Transcriptional regulation of development in time and space

Human development requires the generation of trillions of cells with myriad functions from a single cell. This requires that restriction of stem cell fate competence and proliferation are precisely temporally and spatially patterned as the embryo grows. To accomplish this, the chromatin landscape of individual stem cells progressively constrains gene expression in a context specific manner in order to guide cell behavior. In turn, this context is provided by the cellular environment and intrinsic determinants via the activity of transcription factors.

In paper I, we utilize ChIP-sequencing to study the overlapping and specific activities of the transcription factor sex determining region Y-box 2 (SOX2) in the developing cortex, spinal cord, stomach and lungs. We show that cell type specific binding is associated with tissue specific gene expression, while commonly bound cis-regulatory modules neighbor genes involved in the core processes of stem cell maintenance and proliferation.

In paper II, we use DNase- and ChIP-sequencing to demonstrate that, though the accessible chromatin landscape in the spinal cord and cortex are highly overlapping, SOX2 binding is primarily specific to one region. We find that this is due to an association with the specifically expressed partner transcription factors HOXA9 in spinal cord and LHX2 in cortex, which are capable of respecifying gene expression when misexpressed.

In paper III, we exploit single cell RNA-sequencing to establish that the stem cell population of the early cortex expresses high levels of S o x2, exhibits features of multipotency, and is enriched for genes involved in mitosis, such as Ccnb1/2. In contrast, the committed progenitor pool expresses high levels of the G1/S-phase genes, including Ccnd1, which is capable of inducing differentiation when overexpressed.

In paper IV, we find that Sox2 acts in a dose-dependent fashion to control proliferation in the developing cortex by directly repressing Ccnd1. We show that this is accomplished via the binding of off-consensus sites in the Ccnd1 promoter, and an association with Wnt signal transducing, TCF/LEF, transcription factors and their established co-repressor, TLE1.

List of scientific papers

I. Hagey DW, Zouter C, Bergsland M, Klum S, Kurtsdotter I, Andersson O, and Muhr, J. SOX2 regulates common and specific stem cell features in the CNS and endoderm derived organs. [Manuscript]

II. Hagey DW, Zaouter C, Combeau G, Lendahl MA, Andersson O, Huss M and Muhr J. Distinct transcription factor complexes act on a permissive chromatin landscape to establish regionalized gene expression in CNS stem cells. Genome Research. 2016 Jul; 26(7):908-17.
https://doi.org/10.1101/gr.203513.115

III. Hagey DW, Topcic D, Kee N, Perlmann T and Muhr J. Cell cycle dependent regulation of cortical progenitor multipotency. [Manuscript]

IV. Hagey DW and Muhr J. Sox2 acts in a dose-dependent fashion to regulate proliferation of cortical progenitors. Cell Reports. 2014 Dec 11; 9(5):1908-20.
https://doi.org/10.1016/j.celrep.2014.11.013