Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A vitamin C-derived DNA modification catalyzed by a TET homolog in green alga [RNA-seq]

ABSTRACT: A vitamin C-derived DNA modification catalyzed by a TET homolog in green alga [RNA-seq]

PROVIDER: PRJNA506067 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR8208083_1.fastq.gz	Fastqsanger.gz
	SRR8208083_2.fastq.gz	Fastqsanger.gz
	SRR8208084_1.fastq.gz	Fastqsanger.gz
	SRR8208084_2.fastq.gz	Fastqsanger.gz
	SRR8208085_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 12

Similar Datasets

A vitamin C-derived DNA modification catalyzed by a TET homolog in green alga [Bisulfite-seq]

Project description:A vitamin C-derived DNA modification catalyzed by a TET homolog in green alga [Bisulfite-seq]

| PRJNA506066 | ENA

A vitamin C-derived DNA modification catalyzed by a TET homolog in green alga [Bisulfite-seq]

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

A vitamin C-derived DNA modification catalyzed by a TET homolog in green alga [RNA-seq]

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

TET-catalyzed 5-carboxylcytosine promotes CTCF binding to suboptimal sequences genome-wide

Project description:TET-catalyzed 5-carboxylcytosine promotes CTCF binding to suboptimal sequences genome-wide

| PRJNA507546 | ENA

TET-catalyzed 5-carboxylcytosine promotes CTCF binding to suboptimal sequences genome-wide

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

Proteome analysis of newly identified green alga M. hakoo

Project description:Proteome analysis of total proteins extracted from green alga M. hakoo using LC-MS/MS. The proteome of A. thaliana was also analyzed for comparison.

2022-12-07 | PXD033813 | JPOST Repository

Glucose regulation of oxygenic photosynthesis in green alga C zofingiensis

Project description:Lipid profiling was performed on green alga C. zofingiensis grown with and without glucose in the presence of light. Published in, The Plant Cell, Volume 31, Issue 3, March 2019, Pages 579 to 601, https://doi.org/10.1105/tpc.18.00742

| MSV000090308 | MassIVE

Unicellular green alga

Project description:Comparative genomic analysis of a photosymbiont evolution

| PRJNA832740 | ENA

The Transcriptome of Photo-Biological Hydrogen Production in the Green Alga Chlamydomonas reinhardtii

Project description:Algal photo-bio hydrogen production, a promising method for producing clean and renewable fuel in the form of hydrogen gas, has been studied extensively over the last few decades. In this study, microarray analyses were used to obtain a global expression profile of mRNA abundance in the green alga Chlamydomonas reinhardtii at five different time points before the onset and during the course of sulphur depleted hydrogen production. The present work confirms previous findings on the impacts of sulphur deprivation but also provides new insights into photosynthesis, sulphur assimilation and carbon metabolism under sulphur starvation towards hydrogen production. For instance, while a general trend towards repression of transcripts encoding photosynthetic genes was observed, the abundance of Lhcbm9 (encoding a major light harvesting polypeptide) and LhcSR1 (encoding a chlorophyll binding protein) was strongly elevated throughout the experiment, suggesting remodeling of the photosystem II light harvesting complex as well as an important function of Lhcbm9 under sulphur starvation. This study presents the first global transcriptional analysis of C. reinhardtii during hydrogen production using five major time points at Peak Oxygen, Mid Oxygen, Zero Oxygen, Mid Hydrogen and Peak Hydrogen. Keywords: Time course, sulfur deprivation, hydrogen production.

2008-10-28 | GSE9165 | GEO

Tet-Gabpα cKO ES cells: -Tet vs. +Tet

Project description:We generated tetracycline-inducible myc-GABPα-expressing Gabpα conditional knockout embryonic stem cells (Tet-Gabbpα cKO ES cells), and then compared the transcriptional profiles between control (-Tet) and Gabpα-null (+Tet) cells by an oligo DNA microarray analysis.

2017-07-01 | GSE82231 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data