Genome-wide map of nucleosome acetylation and methylation in yeast.

By Dmitry Pokholok, Christopher T. Harbison, S. Levine, Megan F. Cole, N. Hannett, Tong Ihn Lee, George W. Bell, Kimberly Walker, P. Alex Rolfe, Elizabeth Herbolsheimer and 4 more. Cell, 2005

1,597 citations recorded by the source corpus.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/d688b2b14c671626d30fd6ba7c814477a0c7105f

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Citations in the corpus

Protocol for the fast chromatin immunoprecipitation (ChIP) method (2006, background): “Alternatively, an interaction of the factor with multiple genomic locations can be detected simultaneously by applying the isolated DNA to a DNA microarray (ChIP on chip”
Whole-Genome Analysis of Histone H3 Lysine 27 Trimethylation in Arabidopsis (2007, methodology): “As a control, nucleosomal DNA was isolated by ChIP using an antibody against the C terminus of H3 (regardless of its modifications) [31].”
The role of chromatin during transcription. (2007, background): “Acetylated histones H3 and H4 continue to accumulate during gene activation (Pokholok et al., 2005), and Htz1 K14 is acetylated at active promoters (Millar et al., 2006).”
Histone Marks in the 'Driver's Seat': Functional Roles in Steering the Transcription Cycle. (2017, background): “Chromatin immunoprecipitation assays first followed by microarrays (ChIP-chip), and now sequencing (ChIP-seq) have yielded extensive information about a variety of histone modifications and localizations in the genome [8,9].”
Pyicos: a versatile toolkit for the analysis of high-throughput sequencing data (2011, methodology): “In order to test the performance of Pyicos EA, we compared it to DEGSeq and to a combination of BEDTools (Quinlan and Hall, 2010) with edgeR and DESeq, as these two programs do not accept as input BED files with the regions of interest and the positions of the mapped reads from the samples to be…”
Histone H3 methylation by Set2 directs deacetylation of coding regions by Rpd3S to suppress spurious intragenic transcription. (2005, background): “Genome wide studies indicate that histone H3K4 methylation peaks at the 5# end of transcribed genes and dissipates across the coding region (Ng et al., 2003; Pokholok et al., 2005).”
Lineage-specific polycomb targets and de novo DNA methylation define restriction and potential of neuronal progenitors. (2008, background): “As an indicator for ‘‘active chromatin,’’ we monitored dimethylation of lysine 4 of histone H3, which was previously shown to be a marker of active genes in several eukaryotes tested (Barski et al., 2007; Pokholok et al., 2005; Schübeler et al., 2004).”
HyenaDNA: Long-Range Genomic Sequence Modeling at Single Nucleotide Resolution (2023, methodology): “Epigenetic Marks In the epigenetic marks prediction task, we used the dataset from [35, 36] to predict nucleosome occupancy and modification states in the yeast genome.”