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1.
Figure 2

Figure 2. Influence of Pol II and the Transcription Machinery on Chromatin Architecture. From: Coupling Polymerase Pausing and Chromatin Landscapes for Precise Regulation of Transcription.

A) Nucleosome occupancy was summed across 17,116 Drosophila promoters to create a ‘metagene’ profile revealing the stereotypical promoter nucleosome arrangement. The locations of the nucleosome free region (NFR) and +1, +2, and +3 nucleosomes are indicated. Data are from [19].
B) Separating Pol II-bound promoters (purple) from Pol II-unbound promoters (green) reveals that Pol II binding is coincident with lower nucleosome occupancy upstream of the TSS (the NFR), and paradoxically, higher downstream occupancy and more regular nucleosome spacing.
C) Nucleosome occupancy is significantly lower downstream of highly paused promoters (red, quartile 1 of pausing indices, 1,866 promoters) than downstream of the least paused promoters (blue, quartile 4 of pausing indices, 1,867 promoters). Pausing index is calculated as (Pol II occupancy TSS +/−250 bp)/(Pol II occupancy TSS +500 bp to gene end) as in [19].

Daniel A. Gilchrist, et al. Biochim Biophys Acta. ;1819(7):700-706.
2.
Figure 1

Figure 1. Two Paradigms for Regulation of Inducible Gene Expression. From: Coupling Polymerase Pausing and Chromatin Landscapes for Precise Regulation of Transcription.

A) Transcriptional activation at the S. cerevisiae PHO5 promoter proceeds through a series of ordered events: i) a signal (lightning bolt) leads to binding of transcription factor Pho4 to upstream activating sites (UAS) and removal of nucleosomes by chromatin remodelers (REMOD) permitting ii) recruitment of the transcription machinery and transcription initiation, followed directly by iii) productive RNA synthesis. Chromatin opening follows signaling.
B) In contrast, activation of the Drosophila heat shock genes proceeds through a distinct pathway: i) GAGA recruits chromatin remodeler NURF to remove nucleosomes and open promoter chromatin, allowing ii) Pol II initiation and transition to the paused state, whereupon iii) an activating signal (lightning bolt) triggers pause release and productive RNA synthesis. Note that chromatin opening precedes signaling.

Daniel A. Gilchrist, et al. Biochim Biophys Acta. ;1819(7):700-706.
3.
Figure 3

Figure 3. Paused Promoters are Linked to Distinct Chromatin Landscapes. From: Coupling Polymerase Pausing and Chromatin Landscapes for Precise Regulation of Transcription.

A) The most highly paused promoters in Drosophila S2 cells (quartile 1 of pausing indices, n=1,866 promoters) are frequently in close proximity to ‘state 3’ chromatin [51]. State 3 is characterized by modifications to histone H3 (H3K4me1, H3K27ac, and H3K18ac) and is associated with developmental regulation. Bars indicate the fraction of TSS regions within 0.5 kb of a region of ‘state 3’ chromatin. Total Pol II ChIP-chip data and pausing index calculations are from [19]. Less paused genes in pausing index quartiles 2-4 are shown for comparison, along with control genomic regions selected at random (Cntrl., n=1867).
B) The most highly paused Drosophila promoters frequently overlap with a region of RED chromatin [50]. RED chromatin is characterized by the presence of GAGA, BRM, and MED31, and is linked to developmentally regulated genes that show tissue-restricted expression patterns. Bars indicate the fraction of TSS regions (TSS +/−250 bp) that intersect with a region of RED chromatin. Total Pol II ChIP-chip data from Kc cells were generated by the modENCODE project [52] and pausing indices were calculated as in [19]. Less paused genes in quartiles 2-4 are shown for comparison, along with random control genomic regions.
C) Highly paused Drosophila promoters and those lacking pausing can be differentiated by the relative frequency of occurrence of specific chromatin features as indicated.

Daniel A. Gilchrist, et al. Biochim Biophys Acta. ;1819(7):700-706.

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