Liver Chromatin accessibility landscapes during onset of salmon maturation
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ABSTRACT:
PROVIDER: PRJNA659750 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12534800_1.fastq.gz | Fastqsanger.gz | |||
| SRR12534800_2.fastq.gz | Fastqsanger.gz | |||
| SRR12534801_1.fastq.gz | Fastqsanger.gz | |||
| SRR12534801_2.fastq.gz | Fastqsanger.gz | |||
| SRR12534802_1.fastq.gz | Fastqsanger.gz |
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Project description:We sequenced 12 ATAC-Seq lbraries from four biological replicates before (T1) and after the onset of maturation (T2, T3, T4) from liver. To characterise changes in chromatin state following long light initiation, we defined differentially accessible regions (DARs) where mapping counts differed significantly between T1 and other time points. This revealed a strong early remodelling in the chromatin state landscape, as most DARs were observed at T2 (n=1501) before decreasing in stepwise fashion at T3 (n=477) and T4. The majority of DARs (n=1036 or 57%) exhibit reduced accessibility at T2 compared with T1 and subsequently remained unchanged at later time points (Fig. 5a; Supplementary Figure S14). Similarly, regions that gained accessibility at T2 (n=696 or 38%) also remained unchanged at later timepoints. This left less than 10% of DARs (n=99) that displayed an oscillating pattern following the onset of the maturation. Together, this revealed the ATAC-seq signatures were predominantly stable chromatin state changes.
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Project description:This SuperSeries is composed of the SubSeries listed below.This contains multi-omics datasets transcriptomic (RNA-Seq), methylomic (WGBS), and epigenomics (ATAC-seq) obtained during onset of sexual maturation in Atlantic salmon. We used gene regulatory networks (GRNs) to integrate results from these multi-omic analyses to identify key regulators of maturation.
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Project description:Multitissue transcriptomic profiling during onset of salmon maturation
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Project description:We sequenced mRNA from four biological replicates of each tissue before (T1) and after the onset of maturation (T2, T3, T4). A total of 3.2 billion paired-end reads were mapped against the Atlantic salmon reference genome with 72% mapping efficiency to create an average depth of 50 million reads per library. The number of differentially expressed genes (DEGs) increased with elapsed time following the onset of the long light photoperiod for the two BPG axis tissues (pituitary and ovary). Of these, the ovary underwent the most dramatic remodelling over time with 403, 1,709 and then 3,497 DEGs observed at timepoints T2, T3 and T4 respectively. This increasing trajectory of differential ngene expression, coupled with the elevated GSI following the light stimuli, strongly suggests the experimental approach successfully initiated the onset of maturation. Next, we identified clusters of DEGs in each of the analysed tissues, which describe their physiological roles. The identity of the DEGs, in response to the onset of maturation, revealed the key players involved in the earliest triggers into maturation. Among these, upregulation of genes encoding specififc pituitary hormones such as gonadotropins along with genes encoding transcription factors (such as GATA2) are significant in controlling onset of maturation. In addition, genes encoding pituitary hormone receptors and follicular development were upregulated in ovary.
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Project description:Multitissue DNA methylome profiling during onset of salmon maturation
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Project description:We performed a time course experiment, whereby animals were manipulated with photoperiod before tissues were collected across the time window when animals commence sexual development. We performed whole genome bisulfite sequencing of three salmon tissues (pituitary, ovary and liver) at both the beginning and end of the experiment, to take a first look at the patterns of DNA methylation and examine how they change in response to the onset of an important life history trait. Comparison across timepoints revealed 6,373 differentially methylated regions (DMRs), of which approximately 50% were located within genes (DMGs). The ovary underwent the most profound remodelling, with a strong bias towards increased methylation levels (hyper-methylation). Weak correlation was observed considering all available genes, suggesting methylation may not be the key epigenomic regulator of global expression in the context of our experiment. However, we found a significant overlap between DMGs and differentially expressed genes in the ovary. Taken together, our results suggest chromatin remodelling genes play a role in the commitment of animals to the sexual maturation pathway.
