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Next Generation Sequencing Facilitates Quantitative Analysis of subcutaneous tumors untreated and treated with doxycycline for 4h to activate shST18

ABSTRACT: We report the transcriptome profiling (RNAseq) in hepatoblast-derived tumors, without (untreated) or with ST18 knockdown (4h Doxy) (three independent samples for each condition). We find that ST18 knockdown in hepatoblast-derived tumors affects inflammation-associated genes.

ORGANISM(S): Mus musculus

PROVIDER: GSE72403 | GEO | 2017/12/22

SECONDARY ACCESSION(S): PRJNA293975

REPOSITORIES: GEO

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Project description:Cortical development is a tightly spatiotemporally regulated process in which cell-fate specification is accompanied by stable resetting of transcriptional programs. However, the full repertoire of transcriptional regulators orchestrating such transcriptome changes remains largely incomprehensive. Applying a bioinformatics predictive approach we aimed to identify novel transcription factors contriuting to transcriptional reprogramming during embryonic neurogenesis and identified the neuronal tissue specific transcription factor St18 to be essential for neurogenesis in vitro and in vivo. We find that embryonic stem cells deficient for St18 are not able to efficiently differentiate along neuronal lineage and St18 depleted cells in the developing cortex do not elongate in shape and reside in the VZ/SVZ region but display premature expression of the upper layer neuronal marker Satb2. Relation of St18 binding to genes deregulated upon St18 depletion in vivo revealed St18 to function as transcriptional repressor at the time when neurogenesis is initiated. St18 ensures efficient onset of cortical neurogenesis by inhibiting expression of the self-renewal maintaining factor Hes1 that represses differentiation genes in neuronal progenitors as well as downregulation of genes that are essential for differentiation into mesodermal and endodermal lineage such as Lama5, Traf4 and Tab1. Furthermore we find this transcriptional repressor to be bound to genes that are important for later stages of neurogenesis when the neuronal circuitry is established likely to keep them in repressed state in the time window of neurogenesis when they are not yet required. These genes important for axon guidance and neurite outgrowth are subsequently prematurely upregulated in St18 depleted cortical cells. We further observe St18 to be bound to a significant fraction of intergenic enhancers where it regulates expression of nearest genes that Our data establish St18 as a novel transcriptional regulator during early onset of cortical neurogenesis that is essential to ensure timely expression kinetics of phase and lineage specific genes.

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Next Generation Sequencing Facilitates Quantitative Analysis of subcutaneous tumors untreated and treated with doxycycline for 4h to activate shST18

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