Nucleosome positioning on the MMTV LTR results from the frequency-biased occupancy of multiple frames.

Abstract

The translational positions of nucleosomes in the promoter region of the mouse mammary tumor virus (MMTV) were defined at high resolution. Nucleosome boundaries were determined in primer extension assays using full-length single-stranded mononucleosomal DNA prepared from cells treated with formaldehyde, a reversible protein-DNA cross-linking agent. Multiple boundaries were observed in both the nucleosome A (Nuc-A) and Nuc-B region of the promoter, indicating multiple nucleosome translational frames. The different nucleosome frames in both the Nuc-A and Nuc-B regions were occupied unequally. The most frequently occupied frames were found clustered within 50-60 bases of each other, resulting in a distribution centered in the positions defined previously at low resolution for Nuc-A and Nuc-B. The most abundant 5' ends of the frames in the B region were found between -235 and -187, and the 3' ends between -86 and -36, whereas in the A region the most abundant 5' ends were between -22 and +42, and the 3' ends between + 121 and +186. Although frames in the Nuc-B region of the LTR extend at a low frequency in the 5' direction toward the Nuc-C region, there is a sharp discontinuity in the 3' direction toward Nuc-A, suggesting the presence of a boundary constraint in the A-B linker. The positions and relative occupancies of nucleosome frames, in either the B or the A region, did not change when the promoter was activated with dexamethasone.

Transcriptional Regulation of Mammalian Genes in Vivo

“…Roberts et al (38) observed clear 10-bp periodicities for an in vitro reconstitute that contained five different core positions, demonstrating the difficulty of using this criterion for determination of high resolution positions. Similar data from several other systems (summarized in Fragoso et al (33)) is also consistent with multiply positioned cores within families. Thus, the preponderance of evidence at this time would argue that even in highly organized and reproducible systems, such as the MMTV LTR, considerable complexity exists in nucleosome positioning.…”

“…This structure was originally characterized as a periodic array of micrococcal nuclease and methyldiumpropyl-EDTA-Fe(II) cleavage-sensitive internucleosomal linker regions (35). More recently, using an in vivo cross-linking procedure for determining nucleosome core positions, Fragoso et al (33,37) concluded that the periodic array does not represent precisely positioned nucleosomes but rather consists of a series of nucleosome families (Fig. 1A, A-F) (33).…”

“…More recently, using an in vivo cross-linking procedure for determining nucleosome core positions, Fragoso et al (33,37) concluded that the periodic array does not represent precisely positioned nucleosomes but rather consists of a series of nucleosome families (Fig. 1A, A-F) (33). Each family contains a group of nucleosomes in a frequency-biased distribution among a set of available translational frames.…”

Steroid Hormone Receptor-mediated Histone Deacetylation and Transcription at the Mouse Mammary Tumor Virus Promoter

“…The MMTV-LTR has six well defined positioned nucleosome families, designated nucleosomes (Nuc) A-F. NucA overlaps the TATA region and the transcription start site, and NucF is the farthest 5Ј to the transcription start site (Ϫ1 kilobase) (Fig. 1A) (22,23). Four GR binding sites or hormone response elements (HREs) are located in the NucB region (Fig.…”

Principles and practice of nucleosome positioningin vitro

“…Furthermore, the superantigen sequence is hypervariable and this affects sequences across nucB (Brandt-Carlson et al 1993), so care is needed when comparing results from different isolates and this may have led to different nucleosome mapping assignments (Piña et al 1990;Archer et al 1991;Fragoso et al 1995;Flaus and Richmond 1998).…”