The nucleosome position-encoding WW/SS sequence pattern is depleted in mammalian genes relative to other eukaryotes

Abstract

Nucleosomal DNA sequences generally follow a well-known pattern with ∼10-bp periodic WW (where W is A or T) dinucleotides that oscillate in phase with each other and out of phase with SS (where S is G or C) dinucleotides. However, nucleosomes with other DNA patterns have not been systematically analyzed. Here, we focus on an opposite pattern, namely anti-WW/SS pattern, in which WW dinucleotides preferentially occur at DNA sites that bend into major grooves and SS (where S is G or C) dinucleotides are often found at sites that bend into minor grooves. Nucleosomes with the anti-WW/SS pattern are widespread and exhibit a species- and context-specific distribution in eukaryotic genomes. Unlike non-mammals (yeast, nematode and fly), there is a positive correlation between the enrichment of anti-WW/SS nucleosomes and RNA Pol II transcriptional levels in mammals (mouse and human). Interestingly, such enrichment is not due to underlying DNA sequence. In addition, chromatin remodeling complexes have an impact on the abundance but not on the distribution of anti-WW/SS nucleosomes in yeast. Our data reveal distinct roles of cis- and trans-acting factors in the rotational positioning of nucleosomes between non-mammals and mammals. Implications of the anti-WW/SS sequence pattern for RNA Pol II transcription are discussed.

Figure 1.

Four sequence patterns of nucleosomal DNA in yeast. Shown are frequencies of the combined AA, TT, AT and TA dinucleotides (denoted as WW, shown in blue) and GG, CC, GC and CG dinucleotides (denoted as SS, shown in red) at each nucleosomal position, which were ‘symmetrized’ with respect to the dyad (dashed lines). Three base-pair running averages of the WW and SS frequencies were calculated and plotted: Type 1 (A), Type 2 (B), Type 3 (C) and Type 4 (D). The blue and red shade areas cover the range of minor- and major-GBS, respectively (see ‘Materials and Methods’ section). The Type 1 pattern refers to the WW/SS pattern, whereas the Type 4 pattern refers to the anti-WW/SS pattern.

Figure 2.

Comparison of the fractions of nucleosomal DNA patterns in eukaryotes. Shown is the fractions of four sequence patterns in nucleosomal DNA from yeast, nematode, fruit flies, mice and humans. For chemical mapping data, the ‘unique’ maps of nuleosomal dyad positions were taken from literature (10,13) and the corresponding 147-bp NCP fragments were used in this study. For the paired-end MNase mapping data, the two biological replicates or relevant datasets were taken from literature and 147-bp NCP fragments in these datasets were used for analysis. The fractions of sequence patterns were calculated for each dataset (Supplementary Table S4).

Figure 3.

Nucleosome occupancy profiles around TSS of yeast (A and B), fly (B), nematode (C), mouse (D and E) and human (F) genes. There are two separate nucleosome datasets for yeast and mice, derived from chemical mapping (A and D) and MNase-Seq mapping (B and E), respectively. Nucleosome occupancy signals ±1 kb of verified TSSs are separated into quartiles based on transcriptional levels (Supplementary Table S5). The first 25%-ile represents the least active genes whereas the fourth 25%-ile represents the most active genes. The average nucleosome profile of all genes is shown in black. Nucleosomes −1 to +5 are demarcated by dashed lines and arrows, following the methods used in previous studies (77). These definable zones relative to the TSS (position 0) to which a nucleosome midpoint may be assigned are: −1, +1, +2, +3, +4 and +5 (see Supplementary Table S6 for nucleosome ranges). Note the nucleosome occupancy of the nematode dataset (D) looks noisier than other datasets probably due to low read coverage.

Figure 4.

Nucleosome ΔNPS values for genes separated into quartiles by transcriptional frequencies. The first 25%-ile represents the least active genes whereas the fourth 25%-ile represents the most active genes. The ΔNPS values for all genes are shown in black. The genomic ΔNPS values are denoted by dashed lines.

Figure 5.

DAC function profiles for WW dinucleotides in yeast (A), fly (B), nematode (C), mouse (D) and human (E) DNA. Genomic fragments [−500 bp, +1000 bp] relative to verified TSSs (position 0) were used for analysis. Both raw (thin lines) and 3-bp running average (thick lines) values were plotted.

Figure 6.

Fractions of DNA sequence patterns and ΔNPS values in human repeat families. (A) Fraction of repeat families in human genome. The fractions were taken from literature (78). (B) Fraction of 147-bp human nucleosomes residing in each repeat family. (C) Fraction of four types of nucleosomes in each repeat family. (D) Nucleosome ΔNPS values in genic and repetitive DNA regions. The genomic ΔNPS value is indicated by dashed lines.

Figure 7.

Genomic ΔNPS values in yeast WT and mutant strains. ΔNPS values were calculated by chromosomes and shown in a box-whisker plot, with the mean representing the genomic ΔNPS. The genomic ΔNPS values of WT strains are used as reference points to compare with those of mutant strains (Supplementary Table S12) in which one or more chromatin remodeler genes are knocked out (50).

Figure 8.

ΔNPS values of promoter and downstream nucleosomes in yeast mutant strains. For the sake of comparison, the ranges of nucleosomes are the same for both the WT and mutant strains (Supplementary Table S6). Other notations follow Figure 3.

Figure 9.

Models for the roles of cis and trans factors in rotational positioning of nucleosomes. (A) Species-specific distribution of anti-WW/SS nucleosomes. In mammals, the fraction of anti-WW/SS nucleosomes in nucleosomes −1 to +5 is increased and the fraction of WW/SS nucleosomes is decreased, suggesting that these nucleosomes are unstable (represented by fuzziness of nucleosome positioning). This change is not seen in non-mammalian genes. Nucleosomes −1 to +5 in mammals are depicted in dark brown and other nucleosomes (including those residing in mammalian repetitive DNA) are depicted in light brown. (B) Distinct role of cis and trans factors in rotational positioning of nucleosomes. Both cis-acting factors (e.g. DNA sequences) and trans-acting factors (e.g. chromatin remodeling complexes and RNA Pol II) affect rotational settings of nucleosomes. In non-mammals, DNA sequence plays a more important role than RNA Pol II because (i) the ∼10-bp periodic WW (or SS) patterns are pronounced; (ii) no clear change in the ΔNPS values is seen between highly and lowly transcribed genes. By contrast, in mammalian genes, RNA Pol II plays a more important role because (i) the ∼10-bp periodicity is diminished, and (ii) a clear change in ΔNPS values is seen between highly and lowly transcribed genes. Chromatin remodelers also have an impact on the rotational setting of nucleosomes in non-mammals, but this effect is unclear in mammals.