Using ChIP-seq to study action of Circadian Clock Components in Neurospora crassa
EMSL Project ID
60644
Abstract
Biofuel production using cellulases extracted from fungi has the potential to be a major resource to replace fossil fuels and regulating the synthesis of these and other enzymes is crucial for the economics of biofuel production from lignocellulose. Some of the best inducers of plant cell wall-degrading enzymes are filamentous fungi. However, environmental and cell-intrinsic controls on cellular metabolism are known to modulate the amount of cellulases that can be produced in fungi. The filamentous fungus Neurospora is commonly used in the production of cellulases for biofuel manufacture and it is also the principal fungal model system for the study of the effects of light and circadian clocks. The circadian clock plays a large role in the regulation of the Neurospora genome: as many as 40% of Neurospora genes can be clock regulated, including many genes that regulate metabolism. Although the dominant general role of the clock in metabolic regulation is appreciated, the degree to which the clock controls specific aspects of metabolism is not currently understood.
At the core of the circadian clock, a heterodimeric transcription factor (TF) drives expression of genes whose protein products feedback, physically interact with, and depress the activity of their heterodimeric activator. This negative feedback loop, yielding oscillatory TF activity, is the basis of fungal circadian rhythms. Output from this clock occurs when these TFs regulate genes whose products do not impact the core feedback loop. Neurospora crassa is a well-established model for the cellular circadian system, as well as being a model organism for cellulase over production, and is an extremely tractable system in which to pioneer modeling of these cellular clocks and their influence on metabolism. Previous EMSL cooperative agreements have used proteomics and high-throughput DNA sequencing to understand how the core clock works as well as how time information generated by the clock is transduced into the cell to control metabolic potential. In particular we have collaboratively used EMSL sequencing capabilities to carry out ChIP-seq to reveal how the clock operates and how time sculpts the transcriptional network. The manuscript reporting results of one such study (Wang et al. which includes to co-authors from EMSL staff) is in revision at Nature Communications (Impact factor ~17); however, the EMSL cooperative agreement supporting this collaboration has expired. The only remaining data requested by the Nature editors is replication, using independent biological samples, of ChIP-seq studies previously done at EMSL. This limited Scope Proposal will fund these repeat studies.
Project Details
Project type
Limited Scope
Start Date
2023-05-15
End Date
2023-05-01
Status
Closed
Released Data Link
Team
Principal Investigator