DNA binding preferences of fungal SREBP transcription regulators
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA485525 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR7685430.fastq.gz | Fastqsanger.gz | |||
| SRR7685431.fastq.gz | Fastqsanger.gz | |||
| SRR7685432.fastq.gz | Fastqsanger.gz | |||
| SRR7685433.fastq.gz | Fastqsanger.gz | |||
| SRR7685426.fastq.gz | Fastqsanger.gz |
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Project description:Roquin proteins target specific RNA stem-loop motifs with their unique ROQ domain for mRNA degradation. The cellular levels of mRNAs are controlled by these post-transcriptional cis-regulatory stem-loop elements in the 3'-untranslated region (3'-UTR). Here, we first provide an RBNS (RNA Bind-n-Seq) experiment using pre-structured RNA libraries as input. This sRBNS (structured RBNS) was used to map Roquin's RNA binding preferences at nucleotide resolution, revealing preferences for loop sizes and consensus motifs for CDEs and ADEs.
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Project description:The Aspergillus fumigatus sterol regulatory element binding protein (SREBP) SrbA belongs to the basic Helix-Loop-Helix (bHLH) family of transcription factors and is crucial for antifungal drug resistance and virulence. The latter phenotype is especially striking, as loss of SrbA results in complete loss of virulence in murine models of invasive pulmonary aspergillosis (IPA). How fungal SREBPs mediate fungal virulence is unknown, though it has been suggested that lack of growth in hypoxic conditions accounts for the attenuated virulence. To further understand the role of SrbA in fungal infection site pathobiology, chromatin immunoprecipitation followed by massively parallel DNA sequencing (ChIP-seq) was used to identify genes under direct SrbA transcriptional regulation in hypoxia. These results confirmed the direct regulation of ergosterol biosynthesis and iron uptake by SrbA in hypoxia and revealed new roles for SrbA in nitrate assimilation and heme biosynthesis. Moreover, functional characterization of an SrbA target gene with sequence similarity to SrbA identified a new transcriptional regulator of the fungal hypoxia response and virulence, SrbB. SrbB co-regulates genes involved in heme biosynthesis and demethylation of C4 sterols with SrbA in hypoxic conditions. However, SrbB also has regulatory functions independent of SrbA including regulation of carbohydrate metabolism. Loss of SrbB markedly attenuates A. fumigatus virulence, and loss of both SREBPs further reduces in vivo fungal growth. These data suggest that both A. fumigatus SREBPs are critical for hypoxia adaptation and virulence and reveals new insights into SREBPM-bM-^@M-^Ys complex role in infection site adaptation and fungal virulence. 4 hour and 12 hour ChIP experiments were completed. Input control samples for each set were collected.
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