Werner syndrome protein limits MYC-induced cellular senescence - Supplementary Materials Only

The MYC oncoprotein is a transcription factor that coordinates cell growth and division. MYC overexpression exacerbates genomic instability and sensitizes cells to apoptotic stimuli. Here we demonstrate that MYC directly stimulates transcription of the human Werner syndrome gene, WRN, which encodes a conserved RecQ helicase. Loss-of-function mutations in WRN lead to genomic instability, an elevated cancer risk, and premature cellular senescence. The overexpression of MYC in WRN syndrome fibroblasts or after WRN depletion from control fibroblasts led to rapid cellular senescence that could not be suppressed by hTERT expression. We propose that WRN up-regulation by MYC may promote MYC-driven tumorigenesis by preventing cellular senescence

Some new types of biplot

We give examples of novel biplots based on the ideas developed by Gower and Hand (1996). The basic concept that underpins all these biplots is that of the reference system which acts like sets of high dimensional coordinate axes. We use the term reference system because, although its generality includes the familiar rectangular Cartesian coordinate axes, it also include non-linear axes, termed trajectories, and sets of points termed category level points, which are applicable to categorical, rather than continuous, variables. Like ordinary coordinate axes, the trajectories are equipped with scales by providing markers labelled by numerical values, usually chosen at conveniently equal intervals of the measure associated with the variables. Category level points are labelled by the names of the category levels. A reference system may include both trajectories and sets of category level points. Reference systems act like coordinate axes because they can be constructed so that (i) the coordinates associated with any point in the multidimensional space are given by finding the nearest marker for each variable and (ii) a point may be added to the reference system by taking the vector-sum of the markers associated with its numerical and/or categorical values. For numerical variables, nearest amounts to orthogonal projection onto the trajectories; for categorical variables, nearest merely means determining the nearest category level point for each variable

Nonlinearity effects in multidimensional scaling

When multidimensional scaling of n cases is derived from dissimilarities that are functions of p basic continuous variables, the question arises of how to relate the values of the variables to the configuration of n points. We provide a methodology based on nonlinear biplots that expresses nonlinearity in two ways: (i) each variable is represented by a nonlinear trajectory and (ii) each trajectory is calibrated by an irregular scale. Methods for computing, calibrating and interpreting these trajectories are given and exemplified. Not only are the tools of immediate practical utility but the methodology established assists in a critical appraisal of the consequences of using nonlinear measures in a variety of multidimensional scaling methods.Biplots Graphical representations Matrix approximation Multidimensional scaling Nonlinearity Prediction

Nonlinearity effects in multidimensional scaling

When multidimensional scaling of n cases is derived from dissimilarities that are functions of p basic continuous variables, the question arises of how to relate the values of the variables to the configuration of n points. We provide a methodology based on nonlinear biplots that expresses nonlinearity in two ways: (i) each variable is represented by a nonlinear trajectory and (ii) each trajectory is calibrated by an irregular scale. Methods for computing, calibrating and interpreting these trajectories are given and exemplified. Not only are the tools of immediate practical utility but the methodology established assists in a critical appraisal of the consequences of using nonlinear measures in a variety of multidimensional scaling methods

c-Myc binds to human ribosomal DNA and stimulates transcription of rRNA genes by RNA polymerase I

c-Myc coordinates cell growth and division through a transcriptional programme that involves both RNA polymerase (Pol) II- and Pol III-transcribed genes. Here, we demonstrate that human c-Myc also directly enhances Pol I transcription of ribosomal RNA (rRNA) genes. rRNA synthesis and accumulation occurs rapidly following activation of a conditional MYC-ER allele (coding for a Myc-oestrogen-receptor fusion protein), is resistant to inhibition of Pol II transcription and is markedly reduced by c-MYC RNA interference. Furthermore, by using combined immunofluorescence and rRNA-FISH, we have detected endogenous c-Myc in nucleoli at sites of active ribosomal DNA (rDNA) transcription. Our data also show that c-Myc binds to specific consensus elements located in human rDNA and associates with the Pol I-specific factor SL1. The presence of c-Myc at specific sites on rDNA coincides with the recruitment of SL1 to the rDNA promoter and with increased histone acetylation. We propose that stimulation of rRNA synthesis by c-Myc is a key pathway driving cell growth and tumorigenesis

Continuously tunable nucleic acid hybridization probes

In silico–designed nucleic acid probes and primers often do not achieve favorable specificity and sensitivity tradeoffs on the first try, and iterative empirical sequence-based optimization is needed, particularly in multiplexed assays. We present a novel, on-the-fly method of tuning probe affinity and selectivity by adjusting the stoichiometry of auxiliary species, which allows for independent and decoupled adjustment of the hybridization yield for different probes in multiplexed assays. Using this method, we achieved near-continuous tuning of probe effective free energy. To demonstrate our approach, we enforced uniform capture efficiency of 31 DNA molecules (GC content, 0–100%), maximized the signal difference for 11 pairs of single-nucleotide variants and performed tunable hybrid capture of mRNA from total RNA. Using the Nanostring nCounter platform, we applied stoichiometric tuning to simultaneously adjust yields for a 24-plex assay, and we show multiplexed quantitation of RNA sequences and variants from formalin-fixed, paraffin-embedded samples