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Interactions between the ValRS coiled-coil domain and tRNA^Val (stereo view). The trace of the phosphorus atoms of tRNA^Val is shown as a yellow tube. A20, U18•G55, and C19•G56 of tRNA^Val are shown as a ball-and-stick representation, where the carbon atoms are colored in yellow. The ValRS coiled-coil domain is colored lime green. The ValRS amino acid residues that interact with the D- and TΨC-loops of tRNA^Val are shown as a ball-and-stick representation, where the carbon atoms are colored green.

Hfq promotes RNA-RNA interactions. A) The 5'-UTR of the sodB mRNA is shown with stem-loops a and b. The Shine-Dalgarno sequence is marked in blue, the start condon is circled, and the binding site for Hfq is indicated. The structural changes in the sodB mRNA 5'-UTR upon binding of Hfq are shown. RNAse footprinting experiments with different RNAses were done in the presence and absence of Hfq.38 Red triangles represent RNAse cleavages that are enhanced after binding of Hfq. Black triangles are RNAse cleavage sites that are protected upon the addition of Hfq. The sequence complementary to RyhB RNA is shown within a gray square. B) Electrostatic surface representation of the RNA binding site of the Hfq hexamer. Blue is electropositive and red is electronegative. The RNA is shown as a stick model, with oxygen, nitrogen, carbon and phosphorus atoms colored red, blue, white and yellow, respectively. Figure adapted from reference 4747.

Subnuclear genome organization revealed by studies of DNA replication. A) Late-replicating, condensed inactive X chromosome (Xi, arrowhead) at the nuclear periphery in MEF cells revealed by a 10-minute BrdU pulse labeling during mid-late stages of S-phase. Figure was adapted from Wu et al with permission from Journal of Cell Biology.71 B) Sites of DNA replication in early S (green, a 10-minute CldU pulse in early S) vs late S-phase (red, a 10-minute IdU pulse in late S of the same cell cycle) revealed by a "pulse-chase-pulse" experiment in mouse C127 fibroblast cells. Note that DNA replication during late S-phase takes place preferentially at the nuclear periphery and nucleolar periphery, whereas during early S-phase, it takes place in the interior of the nucleus excluding these two subnuclear compartments. C) Representative 2D DNA-FISH of Zfp42 (also known as Rex2) and Pou5f1 (also known as Oct4) loci in EPL cells and EpiSCs, which model early and late epiblast stages in mice, respectively.8 Zfp42 locus is a representative lineage-independent EtoL locus that completes its EtoL change during the transition from early to late epiblast equivalent stage (see Figure 2, asterisk), during which its timing change traverses the mid-late stages of S-phase. By contrast, Pou5f1 locus is constitutively early replicating. Zfp42 locus (red signals) is repositioned from the interior toward the nuclear periphery in EpiSCs but not EPL cells, whereas Pou5f1 locus (green signals) maintains its internal positioning in both cell types. Figure was adapted from Hiratani et al with permission from Genome Research.8 D) Electron spectroscopic imaging (ESI) analysis of nuclei during ESC differentiation.8 Images from left to right are: ESC, EBM3 (day 3 differentiated cells), EBM6 (day 6 differentiated) and EBM9 (day 9 NPCs). Relative levels of phosphorus and nitrogen levels were used to delineate chromatin (yellow) vs protein and ribonucleoprotein (blue).81 ESC nucleus is a relatively uniform meshwork of 10 nm chromatin fibers with a low degree of chromatin compaction along the nuclear envelope or throughout the nucleoplasm. EBM3 showed a landscape very similar to ESCs. However, note that in EBM6, a dramatic accumulation of compact chromatin was evident near the nuclear periphery, the boundaries of which became further sharpened in EBM9. The EBM3-EBM6 transition roughly corresponds to the early to late epiblast transition, based on gene expression, replication timing profiles and subnuclear position analysis of several gene loci.8 Figure was adapted from Hiratani et al with permission from Genome Research.8