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Genome-wide binding sites of Mss11 in Candida glabrata

ABSTRACT: We found Mss11 as a transcription factor is vital for the adhesion and biofilm formation abilities of C. glabrata, and it consequently impacts its virulence. This modulation is achieved by regulating C. glabrata Epa1 and Epa6 expression. To analyze Mss11 regulation of EPA1 and EPA6 expression further, we constructed the FLAG-tagged Mss11 and conducted ChIP-seq. The results revealed that Mss11 exhibited extensive binding across all chromosomes of C. glabrata, with enriched peaks predominantly concentrated within specific genomic features. In particular, most Mss11 binding sites were located within promoter regions of the genes (89.01%), with a smaller fraction in the upstream regions (4.95%) and the remainder distributed among the exon (3.30%) and intergenic (2.75%) regions. This binding pattern aligned with the expected behavior of Mss11 as a transcription factor. Notably, our investigation revealed that Mss11 binds to approximately 2829 bp upstream of EPA1 and 2576 bp upstream of EPA6, as well as to the promoter regions of the subtelomeric silencing-related genes SIR4, RIP1, and RAP1.

ORGANISM(S): Nakaseomyces glabratus

PROVIDER: GSE244916 | GEO | 2025/10/01

REPOSITORIES: GEO

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Project description:Transcription factors direct gene expression, and so there is much interest in mapping their genome-wide binding locations. M-BM- Current methods do not allow for the multiplexed analysis of TF binding, and this limits their throughput. We describe a novel method for determining the genomic target genes of multiple transcription factors simultaneously. DNA-binding proteins are endowed with the ability to direct transposon insertions into the genome near to where they bind. The transposon becomes a M-bM-^@M-^\Calling CardM-bM-^@M-^] marking the visit of the DNA-binding protein to that location. A unique sequence M-bM-^@M-^\barcodeM-bM-^@M-^] in the transposon matches it to the DNA-binding protein that directed its insertion. The sequences of the DNA flanking the transposon (which reveal where in the genome the transposon landed) and the barcode within the transposon (which identifies the TF that put it there) are determined by massively-parallel DNA sequencing. To demonstrate the methodM-bM-^@M-^Ys feasibility, we determined the genomic targets of eight transcription factors in a single experiment. The Calling Card method promises to significantly reduce the cost and labor needed to determine the genomic targets of many transcription factors in different environmental conditions and genetic backgrounds. These data contain Ty5 insertion sites mapped by an Illumina GAII analyzer in the S. cerevisiae genome for the background strain without any Sir4 present (1 run), in strains expressing Sir4-tagged copies of three well-characterized TFs: Gal4, Leu3, and Gcn4 (1 run each), and a multiplex of eight Sir4-tagged TFs pooled in a single experiment (2 biological replicates), and insertions from the Thi2-Sir4 fusion expressed from its native locus in two conditions (1 run each). The format of each insertions file is [chromosome number] [position of genomic base] [direction of insertion] [number of reads at that position]. Raw sequencing data comes in two varieties. Paired-end data contains a 5 bp barcode at the beginning of read #2. Single-end data contains a 2 bp barcode on the beggining of read #1.

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Genome-wide binding sites of Mss11 in Candida glabrata

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