CTCF binding site classes exhibit distinct evolutionary, genomic, epigenomic and transcriptomic features.

BACKGROUND: CTCF (CCCTC-binding factor) is an evolutionarily conserved zinc finger protein involved in diverse functions ranging from negative regulation of MYC, to chromatin insulation of the beta-globin gene cluster, to imprinting of the Igf2 locus. The 11 zinc fingers of CTCF are known to differentially contribute to the CTCF-DNA interaction at different binding sites. It is possible that the differences in CTCF-DNA conformation at different binding sites underlie CTCF's functional diversity. If so, the CTCF binding sites may belong to distinct classes, each compatible with a specific functional role. RESULTS: We have classified approximately 26,000 CTCF binding sites in CD4+ T cells into three classes based on their similarity to the well-characterized CTCF DNA-binding motif. We have comprehensively characterized these three classes of CTCF sites with respect to several evolutionary, genomic, epigenomic, transcriptomic and functional features. We find that the low-occupancy sites tend to be cell type specific. Furthermore, while the high-occupancy sites associate with repressive histone marks and greater gene co-expression within a CTCF-flanked block, the low-occupancy sites associate with active histone marks and higher gene expression. We found that the low-occupancy sites have greater conservation in their flanking regions compared to high-occupancy sites. Interestingly, based on a novel class-conservation metric, we observed that human low-occupancy sites tend to be conserved as low-occupancy sites in mouse (and vice versa) more frequently than expected. CONCLUSIONS: Our work reveals several key differences among CTCF occupancy-based classes and suggests a critical, yet distinct functional role played by low-occupancy sites.

Influence of optical heterogeneities on reconstruction of spatial phosphorescence lifetime distributions.

We have previously demonstrated that phosphorescence lifetime imaging (PLI) allows for unbiased determination of absolute oxygen levels in homogeneously absorbing/scattering media. We computationally show that tomographic PLI can perform equally well in heterogeneous environments relying only on surface measurements of phosphorescence.

Simultaneous fluorometry and phosphorometry of Langendorff perfused rat heart: ex vivo animal studies.

Fluorescence imaging of intrinsic fluorophores of tissue is a powerful method to assess metabolic changes at the cellular and intracellular levels. At the same time, exogenous phosphorescent probes can be used to accurately measure intravascular tissue oxygenation. Heart failure is the leading cause of death in America. A rat heart can potentially model the human heart to study failures or other abnormalities optically. We report simultaneous fluorescence and phosphorescence measurements performed on a rat heart. We have used two different optical systems to acquire fluorescence signals of flavoprotein and nicotinamide adenine dinucleotide--the two intrinsic fluorophores of mitochondria--and the phosphorescence signal of an intravascular oxygen probe to extract intracellular and intravascular metabolism loads, respectively.

Oxygen pressures in the interstitial space and their relationship to those in the blood plasma in resting skeletal muscle.

This study compared oxygen pressures (Po(2)), measured by oxygen-dependent quenching of phosphorescence, in the intravascular (blood plasma) space in the muscle with those in the interstitial (pericellular) space. Our hypothesis was that the capillary wall would not significantly impede oxygen diffusion from the blood plasma to the pericellular space. A new near-infrared oxygen sensitive probe, Oxyphor G3, was used to obtain oxygen distributions in the interstitial space. Oxyphor G3 is a Pd-tetrabenzoporphyrin encapsulated inside generation 2 poly-arylglycine (AG) dendrimer. The periphery of the dendrimer is modified with oligoethylene glycol residues (average molecular weight 350) to make the probe water soluble and biologically inert. Oxyphor G3 was injected into thigh muscle using a 30-gauge needle. Histograms of the Po(2) in the interstitial space were measured in awake and anesthetized animals and compared with those for Oxyphor G2 in the intravascular (blood plasma) space. For awake mice, the lowest 10% of Po(2) values for the interstitial and intravascular spaces (believed to represent capillary bed) were not significantly different [23.8 (SD 4.5) and 25 Torr (SD 4.3), respectively], whereas, in isoflurane-anesthetized mice, there was a small but significant (P = 0.01) difference [20.4 (SD 6.3) and 27.9 Torr (SD 3.5), respectively]. The peak values for the histograms for the interstitial space in awake and isoflurane-anesthetized mice were 40.8 (SD 7.5) and 36.9 Torr (SD 8.3), respectively, whereas those for the intravascular space were 52.2 (SD 4.9) and 55.9 Torr (SD 8.4), respectively, showing no significant difference due to isoflurane anesthesia. The histograms for the intravascular space were significantly wider, with more contribution at higher Po(2) values. A different anesthetic, ketamine plus xylazine injected intraperitoneally, caused a marked decrease in the tissue Po(2) values in both spaces, with the time course and extent of the decrease dependent on the time after injection and variable among mice. It was, therefore, not further used.

Feasibility of diffuse optical imaging with long-lived luminescent probes.

Long-lived near-infrared phosphors with high quantum yields have recently become available, making it possible to image oxygen distributions in tissue in three dimensions. By numerical simulations we demonstrate that, by using phosphorescent probes with appropriate oxygen quenching constants, one can image hypoxic phantoms in scattering media with adequate spatial resolution, employing simple time-gated measurements. The approach developed will guide experimental imaging of phosphorescence lifetime and oxygen pressure in living tissue.