Table 1. Naturally occurring and synthetic nucleosome-positioning or nucleosome-repelling sequences used in this study.

Sequence Name	Species	Genomic Position	Nucleosome Affinity
poly(dA:dT) (“dA”)	Budding yeast (S. cerevisiae)	Chr III, 38745 – 39785 bp (Ref. [23])	∼3-fold in vivo nucleosome depletion relative to average genomic DNA (Fig. 2E of Ref. [22]); increase in energy of nucleosome formation in vitro relative to 5S (Fig. 8D of Ref. [22]) (estimates based on similar sequences)
GC-rich (“CG”)	Human	Chr Y, 4482107 – 4481956 bp (Ref. [22])	(not determined)
5S	Sea urchin (L. variegatus)	20 bp–165 bp from the Mbo II fragment containing 5S rRNA gene (Ref. [45])	decrease in energy of nucleosome formation compared to E8 in vitro (Ref. [8])
601TA (“TA”)	synthetic, strong nucleosome positioning sequence (Refs. [8], [59], [60])	N/A	decrease in energy of nucleosome formation compared to E8 in vitro (Ref. [8])
E8	synthetic random (Refs. [8], [60])	N/A	(used as a reference)

The sequences described here were chosen because each has been found to have significant effects on in vivo nucleosome positions and/or in vitro nucleosome affinities, as shown in the rightmost column. The exception is the GC-rich sequence from humans: although its nucleosome affinity has not been directly determined either in vivo or in vitro, it is predicted to correlate with high nucleosome occupancy because of its high G+C content [17] and is occupied by a nucleosome(s) in vivo according to micrococcal nuclease digestion [22]. Two-letter abbreviations given in parentheses under each full sequence name will be used in figure legends in the rest of this work.