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| Status |
Public on Sep 01, 2020 |
| Title |
Ancestral function of Inhibitors-of-kappaB regulates Caenorhabditis elegans development (ChIP-Seq) |
| Organism |
Caenorhabditis elegans |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
NF-κB-mediated signaling is maintained silent by the action of IκB proteins, whose canonical role is to sequester NF-κB in the cytoplasm. An alternative chromatin role for IκB members have been shown to affect stemness and cell differentiation but the involvement of NF-κB in this function has not been excluded. NFKI-1 and IKB-1 are IκB homologs in Caenorhabditis elegans, which lacks NF-κB nuclear effectors. nfki-1 and ikb-1 mutants present developmental defects that phenocopy mutations in Polycomb genes and demethylases as utx-1. suggesting a role for C. elegans IKB proteins in chromatin regulation, which is supported by various lines of evidence:(i) we detected NFKI-1 in the nucleus; (ii) NFKI-1 and IKB-1 bind to histones and Polycomb proteins, (iii) NFKI-1 and IKB-1 bind to chromatin in vivo, and (iv) mutations in nfki-1 and ikb-1 alter chromatin marks . Thus, ancestral IκB inhibitors may exert nuclear functions regulating of gene expression and development.
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| Overall design |
To study chromatin alterations in nfki-1(cer1) and ikb-1(nr2027) mutants, we performed ChIP-seq for H3K27me3 and H3K36me3 chromatin marks at L4 stage (36 hours at 25ºC after synchronization, from the same worm extracts used for RNA-seq). cer1 allele is a CRISPR-generated 368 bp deletion near nfki-1 exon 2. nr2027 is a 1911 bp deletion of ikb-1 that includes the ankyrin-repeat domains encoding sequence (Pujol et al., 2001). N2(Bristol) was used as a wildtype control. To detect direct chromatin targets of nfki-1 and ikb-1, we performed ChIP-seq at L1 (5 hours fed 3 hours at 25ºC starved after synchronization) on the endogenous tagged strain CER425[ikb-1(syb267[ikb-1::mCherry])I;nfki-1(cer102[nfki-1::3xFLAG)])X], using 3 independent biological replicates per strain. 50 bp single-end sequencing was done on an Illumina HiSeq 2000.
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| Contributor(s) |
Brena D, Porta-de-la-Riva M, Bertran J, Guillén Y, Espinosa L, Cerón J |
| Citation(s) |
32999373 |
| Submission date |
Mar 09, 2020 |
| Last update date |
Oct 06, 2020 |
| Contact name |
Yolanda Guillén |
| E-mail(s) |
yguillen87@gmail.com
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| Organization name |
IMIM
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| Street address |
Dr. Aiguader 88 Planta 2 IMIM
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| City |
Barcelona |
| ZIP/Postal code |
08003 |
| Country |
Spain |
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| Platforms (1) |
| GPL13657 |
Illumina HiSeq 2000 (Caenorhabditis elegans) |
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| Samples (21)
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| This SubSeries is part of SuperSeries: |
| GSE146655 |
Ancestral function of Inhibitors-of-kappaB regulates Caenorhabditis elegans development |
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| Relations |
| BioProject |
PRJNA611581 |
| SRA |
SRP252083 |
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