High-resolution DNA-binding specificity analysis of yeast transcription factors

Cong Zhu, Kelsey J R P Byers, Rachel Patton McCord, Zhenwei Shi, Michael F. Berger, Daniel E. Newburger, Katrina Saulrieta, Zachary Smith, Mita V. Shah, Mathangi Radhakrishnan, Anthony A. Philippakis, Yanhui Hu, Federico De Masi, Marcin Pacek, Andreas Rolfs, Tal Murthy, Joshua LaBaer, Martha L. Bulyk

Research output: Contribution to journalArticle

286 Citations (Scopus)

Abstract

Transcription factors (TFs) regulate the expression of genes through sequence-specific interactions with DNA-binding sites. However, despite recent progress in identifying in vivo TF binding sites by microarray readout of chromatin im-munoprecipitation (ChIP-chip), nearly half of all known yeast TFs are of unknown DNA-binding specificities, and many additional predicted TFs remain uncharacterized. To address these gaps in our knowledge of yeast TFs and their cis regulatory sequences, we have determined high-resolution binding profiles for 89 known and predicted yeast TFs, over more than 2.3 million gapped and ungapped 8-bp sequences ("k-mers"). We report 50 new or significantly different direct DNA-binding site motifs for yeast DNA-binding proteins and motifs for eight proteins for which only a consensus sequence was previously known; in total, this corresponds to over a 50% increase in the number of yeast DNA-binding proteins with experimentally determined DNA-binding specificities. Among other novel regulators, we discovered proteins that bind the PAC (Polymerase A and C) motif (GATGAG) and regulate ribosomal RNA (rRNA) transcription and processing, core cellular processes that are constituent to ribosome biogenesis. In contrast to earlier data types, these comprehensive k-mer binding data permit us to consider the regulatory potential of genomic sequence at the individual word level. These k-mer data allowed us to reannotate in vivo TF binding targets as direct or indirect and to examine TFs' potential effects on gene expression in ∼1700 environmental and cellular conditions. These approaches could be adapted to identify TFs and cis regulatory elements in higher eukaryotes.

Original languageEnglish (US)
Pages (from-to)556-566
Number of pages11
JournalGenome Research
Volume19
Issue number4
DOIs
StatePublished - Apr 2009
Externally publishedYes

Fingerprint

Transcription Factors
Yeasts
DNA
Fungal Proteins
Binding Sites
DNA-Binding Proteins
Gene Expression
Amino Acid Motifs
Consensus Sequence
Eukaryota
Ribosomes
Chromatin
Proteins

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

Cite this

Zhu, C., Byers, K. J. R. P., McCord, R. P., Shi, Z., Berger, M. F., Newburger, D. E., ... Bulyk, M. L. (2009). High-resolution DNA-binding specificity analysis of yeast transcription factors. Genome Research, 19(4), 556-566. https://doi.org/10.1101/gr.090233.108

High-resolution DNA-binding specificity analysis of yeast transcription factors. / Zhu, Cong; Byers, Kelsey J R P; McCord, Rachel Patton; Shi, Zhenwei; Berger, Michael F.; Newburger, Daniel E.; Saulrieta, Katrina; Smith, Zachary; Shah, Mita V.; Radhakrishnan, Mathangi; Philippakis, Anthony A.; Hu, Yanhui; De Masi, Federico; Pacek, Marcin; Rolfs, Andreas; Murthy, Tal; LaBaer, Joshua; Bulyk, Martha L.

In: Genome Research, Vol. 19, No. 4, 04.2009, p. 556-566.

Research output: Contribution to journalArticle

Zhu, C, Byers, KJRP, McCord, RP, Shi, Z, Berger, MF, Newburger, DE, Saulrieta, K, Smith, Z, Shah, MV, Radhakrishnan, M, Philippakis, AA, Hu, Y, De Masi, F, Pacek, M, Rolfs, A, Murthy, T, LaBaer, J & Bulyk, ML 2009, 'High-resolution DNA-binding specificity analysis of yeast transcription factors', Genome Research, vol. 19, no. 4, pp. 556-566. https://doi.org/10.1101/gr.090233.108
Zhu C, Byers KJRP, McCord RP, Shi Z, Berger MF, Newburger DE et al. High-resolution DNA-binding specificity analysis of yeast transcription factors. Genome Research. 2009 Apr;19(4):556-566. https://doi.org/10.1101/gr.090233.108
Zhu, Cong ; Byers, Kelsey J R P ; McCord, Rachel Patton ; Shi, Zhenwei ; Berger, Michael F. ; Newburger, Daniel E. ; Saulrieta, Katrina ; Smith, Zachary ; Shah, Mita V. ; Radhakrishnan, Mathangi ; Philippakis, Anthony A. ; Hu, Yanhui ; De Masi, Federico ; Pacek, Marcin ; Rolfs, Andreas ; Murthy, Tal ; LaBaer, Joshua ; Bulyk, Martha L. / High-resolution DNA-binding specificity analysis of yeast transcription factors. In: Genome Research. 2009 ; Vol. 19, No. 4. pp. 556-566.
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AU - Hu, Yanhui

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