Gene regulation in the development of the vertebrate nervous system

Abstract

Within the developing vertebrate neural tube, different types of neuron are specified in a stereotypical pattern. This pattern depends on the expression of a set of transcription factors by the secreted protein Sonic Hedgehog (Shh). The transcription factors form a regulatory network that determines the dynamics and patterns of gene expression

A systematic mechanistic understanding of this network remains elusive. To address this, we have generated RNA-seq and ChIP-seq data from neural cells in different states of the network. The aim of this project is to develop methods to analyse these data and to dissect the gene regulatory network.

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References:
[1]

Balaskas et al. (2012) Gene regulatory logic for reading the Sonic Hedgehog signaling gradient in the vertebrate neural tube. Cell 148, 273.

[2]

Park (2009) Chip-Seq: advantages and challenges of a maturing technology. Nature Reviews Genetics 10, 669.

[3]

Biggin (2011) Animal transcription networks as highly connected, quantitative continua. Developmental Cell 21, 611.

[4]

Bolouri & Davidson (2003) Transcriptional regulatory cascades in development: initial rates, not steady state, determine network kinetics. PNAS 100, 9371.

[5]

Shao et al. (2012) MANorm: a robust model for quantitative comparison of Chip-Seq data sets. Genome Biology 12, R16.


Biological Areas:

Neurobiology
Development

BBSRC Area:

Genes, development and STEM approaches to biology