TY  - JOUR
A1  - Lorenzin, Francesca
A1  - Benary, Uwe
A1  - Baluapuri, Apoorva
A1  - Walz, Susanne
A1  - Jung, Lisa Anna
A1  - von Eyss, Björn
A1  - Kisker, Caroline
A1  - Wolf, Jana
A1  - Eilers, Martin
A1  - Wolf, Elmar
T1  - Different promoter affinities account for specificity in MYC-dependent gene regulation
JF  - eLife
N2  - Enhanced expression of the MYC transcription factor is observed in the majority of tumors. Two seemingly conflicting models have been proposed for its function: one proposes that MYC enhances expression of all genes, while the other model suggests gene-specific regulation. Here, we have explored the hypothesis that specific gene expression profiles arise since promoters differ in affinity for MYC and high-affinity promoters are fully occupied by physiological levels of MYC. We determined cellular MYC levels and used RNA- and ChIP-sequencing to correlate promoter occupancy with gene expression at different concentrations of MYC. Mathematical modeling showed that binding affinities for interactions of MYC with DNA and with core promoter-bound factors, such as WDR5, are sufficient to explain promoter occupancies observed in vivo. Importantly, promoter affinity stratifies different biological processes that are regulated by MYC, explaining why tumor-specific MYC levels induce specific gene expression programs and alter defined biological properties of cells.
KW  - MYC
KW  - promoter affinity
KW  - human
KW  - mathematical modeling
KW  - mouse
KW  - ChIP-sequencing
KW  - MIZ1
KW  - cancer biology
KW  - cell biology
KW  - WDR5
Y1  - 2016
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-162913
VL  - 5
ER  - 
TY  - JOUR
A1  - Balkenhol, Johannes
A1  - Kaltdorf, Kristin V.
A1  - Mammadova-Bach, Elmina
A1  - Braun, Attila
A1  - Nieswandt, Bernhard
A1  - Dittrich, Marcus
A1  - Dandekar, Thomas
T1  - Comparison of the central human and mouse platelet signaling cascade by systems biological analysis
JF  - BMC Genomics
N2  - Background 
Understanding the molecular mechanisms of platelet activation and aggregation is of high interest for basic and clinical hemostasis and thrombosis research. The central platelet protein interaction network is involved in major responses to exogenous factors. This is defined by systemsbiological pathway analysis as the central regulating signaling cascade of platelets (CC). 

Results 
The CC is systematically compared here between mouse and human and major differences were found. Genetic differences were analysed comparing orthologous human and mouse genes. We next analyzed different expression levels of mRNAs. Considering 4 mouse and 7 human high-quality proteome data sets, we identified then those major mRNA expression differences (81%) which were supported by proteome data. CC is conserved regarding genetic completeness, but we observed major differences in mRNA and protein levels between both species. Looking at central interactors, human PLCB2, MMP9, BDNF, ITPR3 and SLC25A6 (always Entrez notation) show absence in all murine datasets. CC interactors GNG12, PRKCE and ADCY9 occur only in mice. Looking at the common proteins, TLN1, CALM3, PRKCB, APP, SOD2 and TIMP1 are higher abundant in human, whereas RASGRP2, ITGB2, MYL9, EIF4EBP1, ADAM17, ARRB2, CD9 and ZYX are higher abundant in mouse. Pivotal kinase SRC shows different regulation on mRNA and protein level as well as ADP receptor P2RY12. 

Conclusions 
Our results highlight species-specific differences in platelet signaling and points of specific fine-tuning in human platelets as well as murine-specific signaling differences.
KW  - interspecies comparison
KW  - transcriptome
KW  - proteome
KW  - platelet
KW  - network
KW  - signaling
KW  - mouse
KW  - human
KW  - interactome
KW  - cascade
Y1  - 2020
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-230377
VL  - 21
ER  -