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| Status |
Public on May 04, 2023 |
| Title |
Genome-wide characterization of the Caenorhabditis elegans intestine GATA transcription factor ELT-2 |
| Organism |
Caenorhabditis elegans |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
ELT-2 is the major transcription factor required for Caenorhabditis elegans intestinal development. It initiates in embryos to promote development then persists after hatching through larval and adult stages. Though the sites of ELT-2 binding are characterized and the transcriptional changes that result from ELT-2 depletion are described, a major missing piece has been the lack of an intestine-specific transcriptome profile over developmental time. We generated this dataset by Fluorescence Activated Cell Sorting (FACS) intestine cells at distinct developmental stages. We analyzed this dataset in conjunction with previously conducted ELT-2 studies to evaluate ELT-2’s role in directing the intestinal regulatory network through development. We found that only 33% of intestine-enriched genes in the embryo were direct targets of ELT-2 but that number increased to 75% by the L3 stage. This suggests additional transcription factors promote intestinal transcription especially in the embryo. Furthermore, only half of ELT-2’s direct target genes were dependent on ELT-2 for their proper expression levels, and an equal proportion of those responded to elt-2 depletion with over-expression as with under-expression. That is, ELT-2 can either activate or repress direct target genes. Indeed, we observed that ELT-2 repressed its own promoter, implicating new models for its autoregulation. Together, our results illustrate that ELT-2 impacts roughly 20 – 50% of intestine-specific genes, that ELT-2 both positively and negatively controls its direct targets, and that our current model of the intestinal regulatory network is incomplete as the factors responsible for directing the expression of many intestinal genes remain unknown.
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| Overall design |
mRNA-seq transcriptome profilng performed on FACS sorted C. elegans cells at three developmental stages: mixed embryo, L1 larval stage, and L3 larval stage. FACS enrichme elt-2promoter::GFP marker strain; GFP minus FACS sorted cells and the sum of GFP+ and GFP- cells are included as controls; un-sorted, dissociated cells are included as controls
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| Contributor(s) |
Williams RT, King DC, Mastroianni IR, Hill JL, Apenas NW, Ramirez G, Miner E, Moore A, Coleman K, Nishimura EO |
| Citation missing |
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| Submission date |
Sep 30, 2022 |
| Last update date |
May 07, 2023 |
| Contact name |
Erin Osborne Nishimura |
| E-mail(s) |
erinnish@colostate.edu
|
| Organization name |
Colorado State University
|
| Department |
Biochemistry and Molecular Biology
|
| Street address |
1870 Campus Delivery, 200 W. Lake St.
|
| City |
Fort Collins |
| State/province |
CO |
| ZIP/Postal code |
80523 |
| Country |
USA |
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| Platforms (2) |
| GPL25147 |
HiSeq X Ten (Caenorhabditis elegans) |
| GPL26672 |
Illumina NovaSeq 6000 (Caenorhabditis elegans) |
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| Samples (34)
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| Relations |
| BioProject |
PRJNA885900 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE214581_L1_dissociated_cells_merged.bw |
108.0 Mb |
(ftp)(http) |
BW |
| GSE214581_L1_intestine_cells_merged.bw |
104.6 Mb |
(ftp)(http) |
BW |
| GSE214581_L1_non-intestine_cells_merged.bw |
98.8 Mb |
(ftp)(http) |
BW |
| GSE214581_L1_whole_merged.bw |
138.3 Mb |
(ftp)(http) |
BW |
| GSE214581_L3_dissociated_cells_merged.bw |
134.2 Mb |
(ftp)(http) |
BW |
| GSE214581_L3_intestine_cells_merged.bw |
112.4 Mb |
(ftp)(http) |
BW |
| GSE214581_L3_non-intestine_cells_merged.bw |
122.8 Mb |
(ftp)(http) |
BW |
| GSE214581_L3_whole_merged.bw |
133.7 Mb |
(ftp)(http) |
BW |
| GSE214581_RAW.tar |
2.1 Gb |
(http)(custom) |
TAR (of BW) |
| GSE214581_c_elegans.PRJNA13758.WS263.canonical_geneset.gtf.gz |
2.6 Mb |
(ftp)(http) |
GTF |
| GSE214581_embryo_dissociated_cells_merged.bw |
130.2 Mb |
(ftp)(http) |
BW |
| GSE214581_embryo_intestine_cells_merged.bw |
2.7 Mb |
(ftp)(http) |
BW |
| GSE214581_embryo_non-intestine_cells_merged.bw |
152.5 Mb |
(ftp)(http) |
BW |
| GSE214581_embryo_whole_merged.bw |
3.8 Mb |
(ftp)(http) |
BW |
| GSE214581_intestine_FACS_RNAseq_norm_counts.txt.gz |
3.1 Mb |
(ftp)(http) |
TXT |
| GSE214581_intestine_FACS_RNAseq_raw_counts.txt.gz |
794.4 Kb |
(ftp)(http) |
TXT |
| GSE214581_intestine_FACS_RNAseq_rlog_counts.txt.gz |
3.9 Mb |
(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 |
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