Signals in DNA that affect nucleosome alignment and gene regulation
Abstract
Eukaryotic DNA is packaged into chromatin which contains periodic arrays of nucleosomes. The nucleosome arrays reflect or influence the higher-order chromatin structure and function. Despite their importance in the higher-order chromatin structure and gene regulation, it is unclear how nucleosome arrays are formed. Using an in vitro chromatin assembly system, we first investigated how a shortened nucleosome repeat arises specifically on $\beta$-globin DNA in erythroid cells. Our results indicated that the shortened nucleosome repeat is encoded in the $\beta$-globin DNA sequence and that nucleosome alignment is facilitated by sequences in the $\rm\beta\sp{A}$-$\varepsilon$ intergenic region. We suggested that these nucleosome alignment signals in $\beta$-globin DNA have a dominant effect on chromatin assembly in erythroid cells. Next the effects of introns on transcription and chromatin assembly were examined. We discovered that rat growth hormone gene introns stimulate nucleosome alignment in vitro and in transgenic mice. The presence of well-ordered nucleosome arrays correlated with high levels of transcription. This study suggests one way that transcriptional control may be influenced by chromatin structure. Finally, we investigated chromatin structures assembled on different anonymous genomic DNA clones from chicken in vitro and in chicken liver nuclei. The chromatin structures of genomic DNA assembled in vitro resembled those in chicken liver tissue. The results obtained here suggest that DNA sequence encodes information for nucleosome array formation. Analysis of 45 kbp of contiguous genomic DNAs, isolated from cosmid clones, indicates that well-ordered regions are adjacent to less ordered regions, both in vitro and in animal tissue. These findings, taken together with recent findings of others, challenge the "solenoid" model and have some far-reaching implications for how DNA may function in the context of chromatin.
Degree
Ph.D.
Advisors
Stein, Purdue University.
Subject Area
Molecular biology|Cellular biology
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