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Gallus gallus

ABSTRACT: Genome-wide strategies identify downstream target genes of connective tissue-associated transcription factors [ChIP-seq TFs]

PROVIDER: PRJNA392019 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR5759330.fastq.gz	Fastqsanger.gz
	SRR5759340.fastq.gz	Fastqsanger.gz
	SRR5759331.fastq.gz	Fastqsanger.gz
	SRR5759341.fastq.gz	Fastqsanger.gz
	SRR5759322.fastq.gz	Fastqsanger.gz

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Project description:Genome-wide strategies identify downstream target genes of connective tissue-associated transcription factors [RNA-seq]

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Genome-wide strategies identify downstream target genes of connective tissue-associated transcription factors

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Genome-wide strategies identify downstream target genes of connective tissue-associated transcription factors [RNA-seq]

Project description:Connective tissues support organs and play crucial roles in development, homeostasis and fibrosis, yet our understanding of their formation is still limited. To gain insight into the molecular mechanisms of connective tissue specification, we selected five zinc finger transcription factors - OSR1, OSR2, EGR1, KLF2 and KLF4 - based on their expression patterns and/or known involvement in connective tissue subtype differentiation. RNA-seq and ChIP-seq profiling revealed a set of common genes regulated by all five transcription factors, which we propose as connective tissue core expression set. This common core was enriched in genes associated with axon guidance and myofibroblast signature, including fibrosis-related genes. In addition, each transcription factor regulated a specific set of signalling molecules and extracellular matrix components. This suggests a concept whereby local molecular niches can be created via the expression of specific transcription factors impinging on the specification of local microenvironments. The regulatory network established here identifies common and distinct molecular signatures of limb connective tissue subtypes, provides novel insight into the signalling pathways governing connective tissue specification, and serves as a resource for connective tissue development.

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Protein interaction networks of human transcription factors

Project description:Transcription factors (TFs) engage in protein-protein interactions throughout the process of transcriptional control. In this study, we have successfully identified the protein-protein interactions for more than 100 distinct human transcription factors (TFs) using the techniques of proximity-dependent biotinylation (BioID) and affinity purification mass spectrometry (AP-MS).

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A functional genomics approach identifies the GATA factor SERPENT as a tissue-specific partner of CLOCK/CYCLE in the Drosophila circadian clock

Project description:Broadly expressed transcriptions factors (TFs) control tissue-specific programs of gene expression through interactions with local TF networks. Prime examples are the circadian clock TFs CLOCK (CLK) and CYCLE (CYC or BMAL1): while they control a core transcriptional circuit throughout animal bodies, downstream clock target genes and circadian physiology are tissue-specific. Here, we use ChIP-seq to determine the regulatory targets of Drosophila CLK and CYC, which we epitope-tagged by homologous recombination. Both TFs have distinct binding sites in heads versus bodies, suggesting that they directly control tissue-specific downstream target genes. Analysis of these context-specific binding sites revealed distinct sequence motifs for putative clock partner factors, including a motif for the GATA factor SERPENT (SRP). SRP indeed synergistically enhances CLK/CYC-mediated activity of a cis-regulatory region bound by CLK/CYC specifically in bodies. These results reveal how universal clock circuits can generate tissue-specific outputs and demonstrate an approach to dissect regulatory interactions more generally. We sequenced ChIP and input samples, as well as M-bM-^@M-^\mockM-bM-^@M-^] samples for which we performed ChIP with the V5 antibody from wildtype w- flies (not carrying the V5 tag) for two independent biological replicates each, summing to 24 libraries in total.

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