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Regional specific differentiation of integumentary organs: SATB2 is involved in α- and β-keratin gene cluster switching in the chicken

ABSTRACT: Regional specific differentiation of integumentary organs: SATB2 is involved in α- and β-keratin gene cluster switching in the chicken

PROVIDER: PRJNA739906 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR14877343.fastq.gz	Fastqsanger.gz
	SRR14877344.fastq.gz	Fastqsanger.gz
	SRR14877345.fastq.gz	Fastqsanger.gz
	SRR14877346.fastq.gz	Fastqsanger.gz
	SRR14877347.fastq.gz	Fastqsanger.gz

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Regional specific differentiation of integumentary organs: SATB2 is involved in α- and β-keratin gene cluster switching in the chicken

Project description:Animals develop skin regional specificities to best adapt to their environments. Birds are excellent models in which to study the epigenetic mechanisms that facilitate these adaptions. Patients suffering from SATB2 mutations exhibit multiple defects including ectodermal dysplasia-like changes. The preferential expression of SATB2, a chromatin regulator, in feather-forming compared to scale-forming regions, suggests it functions in regional specification of chicken skin appendages by acting on either differentiation or morphogenesis. Retrovirus mediated SATB2 misexpression in developing feathers, beaks, and claws causes epidermal differentiation abnormalities (e.g. knobs, plaques) with few organ morphology alterations. Chicken β-keratins are encoded in 5 sub-clusters (Claw, Feather, Feather-like, Scale, and Keratinocyte) on Chromosome 25 and a large Feather keratin cluster on Chromosome 27. Type I and II α-keratin clusters are located on Chromosomes 27 and 33, respectively. Transcriptome analyses showed these keratins 1) are often tuned up or down collectively as a sub-cluster, and 2) these changes occur in a temporo-spatial specific manner. This cluster-level suppression is also seen in MMPs on Chromosome 1. SATB2 alters gene expression changes of most other transcripts without this cluster-level switching. These results suggest an organizing role of SATB2 in cluster-level gene co-regulation during skin regional specification.

2021-08-14 | GSE178651 | GEO

Regional specific differentiation of integumentary organs: SATB2 is involved in α- and β-keratin gene cluster switching in the chicken.

Project description:BackgroundAnimals develop skin regional specificities to best adapt to their environments. Birds are excellent models in which to study the epigenetic mechanisms that facilitate these adaptions. Patients suffering from SATB2 mutations exhibit multiple defects including ectodermal dysplasia-like changes. The preferential expression of SATB2, a chromatin regulator, in feather-forming compared to scale-forming regions, suggests it functions in regional specification of chicken skin appendages by acting on either differentiation or morphogenesis.ResultsRetrovirus mediated SATB2 misexpression in developing feathers, beaks, and claws causes epidermal differentiation abnormalities (e.g. knobs, plaques) with few organ morphology alterations. Chicken β-keratins are encoded in 5 sub-clusters (Claw, Feather, Feather-like, Scale, and Keratinocyte) on Chromosome 25 and a large Feather keratin cluster on Chromosome 27. Type I and II α-keratin clusters are located on Chromosomes 27 and 33, respectively. Transcriptome analyses showed these keratins (1) are often tuned up or down collectively as a sub-cluster, and (2) these changes occur in a temporo-spatial specific manner.ConclusionsThese results suggest an organizing role of SATB2 in cluster-level gene co-regulation during skin regional specification.

| S-EPMC8742846 | biostudies-literature

ChIP-seq for Satb2 in E15 cortex

Project description:The goal of the study was to identify the binding site of SATB2 in wild-ype cortex by performing ChIP-seq using SATB2 antibody. E15 cortical tissues were dissected, lysed and fixed. Chromatin was prepared by sonication. Sequences bound by SATB2 protein was precipitated using a SATB2 antibody. Sequencing was performed on Illumina Genome Analyzer II. SATB2 binding peaks were called using MACS. ChIP for Satb2, followed by sequencing on Illumina Genome Analyzer II platform

2015-09-08 | E-GEOD-68910 | biostudies-arrayexpress

Folding Keratin Gene Clusters During Skin Specification

Project description:Regional specification is critical for skin development, regeneration and evolution. The contribution of epigenetics in this process remains unknown. Here using avian epidermis we find two major strategies regulate β-keratin gene clusters. 1) Over the body, macro-regional specificities (scales, feathers, claws, etc) established by typical enhancers control five sub-clusters located within the epidermal differentiation complex on chromosome 25; 2) Within a feather, micro-regional specificities are orchestrated by temporo-spatial chromatin looping of the feather β-keratin gene cluster on chromosome 27. Analyses suggest a 3-factor model for regional specification: competence factors (e.g., AP1) make chromatin accessible, regional specifiers (e.g., Zic1) target specific genome regions, and chromatin organizers (e.g., CTCF, SATB2) establish looping configurations. Gene perturbations disrupt morphogenesis and histo-differentiation. This chicken skin paradigm advances our understanding of how regulation of big gene clusters can set up a two-dimensional body surface map.

2020-06-08 | GSE136224 | GEO

Role of Satb1 and Satb2 in embryonic stem cells

Project description:Satb1 and Satb2 are regulators of higher order chromatin in T cells and osteoblasts repectively. We were interested if Satb1 and Satb2 play a role in the regulation of gene expression in ES cells. This SuperSeries is composed of the following subset Series: GSE17487: Expression data in WT and Satb1-/- ES cells GSE17488: Expression data in WT and ES cells overexpressing Satb1 GSE17489: Expression data in WT and ES cells overexpressing Satb2 Refer to individual Series

2009-09-01 | E-GEOD-17490 | biostudies-arrayexpress

Expression data from Minoxdil, Keratin and microsphere keratin in vivo

Project description:Gene expression profiling reveals a potential effect of microsphere keratin in stimulating hair growth in vivo Mice back was depilated and then treated with 1% milliQ, 1% minoxidil, 1% keratin, 1% microsphere keratin for 20 days. Then the skin was collected and RNA was extracted from thetreatd skin as explained in the following section. The microarray was conducted for two biological replicates

2022-11-15 | GSE217935 | GEO

ChIP-seq for Satb2 in E15 cortex

2015-09-08 | GSE68910 | GEO

Expression data from Minoxdil, Keratin and microsphere keratin in vivo

Project description:Expression data from Minoxdil, Keratin and microsphere keratin in vivo

| PRJNA901424 | ENA

RNA-seq of postnatal day 0 (P0) wild-type and Satb2-/- cortices

Project description:The goal of the study was to compare gene expression of P0 wild-type and P0 Satb2-/- cortices. Total RNAs were isolated from P0 cortices dissected from wild-type and Satb2-/- mice (n=3 for each genotype), following Qiagen RNAeasy kit instruction.Sequence libraries were made following Illumina RNA TruSeq library preparation guide.The libaries were pair-end sequenced (50nt per end). Differentially expressed genes were identified by DESEQ. Total RNAs were isolated from P0 cortices (3 control and 3 mutants), and sequenced on Illumina Genome Analyzer

2015-09-08 | E-GEOD-68911 | biostudies-arrayexpress

Expression data in WT and ES cells overexpressing Satb2

Project description:Satb1 and Satb2 are regulators of higher order chromatin in T cells and osteoblasts repectively. We were interested if Satb1 and Satb2 play a role in the regulation of gene expression in ES cells. ES cells which can inducibly express Satb1 or Satb2 were generated using the tet-ON system. In this experiment, we compared gene expression in uninduced cells to that in cells which had been induced for 24h to express Satb2 ectopcially at very high levels.

2009-09-01 | GSE17489 | GEO

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