Threshold and Flavour Effects in the Renormalization Group Equations of the MSSM I: Dimensionless Couplings

In a theory with broken supersymmetry, gaugino couplings renormalize differently from gauge couplings, as do higgsino couplings from Higgs boson couplings. As a result, we expect the gauge (Higgs boson) couplings and the corresponding gaugino (higgsino) couplings to evolve to different values under renormalization group evolution. We re-examine the renormalization group equations (RGEs) for these couplings in the Minimal Supersymmetric Standard Model (MSSM). To include threshold effects, we calculate the $\beta$-functions using a sequence of (non-supersymmetric) effective theories with heavy particles decoupled at the scale of their mass. We find that the difference between the SM couplings and their SUSY cousins that is ignored in the literature may be larger than two-loop effects which are included, and further that renormalization group evolution induces a non-trivial flavour structure in gaugino interactions. We present here the coupled set of RGEs for these dimensionless gauge and "Yukawa"-type couplings. The RGEs for the dimensionful SSB parameters of the MSSM will be presented in a companion paper.Comment: 67 pages, 5 figures, revtex4, bm.sty, amsmath.sty; Corrected Eqs. (59), (60) and (62) - (64). Results change by less than 0.05

Threshold and Flavour Effects in the Renormalization Group Equations of the MSSM II: Dimensionful couplings

We re-examine the one-loop renormalization group equations (RGEs) for the dimensionful parameters of the minimal supersymmetric Standard Model with broken supersymmetry, allowing for arbitrary flavour structure of the soft SUSY breaking (SSB) parameters. We include threshold effects by evaluating the $\beta$-functions in a sequence of (non-supersymmetric) effective theories with heavy particles decoupled at the scale of their mass. We present the most general form for high scale SSB parameters that obtains if we assume that the supersymmetry breaking mechanism does not introduce new inter-generational couplings. This form, possibly amended to allow additional sources of flavour-violation, serves as a boundary condition for solving the RGEs for the dimensionful MSSM parameters. We then present illustrative examples of numerical solutions to the RGEs. We find that in a SUSY GUT with the scale of SUSY scalars split from that of gauginos and higgsinos, the gaugino mass unification condition may be violated by ${\cal O}$(10%). As another illustration, we show that in mSUGRA, the rate for the flavour-violating $\tilde{t}_1\to c\tilde{Z}_1$ decay obtained using the complete RGE solution is smaller than that obtained using the commonly-used "single-step" integration of the RGEs by a factor 10-25, and so may qualitatively change expectations for topologies from top-squark pair production at colliders. Together with the RGEs for dimensionless couplings presented in a companion paper, the RGEs in Appendix B of this paper form a complete set of one-loop MSSM RGEs that include threshold and flavour-effects necessary for two-loop accuracy.Comment: 96 pages, 14 figures, revtex4, multirow.sty, bm.sty, amsmath.sty; Corrected Fig. 3 and Eqs. (B9), (B11), (B13) - (B20) and (B24). Results change by less than 1

Identifying DNA motifs based on match and mismatch alignment information

The conventional way of identifying DNA motifs, solely based on match alignment information, is susceptible to a high number of spurious sites. A novel scoring system has been introduced by taking both match and mismatch alignment information into account. The mismatch alignment information is useful to remove spurious sites encountered in DNA motif searching. As an example, a correct TATA box site in Homo sapiens H4/g gene has successfully been identified based on match and mismatch alignment information

TBP binding and the rate of transcription initiation from the human β-globin gene.

DNA-protein interaction studies in vitro revealed several factors binding over the TATA box and the region of transcription initiation (cap) site of the human beta-globin promoter; TATA binding protein TBP at -30, Sp1 at -19, GATA-1 at -12 and +5, YY1 at -9 and a novel factor C1 over the site of initiation (-4 to +7). Point mutants which specifically abolish the binding of each of these proteins were tested in a beta-globin locus control region (LCR) construct which allows quantitative comparisons at physiological levels of transcription. Only mutants which drastically affect the binding of TBP resulted in decreased levels of transcription. A threshold value of TBP binding of 15-30% of wild type was sufficient to give normal levels of transcription. This indicates that the association of TF IID with the TATA box is not limiting in the rate of initiation of transcription

A nucleosome-free dG-dC-rich sequence element promotes constitutive transcription of the essential yeast RIO1 gene

RIO1 is an essential gene that encodes a protein serine kinase and is transcribed constitutively at a very low level. Transcriptional activation of RIO1 dispenses with a canonical TATA box as well as with classical transactivators or specific DNAbinding factors. Instead, a dGdCrich sequence element, that is located 40 to 48 bp upstream the single site of mRNA initiation, is essential and presumably constitutes the basal promoter. In addition, we demonstrate here that this promoter element comprises a nucleosomefree gap which is centered at the dGdC tract and flanked by two positioned nucleosomes. This element is both, necessary and sufficient, for basal transcription initiation at the RIO1 promoter and, thus, constitutes a novel type of core promoter element

Molecular mechanisms that distinguish TFIID housekeeping from regulatable SAGA promoters

An important distinction is frequently made between constitutively expressed housekeeping genes versus regulated genes. Although generally characterized by different DNA elements, chromatin architecture and cofactors, it is not known to what degree promoter classes strictly follow regulatability rules and which molecular mechanisms dictate such differences. We show that SAGA-dominated/wTATA-box promoters are more responsive to changes in the amount of activator, even compared to TFIID/TATA-like promoters that depend on the same activator Hsf1. Regulatability is therefore an inherent property of promoter class. Further analyses show that SAGA/TATA-box promoters are more dynamic because TATA-binding protein recruitment through SAGA is susceptible to removal by Mot1. In addition, the nucleosome configuration upon activator depletion shifts on SAGA/TATA-box promoters and seems less amenable to preinitiation complex formation. The results explain the fundamental difference between housekeeping and regulatable genes, revealing an additional facet of combinatorial control: an activator can elicit a different response dependent on core promoter class

The RNA Polymerase II Core Promoter in Drosophila.

Transcription by RNA polymerase II initiates at the core promoter, which is sometimes referred to as the "gateway to transcription." Here, we describe the properties of the RNA polymerase II core promoter in Drosophila The core promoter is at a strategic position in the expression of genes, as it is the site of convergence of the signals that lead to transcriptional activation. Importantly, core promoters are diverse in terms of their structure and function. They are composed of various combinations of sequence motifs such as the TATA box, initiator (Inr), and downstream core promoter element (DPE). Different types of core promoters are transcribed via distinct mechanisms. Moreover, some transcriptional enhancers exhibit specificity for particular types of core promoters. These findings indicate that the core promoter is a central component of the transcriptional apparatus that regulates gene expression

Inhibition of RNA polymerase II transcription in human cells by synthetic DNA-binding ligands

Sequence-specific DNA-binding small molecules that can permeate human cells potentially could regulate transcription of specific genes. Multiple cellular DNA-binding transcription factors are required by HIV type 1 for RNA synthesis. Two pyrrole-imidazole polyamides were designed to bind DNA sequences immediately adjacent to binding sites for the transcription factors Ets-l, lymphoid-enhancer binding factor 1, and TATA-box binding protein. These synthetic ligands specifically inhibit DNA-binding of each transcription factor and HIV type 1 transcription in cell-free assays. When used in combination, the polyamides inhibit virus replication by >99% in isolated human peripheral blood lymphocytes, with no detectable cell toxicity, The ability of small molecules to target predetermined DNA sequences located within RNA polymerase II promoters suggests a general approach for regulation of gene expression, as well as a mechanism for the inhibition of viral replication