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Series GSE150256 Query DataSets for GSE150256
Status Public on Mar 09, 2021
Title DNA affinity purification sequencing and transcriptional profiling reveal new aspects of nitrogen regulation in a filamentous fungus
Organism Neurospora crassa
Experiment type Expression profiling by high throughput sequencing
Summary Sensing available nutrients and efficiently utilizing them is a challenge common to all organisms. The model filamentous fungus Neurospora crassa is capable of utilizing a variety of inorganic and organic nitrogen sources. Nitrogen utilization in N. crassa is regulated by a network of pathway-specific transcription factors in combination with nitrogen catabolite repression regulatory proteins. We identified an uncharacterized pathway-specific transcription factor, amn-1, that is required for utilization of proline, branched chain amino acids, and aromatic amino acids. AMN-1 also plays a role in regulating genes involved in responding to the simple sugar mannose, suggesting an integration of nitrogen and carbon metabolism. The utilization of nonpreferred nitrogen sources is also regulated by the nitrogen catabolite regulator NIT-2. Using RNA sequencing combined with DNA affinity purification sequencing, we performed a survey of the role of NIT-2 and pathway-specific transcription factors in directly regulating genes involved in nitrogen utilization. Our data shows that pathway-specific transcription factors regulate genes involved in the catabolism of specific nitrogen sources, while NIT-2 regulates genes involved in utilization of all nonpreferred nitrogen sources, such as nitrogen transporters. Together, these transcription factors form a nutrient sensing network that allows N. crassa cells to regulate nitrogen utilization.
 
Overall design mRNA profiles of wild type and mutant N. crassa cells exposed to carbon starvation, mannose, nitrogen starvation, alanine, arginine, glutamine, glutamate, glycine, isoleucine, proline, tryptophan, ammonium, and nitrate. There are 27 different strains and conditions each done in at least biological triplicate, which includes wild type controls for a total of 86 samples.
 
Contributor(s) Huberman LB, Wu VW, Kowbel DJ, Grigoriev IV, O'Malley RC, Glass NL
Citation(s) 33753477
Submission date May 11, 2020
Last update date Jun 08, 2021
Contact name Lori B Huberman
Organization name University of California Berkeley
Department Plant and Microbial Biology
Lab Glass Lab
Street address 2151 Berkeley Way
City Berkeley
State/province CA
ZIP/Postal code 94708
Country USA
 
Platforms (2)
GPL16164 Illumina HiSeq 2000 (Neurospora crassa)
GPL23150 Illumina HiSeq 4000 (Neurospora crassa)
Samples (86)
GSM4544352 Wild type Vogel's Minimal Medium Biological Replicate 1
GSM4544353 Wild type Vogel's Minimal Medium Biological Replicate 2
GSM4544354 Wild type Vogel's Minimal Medium Biological Replicate 3
Relations
BioProject PRJNA631679
SRA SRP261087

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

Supplementary file Size Download File type/resource
GSE150256_FPKM_Metafile.xlsx 7.1 Mb (ftp)(http) XLSX
GSE150256_RAW.tar 22.0 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
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