Instruct: Identify the main and secondary category of Arxiv papers based on the titles and abstracts
Query: Classification of Saccharomyces cerevisiae promoter regions into
  distinct chromatin classes reveals the existence of nucleosome-depleted
  hotspots of transcription factor occupancy   Transcription factors (TF) play an essential role in the cell as locus- and
condition-specific recruiters of transcriptional machinery or
chromatin-modifying complexes. However, predicting the in vivo profile of TF
occupancy along the genome, which depends on complex interactions with other
chromatin-associated proteins, from the DNA sequence remains a major challenge.
Through careful reanalysis of ChIP-chip data for 138 TFs obtained in rich
media, we were able to classify the upstream promoter regions of S. cerevisiae
into 15 distinct chromatin types. One of these encompasses 5% of all promoters
and is unique in that it is highly occupied by (essentially) all TFs expressed
in rich media. These "hotspots" of TF occupancy are strongly
nucleosome-depleted and preferentially targeted by chromatin-remodeling
complexes and the origin-of-replication complex (ORC). They are also the only
chromatin type enriched for predicted Rap1p and Pdr1p binding sites, which we
found to work cooperatively with AAA/TTT motifs, known to affect local DNA
structure, to reduce nucleosome occupancy. Taken together, our results reveal
and characterize a new type of local chromatin structure in yeast.

13
The categories of this paper are: quant-ph
33
The categories of this paper are: plasm-ph
34
The categories of this paper are: chem-ph
4
The categories of this paper are: cond-mat
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The categories of this paper are: solv-int
18
The categories of this paper are: econ
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The categories of this paper are: dg-ga
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The categories of this paper are: nucl-th
1
The categories of this paper are: cs
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The categories of this paper are: nucl-ex
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The categories of this paper are: q-fin
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The categories of this paper are: eess
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The categories of this paper are: astro-ph
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The categories of this paper are: nlin
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The categories of this paper are: patt-sol
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The categories of this paper are: hep-lat