Modulated contact frequencies at gene-rich loci support a statistical helix model for mammalian chromatin organization

International audienceABSTRACT: BACKGROUND: Despite its critical role for mammalian gene regulation, the basic structural landscape of chromatin in living cells remains largely unknown within chromosomal territories below the megabase scale. RESULTS: Here, using the 3C-qPCR method, we investigate contact frequencies at high resolution within the interphase chromatin at several mouse loci. We find that, at several gene-rich loci, contact frequencies undergo a periodical modulation (every 90-100 kb) that affects chromatin dynamics over large genomic distances (few hundred kb). Interestingly, this modulation appears to be conserved in human cells and bioinformatic analyses of locus-specific, long-range cis-interactions suggest that it may underlie the dynamics of a significant number of gene-rich domains in mammals, thus contributing to genome evolution. Finally, using an original model derived from polymer physics, we show that this modulation can be understood as a fundamental helix shape that chromatin tends to adopt in gene-rich domains when no significant locus-specific interaction takes place. CONCLUSIONS: Altogether, our work unveils a fundamental aspect of chromatin dynamics in mammals and contributes to a better understanding of genome organization within chromosomal territories

Lines 1352-1449, Regiment of Princes Collation Tables Group MITCH 4

Files in this work belong to a collection of handwritten variant tables compiled by Charles Blyth and a team consisting of David Greetham, Jerome Mitchell, Gail Sigal, Peter Farley, Marcia Marzec, and David Yerkes during the 1980s and 1990s to collate the manuscripts of Thomas Hoccleve's fifteenth-century poem, 'The Regiment of Princes.' Blyth used these tables to help produce his 1999 edition of the poem published by TEAMS. Blyth passed this collection to Elon Lang in 2009. Lang set up the Hoccleve Archive in 2012 at UT-Austin to preserve and publish the collation tables, to collect other materials related to Hoccleve and Hoccleve scholarship, and to develop strategies for building and using digital archives and editions.Digital images of the variant collation tables in this work were produced by UTAustin Liberal Arts ITS staff member Emma Whelan, Rebecca van Kniest, and members of the UT-School of Information Fall 2012 Digitization Methods class when their names are included in a dc.contributer field. Tables are identified in the title field by a line number range from Blyth's edition of 'The Regiment of Princes.' Transcriptions of marginal glosses associated with some lines in the source manuscripts are written on verso sides of these collation tables or on subsequent sheets. Images of these versos or subsequent sheets are identified by suffices appended to the 'table0000' filename.Humanitie

Rhythmic translation of ribosomal proteins in mouse liver.

<p>(A) Temporal expression profiles of microarray probes showing a rhythmic ratio of polysomal to total RNAs, ordered by phase. For visualization, data were mean centered and standardized. Log-ratios are color-coded so that red indicates high and green low relative levels of polysomal mRNAs compared to the total fraction. (B) Examples of temporal expression profiles of a subset of rhythmically translated 5′-TOP genes identified in our microarray experiment. Traces represent the levels of mRNA expression measured by microarray in the total RNA (blue line) and polysomal fraction (red line). Data are represented in log scale following standard normalization. (C) Temporal location of <i>Gapdh</i> and selected genes showing translational regulation mRNA on the different gradients obtained after polysomes purification. Pools of RNA obtained from four animals were used for each fraction at each time point. The color intensity represents for each time point the relative abundance of the mRNA in each fraction. Fractions 1–2 represent heavy polysomes, 2–3, light polysomes, and 9–10, free mRNAs. Note that even for <i>Gapdh</i> mRNA, translation slightly decreases at the end of the light period. (D) Temporal expression of selected rhythmically translated ribosomal proteins in liver cytoplasmic extracts during two consecutive days. Naphtol blue black staining of the membranes was used as a loading control. The lines through gels indicate where the images have been cropped. The zeitgeber times (ZT) at which the animals were sacrificed are indicated on each panel.</p

Temporal activation of signaling pathways controlling translation initiation.

