Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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RNA-seq of 3 day old C. elegans RILs exposes for 240 minutes to 0 mM or 400 mM ethanol

ABSTRACT: In this experiment we evaluate the transcriptional responses of C. elegans to 0 mM and 400 mM ethanol after 240 minutes by mapping expression quantitative trait loci. We used 70 mpRILs and their parental lines (JU1511, JU1926, JU1931, and JU1941). Animals were 3 day old when exposure and tissue collection took place. Growth, maintenance, and exposure was performed at 20 degrees Celsius, For this experiment we did not use biological replicates, except for the 4 parents that have 6 biological replicates. Worms underwent the treatment at VCU Richmond, Virginia, USA (Bettinger lab) and were sent to us (Wageningen, The Netherlands, Kammenga lab) on dry ice. RNA extraction was done in Wageningen. Sequencing was performed by BGI Hong Kong.

INSTRUMENT(S): DNBSEQ-T7, Maxwell® 16 AS2000

ORGANISM(S): Caenorhabditis elegans

SUBMITTER: Mark Sterken

PROVIDER: E-MTAB-15535 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:The essential process of dosage compensation equalizes X-chromosome gene expression between C. elegans XO males and XX hermaphrodites through a dosage compensation complex (DCC) that resembles condensin. The DCC binds to both X chromosomes of hermaphrodites to repress transcription by half. Here we show that post-translational modification by the SUMO conjugation pathway is essential for sex-specific assembly of the DCC onto X. Depletion of the SUMO peptide in vivo severely disrupts binding of particular DCC subunits and causes changes in X-linked gene expression similar to those caused by disrupting genes encoding DCC subunits. Three DCC subunits are themselves SUMOylated, and depletion of SUMO preferentially reduces their binding to X, suggesting that SUMOylation of DCC subunits is essential for robust association with X. DCC SUMOylation is triggered by the signal that initiates DCC assembly onto X. The initial step of assembly--binding of X-targeting factors to recruitment sites on X (rex sites)--is independent of SUMOylation, but robust binding of the complete complex requires SUMOylation. SUMOylated DCC subunits are enriched at rex sites, and SUMOylation enhances interactions between X-targeting factors and condensin subunits that facilitate DCC binding beyond the low level achieved without SUMOylation. DCC subunits also participate in condensin complexes essential for chromosome segregation, but their SUMOylation occurs only in the context of the DCC. Our results reinforce a newly emerging theme in which multiple proteins of a complex are SUMOylated in response to a specific stimulus, leading to accelerated complex formation and enhanced function. ChIP-chip experiments using antibodies against DPY-27, SDC-3, DPY-30, DPY-26, DPY-28 and FLAG-tagged SDC-2 in wild-type and smo-1 RNAi treated mixed embryos, with IGG controls. Also, sequential ChIP-chip experiments: (1) ChIP using FLAG antibodies to determine the genome-wide binding sites for SUMOylated proteins, (2) ChIP using FLAG antibodies followed by re-ChIP of eluted protein-chromatin complexes with DPY-27 antibodies to determine genome-wide binding sites for SUMOylated DPY-27 (referred to as DPY-27 re-ChIP experiments), (3) ChIP using FLAG antibodies followed by re-ChIP of eluted protein-chromatin with IGG antibodies to determine background binding (referred to as IGG re-ChIP experiments, and (4) ChIP using DPY-27 antibodies as a control to assess the efficiency of DPY-27 binding and detection in control vs. FLAG-tagged strains.

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RNA-seq of 3 day old C. elegans RILs exposes for 240 minutes to 0 mM or 400 mM ethanol

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