Chromatin organization at promoters in yeast cells

Our genome is very large and very complicated because it is full of junk DNA. It contains thousand of sites where DNA binding proteins can bind just by chance. This leads to the reorganization of nucleosomes in a way that mimics functional sites. It's difficult to distinguish these spurious sites from real functional sites and that has led to much confusion in the scientific literature.¹

The yeast genome is much more simple and it's safe to assume that almost all of the sites detected by the standard chromatin assays are genuine, biologically relevant, sites. In that sense, it serves as a model for what functional sites looks like. A recent paper in Nature (April 8, 2021) reports on the mapping of most of the sites in the yeast genome where DNA binding proteins are found.

Rossi, M.J., Kuntala, P.K., Lai, W.K., Yamada, N., Badjatia, N., Mittal, C., Kuzu, G., Bocklund, K., Farrell, N.P., Blanda, T.R.M., Joshua D, V, B.A., Mistretta, K.S., Rocco, D.J., Perkinson, E.S., Kellogg, G.D., Mahony, S. and Pugh, B.F. (2021) A high-resolution protein architecture of the budding yeast genome. Nature 592:309-314. [doi: 10.1038/s41586-021-03314-8]

Origins of replication

Origins of replication are also called autonomously replicating sequence consensus sequences (ACS). There are 253 of them in the yeast genome and they are characterized by a 300 bp nucloeosome-free region that's occupied by the origin recognition complex (ORC) and the helicase MCM.

Telomeres

Telomeres are bound by a number of proteins including silent information regulators (SIRs). There's a nucleosome-free region of about 300 bp. where these proteins are located.

Centromeres

The nucleosome-free region at centromeres covers only 170 bp where a number of centromere binding proteins are located. The absence of nucleosomes at the centromere is a surprise since it was though that centromere DNA was bound by modified nucleosomes containing a specific histone variant.

Class I genes (RNA polymerase I)

The promoter region of ribosomal RNA genes covers about 200 bp and the genes themselves are depleted of nucleosomes because of extensive transcription from the promoter.

Class II genes (RNA polymerase II)

There are about 7,500 polymerase II genes and 80% of them are protein-coding genes. About two-thirds of the transcription initiation sites appear to be localized to the promoter region with no evidence of any upstream regulatory sites. This suggests that most yeast genes are constituitively expressed. For those genes, the nucleosome free region is quite small. The remaining genes fall into several subcategories but they all have an extended nuclesome-free region where regulatory proteins are bound.

Class III genes (RNA polymerase III)

As expected, the promoter regions of these genes are occupied by RNA polymerase and so are the internal regulatory sites (A and B). The nucleosome-depleted regions cover about 100 bp downstream of the transcription initiation site.

Ty transposons

The Ty elements are usually transcribed by RNA polymerase III. Most of them didn't have a well-defined preinitiation complex but there was a subset where the LTR was occupied by DNA binding proteins.

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1. The confusion is caused by scientists who don't understand junk DNA and don't understand how DNA binding proteins work.