<p>(A) Temporal expression and phosphorylation of representative proteins of key signaling pathways regulating translation initiation in mouse liver during two consecutive days. Western blots were performed on total liver extracts. Naphtol blue black staining of the membranes was used as a loading control. (B) Temporal binding of EIF4E and 4E-BP1 to 7-methyl-GTP-sepharose during two consecutive days. Total liver extracts were incubated with 7-methyl-GTP beads mimicking the mRNA cap structure. After washing of the beads, bound proteins were analyzed by Western blotting. The zeitgeber times (ZT), with ZT0, lights on; ZT12, lights off, at which the animals were sacrificed, are indicated on each panel. The lines through gels indicate where the images have been cropped.</p

Temporal expression and phosphorylation of translation initiation factors.

<p>(A) Temporal mRNA expression profile of translation initiation factors in mouse liver. For each time point, data are mean ± standard error of the mean (SEM) obtained from four independent animals. (B) Temporal protein expression and phosphorylation of translation initiation factors in mouse liver during two consecutive days. Western blots were realized on total or nuclear (PER2 and BMAL1) liver extracts. PER2 and BMAL1 accumulations are shown as controls for diurnal synchronization of the animals. Naphtol blue black staining of the membranes was used as a loading control. The lines through gels indicate where the images have been cropped. The zeitgeber times (ZT), with ZT0, lights on; ZT12, lights off, at which the animals were sacrificed, are indicated on each panel.</p

Rhythmic transcription of RP mRNA and rRNA through circadian clock regulated expression of UBF1.

<p>(A) Temporal real-time RT-PCR profile of RP pre-mRNA and 45S rRNA precursor expression in mouse liver. For each time point, data are mean ± standard error of the mean (SEM) obtained from four independent animals. (B) Temporal <i>Ubf1</i> mRNA (upper panel) and protein (lower panel) expression in mouse liver. mRNA were measured by real-time RT-PCR and, for each time point, data are mean ± SEM obtained from four independent animals. UBF1 protein expression was measured by Western blot on nuclear extracts during two consecutive days. The lines through gels indicate where the images have been cropped. (C–D) Temporal <i>Ubf1</i> expression in mice devoid of a functional circadian clock. <i>Ubf1</i> expression was measured by real-time RT-PCR with liver RNAs obtained from arrhythmic <i>Cry1</i>/<i>Cry2</i> (C) and <i>Bmal1</i> (D) KO mice and their control littermates (upper panel). Data are mean ± SEM obtained from three and two animals, respectively. Black line corresponds to the WT animals and red line to the KO. Protein levels (lower panel) were measured by Western blot on nuclear extracts. The zeitgeber times (ZT) at which the animals were sacrificed are indicated on each panel. Naphtol blue black staining of the membranes was used as a loading control.</p

Model describing the coordination of ribosome biogenesis by the circadian clock.

<p>The molecular oscillator in the master circadian pacemaker localized in the SCN of the hypothalamus synchronizes peripheral clocks, including liver clock, and, in parallel, regulates feeding behavior, which itself influences peripheral oscillator. The liver circadian clock controls expression of translation initiation factors, and rRNA, and conceivably RP mRNA, through regulation of UBF1. In addition, in association with signals from nutrients, the molecular clock, via the TORC1 pathway, coordinates the rhythmic activation of signaling pathways controlling translation of RP and, in turn, ribosome biogenesis. This succession of events coordinated by the circadian clock finally leads to a subtle rhythmic change of general translation in mouse liver.</p

Rhythmic RNA expression of factors involved in ribosomes biogenesis is disrupted in arrhythmic <i>Cry1</i>/<i>Cry2</i> and <i>Bmal1</i> KO mice.

<p>Temporal expression of factors involved in ribosomes biogenesis in <i>Cry1</i>/<i>Cry2</i> (A) and <i>Bmal1</i> (B) KO mice and their control littermates. Temporal real-time RT-PCR expression profile of 45S rRNA precursor, <i>Rpl23</i> pre-mRNA, and translation initiation factors expression in mouse liver. Black line corresponds to the WT animals and red line to the KO. For each time point, data are mean ± SEM obtained from three (A) and two (B) independent animals. The zeitgeber times (ZT) at which the animals were sacrificed are indicated on each panel.</p