Supplementary Data Sets:
SD1. 346 manually cloned cores
SD2. 312,492 pyrosequencing reads
SD3. Inferred positions and sequences of uniquely placed cores.
Figure Legends
Supplementary Figure 1. Length histogram for manually cloned nucleosome cores. Nine different Micrococcal nuclease digestion conditions (#1 to #9) were considered for isolation of nucleosome core fragments, as detailed in Table 1 of the text. Fragments were treated with a variety of combinations of post-isolation processing [P: removal of 3' phosphate; F(ill): polishing of ends with T4 DNA polymerase; None: No treatment], ligated to a standard cloning vector, and sizes for a small number of clones determined by DNA sequencing. Several conditions and treatments were used in duplicate to test consistency (designated A, B).
Supplementary Figure 2. Position of unique/unambiguous pyro-core reads on the C. elegans genome. Pyro-core sequences showing a unique best match to the C. elegans genome (see Methods) were placed on the C. elegans genome, as were a set of randomly generated virtual cores. Graphs show normalized ratio between the two samples for bins of 100,000 adjacent residues tiling the length of the C. elegans genome. Values close to 1 indicate no substantial deviation from expected core coverage in a given 100,000bp region. Several regions exhibiting apparent under-and over-representation are indicated and are the subjects of current investigation.
Supplementary Figure 3. Sequence specific preference of Micrococcal nuclease seen in nucleotide occurrence upstream and at the start of pyro-core sequences. (A)Positional occurrence of A (green), C (blue), G (black) and T (red) at positions from 25nt downstream through 35nt upstream of the pyro-core starts. (B) Positional occurrence of A (green), C (blue), G (black) and T (red) at positions from 25nt downstream through 171nt upstream of the pyro-core starts.
Supplementary Figure 4. Positional AA and TT dinucleotide abundance in all pyro-core reads, and subsets of pyro-core reads which have been filtered using various criteria. (Top): All pyro-core reads, (Middle): An equivalent graph which has been limited to reads that contain an AA or TT at position -1/1 (Bottom) Equivalent graph limited to reads that lack AA or TT at positions -2/-1, -1/1, and 1/2. AA/TT periodicity is retained in all three sets. AA and TT dinucleotide abundance is analyzed for every set for the entire pyro-core (positions 1-146) and in the 20nt proceeding and following the pyro-core.
Supplementary Figure 5. Fourier analysis of periodicity occurring in start-to-start pyro-core data. (A) Analysis of periodicities from 100 to 300 bases shows a major peak between 157 and 171bp consistent with a linker size of 11-25bp. (B) Analysis of periodicities from 8 to 14 bases show a major peak at 9.9bp consistent with possible rotational positioning of nucleosomes.
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C. elegans chromatin landscape Johnson, Tan, McCullough, Riordan and Fire08/31/06