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Series GSE224076 Query DataSets for GSE224076
Status Public on Jan 29, 2024
Title The chromatin factors SET-26 and HCF-1 oppose the histone deacetylase HDA-1 in longevity and gene regulation in C. elegans [CUT&RUN]
Organism Caenorhabditis elegans
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary SET-26, HCF-1, and HDA-1 are highly conserved chromatin factors with key roles in development and aging. Here we present mechanistic insights into how these factors regulate gene expression and modulate longevity in C. elegans. We show that SET-26 and HCF-1 cooperate to regulate a common set of genes, and both antagonize the histone deacetylase HDA-1 to limit longevity. We propose a model in which SET-26 recruits HCF-1 to chromatin in somatic cells, where they stabilize each other at the promoters of a subset of genes, particularly mitochondrial function genes, and regulate their expression. HDA-1 opposes SET-26 and HCF-1 on the regulation of a subset of their common target genes and in longevity. Our findings suggest that SET-26, HCF-1, and HDA-1 comprise a mechanism to fine-tune gene expression and longevity and likely have important implications for the mechanistic understanding of how these factors function in diverse organisms, particularly in aging biology.
 
Overall design CUT&RUN chromatin binding profiles of C. elegans proteins SET-26, HCF-1, and HDA-1 at day 1 of adulthood in somatic-only or whole worm samples, in set-26(tm2467) or hcf-1(pk924) mutant backgrounds. Profiles were obtained using CRISPR knock-in strains for each factor. Two replicates are included for each experiment, and normalization tracks (either antibody background or H3 immunoprecipitated in parallel) are included for each experiment.
 
Contributor(s) Emerson FJ, Lee S
Citation(s) 38485937
NIH grant(s)
Grant ID Grant title Affiliation Name
R01 AG024425 Genetic and Epigenetic Determinants of Longevity Cornell University Siu Sylvia Lee
Submission date Jan 30, 2023
Last update date Mar 20, 2024
Contact name Siu Sylvia Lee
E-mail(s) leelabcornell@gmail.com
Organization name Cornell University
Street address 520 Campus road
City Ithaca
State/province NY
ZIP/Postal code 14850
Country USA
 
Platforms (1)
GPL19757 Illumina NextSeq 500 (Caenorhabditis elegans)
Samples (83)
GSM7011391 Somatic SET-26 binding profile, germline-less glp-1(e2141) background, rep 1
GSM7011392 Somatic SET-26 binding profile, germline-less glp-1(e2141) background, rep 2
GSM7011393 Somatic HCF-1 binding profile, germline-less glp-1(e2141) background, rep 1
This SubSeries is part of SuperSeries:
GSE224078 The chromatin factors SET-26 and HCF-1 oppose the histone deacetylase HDA-1 in longevity and gene regulation in C. elegans
Relations
BioProject PRJNA929523

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
GSE224076_HCF-1.vs.H3_L4440_MergedReps.bigwig 38.4 Mb (ftp)(http) BIGWIG
GSE224076_HCF-1.vs.H3_L4440_MergedReps_narrow_peaks_peaks.narrowPeak.gz 259.4 Kb (ftp)(http) NARROWPEAK
GSE224076_HCF-1.vs.H3_L4440_MergedReps_narrow_peaks_peaks.txt.gz 299.9 Kb (ftp)(http) TXT
GSE224076_HCF-1.vs.H3_glp-1RNAi_MergedReps.bigwig 38.4 Mb (ftp)(http) BIGWIG
