title: Major transcriptome re-organisation and abrupt changes in signalling, cell cycle and chromatin regulation at neural differentiation in vivo.
abstract: Here, we exploit the spatial separation of temporal events of neural differentiation in the elongating chick body axis to provide the first analysis of transcriptome change in progressively more differentiated neural cell populations in vivo. Microarray data, validated against direct RNA sequencing, identified: (1) a gene cohort characteristic of the multi-potent stem zone epiblast, which contains neuro-mesodermal progenitors that progressively generate the spinal cord; (2) a major transcriptome re-organisation as cells then adopt a neural fate; and (3) increasing diversity as neural patterning and neuron production begin. Focussing on the transition from multi-potent to neural state cells, we capture changes in major signalling pathways, uncover novel Wnt and Notch signalling dynamics, and implicate new pathways (mevalonate pathway/steroid biogenesis and TGFβ). This analysis further predicts changes in cellular processes, cell cycle, RNA-processing and protein turnover as cells acquire neural fate. We show that these changes are conserved across species and provide biological evidence for reduced proteasome efficiency and a novel lengthening of S phase. This latter step may provide time for epigenetic events to mediate large-scale transcriptome re-organisation; consistent with this, we uncover simultaneous downregulation of major chromatin modifiers as the neural programme is established. We further demonstrate that transcription of one such gene, HDAC1, is dependent on FGF signalling, making a novel link between signals that control neural differentiation and transcription of a core regulator of chromatin organisation. Our work implicates new signalling pathways and dynamics, cellular processes and epigenetic modifiers in neural differentiation in vivo, identifying multiple new potential cellular and molecular mechanisms that direct differentiation.
authors: Division of Cell and Developmental Biology, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK.
authors: Isabel
authors: I
authors: Olivera-Martinez
authors: Division of Computational Biology, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK.
authors: Nick
authors: N
authors: Schurch
authors: Division of Cell and Developmental Biology, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK.
authors: Roman A
authors: RA
authors: Li
authors: Division of Cell and Developmental Biology, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK.
authors: Junfang
authors: J
authors: Song
authors: Division of Cell and Developmental Biology, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK.
authors: Pamela A
authors: PA
authors: Halley
authors: Division of Cell and Developmental Biology, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK.
authors: Raman M
authors: RM
authors: Das
authors: Department of Genomics and Genetics, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK.
authors: Dave W
authors: DW
authors: Burt
authors: Division of Computational Biology, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK.
authors: Geoffrey J
authors: GJ
authors: Barton
authors: Division of Cell and Developmental Biology, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK k.g.storey@dundee.ac.uk.
authors: Kate G
authors: KG
authors: Storey
mesh_terms: D000818:Animals; D019521:Body Patterning; D002453:Cell Cycle; D002454:Cell Differentiation; D019070:Cell Lineage; D002642:Chick Embryo; D002843:Chromatin / Q000378:metabolism*; D044127:Epigenesis, Genetic; D005346:Fibroblast Growth Factors / Q000378:metabolism; D018507:Gene Expression Regulation, Developmental; D056284:Histone Deacetylase 1 / Q000378:metabolism; D051379:Mice; D055495:Neurogenesis / Q000502:physiology*; D009474:Neurons / Q000166:cytology*; D020411:Oligonucleotide Array Sequence Analysis; D017423:Sequence Analysis, RNA; D015398:Signal Transduction; D013116:Spinal Cord / Q000196:embryology; D013997:Time Factors; D059467:Transcriptome; D016212:Transforming Growth Factor beta / Q000378:metabolism
chemical_list: D002843:Chromatin; D016212:Transforming Growth Factor beta; D005346:Fibroblast Growth Factors; D056284:Histone Deacetylase 1
keywords: Cell cycle; Chick embryo; Chromatin; FGF signalling; Neural differentiation; Transcriptome