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Branchiostoma japonicum

ABSTRACT: Genic analysis of amphioxus adult notochord

PROVIDER: PRJDB16674 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	DRR503888_subreads.fastq.gz	Fastqsanger.gz
	DRR503889_1.fastq.gz	Fastqsanger.gz
	DRR503889_2.fastq.gz	Fastqsanger.gz

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microRNA expression changes after lipopolysaccharide treatment in gills of amphioxus Branchiostoma belcheri

Project description:Recently, amphioxus has served as a model for studying the origin and evolution of vertebrate immunity. However, little is known about how microRNAs (miRNAs) are involved in the immune defense in amphioxus. In this article, we identified the amphioxus miRNAs in the acute-phase response to Lipopolysaccharide (LPS). First, we determined the time point for the peak of immune response in amphioxus after LPS challenge by evaluating the expression of TLR4 and NF-κb(v-rel) which were commonly used immune response indicators. Then we performed miRNA microarray analysis on gill samples collected at the time point to select the differentially expressed miRNAs. Finally, we used real-time quantitative PCR to detect the expression patterns of amphioxus miRNAs under effective LPS challenge during the time course. The microarray data revealed that the miRNA expression file was significantly changed after LPS stimulation. The changes of the most upregulated and most downregualted miRNAs in gills of the amphioxus following challenge with LPS revealed a temporal induction kinetic. Our current study will provide valuable information to take an insight into molecular mechanism of innate immune and the evolution of the miRNA family.

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Branchiostoma belcheri

Project description:transcriptome analysis of different developmental stages of amphioxus (Branchiostoma belcheri)

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Base resolution methylome profiling of Branchiostoma lanceolatum embryos and adult tissues

Project description:To be able to fully comprehend the contribution of the epigenome to embryonic development, it is important to understand how various components of the epigenome evolved. To date, a number of studies have thoroughly described various epigenetic mechanisms in both vertebrates and invertebrates, however there is currently a lack of high resolution epigenomic data corresponding to animals that form the invertebrate-vertebrate boundary. To that end, we have sequenced the genome of the European amphioxus (Branchiostoma lanceolatum) and explored various layers of its epigenome. Our whole genome bisulfite sequencing (MethylC-seq) approach revealed that amphioxus displays invertebrate-like, mosaic DNA methylation patterns. Nevertheless, we found significant DNA methylation remodeling events taking place during tissue differentiation, mostly consisting of developmental hypomethylation. This developmental loss of DNA methylation temporally coincides with the activation of the Tet protein orthologue in the amphioxus genome, suggestive of active demethylation. Furthermore, comparisons with chromatin accessibility data (ATAC-seq) demonstrate that this demethylation event affects cis regulatory elements, as previously described in vertebrates. Altogether, our study provides a rich developmental resource for studying epigenome evolution and demonstrates for the first time the existence of embryonic DNA methylation remodeling in an invertebrate chordate.

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Project description:Solexa sequencing of small RNAs in Chinese Amphioxus

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Project description:Branchiostoma japonicum overview

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Branchiostoma japonicum

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Solexa sequencing of small RNAs in Chinese Amphioxus

Project description:We applied Solexa sequencing technology to identify Amphioxus microRNA genes. We identified 113 amphioxus microRNA genes, 55 were conserved across species and coded for 45 nonredundant mature miRNAs, whereas 58 were amphioxus-specific and accounted for 53 mature miRNAs. Analyzing the evolutionary history of amphioxus miRNAs, we found amphioxus possessed many miRNAs that are also found in chordates and vertebrates, suggesting these miRNAs may represent cephalochordate lineage innovation. By detailed comparison of the miRNA phylogenetic histories, we further found that amphioxus is more vertebrate-like than tunicates. Keywords: Small RNA 18-30 nt small RNAs from 12 adult Chinese Amphioxus were sequenced in one Solexa lane.

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