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| Status |
Public on Sep 13, 2016 |
| Title |
ChIP-seq analysis of the C. elegans CEBP-1 protein |
| Organism |
Caenorhabditis elegans |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
Purpose: The goal of this study is to identify genes selectively associated with C. elegans CEBP-1.
Methods: We generated transgenic animals expressing FLAG-tagged CEBP-1 in a cebp-1(tm2807) mutant background (cebp-1(0); juIs418 [Pcebp-1::FLAG::CEBP-1::cebp-1 3’UTR]) and then immunoprecipitated FLAG-CEBP-1-associated DNA fragments using anti-FLAG antibodies (M2 anti-FLAG magnetic beads; Sigma). We collected mixed stage worms grown at 20˚C on NGM plates followed by 2% formaldehyde and sonicated the samples as described (Mukhopadhyay et al., 2008). We next generated ChIP-seq DNA libraries. Briefly, both ChIPed DNA and input genomic DNA were ligated to specific adaptors and amplified by barcode primers followed by sequencing on the Illumina HiSeq-2000 platform. We performed two independent ChIP-seq experiments, with parallel genomic DNA controls prepared from the same strain. We conducted peak-calling using CLC genomics workbench 6.0 (CLCbio). To define genes associated with the peaks, we used the annotation of transcription start site (TSS) and transcription end site (TES) from WS220 and annotated the peak if it overlapped the gene or the 3 kb upstream of the TSS. We then manually confirmed the peaks and associated genes using UCSC browser and update to WS252.
Results: We found 209 CEBP-1 ChIP-seq peaks in the genome that were associated with 212 coding genes. Through motif discovery tools, we also found that CEBP-1 binds conserved DNA motifs.
Conclusions: The conservation of C.elegans CEBP-1 binding motif supports functional parallels between C. elegans CEBP-1 and vertebrate C/EBPs.
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| Overall design |
CEBP-1 ChIP and input sample
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| Contributor(s) |
Kim K, Jin Y |
| Citation(s) |
27927209 |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| R01 NS035546 |
GABAergic Neuron Differentiation in C. elegans: GABAERGIC NEURON DIFFERENTIATION IN C ELEGANS: GABAergic Neuron Differentiation in C. elegans: GABAergic Neuron Differentiation in C. elegans: GABAergic Neuron Differentiation in C. elegans: GABAergic Neuron Differentiation in C. elegans: GABAERGIC NEURON DIFFERENTIATION IN C ELEGANS: GABAERGIC NEURON DIFFERENTIATION IN C ELEGANS: GABAERGIC NEURON DIFFERENTIATION IN C ELEGANS: GABAERGIC NEURON DIFFERENTIATION IN C ELEGANS |
THE REGENTS OF THE UNIV. OF CALIF., UNIV. OF CALIF., SAN DIEGO |
Jin |
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| Submission date |
Jun 14, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Kyung Won Kim |
| E-mail(s) |
kwkim3@gmail.com
|
| Organization name |
University of California, San Deigo
|
| Department |
Section of Neurobiology, Division of Biological Sciences
|
| Lab |
Yishi Jin lab
|
| Street address |
9500 Gilman Drive
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
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| Platforms (1) |
| GPL13657 |
Illumina HiSeq 2000 (Caenorhabditis elegans) |
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| Samples (2) |
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| Relations |
| BioProject |
PRJNA325627 |
| SRA |
SRP076537 |
