Transcriptional interaction-assisted identification of dynamic nucleosome positioning

DNA sequence preferences of transcriptional activators correlate more strongly than repressors with nucleosomes

Transcription factors (TFs) and histone octamers are two abundant classes of DNA binding proteins that coordinate the transcriptional program in cells. Detailed studies of individual TFs have shown that TFs bind to nucleosome-occluded DNA sequences and induce nucleosome disruption/repositioning, while recent global studies suggest this is not the only mechanism used by all TFs. We have analyzed to what extent the intrinsic DNA binding preferences of TFs and histones play a role in determining nucleosome occupancy, in addition to nonintrinsic factors such as the enzymatic activity of chromatin remodelers. The majority of TFs in budding yeast have an intrinsic sequence preference overlapping with nucleosomal histones. TFs with intrinsic DNA binding properties highly correlated with those of histones tend to be associated with gene activation and might compete with histones to bind to genomic DNA. Consistent with this, we show that activators induce more nucleosome disruption upon transcriptional activation than repressors.

Characterizing nucleosome dynamics from genomic and epigenetic information using rule induction learning

BACKGROUND

Eukaryotic genomes are packaged into chromatin, a compact structure containing fundamental repeating units, the nucleosomes. The mobility of nucleosomes plays important roles in many DNA-related processes by regulating the accessibility of regulatory elements to biological machineries. Although it has been known that various factors, such as DNA sequences, histone modifications, and chromatin remodelling complexes, could affect nucleosome stability, the mechanisms of how they regulate this stability are still unclear.

RESULTS

In this paper, we propose a novel computational method based on rule induction learning to characterize nucleosome dynamics using both genomic and histone modification information. When applied on S. cerevisiae data, our method produced totally 98 rules characterizing nucleosome dynamics on chromosome III and promoter regions. Analyzing these rules we discovered that, some DNA motifs and post-translational modifications of histone proteins play significant roles in regulating nucleosome stability. Notably, these DNA motifs are strong determinants for nucleosome forming and inhibiting potential; and these histone modifications have strong relation with transcriptional activities, i.e. activation and repression. We also found some new patterns which may reflect the cooperation between these two factors in regulating the stability of nucleosomes.

CONCLUSION

DNA motifs and histone modifications can individually and, in some cases, cooperatively regulate nucleosome stability. This suggests additional insights into mechanisms by which cells control important biological processes, such as transcription, replication, and DNA repair.