Developmental transcriptomes of the two sexes in Caenorhabditis elegans during sexual maturation
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ABSTRACT: We compare whole-animal RNA-seq transcriptomes for C. elegans males and hermaphrodites from the late L3 larval stage to young adulthood. During this interval, male sexual structures develop, including extensive neurogenesis and synaptogenesis that nearly doubles the size of the nervous system. Previous genome-wide expression studies in C. elegans have usually focused on only one sex â the hermaphrodite, and there are a relatively large number of predicted genes that still remain without meaningful annotation. In the present study, differential expression analysis of the RNA-seq data revealed 1,751 genes expressed at a higher level in the male. By differential expression analysis, unbiased gene correlation analysis, and a guilt-by-association approach, we identified new transcription factors required for differentiation of male genital structures, semen proteins, and candidates for previously-unknown components for synapse function. The results validate the dataset as a rich resource for future gene discovery in C. elegans. To analyze gene expression during sexual maturation in C. elegans, we performed RNA-seq for five samples for each sex ranging at 6 hr intervals from late L3 to young adult stages
Project description:We compare whole-animal RNA-seq transcriptomes for C. elegans males and hermaphrodites from the late L3 larval stage to young adulthood. During this interval, male sexual structures develop, including extensive neurogenesis and synaptogenesis that nearly doubles the size of the nervous system. Previous genome-wide expression studies in C. elegans have usually focused on only one sex – the hermaphrodite, and there are a relatively large number of predicted genes that still remain without meaningful annotation. In the present study, differential expression analysis of the RNA-seq data revealed 1,751 genes expressed at a higher level in the male. By differential expression analysis, unbiased gene correlation analysis, and a guilt-by-association approach, we identified new transcription factors required for differentiation of male genital structures, semen proteins, and candidates for previously-unknown components for synapse function. The results validate the dataset as a rich resource for future gene discovery in C. elegans.
Project description:Identification of genes expressed in the germ line of C. elegans. This SuperSeries is composed of the following subsets: Direct comparison of fem-3(gf) vs fem-1(lf): GSE725: oocytes vs sperm Indirect comparisons between males and hermaphrodites with and without a germline: GSE715: glp-4 adults GSE716: glp-4 L2 GSE717: glp-4 L3 GSE718: glp-4 L4 GSE719: wt L2 GSE720: wt L3 GSE721: wt L4 GSE722: wt adults GSE723: adult males vs reference GSE724: no germline males vs reference Temporal analysis of wild-type larval and adult gene expression: GSE726: TP01 mid-L3 GSE727: TP02 late-L3 GSE728: TP03 late L3/early L4 GSE729: TP04 early L4 GSE730: TP05 late L4 GSE731: TP06 late L4/young adult GSE732: TP07 early young adult GSE733: TP08 late young adult GSE734: TP09 adult GSE735: TP10 adult with embs 1 GSE736: TP11 adult with emb 2 GSE737: TP12 adult with emb 3 Keywords: SuperSeries Refer to individual Series
Project description:The Drosophila genitalia develop from an imaginal disc that is patterned during the larval period and undergoes morphogenesis during the pupal period. Although the genetic hierarchy that controls sexual identity in Drosophila is well characterized, the downstream genes that effect sexually dimorphic development of the genitalia are largely unknown. We used microarrays to profile gene expression in female and male genital imaginal discs at three time points during development: late third-instar larvae (L3), pupae approximately 6 hours after puparium formation (P6) and pupae approximately 20 hours after puparium formation (P20). We identified genes that are sex-differentially expressed in the developing genital disc, including three genes encoding transcription factors that are expressed in the genital disc of one sex but not the other. Through genetic analysis, we showed how the master regulator of sexual identity, Doublesex, limits expression of each of these three genes to one sex. We also determined which genital structures fail to develop properly in the absence of each of the three genes.
Project description:In this study, we profiled genome-wide pattern of tri-methylation of lysine 4 on histone H3 (H3K4me3) in the somatic cells of young and old C. elegans to investigate the changes of H3K4me3 during aging. In addition, we profiled H3K4me3 pattern in developmental stage L3. We found that H3K4me3 pattern in L3 is largely maintained in adults and the age-dynamic H3K4me3 are mainly adult stage specific. We profiled gene expression in young and old C. elegans somatic cells with ribo-RNAseq. The changes of H3K4me3 and RNA abundance are positively correlated.
