Design of Compact, Universal DNA Microarrays for Protein Binding Microarray Experiments

Philippakis, Anthony; Qureshi, Aaron M.; Berger, Michael F.; Bulyk, Martha L.

doi:10.1007/978-3-540-71681-5_30

Cited by 9 publications

(9 citation statements)

References 19 publications

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“…We constructed microarrays covering all 10-bp sequence variants (Berger et al 2006;Philippakis et al 2008) by converting highdensity single-stranded oligonucleotide arrays to double-stranded DNA arrays (Berger et al 2006;Berger and Bulyk 2009). Using these universal arrays, we measured the relative preferences of a TF for all possible contiguous 8-mers, as well as gapped 8-mers spanning up to 10 total positions.…”

Section: Protein-binding Microarrays (Pbms)mentioning

confidence: 99%

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

Zhu¹,

Byers²,

McCord³

et al. 2009

Genome Res.

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375

497

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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 immunoprecipitation (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.

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Section: Protein-binding Microarrays (Pbms)mentioning

confidence: 99%

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

Zhu¹,

Byers²,

McCord³

et al. 2009

Genome Res.

Self Cite

375

497

View full text Add to dashboard Cite

show abstract

“…The Hmo1 DNA-binding sequence motif was derived using a kinetic MITOMI approach (Geertz et al 2012b). A De Bruijn sequence covering all 8-mer sequence variants was calculated (Philippakis et al 2008) and then synthesized as overlapping oligonucleotide pairs that were converted to dsDNA using Cy3 and Cy5 extension primers (Geertz et al 2012a). Kinetic MITOMI measurements were performed to derive dissociation rate constants for all 8-mer De Bruijn sequence oligonucleotides, which were then ranked by inferred k off values.…”

Section: Mitomi Measurements and Motif-finding Analysesmentioning

confidence: 99%

Two distinct promoter architectures centered on dynamic nucleosomes control ribosomal protein gene transcription

et al. 2014

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In yeast, ribosome production is controlled transcriptionally by tight coregulation of the 138 ribosomal protein genes (RPGs). RPG promoters display limited sequence homology, and the molecular basis for their coregulation remains largely unknown. Here we identify two prevalent RPG promoter types, both characterized by upstream binding of the general transcription factor (TF) Rap1 followed by the RPG-specific Fhl1/Ifh1 pair, with one type also binding the HMG-B protein Hmo1. We show that the regulatory properties of the two promoter types are remarkably similar, suggesting that they are determined to a large extent by Rap1 and the Fhl1/Ifh1 pair. Rapid depletion experiments allowed us to define a hierarchy of TF binding in which Rap1 acts as a pioneer factor required for binding of all other TFs. We also uncovered unexpected features underlying recruitment of Fhl1, whose forkhead DNA-binding domain is not required for binding at most promoters, and Hmo1, whose binding is supported by repeated motifs. Finally, we describe unusually micrococcal nuclease (MNase)-sensitive nucleosomes at all RPG promoters, located between the canonical +1 and -1 nucleosomes, which coincide with sites of Fhl1/Ifh1 and Hmo1 binding. We speculate that these ''fragile'' nucleosomes play an important role in regulating RPG transcriptional output.

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“…Two major limiting factors in building TRNs for TFs have been (1) identification TF DNA‐binding motifs and (2) determination of the biological significance of such motifs throughout the genome. The development of protein‐binding microarrays (PBMs) has led to the identification of motifs for several hundred DNA‐binding proteins 179–185. This technology provides an opportunity to identify cis ‐regulatory ‘codes’ or ‘modules’ for coregulated genes.…”

Section: Novel Tools and Approaches In Systems‐level Analysismentioning

confidence: 99%

Building the developmental oculome: systems biology in vertebrate eye development and disease

Lachke

Maas

2010

WIREs Mechanisms of Disease

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The vertebrate eye is a sophisticated multi-component organ that has been actively studied for over a century, resulting in the identification of the major embryonic and molecular events involved in its complex developmental program. Data gathered so far provides sufficient information to construct a rudimentary network of the various signaling molecules, transcription factors and their targets for several key stages of this process. With the advent of genomic technologies, there has been a rapid expansion in our ability to collect and process biological information, and the use of systems-level approaches to study specific aspects of vertebrate eye development has already commenced. This is beginning to result in the definition of the dynamic developmental networks that operate in ocular tissues, and the interactions of such networks between coordinately developing ocular tissues. Such an integrative understanding of the eye by a comprehensive systems-level analysis can be termed the “oculome”, and that of serial developmental stages of the eye as it transits from its initiation to a fully formed functional organ represents the “developmental oculome”. Construction of the developmental oculome will allow novel mechanistic insights that are essential for organ regeneration-based therapeutic applications, and the generation of computational models for eye disease states to predict the effects of drugs. This review discusses our present understanding of two of the individual components of the developing vertebrate eye – the lens and retina – at both the molecular and systems levels, and outlines the directions and tools required for construction of the developmental oculome.

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Design of Compact, Universal DNA Microarrays for Protein Binding Microarray Experiments

Cited by 9 publications

References 19 publications

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

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

Two distinct promoter architectures centered on dynamic nucleosomes control ribosomal protein gene transcription

Building the developmental oculome: systems biology in vertebrate eye development and disease

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