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Series GSE67650 Query DataSets for GSE67650
Status Public on Nov 09, 2015
Title Developmental dynamics of C. elegans dosage compensation
Organisms Caenorhabditis briggsae; Caenorhabditis elegans
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary In Caenorhabditis elegans, the dosage compensation complex (DCC) specifically binds to and represses transcription from both X chromosomes in hermaphrodites. The DCC is composed of an X-specific condensin complex that interacts with several proteins. During embryogenesis, DCC starts localizing to the X chromosomes around the 40-cell stage, and is followed by X-enrichment of H4K20me1 between 100-cell to comma stage. Here, we analyzed dosage compensation of the X chromosome between sexes, and the roles of dpy-27 (condensin subunit), dpy-21 (non-condensin DCC member), set-1 (H4K20 monomethylase) and set-4 (H4K20 di-/tri-methylase) in X chromosome repression using mRNA-seq and ChIP-seq analyses across several developmental time points. We found that the DCC starts repressing the X chromosomes by the 40-cell stage, but X-linked transcript levels remain significantly higher in hermaphrodites compared to males through the comma stage of embryogenesis. Dpy-27 and dpy-21 are required for X chromosome repression throughout development, but particularly in early embryos dpy-27 and dpy-21 mutations produced distinct expression changes, suggesting a DCC independent role for dpy-21. We previously hypothesized that the DCC increases H4K20me1 by reducing set-4 activity on the X chromosomes. Accordingly, in the set-4 mutant, H4K20me1 increased more from the autosomes compared to the X, equalizing H4K20me1 level between X and autosomes. H4K20me1 increase on the autosomes led to a slight repression, resulting in a relative effect of X derepression. H4K20me1 depletion in the set-1 mutant showed greater X derepression compared to equalization of H4K20me1 levels between X and autosomes in the set-4 mutant, indicating that H4K20me1 level is important, but X to autosomal balance of H4K20me1 contributes only slightly to X-repression. Thus H4K20me1 by itself is not a downstream effector of the DCC. In summary, X chromosome dosage compensation starts in early embryos as the DCC localizes to the X, and is strengthened in later embryogenesis by H4K20me1.
 
Overall design RNA-Seq profiles of C. elegans wild type hermaphrodite, mixed sex, at 5 time points and dpy-27, set-4, dpy-21, set-1 and RNAi at 2-3 time points with 3-4 replicates each.

RNA-Seq profiles of C. elegans. Strains are N2 (wild type), BS553 fog-2(oz40) V, CB428 dpy-21(e428) V, MK4 dpy-27(y56) III, MT14911 set-4 (n4600) II, SS1075 set-1(tm1821)/hT2g[bli-4(e937) let-?(q782) qIs48] (I;III). Set-1 collections made as heterozygotes and dpy-27(y56) homozygotes. Spike in RNA-seq libraries have AF16 wild type C. briggsae L1s added at a 1:10 ratio. Timepoints are early embryos (synchronized collection, <40 cells), comma embryos (synchronized early embryos aged for 4 hours), mixed embryos (mixed stage embryos from unsynchronized population), L1 (synchronized L1 larvae), L3 (synchronized L3 larvae), and YA (synchronized young adults, collected before embryos present in hermaphrodite gonad). Biological replicates for each strain/stage listed separately.

ChIP-seq profiles of C. elegans DCC subunit dpy-27, H4K20me1 histone modification and RNA pol II large subunit ama-1 in 3-6 replicates from mixed stage (unsynchronized) embryos and synchronized L3 larvae. Corresponding inputs are labelled with "Input_" plus ChIP name.
 
Contributor(s) Kramer ML, Kranz A, Ercan S
Citation(s) 26641248, 27356611
Submission date Apr 07, 2015
Last update date May 15, 2019
Contact name Sevinc Ercan
Organization name New York University
Department Biology
Street address 12 Waverly Place
City New York
State/province NY
ZIP/Postal code 10003
Country USA
 
Platforms (3)
GPL13657 Illumina HiSeq 2000 (Caenorhabditis elegans)
GPL13776 Illumina Genome Analyzer IIx (Caenorhabditis elegans)
GPL20977 Illumina HiSeq 2000 (Caenorhabditis briggsae; Caenorhabditis elegans)
Samples (146)
GSM1652671 DPY27 CB428 MxEmb Rep1 ChIPSeq
GSM1652672 DPY27 CB428 MxEmb Rep2 ChIPSeq
GSM1652673 DPY27 CB428 MxEmb Rep3 ChIPSeq
Relations
BioProject PRJNA280541
SRA SRP056941

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
GSE67650_RNAseq_FPKMs.txt.gz 5.7 Mb (ftp)(http) TXT
GSE67650_RNAseq_spikeins_counts_Cbriggsae_updated.txt.gz 126.6 Kb (ftp)(http) TXT
GSE67650_RNAseq_spikeins_counts_updated.txt.gz 316.0 Kb (ftp)(http) TXT
GSE67650_all_peak_files.bed.tar.gz 482.8 Kb (ftp)(http) TAR
GSE67650_all_wig_files.tar.gz 4.6 Gb (ftp)(http) TAR
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Raw data are available in SRA
Processed data are available on Series record

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