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BMC Genomics 2013 Nov 06;14:762. doi: 10.1186/1471-2164-14-762.
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A genome-wide survey of maternal and embryonic transcripts during Xenopus tropicalis development.

Paranjpe SS , Jacobi UG , van Heeringen SJ , Veenstra GJ .

BACKGROUND: Dynamics of polyadenylation vs. deadenylation determine the fate of several developmentally regulated genes. Decay of a subset of maternal mRNAs and new transcription define the maternal-to-zygotic transition, but the full complement of polyadenylated and deadenylated coding and non-coding transcripts has not yet been assessed in Xenopus embryos. RESULTS: To analyze the dynamics and diversity of coding and non-coding transcripts during development, both polyadenylated mRNA and ribosomal RNA-depleted total RNA were harvested across six developmental stages and subjected to high throughput sequencing. The maternally loaded transcriptome is highly diverse and consists of both polyadenylated and deadenylated transcripts. Many maternal genes show peak expression in the oocyte and include genes which are known to be the key regulators of events like oocyte maturation and fertilization. Of all the transcripts that increase in abundance between early blastula and larval stages, about 30% of the embryonic genes are induced by fourfold or more by the late blastula stage and another 35% by late gastrulation. Using a gene model validation and discovery pipeline, we identified novel transcripts and putative long non-coding RNAs (lncRNA). These lncRNA transcripts were stringently selected as spliced transcripts generated from independent promoters, with limited coding potential and a codon bias characteristic of noncoding sequences. Many lncRNAs are conserved and expressed in a developmental stage-specific fashion. CONCLUSIONS: These data reveal dynamics of transcriptome polyadenylation and abundance and provides a high-confidence catalogue of novel and long non-coding RNAs.

PubMed ID: 24195446
PMC ID: PMC3907017
Article link: BMC Genomics
Grant support: [+]

Species referenced: Xenopus tropicalis
Genes referenced: aurka aurkb birc5 bmp4 cbx4 ccnb1 cdc25c cdk2 celf1 celf3 cer1 chrd eomes ezh2 fbxo43 fbxo5 fgf8 foxa2 foxc1 foxc2 gata1 gata4 gsc h2ac16 h2ac21 h2ac7 h4c12 hdac3 hes7.1 irx5 kif11 lef1 lhx1 mos myod1 neurog1 nkx2-5 nodal3.2 nodal5 nodal6 pax6 sia1 sia2 tacc3 tal1 tbxt tcf3 wnt4

GEO Series: GSE43652: Xenbase,  NCBI

Article Images: [+] show captions
References [+] :
Aanes, Zebrafish mRNA sequencing deciphers novelties in transcriptome dynamics during maternal to zygotic transition. 2011, Pubmed