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Des poétiques autour de l'oralité, de la spécificité des discours, de la modernité, des sémiotiques, plutôt greimassiennes ou peircéennes, d'autres poétiques..

CLAMP and MSL complex promote accessibility at CES.

<p>A) MACC values at Chromatin Entry Sites (CES) in male (S2) cells are greatest at the peak center (control RNAi, blue). RNAi treatment of <i>clamp</i> reduces accessibility at the CES peak and +/- 500 bp beyond the peak (green). For all panels, the lighter color indicates 95% confidence intervals, while the darker line represents the average MACC value. B.) A reduction in MSL complex following <i>msl2</i> RNAi only reduces accessibility directly at the CES peak (purple). C) The average MACC scores around CES in female Kc cells indicates a reduction in MACC values distal to the CES center, extending +/- 500bp beyond the peak. D) MACC scores at the three subgroups of CES indicate <i>clamp</i> RNAi (green) results in a decrease in accessibility in CES Groups A and B, but not in Group C. E) RNAi targeting <i>msl2</i> (purple) results in a loss of accessibility at Group A CES only at the CES peak. There is a small reduction in accessibility in Group B sites and no effect of <i>msl2</i> RNAi treatment at Group C sites. F) MACC scores from Kc cells are plotted for the three subgroups of CES. In females, <i>clamp</i> RNAi (green) results in a decrease in MACC values around CES in Group A, and to a lesser extent Group B. CES in Group C exhibit an increase in MACC values following <i>clamp</i> RNAi.</p

CLAMP directly affects accessibility of X-linked gene bodies in both males and females.

<p>A) The difference in MACC value (RNAi treatment—control) over gene bodies of all annotated genes was ranked by the magnitude of decrease (top) to increase (bottom) in accessibility. RNAi of <i>msl2</i> shows only a modest change in accessibility, whereas <i>clamp</i> RNAi results in accessibility changes in both males and females. Shown to the right of each heat map is the percent of genes that decrease (MACC<0, blue line) or increase (MACC>0, red line) in accessibility following the indicated RNAi treatment. B) Average MACC profiles across gene bodies are shown for male (S2) and female (Kc) cells separated by X-chromosomes and autosomes. X-linked gene bodies in both males and females have reduced accessibility after <i>clamp</i> RNAi treatment (green). The dark line represents the average MACC value, while 95% confidence intervals are represented by the lighter shading. C) The difference in MACC scores (Δ MACC) between control and RNAi over gene bodies was calculated. Plotted is the distribution of difference values for all chromosomes together (all), or separately for the X-chromosome and autosomes. Plotted is the median difference in MACC scores with the 95% confidence interval indicated by a notch around the median line.</p

CLAMP promotes nucleosome positioning at 5’ends genome-wide.

<p>A) Average MACC profiles around transcription start sites (TSS) are shown for male (S2) and female (Kc) cells separated by X-chromosomes and autosomes. TSS at genes with highly bound CLAMP in both males and females are reduced in accessibility after <i>clamp</i> RNAi treatment (green) compared to control (blue). The dark line represents the average MACC value, while 95% confidence intervals are represented by the lighter colors. B) Average MNase-seq read frequency was calculated for the four MNase experiments and plotted +/- 1 Kb flanking annotated TSS. Upon <i>clamp</i> RNAi (green), there is a decrease in read frequency upstream of the TSS with a concurrent increase in occupancy within gene bodies.</p

CLAMP functions to regulate transcription genome wide through regulating nucleosome positioning.

<p>A) Of the total number of transcripts aligned to the genome in males, approximately 12% (X-chromosome, blue) and 10% (autosomes, red) are significantly (p<0.05) changed following <i>clamp</i> RNAi treatment. The percentage of significantly changed transcripts in females is roughly equivalent for the X-chromosome and autosomes and is ~7%. B) The percent of significantly changed transcripts (p<0.05) that decrease in abundance after <i>clamp</i> RNAi (Positive regulation, un-hatched) or increase in abundance after <i>clamp</i> RNAi (Negative regulation, hatched) is plotted. CLAMP functions predominantly to promote transcription on the male X-chromosome, while on the male autosomes, it functions more frequently as a negative regulator. In females, CLAMP functions positively and negatively on all chromosomes at approximately equal frequencies. C) Average read frequency from all MNase titrations was plotted +/- 1 kb centered around obsTSS on the X and autosomes for genes with a CLAMP peak within +/- 200 bp of the obsTSS. There is a decrease in nucleosome positioning upstream of the TSS and an increase downstream of TSS on all chromosomes in both males (left) and females (right). D and E) X-chromosome and autosome obsTSS were categorized into quartiles based on the change in transcript abundance following <i>clamp</i> RNAi as measured by Start-seq. The two graphs on the left are for males while the graphs on the right are for females. Shown are average MNase-seq read frequency profiles for the quartiles with the largest decrease in transcription after <i>clamp</i> RNAi (D) (positively regulated) and largest increase in transcription after <i>clamp</i> RNAi (E) (negatively regulated).</p

CLAMP establishes the global open chromatin environment on the male X-chromosome.

<p>A) Chromatin is separated into four samples which are digested under differing concentrations of MNase. The digested samples are prepared for high-throughput sequencing and the number of reads obtained within a region of the genome is plotted for all MNase concentrations from highest to lowest. A linear regression line is fit to the data points, and the slope of the line derives the MNase accessibility (MACC) score. B) The overall distribution of accessibility scores measured by the MACC value is shown for the X-chromosome (blue) and autosomes (red) of Control (<i>gfp</i>), <i>clamp</i>, and <i>msl2</i> RNAi treated male (S2) and female (Kc) cells. The male X-chromosome has overall higher MACC values than the autosomes. This accessibility is reduced after <i>clamp</i> RNAi. In females, MACC values for the X-chromosomes and autosomes are similar and are reduced slightly following <i>clamp</i> RNAi treatment. For all box and whisker plots, the 95% confidence interval is shown with a notch around the median line. C) For both the X-chromosomes and autosomes, the difference in MACC value (Δ MACC) between control and RNAi treatment for an individual 100bp bin was calculated to account for differences in chromosome number. In males, the change in MACC scores indicates a reduction in X-chromosome accessibility following <i>clamp</i> RNAi but not <i>msl2</i> RNAi. D) The location of significant changes in accessibility (p-value < 0.01) was classified as either within a gene body (blue), at TSS or TTS (red), at enhancers (green), or in unannotated regions (purple). Details for region definitions are in the Methods. For all RNAi treatments, the largest proportion of accessibility changes is located within gene bodies. E) Average MACC values were plotted over a 20kb window centered on a CLAMP ChIP-seq peak [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0186855#pone.0186855.ref009" target="_blank">9</a>] for both control RNAi (blue) and <i>clamp</i> RNAi (green) conditions. The lighter shading surrounding the darker average line represents the 95% confidence interval. On both male and female X-chromosomes there is a strong reduction in accessibility that extends approximates +/- 7kb from the peak center. A similar, but less pronounced effect is also seen on autosomes in males and females.</p