YEP paper abstract updated

Author: Ali Nematbakhsh

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@@ -15,21 +15,9 @@ <h4>Yeast Epigenome Project</h4>
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         <h5>Abstract</h5>
-        <p>Proteins are architected along eukaryotic chromosomes to maintain chromosome integrity and
-        regulate thousands of genes. There exists no holistic single-base resolution map of their
-        structural organization that reflects on genome function. Here we use ChIP-exo to define this
-        structure in the yeast Saccharomyces. We identified 21 meta-assemblages consisting of >400
-        proteins related to replication origins, centromeres, subtelomeric regions, transposons, and RNA
-        polymerase (Pol) I, II, and III transcription units. Most Pol II promoters lacked a regulatory
-        region by design. These essentially constitutive promoters comprised a short nucleosome-free
-        region adjacent to a +1 nucleosome, which together bound TFIID to formed a pre-initiation
-        complex (PIC). Positioned insulators protected core promoters from upstream events. Only 1/5th
-        of all promoters were architected for inducible regulation, wherein combinations of 78 sequence24 specific transcription factors bound upstream to create a nucleosome-depletable regulatory
-        region. We describe their structural interactions with the genome and cognate cofactors,
-        including nucleosomal and transcriptional regulators RPD3-L, SAGA, NuA4, Tup1, Mediator,
-        and SWI/SNF. Together their assemblages are linked to PIC assembly involving primarily TBP
-        rather than TFIID to achieve a defined integrated network of regulated transcription.
-        </p>
+        <p>
+The genome-wide architecture of chromatin-associated proteins that maintains chromosome integrity and gene regulation is ill defined. Here we use chromatin immunoprecipitation, exonuclease digestion and DNA sequencing (ChIP–exo/seq) to define this architecture in Saccharomyces cerevisiae. We identify 21 meta-assemblages consisting of roughly 400 different proteins that are related to DNA replication, centromeres, subtelomeres, transposons, and transcription by RNA polymerase (Pol) I, II and III. Replication proteins engulf a nucleosome, centromeres lack a nucleosome, and repressive proteins encompass three nucleosomes at subtelomeric X-elements. We find that most promoters associated with Pol II evolved to lack a regulatory region, having only a core promoter. These constitutive promoters comprise a short nucleosome-free region (NFR) adjacent to a +1 nucleosome, which together bind the transcription-initiation factor TFIID to form a preinitiation complex (PIC). Positioned insulators protect core promoters from upstream events. A small fraction of promoters evolved an architecture for inducibility, whereby sequence-specific transcription factors (ssTFs) create a nucleosome-depleted region (NDR) that is distinct from an NFR. We describe structural interactions among ssTFs, their cognate cofactors and the genome. These interactions include the nucleosomal and transcriptional regulators RPD3-L, SAGA, NuA4, Tup1, Mediator and SWI–SNF. Surprisingly, we do not detect interactions between ssTFs and TFIID, suggesting that such interactions do not stably occur. Our model for gene induction involves ssTFs, cofactors and general factors such as TBP and TFIIB, but not TFIID. By contrast, constitutive transcription involves TFIID but not ssTFs and cofactors. From this, we define a highly integrated network of gene regulation by ssTFs.
+                </p>
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