine evicts CTCF, leading to exon exclusion. However, the mechanisms governing dynamic DNA methylation at CTCF-binding sites were unclear. Here, we reveal the methylcytosine dioxygenases TET1 and TET2 as active regulators of CTCF-mediated alternative splicing through conversion of 5-methylcytosine to its oxidation derivatives. 5-hydroxymethylcytosine and 5-carboxylcytosine are enriched at an intragenic CTCF-binding sites in the CD45 model gene and are associated with alternative exon inclusion. Reduced TET levels culminate in increased 5-methylcytosine, resulting in CTCF eviction and exon exclusion. In vitro analyses establish the oxidation derivatives are not sufficient to stimulate splicing, but efficiently promote CTCF association. We further show genomewide that reciprocal exchange of 5-hydroxymethylcytosine and 5-methylcytosine at downstream CTCF-binding sites is a general feature of alternative splicing in naïve and activated CD4(+) T cells. These findings significantly expand our current concept of the pre-mRNA "splicing code" to include dynamic intragenic DNA methylation catalyzed by the TET proteins.
| S-EPMC4741300 | biostudies-literature
Project description:DNA methylation at 5-position of cytosine (5mC) is one of the best studied epigenetic modifications that plays important roles in diverse biological processes. Iterative oxidation of 5mC by the Ten-eleven translocation (Tet) family of proteins generates 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC), which can be further processed by DNA repair proteins leading to DNA demethylation. Functional characterization of the Tet proteins has been complicated by the redundancy between the three Tet proteins. Using the CRISPR/Cas9 technology, we have generated mouse embryonic stem cells (ESCs) deficient for all three Tet proteins (TKO). Whole genome bisulphite sequencing (WGBS) analysis revealed that Tet-mediated DNA demethylation mainly occurs distal enhancers as well as promoters that significantly overlap with 5hmC, 5fC and 5caC. Characterization of the Tet TKO ESCs revealed a function for Tet proteins in cell fate restriction as Tet TKO ESCs tend to adopt both primed pluripotent stem cell-like state and 2-cell embryo-like state. In addition, Tet TKO ESCs exhibit elongated telomeres. Thus, our study reveals a role of Tet proteins not only in DNA demethylation, but also in cell fate restriction and telomere maintenance.
2014-09-22 | GSE56986 | GEO
Project description:A vitamin C-derived DNA modification catalyzed by a TET homolog in green alga [Bisulfite-seq]
| PRJNA506066 | ENA
Project description:A vitamin C-derived DNA modification catalyzed by a TET homolog in green alga [RNA-seq]
| PRJNA506067 | ENA
Project description:TET family enzymes successively oxidize 5-methylcytosine to 5-hydroxymethylcytosine, 5-formylcytosine and 5-carboxylcytosine, leading to eventual demethylation. 5hmC and TET enzymes occupy distinct chromatin regions, suggesting unknown mechanisms controlling the fate of 5hmC within diverse chromatin environments. Here, we report that SALL4A preferentially associates with 5hmC in vitro and occupies enhancers in mouse embryonic stem cells in a largely TET1-dependent manner. While most 5hmC at SALL4A peaks undergoes further oxidation, this process is abrogated upon deletion of Sall4 gene, with a concomitant reduction of TET2 at these regions. Thus, SALL4A facilitates further oxidation of 5hmC at its binding sites, which requires its 5hmC binding activity and TET2, supporting a collaborative action between SALL4A and TET proteins in regulating stepwise oxidation of 5mC at enhancers. Our study identifies SALL4A as a 5hmC binder, which facilitates 5hmC oxidation by stabilizing TET2 association, thereby fine-tuning expression profiles of developmental genes in mouse embryonic stem cells.
2016-10-07 | GSE57700 | GEO
Project description:Methylation of cytosine to 5-methylcytosine (5mC) is a prevalent DNA modification found in many organisms. Sequential oxidation of 5mC by TET dioxygenases results in a cascade of additional epigenetic marks and promotes DNA demethylation in mammals. However, the enzymatic activity and the function of TET homologs present in lower eukaryotes remains largely unexplored. In our study of TET homologs in the green alga Chlamydomonas reinhardtii (C. reinhardtii), we have found a 5mC-modifying enzyme (CMD1) that catalyzes conjugation of a glyceryl moiety onto the methyl group of 5mC through a carbon-carbon bond, resulting in two novel stereoisomeric nucleotide products. The catalytic activity of CMD1 requires Fe(II) and the integrity of its His-x-Asp (HxD) binding motif, which is conserved in Fe-dependent oxygenases. However, unlike all previous described TET enzymes which utilize 2-oxoglutarate (2-OG) as a co-substrate, CMD1 utilizes L-ascorbic acid (vitamin C, VC) as an essential co-substrate. VC itself is the source of the glyceryl moiety that modifies 5mC, with concurrent formation of glyoxylic acid and CO2. The VC-derived DNA modification is present in the genome of C. reinhardtii and its level decreases significantly in a CMD1 mutant strain. The fitness of CMD1 mutant cells to high light exposure is reduced, mainly due to deficient expression of the critical non-photochemical quenching (NPQ) effector gene LHCSR3, which is hypermethylated in the mutant cells. Our study thus reveals a new eukaryotic DNA base modification, and its involvement in a functionally conserved but mechanistically divergent DNA demethylation pathway for the epigenetic regulation of photosynthesis.
2019-05-04 | GSE122717 | GEO
Project description:Methylation of cytosine to 5-methylcytosine (5mC) is a prevalent DNA modification found in many organisms. Sequential oxidation of 5mC by TET dioxygenases results in a cascade of additional epigenetic marks and promotes DNA demethylation in mammals1,2. However, the enzymatic activity and the function of TET homologs present in lower eukaryotes remains largely unexplored. In our study of TET homologs in the green alga Chlamydomonas reinhardtii (C. reinhardtii), we have found a 5mC-modifying enzyme (CMD1) that catalyzes conjugation of a glyceryl moiety onto the methyl group of 5mC through a carbon-carbon bond, resulting in two novel stereoisomeric nucleotide products. The catalytic activity of CMD1 requires Fe(II) and the integrity of its His-x-Asp (HxD) binding motif, which is conserved in Fe-dependent oxygenases3. However, unlike all previous described TET enzymes which utilize 2-oxoglutarate (2-OG) as a co-substrate4, CMD1 utilizes L-ascorbic acid (vitamin C, VC) as an essential co-substrate. VC itself is the source of the glyceryl moiety that modifies 5mC, with concurrent formation of glyoxylic acid and CO2. The VC-derived DNA modification is present in the genome of C. reinhardtii and its level decreases significantly in a CMD1 mutant strain. The fitness of CMD1 mutant cells to high light exposure is reduced, mainly due to deficient expression of the critical non-photochemical quenching (NPQ) effector gene LHCSR3, which is hypermethylated in the mutant cells. Our study thus reveals a new eukaryotic DNA base modification, and its involvement in a functionally conserved but mechanistically divergent DNA demethylation pathway for the epigenetic regulation of photosynthesis.
2019-05-04 | GSE122718 | GEO