 |
 |
GEO help: Mouse over screen elements for information. |
|
| 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 [hMeRIP] |
| Organism |
Drosophila melanogaster |
| Experiment type |
Expression 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 |
To study the function of Tet in mRNA 5-hydroxymethyl-Cytosine modification, we did hMeRIP-seq (5-hydroxymethyl-cytosine RNA Immunoprecipitation sequencing) in Drosophila melanogaster 0-12h embryo and third instar larval brain fraction (LBF, containing larval brain and imaginal discs). The hMeRIP-seq was conducted on both wild type control and Tet deletion genotypes (Tetnull, Delatte et.al., Science, 2016; Wang et.al. PloSONE, 2018) in larva samples. hMeRIP-seq was conducted on only 0-12h wild type embryo samples. RNA-seq was also performed at the same time with the hMeRIP-seq as input controls.
|
| Web link |
https://doi.org/10.1371/journal.pone.0293894
|
| |
|
| Contributor(s) |
Singh BN, Tran H, 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 |
| E-mail(s) |
steward@waksman.rutgers.edu
|
| 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) |
| GPL19806 |
Illumina HiScanSQ (Drosophila melanogaster) |
|
| Samples (10)
|
| GSM7061222 |
hMeRIP, WT, LBF, rep2 |
| GSM7061223 |
Input, WT, LBF, rep1 |
| GSM7061224 |
Input, WT, LBF, rep2 |
| GSM7061225 |
hMeRIP, Tetnull, LBF, rep1 |
| GSM7061226 |
hMeRIP, Tetnull, LBF, rep2 |
| GSM7061227 |
Input, WT, Tetnull, rep1 |
| GSM7061228 |
Input, WT, Tetnull, rep2 |
|
| This SubSeries is part of SuperSeries: |
| GSE225980 |
Tet-dependent 5-hydroxymethyl-Cytosine modification of mRNA regulates axon guidance genes in Drosophila |
|
| Relations |
| BioProject |
PRJNA938138 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE225979_RAW.tar |
38.2 Mb |
(http)(custom) |
TAR (of BW) |
| GSE225979_hMeRIP-seq_0-12hembryo_anno.txt.gz |
52.0 Kb |
(ftp)(http) |
TXT |
| GSE225979_hMeRIP-seq_LBF_Tetnull_anno.txt.gz |
330.4 Kb |
(ftp)(http) |
TXT |
| GSE225979_hMeRIP-seq_LBF_WT_anno.txt.gz |
232.7 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
|
|
|
|
 |
Less...
More...