Details

Autor(en) / Beteiligte

• Shah, Vrutant V.
• Soibam, Benjamin
• Ritter, Ruth A.
• Benham, Ashley
• Oomen, Jamina
• Sater, Amy K.

Titel

MicroRNAs and ectodermal specification I. Identification of miRs and miR-targeted mRNAs in early anterior neural and epidermal ectoderm

Ist Teil von

• Developmental biology, 2017-06, Vol.426 (2), p.200-210

Ort / Verlag

United States: Elsevier Inc

Erscheinungsjahr

2017

Link zum Volltext

Quelle

Access via ScienceDirect (Elsevier)

Beschreibungen/Notizen

• The establishment of cell lineages occurs via a dynamic progression of gene regulatory networks (GRNs) that underlie developmental commitment and differentiation. To investigate how microRNAs (miRs) function in this process, we compared miRs and miR targets at the initiation of the two major ectodermal lineages in Xenopus. We used next-generation sequencing to identify over 170 miRs expressed in midgastrula ectoderm expressing either noggin or a constitutively active BMP receptor, reflecting anterior neural or epidermal ectoderm, respectively; 125 had not previously been identified in Xenopus. We identified the locations of the pre-miR sequences in the X. laevis genome. Neural and epidermal ectoderm express broadly similar sets of miRs. To identify targets of miR-dependent translational control, we co-immunoprecipitated Argonaute-Ribonucleoprotein (Ago-RNP) complexes from early neural and epidermal ectoderm and sequenced the associated RNA. The Ago-RNP RNAs from these tissues represent overlapping, yet distinct, subsets of genes. Moreover, the profile of Ago-RNP associated genes differs substantially from the profile of total RNAs in these tissues. We generated target predictions for the “high confidence” Ago-RNP RNAs using the identified ectodermal miRs; These RNAs generally had target sites for multiple miRs. Oct4 orthologues, as well as many of their previously identified transcriptional targets, are represented in the Ago-RNP pool in both tissues, suggesting that miR-dependent regulation contributes to the downregulation of the oct4 gene regulatory network and the reduction in ectodermal pluripotency. •Over 170 microRNAs were identified from midgastrula neural and epidermal ectoderm.•Over 6000 mRNAs were identified from Argonaute-RNP RNAs; these transcripts are candidate targets of microRNA-dependent regulation.•Target predictions of interactions between the ectodermal microRNAs and over 800 mRNAs that are enriched in Argonaute-RNP over total RNA suggest that these mRNAs include multiple target sites for microRNA binding.•Both the pou5f3 orthologues and the conserved targets of pou5f3 are predicted to interact with multiple microRNAs, suggesting that microRNA-dependent regulation of the pou5f3 network is highly robust.