GSE224076_HCF-1.vs.H3_glp-1RNAi_MergedReps_narrow_peaks_peaks.narrowPeak.gz 392.5 Kb (ftp)(http) NARROWPEAK
GSE224076_HCF-1.vs.H3_glp-1RNAi_MergedReps_narrow_peaks_peaks.txt.gz 458.3 Kb (ftp)(http) TXT
GSE224076_HCF-1.vs.H3_glp-1mut_OP50_MergedReps.bigwig 38.7 Mb (ftp)(http) BIGWIG
GSE224076_HCF-1.vs.H3_glp-1mut_OP50_MergedReps_narrow_peaks_peaks.narrowPeak.gz 496.9 Kb (ftp)(http) NARROWPEAK
GSE224076_HCF-1.vs.H3_glp-1mut_OP50_MergedReps_narrow_peaks_peaks.txt.gz 578.3 Kb (ftp)(http) TXT
GSE224076_HCF-1.vs.antibodybackground_wildtype_OP50_MergedReps.bigwig 38.6 Mb (ftp)(http) BIGWIG
GSE224076_HCF-1.vs.antibodybackground_wildtype_OP50_MergedReps_narrow_peaks_peaks.narrowPeak.gz 265.6 Kb (ftp)(http) NARROWPEAK
GSE224076_HCF-1.vs.antibodybackground_wildtype_OP50_MergedReps_narrow_peaks_peaks.txt.gz 316.0 Kb (ftp)(http) TXT
GSE224076_HCF-1_somatic.vs.antibodybackground_glp-1_OP50_MergedReps_narrow_peaks_peaks.txt.gz 419.9 Kb (ftp)(http) TXT
GSE224076_HCF-1_somatic.vs.antibodybackground_glp1_OP50_MergedReps.bigwig 38.6 Mb (ftp)(http) BIGWIG
GSE224076_HCF-1_somatic.vs.antibodybackground_glp1_OP50_MergedReps_narrow_peaks_peaks.narrowPeak.gz 356.9 Kb (ftp)(http) NARROWPEAK
GSE224076_HDA-1.vs.H3_L4440_mergedreps.bigwig 38.7 Mb (ftp)(http) BIGWIG
GSE224076_HDA-1.vs.H3_L4440_mergedreps_narrow_peaks_peaks.narrowPeak.gz 246.7 Kb (ftp)(http) NARROWPEAK
GSE224076_HDA-1.vs.H3_L4440_mergedreps_narrow_peaks_peaks.txt.gz 291.4 Kb (ftp)(http) TXT
GSE224076_HDA-1.vs.H3_glp-1RNAi_mergedreps.bigwig 38.7 Mb (ftp)(http) BIGWIG
GSE224076_HDA-1.vs.H3_glp-1RNAi_mergedreps_narrow_peaks_peaks.narrowPeak.gz 420.4 Kb (ftp)(http) NARROWPEAK
GSE224076_HDA-1.vs.H3_glp-1RNAi_mergedreps_narrow_peaks_peaks.txt.gz 483.8 Kb (ftp)(http) TXT
GSE224076_HDA-1.vs.antibodybackground_wildtype_OP50_MergedReps.bigwig 38.7 Mb (ftp)(http) BIGWIG
GSE224076_HDA-1.vs.antibodybackground_wildtype_OP50_MergedReps_narrow_peaks_peaks.narrowPeak.gz 226.5 Kb (ftp)(http) NARROWPEAK
GSE224076_HDA-1.vs.antibodybackground_wildtype_OP50_MergedReps_narrow_peaks_peaks.txt.gz 263.7 Kb (ftp)(http) TXT
GSE224076_HDA-1_somatic.vs.antibodybackground_glp-1_OP50_MergedReps.bigwig 38.7 Mb (ftp)(http) BIGWIG
GSE224076_HDA-1_somatic.vs.antibodybackground_glp-1_OP50_MergedReps_narrow_peaks_peaks.narrowPeak.gz 419.5 Kb (ftp)(http) NARROWPEAK
GSE224076_HDA-1_somatic.vs.antibodybackground_glp-1_OP50_MergedReps_narrow_peaks_peaks.txt.gz 493.0 Kb (ftp)(http) TXT
GSE224076_SET-26.vs.H3_L4440_MergedReps.bigwig 38.7 Mb (ftp)(http) BIGWIG
GSE224076_SET-26.vs.H3_L4440_MergedReps_narrow_peaks_peaks.narrowPeak.gz 431.7 Kb (ftp)(http) NARROWPEAK
GSE224076_SET-26.vs.H3_L4440_MergedReps_narrow_peaks_peaks.txt.gz 496.9 Kb (ftp)(http) TXT
GSE224076_SET-26.vs.H3_glp-1RNAi_MergedReps.bigwig 38.5 Mb (ftp)(http) BIGWIG
GSE224076_SET-26.vs.H3_glp-1RNAi_MergedReps_narrow_peaks_peaks.narrowPeak.gz 545.0 Kb (ftp)(http) NARROWPEAK
GSE224076_SET-26.vs.H3_glp-1RNAi_MergedReps_narrow_peaks_peaks.txt.gz 625.0 Kb (ftp)(http) TXT
GSE224076_SET-26.vs.antibodybackground_wildtype_OP50_MergedReps.bigwig 38.5 Mb (ftp)(http) BIGWIG
GSE224076_SET-26.vs.antibodybackground_wildtype_OP50_MergedReps_narrow_peaks_peaks.narrowPeak.gz 549.8 Kb (ftp)(http) NARROWPEAK
GSE224076_SET-26.vs.antibodybackground_wildtype_OP50_MergedReps_narrow_peaks_peaks.txt.gz 629.5 Kb (ftp)(http) TXT
