GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE225970 Query DataSets for GSE225970
Status Public on Feb 23, 2024
Title Tet-dependent 5-hydroxymethyl-Cytosine modification of mRNA regulates the axon guidance genes robo2 and slit in Drosophila [ChIP LBF]
Organism Drosophila melanogaster
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Modifications of mRNA, especially methylation of adenosine, have recently drawn much attention. The much rarer modification, 5-hydroxymethylation of cytosine (5hmC), is not well understood and is the subject of this study. Vertebrate Tet proteins are 5-methylcytosine (5mC) hydroxylases enzymes catalyzing the transition of 5mC to 5hmC in DNA and have recently been shown to have the same function in messenger RNAs in both vertebrates and in Drosophila. The Tet gene is essential in Drosophila because Tet knock-out animals do not reach adulthood. We describe the identification of Tet-target genes in the embryo and larval brain by determining Tet DNA-binding sites throughout the genome and by mapping the Tet-dependent 5hmrC modifications transcriptome-wide. 5hmrC-modified sites can be found along the entire transcript and are preferentially located at the promoter where they overlap with histone H3K4me3 peaks. The identified mRNAs are frequently involved in neuron and axon development and Tet knock-out led to a reduction of 5hmrC marks on specific mRNAs. Among the Tet-target genes were the robo2 receptor and its slit ligand that function in axon guidance in Drosophila and in vertebrates. Tet knock-out embryos show overlapping phenotypes with robo2 and are sensitized to reduced levels of slit. Both Robo2 and Slit protein levels were markedly reduced in Tet KO larval brains. Our results establish a role for Tet-dependent 5hmrC in facilitating the translation of modified mRNAs, primarily in developing nerve cells.
Overall design Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for Tet-GFP fusion protein in Drosophila melanogaster 0-12h embryo and third instar larva brain fraction (LBF, larval brain and imaginal discs).
Web link
Contributor(s) Singh BN, Tran HH, Kramer J, Kirishenko E, Changela N, Wang F, Feng Y, Kumar D, Tu M, Lan J, Bizet M, Fuks F, Steward R
Citation(s) 38381741
NIH grant(s)
Grant ID Grant title Affiliation Name
R01 GM120405 RNA processing in Drosophila development RUTGERS, THE STATE UNIVERSITY OF NEW JERSEY Ruth M Steward
Submission date Feb 23, 2023
Last update date Feb 24, 2024
Contact name Ruth Steward
Phone +1-848-445-3918
Organization name Rutgers University
Department Waksman Institute of Microbiology
Street address 190 Frelinghuysen Rd
City Piscataway
State/province New Jersey
ZIP/Postal code 08854
Country USA
Platforms (1)
GPL16479 Illumina MiSeq (Drosophila melanogaster)
Samples (2)
GSM7061119 Tet-GFP, LBF (third instar larva brain fraction)
GSM7061120 w1118 (wild-type), LBF (third instar larva brain fraction)
This SubSeries is part of SuperSeries:
GSE225980 Tet-dependent 5-hydroxymethyl-Cytosine modification of mRNA regulates axon guidance genes in Drosophila
BioProject PRJNA938124

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE225970_RAW.tar 337.6 Mb (http)(custom) TAR (of BW, TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap