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| Status |
Public on Sep 01, 2015 |
| Title |
Identification of direct target genes of the Neurospora crassa essential plant biomass deconstruction transcription factors CLR-1, CLR-2 and XLR-1 (ChIP-Seq) |
| Organism |
Neurospora crassa |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
abstract: The plant cell wall is composed of many complex polymers, and its deconstruction requires an equally complex orchestration of a wide array of enzymes. In Neurospora crassa, clr-1, clr-2 and xlr-1 have been identified as the key transcription factors involved in cell wall breakdown. In order to define their regulons, we performed ChIPseq upon these three transcription factors. CLR-1, CLR-2 and XLR-1 each bind to the most highly and differentially expressed gene populations, which include the cellulases for the CLRs and the hemicellulases for XLR-1. CLR-1 also bound to its regulon under non-inducing conditions; however, this did not translate into gene expression. Motif analysis of the bound genes revealed conserved DNA binding motifs, with the CLR-2 motif matching that of its closest yeast homolog, GAL4. Co-immunoprecipitation studies were able to show that CLR-1 and CLR-2 act as homodimers. Finally, we report on a conserved XLR-1 point mutation that is sufficient to drive hemicellulase expression under non-inducing conditions. Understanding how these transcription factors work in concert to break down plant biomass can inform decisions on how to best engineer future fungal strains for decreased enzyme costs.
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| Overall design |
RNAseq and ChIPseq upon knockout mutants and sild type growing on various carbon sources to determin the role of the transcription factors: CLR-1, CLR-2, and XLR-1 in plant cell wall degradation
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| Contributor(s) |
Craig J, Coradetti S, Starr T, Glass NL |
| Citation(s) |
26463163 |
| |
| Submission date |
May 04, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
James Craig |
| E-mail(s) |
jimcraig134@gmail.com
|
| Organization name |
UC Berkeley
|
| Department |
Plant & Microbial Biology
|
| Lab |
N. Louise Glass
|
| Street address |
341A Koshland Hall
|
| City |
Berkeley |
| State/province |
CA |
| ZIP/Postal code |
94720 |
| Country |
USA |
| |
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| Platforms (1) |
| GPL16164 |
Illumina HiSeq 2000 (Neurospora crassa) |
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| Samples (22)
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| This SubSeries is part of SuperSeries: |
| GSE68517 |
Identification of direct target genes of the Neurospora crassa essential plant biomass deconstruction transcription factors CLR-1, CLR-2 and XLR-1 |
|
| Relations |
| BioProject |
PRJNA282962 |
| SRA |
SRP057990 |
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