Project description:The goal of this study is to identify and characterize sites in the C. elegans genome bound by the transcription factor TRA-1. TRA-1 ChIP-seq was performed in the following stages of animals in duplicate: 1) L2 stage of C. elegans wild-type N2 strain; 2) L3 stage of C. elegans wild-type N2 strain; 3) young adult stage of C. elegans glp-4(bn2) mutant; 4) young adult stage of C. elegans spe-11(hc77) mutant; 5) L3 stage of C. briggsae wild-type AF16 strain. As a negative control, TRA-1 ChIP-seq was also performed in C. elegans L3 stage with tra-1(e1834) homozygous and heterozygous mutation. Input DNA was also sequenced in each condition.
Project description:Piwi-related Argonaute proteins play important roles in maintaining germline integrity and fertility and have been linked to a class of germline-enriched small RNAs termed piRNAs. Caenorhabditis elegans encodes two Piwi family proteins called PRG-1 and PRG-2, and PRG-1 interacts with the C. elegans piRNAs (21U-RNAs). Previous studies found that the prg-1 mutation causes a marked reduction in the expression of 21U-RNAs, temperature-sensitive defects in fertility and other phenotypic defects.To systematically demonstrate the function of PRG-1 on regulating small RNAs and their targets. We use recent advances in high-throughput sequencing technology to show that expression of non-coding small RNAs in six stages(embryo,L1,L2,L3,L4,young audlt) and mRNAs in four stages (L1,L2,L3,L4) after prg-1 mutation. prg-1 mutation can not only lead to a decrease in the expression of 21U-RNAs, but also cause 35~40% of miRNAs to be significantly down-regulated; approximately 3% (6.00% in L4) of protein-coding genes are differentially expressed after mutating prg-1, and 60~70% of these substantially changed protein-coding genes are up-regulated. Examination of small RNA expression in six different developmental stages (embryo, L1, L2, L3, L4, young adult) and mRNA expression in four stages (L1,L2,L3,L4) of C. elegans prg-1 mutant (wm161) .
Project description:Piwi-related Argonaute proteins play important roles in maintaining germline integrity and fertility and have been linked to a class of germline-enriched small RNAs termed piRNAs. Caenorhabditis elegans encodes two Piwi family proteins called PRG-1 and PRG-2, and PRG-1 interacts with the C. elegans piRNAs (21U-RNAs). Previous studies found that the prg-1 mutation causes a marked reduction in the expression of 21U-RNAs, temperature-sensitive defects in fertility and other phenotypic defects.To systematically demonstrate the function of PRG-1 on regulating small RNAs and their targets. We use recent advances in high-throughput sequencing technology to show that expression of non-coding small RNAs in six stages(embryo,L1,L2,L3,L4,young audlt) and mRNAs in four stages (L1,L2,L3,L4) after prg-1 mutation. prg-1 mutation can not only lead to a decrease in the expression of 21U-RNAs, but also cause 35~40% of miRNAs to be significantly down-regulated; approximately 3% (6.00% in L4) of protein-coding genes are differentially expressed after mutating prg-1, and 60~70% of these substantially changed protein-coding genes are up-regulated. Examination of small RNA expression in six different developmental stages (embryo, L1, L2, L3, L4, young adult) and mRNA expression in four stages (L1,L2,L3,L4) of C. elegans prg-1 mutant (wm161) .
Project description:We comprehensively compared the chromatin structures and transcriptomes in successive substages of female and male mouse meiotic prophase by using sisHi-C and RNA-Seq methods. Interestingly, the transcriptional change happened earlier than chromatin structures reprograming that chromatin structures largely maintained the pre-meiotic condition in leptotene. Also, compartments and TADs gradually disappeared and then slowly recovered in both oocytes and spermatocytes. We characterized the events of homologous chromosomes pairing and found homologues adopted two sex-conserved pairing strategies prior to and after leptotene-to-zygotene transition, which firstly contacted more frequently in LINE enriched compartment B and then switched to SINE enriched compartment A. The sexual difference of transcriptome was most obvious in late meiotic prophase, which reflected in gamete morphology and function differences. We also complemented marker genes for each substage of oocytes and spermatocytes meiotic prophase, and predicted the sex-specific meiotic functional genes, whose mutation or deletion may cause sex different effects on fertility. In summary, this study revealed the sexual similarities and dimorphic of higher-order chromatin architecture, homologous pairing and transcriptome during meiotic prophase of both oogenesis and spermatogenesis.