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Series GSE54831 Query DataSets for GSE54831
Status Public on Feb 11, 2014
Title Transcription Factor Regulation and Chromosome Dynamics in Pseudohyphal Growth
Organism Saccharomyces cerevisiae
Experiment type Expression profiling by high throughput sequencing
Summary Pseudohyphal growth is a developmental pathway seen in some strains of yeast, in which cells elongate and form multicellular filaments in response to environmental stresses. Regulation of this process is complex and involves multiple signaling pathways and a large number of transcription factors (TFs). We used multiplexed transposon “Calling Cards” to simultaneously record the genome-wide binding patterns of 28 TFs in nitrogen-starved yeast. We were able to identify TF targets relevant for pseudohyphal growth, producing a detailed map of the regulatory network that governs this process. Using tools from graph theory, we identified 8 transcription factors that lie at the center of this network, including Flo8, Mss11, and Mfg1, which bind as a complex. Surprisingly, the DNA binding preferences for these key transcription factors were not known. Using Calling Card data, we predicted the in vivo DNA binding motif for the Flo8-Mss11-Mfg1 complex and validated it using a reporter assay. We found that this complex binds several important targets, including FLO11, at both their promoter and termination sequences. We demonstrated that this binding pattern is the result of DNA-looping, which regulates the transcription of these targets and is stabilized by an interaction with the nuclear pore complex. This looping provides yeast cells with a transcriptional memory, enabling them to more rapidly execute the filamentous growth program when nitrogen-starved if they have been previously exposed to this condition.
Overall design These data contain mapped insertion sites from Ty5 transposon "Calling Cards" in Σ1278b yeast sequenced using an Illumina Hiseq. Other sequencing data present are RNA-seq reads.
Contributor(s) Mitra R
Citation(s) 25009286
Submission date Feb 10, 2014
Last update date May 15, 2019
Contact name David Mayhew
Organization name GlaxoSmithKline
Department Target Sciences, Computation Biology, R&D
Street address 1250 South Collegeville Road
City Collegeville
State/province PA
ZIP/Postal code 19426
Country USA
Platforms (1)
GPL13821 Illumina HiSeq 2000 (Saccharomyces cerevisiae)
Samples (30)
GSM1324530 Calling Cards - Flo8 insertions
GSM1324531 Calling Cards - Mss11 insertions
GSM1324532 Calling Cards - Mfg1 insertions
BioProject PRJNA237777
SRA SRP037541

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
GSE54831_CallingCards_pValue.txt.gz 260.4 Kb (ftp)(http) TXT
GSE54831_Expression_RPKM.txt.gz 128.5 Kb (ftp)(http) TXT
GSE54831_RAW.tar 2.0 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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