Transcriptional Bursting and Co-bursting Regulation by Steroid Hormone Release Pattern and Transcription Factor Mobility.

Genes are transcribed in a discontinuous pattern referred to as RNA bursting, but the mechanisms regulating this process are unclear. Although many physiological signals, including glucocorticoid hormones, are pulsatile, the effects of transient stimulation on bursting are unknown. Here we characterize RNA synthesis from single-copy glucocorticoid receptor (GR)-regulated transcription sites (TSs) under pulsed (ultradian) and constant hormone stimulation. In contrast to constant stimulation, pulsed stimulation induces restricted bursting centered around the hormonal pulse. Moreover, we demonstrate that transcription factor (TF) nuclear mobility determines burst duration, whereas its bound fraction determines burst frequency. Using 3D tracking of TSs, we directly correlate TF binding and RNA synthesis at a specific promoter. Finally, we uncover a striking co-bursting pattern between TSs located at proximal and distal positions in the nucleus. Together, our data reveal a dynamic interplay between TF mobility and RNA bursting that is responsive to stimuli strength, type, modality, and duration.

Topological Structure Determination of RNA Using Small-Angle X-Ray Scattering.

Knowledge of RNA three-dimensional topological structures provides important insight into the relationship between RNA structural components and function. It is often likely that near-complete sets of biochemical and biophysical data containing structural restraints are not available, but one still wants to obtain knowledge about approximate topological folding of RNA. In this regard, general methods for determining such topological structures with minimum readily available restraints are lacking. Naked RNAs are difficult to crystallize and NMR spectroscopy is generally limited to small RNA fragments. By nature, sequence determines structure and all interactions that drive folding are self-contained within sequence. Nevertheless, there is little apparent correlation between primary sequences and three-dimensional folding unless supplemented with experimental or phylogenetic data. Thus, there is an acute need for a robust high-throughput method that can rapidly determine topological structures of RNAs guided by some experimental data. We present here a novel method (RS3D) that can assimilate the RNA secondary structure information, small-angle X-ray scattering data, and any readily available tertiary contact information to determine the topological fold of RNA. Conformations are firstly sampled at glob level where each glob represents a nucleotide. Best-ranked glob models can be further refined against solvent accessibility data, if available, and then converted to explicit all-atom coordinates for refinement against SAXS data using the Xplor-NIH program. RS3D is widely applicable to a variety of RNA folding architectures currently present in the structure database. Furthermore, we demonstrate applicability and feasibility of the program to derive low-resolution topological structures of relatively large multi-domain RNAs.

Software-based PET-MR image coregistration: combined PET-MRI for the rest of us!

BACKGROUND: With the introduction of hybrid positron emission tomography/magnetic resonance imaging (PET/MRI), a new imaging option to acquire multimodality images with complementary anatomical and functional information has become available. Compared with hybrid PET/computed tomography (CT), hybrid PET/MRI is capable of providing superior anatomical detail while removing the radiation exposure associated with CT. The early adoption of hybrid PET/MRI, however, has been limited. OBJECTIVE: To provide a viable alternative to the hybrid PET/MRI hardware by validating a software-based solution for PET-MR image coregistration. MATERIALS AND METHODS: A fully automated, graphics processing unit-accelerated 3-D deformable image registration technique was used to align PET (acquired as PET/CT) and MR image pairs of 17 patients (age range: 10 months-21 years, mean: 10 years) who underwent PET/CT and body MRI (chest, abdomen or pelvis), which were performed within a 28-day (mean: 10.5 days) interval. MRI data for most of these cases included single-station post-contrast axial T1-weighted images. Following registration, maximum standardized uptake value (SUVmax) values observed in coregistered PET (cPET) and the original PET were compared for 82 volumes of interest. In addition, we calculated the target registration error as a measure of the quality of image coregistration, and evaluated the algorithm's performance in the context of interexpert variability. RESULTS: The coregistration execution time averaged 97±45 s. The overall relative SUVmax difference was 7% between cPET-MRI and PET/CT. The average target registration error was 10.7±6.6 mm, which compared favorably with the typical voxel size (diagonal distance) of 8.0 mm (typical resolution: 0.66 mm × 0.66 mm × 8 mm) for MRI and 6.1 mm (typical resolution: 3.65 mm × 3.65 mm × 3.27 mm) for PET. The variability in landmark identification did not show statistically significant differences between the algorithm and a typical expert. CONCLUSION: We have presented a software-based solution that achieves the many benefits of hybrid PET/MRI scanners without actually needing one. The method proved to be accurate and potentially clinically useful.