GSE224076_SET-26_somatic.vs.antibodybackground_glp-1_OP50_MergedReps.bigwig 38.6 Mb (ftp)(http) BIGWIG
GSE224076_SET-26_somatic.vs.antibodybackground_glp-1_OP50_MergedReps_narrow_peaks_peaks.narrowPeak.gz 519.6 Kb (ftp)(http) NARROWPEAK
GSE224076_SET-26_somatic.vs.antibodybackground_glp-1_OP50_MergedReps_narrow_peaks_peaks.txt.gz 611.7 Kb (ftp)(http) TXT
GSE224076_hcf-1mutant_HDA-1.vs.H3_L4440_mergedreps.bigwig 38.7 Mb (ftp)(http) BIGWIG
GSE224076_hcf-1mutant_HDA-1.vs.H3_L4440_mergedreps_narrow_peaks_peaks.narrowPeak.gz 227.7 Kb (ftp)(http) NARROWPEAK
GSE224076_hcf-1mutant_HDA-1.vs.H3_L4440_mergedreps_narrow_peaks_peaks.txt.gz 268.8 Kb (ftp)(http) TXT
GSE224076_hcf-1mutant_HDA-1.vs.H3_glp-1RNAi_mergedreps.bigwig 38.7 Mb (ftp)(http) BIGWIG
GSE224076_hcf-1mutant_HDA-1.vs.H3_glp-1RNAi_mergedreps_narrow_peaks_peaks.narrowPeak.gz 321.9 Kb (ftp)(http) NARROWPEAK
GSE224076_hcf-1mutant_HDA-1.vs.H3_glp-1RNAi_mergedreps_narrow_peaks_peaks.txt.gz 372.9 Kb (ftp)(http) TXT
GSE224076_hcf-1mutant_SET-26.vs.H3_L4440_MergedReps.bigwig 38.6 Mb (ftp)(http) BIGWIG
GSE224076_hcf-1mutant_SET-26.vs.H3_L4440_MergedReps_narrow_peaks_peaks.narrowPeak.gz 464.8 Kb (ftp)(http) NARROWPEAK
GSE224076_hcf-1mutant_SET-26.vs.H3_L4440_MergedReps_narrow_peaks_peaks.txt.gz 534.6 Kb (ftp)(http) TXT
GSE224076_hcf-1mutant_SET-26.vs.H3_glp-1RNAi_MergedReps.bigwig 38.7 Mb (ftp)(http) BIGWIG
GSE224076_hcf-1mutant_SET-26.vs.H3_glp-1RNAi_MergedReps_narrow_peaks_peaks.narrowPeak.gz 447.5 Kb (ftp)(http) NARROWPEAK
GSE224076_hcf-1mutant_SET-26.vs.H3_glp-1RNAi_MergedReps_narrow_peaks_peaks.txt.gz 525.8 Kb (ftp)(http) TXT
GSE224076_set-26mutant_HCF-1.vs.H3_L4440_MergedReps.bigwig 38.5 Mb (ftp)(http) BIGWIG
GSE224076_set-26mutant_HCF-1.vs.H3_L4440_MergedReps_narrow_peaks_peaks.narrowPeak.gz 119.9 Kb (ftp)(http) NARROWPEAK
GSE224076_set-26mutant_HCF-1.vs.H3_L4440_MergedReps_narrow_peaks_peaks.txt.gz 141.4 Kb (ftp)(http) TXT
GSE224076_set-26mutant_HCF-1.vs.H3_glp-1RNAi_MergedReps.bigwig 38.5 Mb (ftp)(http) BIGWIG
GSE224076_set-26mutant_HCF-1.vs.H3_glp-1RNAi_MergedReps_narrow_peaks_peaks.narrowPeak.gz 41.5 Kb (ftp)(http) NARROWPEAK
GSE224076_set-26mutant_HCF-1.vs.H3_glp-1RNAi_MergedReps_narrow_peaks_peaks.txt.gz 48.9 Kb (ftp)(http) TXT
GSE224076_set-26mutant_HCF-1.vs.H3_glp-1mut_OP50_MergedReps.bigwig 38.8 Mb (ftp)(http) BIGWIG
GSE224076_set-26mutant_HCF-1.vs.H3_glp-1mut_OP50_MergedReps_narrow_peaks_peaks.narrowPeak.gz 159.0 Kb (ftp)(http) NARROWPEAK
GSE224076_set-26mutant_HCF-1.vs.H3_glp-1mut_OP50_MergedReps_narrow_peaks_peaks.txt.gz 188.7 Kb (ftp)(http) TXT
GSE224076_set-26mutant_HDA-1.vs.H3_L4440_mergedreps.bigwig 38.7 Mb (ftp)(http) BIGWIG
GSE224076_set-26mutant_HDA-1.vs.H3_L4440_mergedreps_narrow_peaks_peaks.narrowPeak.gz 107.4 Kb (ftp)(http) NARROWPEAK
GSE224076_set-26mutant_HDA-1.vs.H3_L4440_mergedreps_narrow_peaks_peaks.txt.gz 127.0 Kb (ftp)(http) TXT
GSE224076_set-26mutant_HDA-1.vs.H3_glp-1RNAi_mergedreps.bigwig 38.8 Mb (ftp)(http) BIGWIG
GSE224076_set-26mutant_HDA-1.vs.H3_glp-1RNAi_mergedreps_narrow_peaks_peaks.narrowPeak.gz 297.1 Kb (ftp)(http) NARROWPEAK
GSE224076_set-26mutant_HDA-1.vs.H3_glp-1RNAi_mergedreps_narrow_peaks_peaks.txt.gz 343.3 Kb (ftp)(http) TXT
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