Ribosome Profiling over a Zebrafish Developmental Timecourse
ABSTRACT: To experimentally-validate the non-coding status of annotated lncRNAs, we performed ribosome profiling over a developmental timecourse that matched our previously-published (Pauli et al. 2012) developmental transcriptome. We find that many previously-annotated lncRNAs appear to be translated, but in a pattern more akin to 5' leaders of coding genes. Ribosome profiling over 8 stages in early zebrafish development: 2-4 cell, 256 cell, 1K cell, Dome, Shield, Bud, 28hpf and 5dpf
Project description:microRNAs (miRNAs) are an evolutionarily conserved class of non-coding RNA molecules, which regulate kinds of biological processes at post-transcriptional level. Investigation of miRNAs expression profiles using high-throughput strategies is efficiently conductive to identify and characterize miRNAs. In this study, through Solexa deep sequencing approach, we obtained 115 orange spotted grouper (Epinephelus coioides) encoded miRNAs. Among them, 107 miRNAs shared high similarity with miRNAs encoded by zebrafish (Danio rerio) and other four vertebrates, indicating that cellular miRNAs are highly conserved between species. 18-26 nt small RNAs from GS cells were sequenced in one Solexa lane
Project description:DNA methylation undergoes dynamic changes during development and cell differentiation. Recent genome-wide studies discovered that tissue-specific differentially methylated regions (DMRs) often overlap tissue-specific distal cis-regulatory elements. However, developmental DNA methylation dynamics of the majority of the genomic CpGs outside gene promoters and CpG islands has not been extensively characterized. Here we generate and compare comprehensive DNA methylome maps of zebrafish developing embryos. From these maps, we identify thousands of developmental stage-specific DMRs (dsDMRs) across zebrafish developmental stages. The dsDMRs contain evolutionarily conserved sequences, are associated with developmental genes and are marked with active enhancer histone posttranslational modifications. Their methylation pattern correlates much stronger than promoter methylation with expression of putative target genes. When tested in vivo using a transgenic zebrafish assay, 20 out of 20 selected candidate dsDMRs exhibit functional enhancer activities. Our data suggest that developmental enhancers are a major target of DNA methylation changes during embryogenesis. MRE profiles of sperm and 2.5-hpf, 3.5-hpf, 4.5-hpf, 6-hpf and 24-hpf embryos were generated using Illumina HiSeq sequencing.
Project description:MicroRNAs regulate gene expression through deadenylation, repression and mRNA decay. However, the contribution of each mechanism in non-steady-state situations remains unclear. We monitored the impact of miR-430 on ribosome occupancy of endogenous mRNAs in wild type and dicer mutants lacking mature miR-430. Our results indicate that miR-430 reduces the number of ribosomes on target mRNAs before causing mRNA decay. Translational repression occurs before complete deadenylation, and disrupting deadenylation using an internal poly(A) tail did not block target repression. Finally, we observe that ribosome density along the length of the target mRNA remains constant, suggesting that translational repression occurs by reducing the initiation rate rather than reducing elongation or causing ribosomal drop-off. In summary, our results show that miR-430 regulates translation initiation before inducing mRNA decay. Time course parallel ribosome profiling and input mRNA quantification in wildtype and MZdicer mutant embryos
Project description:Zic3 regulates early embryonic patterning in vertebrates. Its loss-of-function disrupts gastrulation, left-right patterning, and neurogenesis. We use the zebrafish as a model to study the developmental role of Zic3 in vivo. Using a combination of two genomics approaches – ChIP-seq and microarray, we identified Zic3 targets, which include genes from the Nodal and Wnt pathways, and show for the first time cis-regulation of these genes by Zic3 using in vivo enhancer assay. We uncovered a previously unrecognized link between Zic3 and the non-canonical Wnt pathway in gastrulation and left-right patterning, and identified neural pre-pattern genes as Zic3 targets during the early steps of neural induction. Zic3 preferably binds to distal intergenic regions, some of which contain evolutionarily conserved functional enhancers. Our study establishes the zebrafish as an excellent model for genome-wide study of a transcription factor in vivo. Zic3 ChIP of wild type and sqet33 transgenic
Project description:Analysis of the binding sites of Hif-1α in both wild-type and von Hippel Lindau mutant zebrafish lines at 4dpf by ChIP linked next generation sequencing. The von Hippel Lindau mutant displays a systemic hypoxic response under normoxic conditions. Results show the extent of Hif-1α binding to the genome, and provide a basis for analysis of the transcriptional response to genetically induced hypoxia in zebrafish. Analysis of the DNA binding sites of Hif-1α in both wild-type and von Hippel Lindau mutant zebrafish lines at 4dpf. The von Hippel Lindau mutant displays a systemic hypoxic response under normoxic conditions. Results show the extent of Hif-1α binding to the genome, and provide a basis for analysis of the dependency of the transcriptional response on Hif-1α in conditions of genetically induced hypoxia in zebrafish.
Project description:ATF6 is a key regulator of the unfolded protein response. Through use of zebrafish and cultured cells we demonstrate that ATF6 drives fatty liver disease by interaction with fatty acid synthase (FASN). Total small RNA from livers of 5 dpf larval zebrafish were collected: 2 batches of Tg(fabp10:nls-mCherry) control larvae, 2 batches of ethanol-treated Tg(fabp10:nls-mCherry) larvae, and 1 batch of Tg(fabp10:nAtf6-cherry; cmlc2:GFP). Each batch was purified for preparation of high-throughput sequencing libraries.
Project description:UHRF1 is an essential regulator of DNA methylation that is highly expressed in many cancers. Using transgenic zebrafish, cultured cells and human tumors, we demonstrate that UHRF1 is an oncogene. RNAseq was used to assess the variation in gene expression between control and experimental samples. Total small RNA from 2 batches of Tg(fabp10:has.UHRF1-GFP)High and age matched Tg(fabp10:nls-mCherry) control 5 dpf zebrafish livers was purified for preparation of high-throughput sequencing libraries.
Project description:Sequencing libraries were generated from total RNA samples following the mRNAseq protocol for the generation of single end (16-36 hpf, 5 day larvae, adult head and adult tail) or paired end (24 hpf) libraries (Illumina). Single end reads of 36 nucleotides and paired end reads (2 x 76 nucleotides) were obtained with a GAIIx (Illumina). Gene expression at the different stages/tissu was assessed by cufflinks and HTseq. RNAseq on 5 differents samples: 24hpf embryos, pool of 16 hour to 36 hour embryos, 5 days old larvea, adult head and adult tail
Project description:Zebrafish is an important model system for the study of vertebrate embryonic development and adaptive immunese response. Recent years have seen great advancement in the understanding of the regulatory mechanisms during zebrafish embryogenesis and immune processes, yet large gaps still remain in the functional pathways critical for each developmental stage, especially for the late embryonic development. We sequenced the polyA-extracted mRNA from 9 stages covering 7 major developmental periods of zebrafish. Whole genome gene expression pattern were analyzed to reveal unknown pathways or factors with implicated roles during each stage of vertebrate development. Analysis of total mRNA by highthroughput sequencing in 9 stages covering 7 periods during the embryonic and larval development of zebrafish