Promoter-specific binding of Rap1 revealed by genome-wide maps of protein–DNA association

By J. Lieb, Xiaole Shirley Liu, David Botstein, Patrick O. Brown. Nature Genetics, 2001

710 citations recorded by the source corpus.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/86c3c27a2e191ae9a26a0b9820ec23d702a4ab7c

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Citations in the corpus

Computational prediction of transcription-factor binding site locations (2003, background): “There is a general lack of data on the function of TFBSs within coding regions, although one recent ChIP-chip study on the yeast TF Rap1 found that binding sites within coding regions were much less likely to be bound in vivo [12].”
Identification and distinct regulation of yeast TATA box-containing genes. (2004, background): “The frequency of these “TATA” containing genes was plotted as a function of “geneness” (Lieb et al., 2001).”
Genomic targets of the human c-Myc protein. (2003, background): “The Gal4 protein, for example, was detected on only 10 target promoters (Ren et al. 2000), and Rap1 bound ∼ 5% of all yeast genes (Lieb et al. 2001).”
Mapping of genetic and epigenetic regulatory networks using microarrays (2005, background): “Such complete maps have been generated in Saccharomyces cerevisiae”
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia (2012, methodology): “Methods for mapping transcription-factor occupancy across the genome by chromatin immunoprecipitation (ChIP) were developed more than a decade ago (Ren et al. 2000; Iyer et al. 2001; Lieb et al. 2001; Horak and Snyder 2002; Weinmann et al. 2002).”
Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCE (2006, methodology): “However, genomescale, quantitative measurements of TF occupancies of intergenic regions are now available due to the advent of in vivo chromatin immunoprecipitation microarrays (Ren et al., 2000; Iyer et al., 2001; Lieb et al., 2001; Simon et al., 2001; Lee et al., 2002; Harbison et al., 2004), in v”
Insulators: many functions, many mechanisms. (2002, background): “The silencer proteins do not spread beyond the HMR barrier elements described above.”
Comprehensive Genome-wide Protein-DNA Interactions Detected at Single Nucleotide Resolution (2011, background): “Selective Motif Usage by Rap1 at Ribosomal Protein Genes and Telomeres Rap1 is a yeast sequence-specific repressor and activator protein that regulates telomeres and ribosomal protein (RP) genes (Lieb et al., 2001; Moehle and Hinnebusch, 1991).”
Extensive Association of Functionally and Cytotopically Related mRNAs with Puf Family RNA-Binding Proteins in Yeast (2004, methodology): “Finally, the list of target mRNAs did not change substantially by application of other statistical methods for selection (see Lieb et al. 2001).”
Zelda is differentially required for chromatin accessibility, transcription factor binding, and gene expression in the early Drosophila embryo (2015, background): “Inparticular,while transcriptionfactors recognizeandbindspecific DNAmotifs, onlya small fractionof theirpotentialbindingsites are occupied at a given time point (Carr and Biggin 1999; Iyer et al. 2001; Lieb et al. 2001; Liu et al. 2006; Yang et al. 2006; Li et al. 2008).”
ChIP-chip: considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments. (2004, methodology): “The median percentile rank approach is particularly useful for identifying targets when more than approximately 4% of the total elements on the array report IP enrichment [1,15], but is less effective for analysis of proteins with fewer targets.”