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Project description:Chromatin accessibility landscapes across B-ALL
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Project description:The maturation-inducing hormone 17alpha,20beta-dihydroxy-4-pregnen-3-one (DHP) was first identified in the amago salmon. However, although carbonyl reductase-like 20beta-hydroxysteroid dehydrogenase (CR/20beta-HSD) was reported to convert 17alpha-hydroxyprogesterone (17alpha-P) to DHP in rainbow trout, we previously found that CR/20beta-HSD mRNA was not up-regulated in stimulated granulosa cells from masu salmon, which suggests that DHP is synthesized by a different enzyme. Accordingly, the present study aimed to identify the specific 20beta-hydroxysteroid dehydrogenase (20beta-HSD) responsible for DHP production by granulosa cells during final oocyte maturation in masu salmon. Granulosa layers were isolated from ovarian follicles at one month before ovulation and incubated with or without forskolin, which was used to mimic luteinizing hormone. Subsequent RNA-sequencing yielded ~12 million reads, with an average length of 51 bp, and 71,062 contigs of >100 bp were constructed. Of the 953 contigs that were exclusively constructed from the reads of forskolin-induced granulosa layers, tBlastx analysis identified one contig (#f103496) that matched 17beta-hydroxysteroid dehydrogenase type 12. We found that mammalian cells transfected with full-length omhsd17beta12l exhibited considerable 20beta-HSD activity, as indicated by efficient conversion of exogenous 17alpha-P to DHP. In addition, we found that omhsd17beta12l mRNA levels were consistently low in follicles during vitellogenic growth; however, the levels increased significantly during final oocyte maturation. The levels of omhsd17beta12l mRNA were also considerably increased in granulosa layers in which 20beta-HSD activity was induced by salmon pituitary extract. Therefore, we suggest that omhsd17beta12l, not CR/20beta-HSD, is the 20beta-HSD responsible for DHP production by granulosa cells in masu salmon during final oocyte maturation.
2016-08-04 | GSE85134 | GEO
Project description:The maturation-inducing hormone 17alpha,20beta-dihydroxy-4-pregnen-3-one (DHP) was first identified in the amago salmon. However, although carbonyl reductase-like 20beta-hydroxysteroid dehydrogenase (CR/20beta-HSD) was reported to convert 17alpha-hydroxyprogesterone (17alpha-P) to DHP in rainbow trout, we previously found that CR/20beta-HSD mRNA was not up-regulated in stimulated granulosa cells from masu salmon, which suggests that DHP is synthesized by a different enzyme. Accordingly, the present study aimed to identify the specific 20beta-hydroxysteroid dehydrogenase (20beta-HSD) responsible for DHP production by granulosa cells during final oocyte maturation in masu salmon. Granulosa layers were isolated from ovarian follicles at one month before ovulation and incubated with or without forskolin, which was used to mimic luteinizing hormone. Subsequent RNA-sequencing yielded ~12 million reads, with an average length of 51 bp, and 71,062 contigs of >100 bp were constructed. Of the 953 contigs that were exclusively constructed from the reads of forskolin-induced granulosa layers, tBlastx analysis identified one contig (#f103496) that matched 17beta-hydroxysteroid dehydrogenase type 12. We found that mammalian cells transfected with full-length omhsd17beta12l exhibited considerable 20beta-HSD activity, as indicated by efficient conversion of exogenous 17alpha-P to DHP. In addition, we found that omhsd17beta12l mRNA levels were consistently low in follicles during vitellogenic growth; however, the levels increased significantly during final oocyte maturation. The levels of omhsd17beta12l mRNA were also considerably increased in granulosa layers in which 20beta-HSD activity was induced by salmon pituitary extract. Therefore, we suggest that omhsd17beta12l, not CR/20beta-HSD, is the 20beta-HSD responsible for DHP production by granulosa cells in masu salmon during final oocyte maturation. Comparison of mRNA levels between control and forskolin-incubated sample.
2016-08-04 | E-GEOD-85134 | biostudies-arrayexpress