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Series GSE68514 Query DataSets for GSE68514
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 (RNA-Seq)
Organism Neurospora crassa
Experiment type Expression 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.
Overall design RNAseq and ChIPseq was performed upon knockout mutants and wild type strains 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
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
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
Platforms (1)
GPL16164 Illumina HiSeq 2000 (Neurospora crassa)
Samples (11)
GSM1674169 2489_4X_Vogels1
GSM1674170 2489_4X_Vogels2
GSM1674171 2489_4X_Vogels3
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
BioProject PRJNA282963
SRA SRP057989

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SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE68514_RAW.tar 3.3 Mb (http)(custom) TAR (of TXT)
GSE68514_cuffdiff_2489_4N_vs_2489_4X_summary.txt.gz 440.1 Kb (ftp)(http) TXT
GSE68514_cuffdiff_2489_4N_vs_6971-const_4N_summary.txt.gz 438.2 Kb (ftp)(http) TXT
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Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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