Short-lived AUF1 p42-binding mRNAs of RANKL and BCL6 have two distinct instability elements each.

Regulation of mRNA stability by RNA-protein interactions contributes significantly to quantitative aspects of gene expression. We have identified potential mRNA targets of the AU-rich element binding protein AUF1. Myc-tagged AUF1 p42 was induced in mouse NIH/3T3 cells and RNA-protein complexes isolated using anti-myc tag antibody beads. Bound mRNAs were analyzed with Affymetrix microarrays. We have identified 508 potential target mRNAs that were at least 3-fold enriched compared to control cells without myc-AUF1. 22.3% of the enriched mRNAs had an AU-rich cluster in the ARED Organism database, against 16.3% of non-enriched control mRNAs. The enrichment towards AU-rich elements was also visible by AREScore with an average value of 5.2 in the enriched mRNAs versus 4.2 in the control group. Yet, numerous mRNAs were enriched without a high ARE score. The enrichment of tetrameric and pentameric sequences suggests a broad AUF1 p42-binding spectrum at short U-rich sequences flanked by A or G. Still, some enriched mRNAs were highly unstable, as those of TNFSF11 (known as RANKL), KLF10, HES1, CCNT2, SMAD6, and BCL6. We have mapped some of the instability determinants. HES1 mRNA appeared to have a coding region determinant. Detailed analysis of the RANKL and BCL6 3'UTR revealed for both that full instability required two elements, which are conserved in evolution. In RANKL mRNA both elements are AU-rich and separated by 30 bases, while in BCL6 mRNA one is AU-rich and 60 bases from a non AU-rich element that potentially forms a stem-loop structure

Static light scattering and electric birefringence experiments on saltfree solutions of poly(styrenesulfonate)

Static light scattering and electric birefringence measurements on aqueous solutions of charged poly(styrenesulfonate) (PSS) with different molecular weights between 10$^5$ and $1.1 \times 10^6$ g/mol are presented. All experiments were performed in the dilute and the semidilute concentration regime (0.0005 mg/ml $<$ $c$ $<$ 10 mg/ml) at minimum ionic strength (down to $\approx$ 10$^{-6}$ M). The static light scattering experiments show a single broad peak in the scattered intensity. The scattering vectors of these peaks increase with increasing concentrations $c$ and scale either with $c^{1/3}$ or with $c^{1/2}$ only depending on a relative concentration but not on the molecular weight : below about 20 $c^*$ (1 $c^*$ := overlap concentration of extended chains = 1 particle/(contour length $\ell_{\rm c}$)$^3$) we found a $c^{1/3}$ dependence of the scattering vector, above 20 $c^*$ a $c^{1/2}$ law is valid. A similar behaviour has been observed for rigid rods [1]. Our results are compared with previous light-[2, 3], small angle neutron-[4, 5], and small angle X-ray [6] scattering investigations. Nearly all of these studies are in a very good agreement with the $c^{1/3}$-and $c^{1/2}$-law. The relaxation of the electric birefringence signal after an applied rectangular electric field is monoexponential in nearly all cases. Again the concentration 20 $c^*$, independent of the molecular weight, seems to be a critical concentration : below 20 $c^*$ we found a normal (negative) birefringence signal, above an anomal (positive) signal. These results are compared with results of electric birefringence measurements on aqueous solutions of rigid rods [7, 8] and PSS- at different ionic strengths [9-11]. It is claimed that our results can be explained by a small flexibility of strongly elongated PSS–rods which increases slightly with increasing molecular weight and distinctly with raising concentration. The concentration $c^*$ is shown to be a reasonable quantity to describe polyelectrolyte solutions without added salt, independent of the molecular weight, respectively the contour length. By rescaling comparable data published by other authors we can establish the critical concentration 20 $c^*$, which seems to be universally valid

Electro-optic effects of aqueous fd-virus suspensions at very low ionic strength

The orientation in external electric fields of rod-like fd-virus particles (length $\ell = 895$ nm, diameter $d = 9$ nm) in aqueous suspensions is examined by the electric birefringence method. In aqueous suspensions the negatively charged fd-particles are surrounded by a diffuse Debye cloud of counterions, which is characterized by the Debye-Hückel parameter $\kappa$. A special experimental set-up is used to vary the ionic strength of the suspension, i.e. the Debye-Hückel parameter, and therefore the electrostatic interparticle interaction. The birefringence signal $\Delta n$ is measured as a function of the strength and frequency of the applied electric field in suspensions of very low ionic strength (10$^{-6}\,$M-10$^{-4}\,$M). At low field strengths Kerr-behaviour is found. From the dependence of the electric anisotropy $\Delta \alpha_{\rm el}$ on the Debye-Hückel parameter $\kappa$ it is concluded that the orientation of the fd-particles is correlated to an induced dipole due to a deformation of the diffuse Debye cloud. Saturation electric birefringence values are far from that theoretically expected. This can be interpreted as a destruction of the diffuse Debye cloud at high electric fields. At low field strengths the frequency dispersion below 1 kHz of $\Delta n$ of the electrostatically interacting fd-virus suspensions shows anomalous behaviour. This negative electro-optic effect is an evidence for the orientation of the particle's long symmetry axis perpendicular to the applied electric field. The dispersion has a positive maximum at about 2 kHz. This maximum could be explained by different frequency dependencies of the electric polarizabilities parallel and perpendicular to the long symmetry axis of the fd-rods