Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Sequentially acting Sox transcription factors in neural lineage development [ChIP-seq]

ABSTRACT: We report sequential binding but unique functions of different Sox transcription factors during distinct stages of neural differentiation Examination of genome-wide Sox2, Sox3 and Sox11 transcription factor binding during different stages of neurogenesis.

ORGANISM(S): Mus musculus

SUBMITTER: Rickard Sandberg

PROVIDER: E-GEOD-33059 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Sequentially acting Sox transcription factors in neural lineage development.

Bergsland Maria M Ramsköld Daniel D Zaouter Cécile C Klum Susanne S Sandberg Rickard R Muhr Jonas J

Genes & development 20111115 23

Pluripotent embryonic stem (ES) cells can generate all cell types, but how cell lineages are initially specified and maintained during development remains largely unknown. Different classes of Sox transcription factors are expressed during neurogenesis and have been assigned important roles from early lineage specification to neuronal differentiation. Here we characterize the genome-wide binding for Sox2, Sox3, and Sox11, which have vital functions in ES cells, neural precursor cells (NPCs), and ...[more]

PMID: 22085726

Similar Datasets

Sequentially acting Sox transcription factors in neural lineage development [RNA-seq]

Project description:We report sequential binding but unique functions of different Sox transcription factors during distinct stages of neural differentiation Loss of function experiment for Sox2/Sox3 in neural progenitor cells and gene expression profile for Sox11 expressing (PSA NCAM sorted) early formed neurons.

2011-11-01 | E-GEOD-33060 | biostudies-arrayexpress

Sequentially acting Sox transcription factors in neural lineage development [microarray]

Project description:We report sequential binding but unique functions of different Sox transcription factors during distinct stages of neural differentiation We used microarray to examine the molecular function of Sox3 in neural progenitor cells. Over-expression of Sox3 under Nestin-promoter in neural progenitor cells. Cells are transgenic for GFP in Sox1 locus and were FACS sorted to obtain pure populations.

2011-11-01 | E-GEOD-33061 | biostudies-arrayexpress

Sequentially acting Sox transcription factors in neural lineage development

Project description:This SuperSeries is composed of the following subset Series: GSE33059: Sequentially acting Sox transcription factors in neural lineage development [ChIP-seq] GSE33060: Sequentially acting Sox transcription factors in neural lineage development [RNA-seq] GSE33061: Sequentially acting Sox transcription factors in neural lineage development [microarray] Refer to individual Series

2011-11-01 | E-GEOD-33024 | biostudies-arrayexpress

Identification of Highly Conserved Putative Developmental Enhancers Bound by SOX3 in Neural Progenitors Using ChIP-Seq

Project description:SOX3 is highly expressed in neural progenitor cells (NPC) within the developing mouse cetral nervous system. A ChIP-Seq experiement was performed for SOX3 in NPCs derived from embryonic stem cells. Identification of SOX3 binidng sites from 3 independent ChIP-seq samples in NPCs

2014-08-31 | E-GEOD-57186 | biostudies-arrayexpress

Sequentially acting Sox transcription factors in neural lineage development [microarray]

2011-11-01 | GSE33061 | GEO

Sequentially Acting SOX Proteins Orchestrate Astrocyte and Oligodendrocyte Specific Gene Expression

Project description:SOX transcription factors have important roles during astrocyte and oligodendrocyte development, but how glial genes are specified and activated in a sub-lineage specific fashion remains unknown. To address this question, we have defined glial specific gene expression in the developing spinal cord using single-cell RNA-sequencing. Moreover, conducting ChIP-seq analyses we show that these glial gene sets are extensively preselected already in multipotent neural precursor cells through the prebinding by SOX3. In the subsequent lineage-restricted glial precursor cells, astrocyte genes become additionally targeted by SOX9 at DNA-regions strongly enriched for Nfi binding-motifs, whereas oligodendrocyte genes become prebound by SOX9 only, at sites that during oligodendrocyte maturation are targeted by SOX10. Interestingly, reporter gene assays and functional studies in the spinal cord revealed that SOX3 binding represses the synergistic activation of astrocyte genes by SOX9 and NFIA, whereas oligodendrocyte genes are activated in a combinatorial manner by SOX9 and SOX10. These genome-wide studies demonstrate how sequentially expressed SOX proteins act on lineage-specific regulatory DNA-elements to coordinate glial gene expression both in a temporal and sub-lineage specific fashion.

2018-08-02 | GSE117997 | GEO

Sequentially acting Sox transcription factors in neural lineage development [RNA-seq]

Project description:We report sequential binding but unique functions of different Sox transcription factors during distinct stages of neural differentiation

2011-11-01 | GSE33060 | GEO

Sequentially acting Sox transcription factors in neural lineage development [ChIP-seq]

Project description:We report sequential binding but unique functions of different Sox transcription factors during distinct stages of neural differentiation

2011-11-01 | GSE33059 | GEO

Sequentially acting Sox transcription factors in neural lineage development.

Project description:Pluripotent embryonic stem (ES) cells can generate all cell types, but how cell lineages are initially specified and maintained during development remains largely unknown. Different classes of Sox transcription factors are expressed during neurogenesis and have been assigned important roles from early lineage specification to neuronal differentiation. Here we characterize the genome-wide binding for Sox2, Sox3, and Sox11, which have vital functions in ES cells, neural precursor cells (NPCs), and maturing neurons, respectively. The data demonstrate that Sox factor binding depends on developmental stage-specific constraints and reveal a remarkable sequential binding of Sox proteins to a common set of neural genes. Interestingly, in ES cells, Sox2 preselects for neural lineage-specific genes destined to be bound and activated by Sox3 in NPCs. In NPCs, Sox3 binds genes that are later bound and activated by Sox11 in differentiating neurons. Genes prebound by Sox proteins are associated with a bivalent chromatin signature, which is resolved into a permissive monovalent state upon binding of activating Sox factors. These data indicate that a single key transcription factor family acts sequentially to coordinate neural gene expression from the early lineage specification in pluripotent cells to later stages of neuronal development.

| S-EPMC3243056 | biostudies-literature

Sequentially acting SOX proteins orchestrate astrocyte- and oligodendrocyte-specific gene expression.

Project description:SOX transcription factors have important roles during astrocyte and oligodendrocyte development, but how glial genes are specified and activated in a sub-lineage-specific fashion remains unknown. Here, we define glial-specific gene expression in the developing spinal cord using single-cell RNA-sequencing. Moreover, by ChIP-seq analyses we show that these glial gene sets are extensively preselected already in multipotent neural precursor cells through prebinding by SOX3. In the subsequent lineage-restricted glial precursor cells, astrocyte genes become additionally targeted by SOX9 at DNA regions strongly enriched for Nfi binding motifs. Oligodendrocyte genes instead are prebound by SOX9 only, at sites which during oligodendrocyte maturation are targeted by SOX10. Interestingly, reporter gene assays and functional studies in the spinal cord reveal that SOX3 binding represses the synergistic activation of astrocyte genes by SOX9 and NFIA, whereas oligodendrocyte genes are activated in a combinatorial manner by SOX9 and SOX10. These genome-wide studies demonstrate how sequentially expressed SOX proteins act on lineage-specific regulatory DNA elements to coordinate glial gene expression both in a temporal and in a sub-lineage-specific fashion.

| S-EPMC6216240 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data