Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcriptome-wide analysis of small RNA expression in early zebrafish development

ABSTRACT: During early vertebrate development, a large number of noncoding RNAs are maternally inherited or expressed upon activation of zygotic transcription. The exact identity, expression levels, and function during early vertebrate development for most of these noncoding RNAs remains largely unknown. miRNAs (microRNAs) and piRNAs (piwi-interacting RNAs) are two classes of small non-coding RNAs that play important roles in gene regulation during early embryonic development. Here, we utilized Illumina next generation sequencing technology to determine temporal expression patterns for both miRNAs and piRNAs during four distinct stages of early vertebrate development using zebrafish as a model system. For miRNAs, the expression patterns for 192 known miRNAs and 12 novel miRNAs within 123 different miRNA families were determined. Significant sequence variation was observed at the 5' and 3' ends of miRNAs with a large number of extra nucleotides added in a non-template directed manner. We also identified a large and diverse set of piRNAs expressed during early development, far beyond that expected if piRNA expression is restricted to germ cells. Our analyses represent the deepest investigation to date of small RNA expression during early vertebrate development and suggest important novel functions for small RNAs during embryogenesis. Identify the expression of small RNAs in zebrafish embryos of four different developmental stages using high through-put sequencing

ORGANISM(S): Danio rerio

SUBMITTER: Chunyao Wei

PROVIDER: E-GEOD-27722 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Transcriptome-wide analysis of small RNA expression in early zebrafish development.

Wei Chunyao C Salichos Leonidas L Wittgrove Carli M CM Rokas Antonis A Patton James G JG

RNA (New York, N.Y.) 20120308 5

During early vertebrate development, a large number of noncoding RNAs are maternally inherited or expressed upon activation of zygotic transcription. The exact identity, expression levels, and function for most of these noncoding RNAs remain largely unknown. miRNAs (microRNAs) and piRNAs (piwi-interacting RNAs) are two classes of small noncoding RNAs that play important roles in gene regulation during early embryonic development. Here, we utilized next-generation sequencing technology to determi ...[more]

PMID: 22408181

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Project description:Eukaryotic cells express several classes of small RNAs that regulate gene expression and ensure genome maintenance. Endogenous siRNAs (endo-siRNAs) and Piwi-interacting RNAs (piRNAs) mainly control gene and transposon expression in the germline, while microRNAs (miRNAs) generally function in post-transcriptional gene silencing in both somatic and germline cells. To provide an evolutionary and developmental perspective on small RNA pathways in nematodes, we identified and characterized known and novel small RNA classes through gametogenesis and embryo development in the parasitic nematode Ascaris suum and compared them with known small RNAs of Caenorhabditis elegans. piRNAs, Piwi-clade Argonautes, and other proteins associated with the piRNA pathway have been lost in Ascaris. miRNAs are synthesized immediately following fertilization in utero, prior to pronuclear fusion, and before the first cleavage of the zygote. This is the earliest expression of small RNAs ever described at a developmental stage long thought to be transcriptionally quiescent. A comparison of the two classes of Ascaris endo-siRNAs, 22G-RNAs and 26G-RNAs, to those in C. elegans, suggests great diversification and plasticity in the use of small RNA pathways during spermatogenesis in different nematodes. Our data reveal conserved characteristics of nematode small RNAs as well as features unique to Ascaris that illustrate significant flexibility in the use of small RNAs pathways, some of which are likely an adaptation to AscarisM-bM-^@M-^Y life cycle and parasitism. We constructed and analyzed 51 libraries from discrete regions of gametogenesis and synchronized stages of embryo development in the parasitic nematode Ascaris, using three types of small RNA libraries preparation methods: 1) 28 libraries of 18-34 or 18-40 nt RNAs with a 5M-bM-^@M-^Y monophosphate (5M-bM-^@M-^Y monophosphate libraries), 2) 4 libraries of 18-34 nt RNAs with a 5M-bM-^@M-^Y monophosphate but treated with periodate to enrich for small RNAs with 3M-bM-^@M-^Y end modifications (5M-bM-^@M-^Y monophosphate, 3M-bM-^@M-^Y end modified), and 3) 19 libraries of 18-28 or 18-40 nt RNAs with a 5M-bM-^@M-^Y triphosphate, diphosphate, or monophosphate (5M-bM-^@M-^Y allphosphate). These libraries enabled us to identify different small RNAs, characterize their different 5M-bM-^@M-^Y and 3M-bM-^@M-^Y ends, and their expression profiles through gametogenesis and embryogenesis.

Dataset Information

Transcriptome-wide analysis of small RNA expression in early zebrafish development

Publications

Transcriptome-wide analysis of small RNA expression in early zebrafish development.

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