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Binding of High Mobility Group A proteins to the mammalian genome occurs as a function of AT-content

ABSTRACT: Binding of High Mobility Group A proteins to the mammalian genome occurs as a function of AT-content

PROVIDER: PRJNA391931 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR5749540.fastq.gz	Fastqsanger.gz
	SRR5749550.fastq.gz	Fastqsanger.gz
	SRR5749560.fastq.gz	Fastqsanger.gz
	SRR5749570.fastq.gz	Fastqsanger.gz
	SRR5749580.fastq.gz	Fastqsanger.gz

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Binding of High Mobility Group A proteins to the mammalian genome occurs as a function of AT-content [RNA-Seq]

Project description:High mobility group (HMG) proteins are of similar size as histones with HMGA1 and HMGA2 being particularly abundant in replicating normal tissues and in cancerous cells. While numerous roles for HMGA proteins have been proposed we lack a comprehensive description of their genomic location as a function of chromatin, DNA sequence and functional domains. Here we report such a characterization of HMGA proteins in mouse embryonic stem cells in which we introduce biotin-tagged constructs of wild-type and DNA binding domain mutants. Comparative analysis of their genome-wide distribution reveals pervasive binding, a feature that critically depends on a functional DNA binding domain and which is shared by both HMGA proteins. Assessment of the underlying queues instructive for this binding modality identifies AT richness as the major criteria for local binding. Additionally, we show that other chromatin states such as those linked to cis-regulatory regions have little impact on HMGA binding both in stem and differentiated cells. As a consequence HMGA proteins are found most enriched at regions of higher AT density such as constitutively heterochromatic regions but are absent from enhancers and promoters arguing for a limited role in regulating individual genes. In line with this model we show that genetic deletion of HMGA proteins in stem cells causes limited transcriptional effects and that binding is conserved in neuronal progenitors.

2017-12-21 | GSE100406 | GEO

Binding of High Mobility Group A proteins to the mammalian genome occurs as a function of AT-content [ChIP-Seq]

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Binding of High Mobility Group A proteins to the mammalian genome occurs as a function of AT-content

Project description:This SuperSeries is composed of the SubSeries listed below.

2017-12-21 | GSE100407 | GEO

Binding of high mobility group A proteins to the mammalian genome occurs as a function of AT-content.

Project description:Genomic location can inform on potential function and recruitment signals for chromatin-associated proteins. High mobility group (Hmg) proteins are of similar size as histones with Hmga1 and Hmga2 being particularly abundant in replicating normal tissues and in cancerous cells. While several roles for Hmga proteins have been proposed we lack a comprehensive description of their genomic location as a function of chromatin, DNA sequence and functional domains. Here we report such a characterization in mouse embryonic stem cells in which we introduce biotin-tagged constructs of wild-type and DNA-binding domain mutants. Comparative analysis of the genome-wide distribution of Hmga proteins reveals pervasive binding, a feature that critically depends on a functional DNA-binding domain and which is shared by both Hmga proteins. Assessment of the underlying queues instructive for this binding modality identifies AT richness, defined as high frequency of A or T bases, as the major criterion for local binding. Additionally, we show that other chromatin states such as those linked to cis-regulatory regions have little impact on Hmga binding both in stem and differentiated cells. As a consequence, Hmga proteins are preferentially found at AT-rich regions such as constitutively heterochromatic regions but are absent from enhancers and promoters arguing for a limited role in regulating individual genes. In line with this model, we show that genetic deletion of Hmga proteins in stem cells causes limited transcriptional effects and that binding is conserved in neuronal progenitors. Overall our comparative study describing the in vivo binding modality of Hmga1 and Hmga2 identifies the proteins' preference for AT-rich DNA genome-wide and argues against a suggested function of Hmga at regulatory regions. Instead we discover pervasive binding with enrichment at regions of higher AT content irrespective of local variation in chromatin modifications.

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CpG islands and GC content dictate nucleosome depletion in a transcription independent manner at mammalian promoters

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Mammalian oocytes store proteins in cytoplasmic lattices

Project description:Mammalian oocytes store proteins in cytoplasmic lattices

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