RNA-seq transcriptome profiling of 1) C. elegans male germlines vs. oogenic germlines, and 2) male germlines, sperm, and F1 offspring germlines when offspring inherited sperm chromatin lacking H3K27me3.
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA475797 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR7298300.fastq.gz | Fastqsanger.gz | |||
| SRR7298310.fastq.gz | Fastqsanger.gz | |||
| SRR7298301.fastq.gz | Fastqsanger.gz | |||
| SRR7298311.fastq.gz | Fastqsanger.gz | |||
| SRR7298292.fastq.gz | Fastqsanger.gz |
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Project description:The role that gamete-inherited chromatin states serve in regulating gene expression across generations is poorly understood. To interrogate how histone marks inherited on parental genomes influence gene expression in offspring, we profiled different tissue contexts in worms that inherited the sperm genome lacking the repressive mark H3K27me3. We found that worms that inherited the sperm genome lacking H3K27me3 upregulated genes in all tissues profiled, which included hermaphrodite and male germlines and mixed soma. We found that most upregulated genes were upregulated specifically from sperm alleles and in a tissue-specific manner, highlighting the importance of cellular context in determining which genes are sensitive to upregulation when H3K27me3 repression is absent. To determine whether chromatin states can impact gene expression transgenerationally, i.e. across 3 generations, we profiled gene expression and chromatin states in the germlines of worms that inherited the sperm genome lacking H3K27me3 (F1 generation) and in the germlines of their offspring (F2 generation). We found that genes upregulated in F1 germlines maintained the H3K27me3(-) state of sperm alleles and that the upregulated and H3K27me3(-) state of sperm alleles was maintained in the germlines of their offspring (F2 generation). These findings demonstrate that histone marks can serve as a transgenerational carrier.
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Project description:PUF RNA-binding proteins control stem cells in diverse species, including mammalian, arthropod, and nematode, in addition to other biological functions. The C. elegans PUF protein FBF serves as a paradigm for metazoan PUFs. FBF is essential for the maintenance of germline stem cells but also regulates the hermpahrodite sperm/oocyte cell fate switch and is critical for the process of spermatogenesis. We have attempted to “disentangle” the different roles of FBF by comparing its targets in spermatogenic and oogenic germlines. To this end, we used FBF iCLIP to learn its binding profile in an adult hermaphrodite germline that is sexually transformed and makes only sperm due to a temperature-sensitive sex-determination mutant. As a control, we analyzed FBF iCLIP data from oogenic germlines at the same temperature. Using a modified peak calling algorithm, we identified FBF binding sites in oogenic animals at 20°C, oogenic animals at 25°C, and spermatogenic animals at 25°C. Oogenic FBF targets were similar at 20°C and 25°C. By contrast, FBF mRNA targets in spermatogenetic animals had a distinct profile, revealing sperm-specific targets that are likely critical for the FBF role in spermatogenesis. Most importantly, we found FBF bound to mRNAs regardless of germline gender. In particular, a group of 22 mRNAs clustered as bound with high frequency in a gender- and temperature-independent manner. These 22 mRNAsencode RNA-binding proteins and stem cell regulators and may be crucial for the FBF role in in stem cell maintenance.
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