biostudies-arrayexpressUnknownTranscriptomicsGenomicsProteomicsLeo ZeefIllumina HiSeq 2500RNA-seq of coding RNACaenorhabditis elegansCaenorhabditis eleganshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-15080Enrichment in the deposition of methyl groups at Histone 3 lysine 4 (H3K4) is associated with active transcription and bivalent chromatin. In yeast, there is evidence additionally supporting a role in repression during stress, In metazoans, H3K4 methylation levels are controlled by a conserved scaffold complex comprised of WDR5, ASH2L, and RBBP5 acting in association with one of the many H3K4 methyltransferases available. RBBP5 facilitates the assembly of the complex and association with the nucleosome. WDR5 coordinates the interaction between RBBP5 and the enzyme to facilitate methylation. WDR5 has moonlighting activities and is found in additional complexes, raising questions about WDR-5’s specific role in H3K4 methylation. Using the C. elegans embryo system coupled with spike-in ChIP-seq and null alleles for wdr-5 and rbbp-5, we defined the impact that these two scaffolding components have on the deposition of H3K4 mono-, di-, and tri-methylation and on gene expression.biostudies-arrayexpressLibrary Construction - Illumina TruSeq Stranded mRNA Library Prep KitSequencing - Paired end sequencingSample Collection - We used six C. elegans strains: N2(wild type), wdr-5(ok1417) III, rbbp-5(tm3463) II, ash-2(tm1905) II, and the double mutants  wdr-5(ok1417) III; rbbp-5(tm3463) II and ash-2(tm1905) II; wdr-5(ok1417) III. Strains were kept at 20°C. 20 x 10cm plates of gravid adults were bleached and synchronised L1s were seeded on 2 X Corning tissue culture dishes (245 x 245 mm) seede with 20x OP50. When the synchronised young gravid mothers started to lay eggs, they were bleached to obtained embryos. These embryos were scored to ensure comparative stages between wild type and the mutants. About 10-12% of embryos are at <28-cell stage, 25-30% of embryos are between the 28-cell stage and 100-cell stage, 45-55% are between ~100-cell stage and pre-coma stage (~400 cell), and 5-15% are post-coma stage. Three independent biological replicates were prepared for RNA-seq.Nucleic Acid Extraction - Total RNA was extracted using TRIzol (Invitrogen) and samples were frozen at -80°C. First strand cDNA synthesis was performed using the SuperScript VILO cDNA Synthesis Kit (Invitrogen), according to the manufacturer's instructions.OrganizationMINSEQE ScoreAssays and DataMAGE-TAB FilesLeo ZeeffalseWDR-5 exhibits H3K4 methylation-independent activity, whereas RBBP-5 is essential for H3K4 methylation during embryonic development in C. elegansEnrichment in the deposition of methyl groups at Histone 3 lysine 4 (H3K4) is associated with active transcription and bivalent chromatin. In yeast, there is evidence additionally supporting a role in repression during stress, In metazoans, H3K4 methylation levels are controlled by a conserved scaffold complex comprised of WDR5, ASH2L, and RBBP5 acting in association with one of the many H3K4 methyltransferases available. RBBP5 facilitates the assembly of the complex and association with the nucleosome. WDR5 coordinates the interaction between RBBP5 and the enzyme to facilitate methylation. WDR5 has moonlighting activities and is found in additional complexes, raising questions about WDR-5’s specific role in H3K4 methylation. Using the C. elegans embryo system coupled with spike-in ChIP-seq and null alleles for wdr-5 and rbbp-5, we defined the impact that these two scaffolding components have on the deposition of H3K4 mono-, di-, and tri-methylation and on gene expression.2025-05-10T00:00:00Z2025-04-24T12:48:31.542Z2025-04-24T12:48:31.542ZE-MTAB-15080ERP171938EFO_0002944EFO_0004170EFO_0005518EFO_0003738EFO_0004184