Unknown,Transcriptomics,Genomics,Proteomics

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MRNA-Seq and microRNA-Seq whole-transcriptome analysis of rhesus monkey ESC neural differentiation revealed the potential rosette neural stem cell regulators

ABSTRACT: Rosette neural stem cells (R-NSCs) represent early stage of neural development and possess full neural differentiation and regionalization capacities. R-NSCs are considered as stem cells of neural lineage and have important implications in study of neurogenesis and cell replacement therapy. However, the molecules regulating their functional properties remain largely unknown. Rhesus monkey is ideal model to study human neural degenerative diseases and plays intermediate translational roles as therapeutic strategies evolve from rodent systems to human clinical applications. In this study, we derived R-NSCs from rhesus monkey embryonic stem cells (rESCs) and systematically investigated the unique expressions of mRNAs, microRNAs, and signaling pathways by genome-wide comparison of the mRNA and microRNA profilings of ESCs, R-NSCs at early (R-NSCP1) and late passages (R-NSCP6) and neural progenitor cells (NPCs). Apart from the R-NSCP1 specific protein-coding genes and microRNAs, we identified several pathways including Hedgehog and Wnt highly activated in R-NSCP1. The possible regulatory interactions among the microRNAs, protein-coding genes and signaling pathways were proposed. Besides, many genes with alternative splicing switch were identified at R-NSCP1. These data provided valuable resource to understand the regulation of early neurogenesis and to better manipulate the R-NSCs for cell replacement therapy. mRNA and miRNA profiles for four stages in rhesus embryonic stem cell neural differentiation, eight samples in all

ORGANISM(S): Macaca mulatta

SUBMITTER: Yuqi Zhao

PROVIDER: E-GEOD-53260 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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mRNA-Seq and microRNA-Seq whole-transcriptome analyses of rhesus monkey embryonic stem cell neural differentiation revealed the potential regulators of rosette neural stem cells.

Zhao Yuqi Y Ji Shuang S Wang Jinkai J Huang Jingfei J Zheng Ping P

DNA research : an international journal for rapid publication of reports on genes and genomes 20140617 5

Rosette neural stem cells (R-NSCs) represent early stage of neural development and possess full neural differentiation and regionalization capacities. R-NSCs are considered as stem cells of neural lineage and have important implications in the study of neurogenesis and cell replacement therapy. However, the molecules regulating their functional properties remain largely unknown. Rhesus monkey is an ideal model to study human neural degenerative diseases and plays intermediate translational roles ...[more]

PMID: 24939742

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Project description:Human pluripotent stem cell derived models that accurately recapitulate neural development in vitro and allow for the generation of specific neuronal subtypes are of major interest to the stem cell and biomedical community. Notch signaling, particularly through the Notch effector HES5, is a major pathway critical for the onset and maintenance of neural progenitor cells (NPCs) in the embryonic and adult nervous system1-3. Use of a HES5 reporter enables the isolation distinct populations of human embryonic stem (ES) cell derived NPCs that represent building blocks of cortical development in vitro4. Here, we report the transcriptional and epigenomic analysis of six consecutive stages of human ES cell differentiation along the neural lineage aimed at modeling key cell fate decisions including specification, expansion and patterning during the ontogeny of neural stem and progenitor cells. In order to dissect the regulatory mechanisms that orchestrate the stage-specific differentiation process we developed a computational framework to infer key regulators of each cell state transition based on the progressive remodeling of the epigenetic landscape and then validated these through a pooled shRNA screen. We were also able to refine our previous observations on epigenetic priming at transcription factor binding sites and show here that they are mediated by combinations of core and stage-specific factors. Taken together, we demonstrate the utility of our reference maps and outline a general framework, not limited to the context of the neural lineage, to dissect regulatory circuits of differentiation. hESC were differentiated in vitro into 5 different NPC populations (NE, ERG, MRG, LRG and LNP) over a time period of 220 days. The hESCs and the first 3 NPC populations (NE, ERG, MRG) were subjected to ChIP-Seq for H3K4m3, H3K4me1, H3K27ac and H3K27me3 as well as RNA-Seq with two biological replicates each as well as whole genome bisulfite sequencing in singlicate. The last two populations (LRG, LNP) were both profiled by RRBS and the LRG populations also by RNA-Seq. In addition, each of the first three NPC populations were differentiated into more mature neuronal populations (NEdN, ERGdN, MRGdN). The LRG population was differentiated along the astrocyte fate (LRGdA). Each of these more mature populations was subjected to RNA-Seq in replicate. Finally, the NE and MRG populations were profiled for the transcription facctor OTX2 by ChIP-Seq.