Zeidler, Sebastian

[["dc.bibliographiccitation.artnumber","33"],["dc.bibliographiccitation.firstpage","1"],["dc.bibliographiccitation.journal","Frontiers in Genetics"],["dc.bibliographiccitation.lastpage","17"],["dc.bibliographiccitation.volume","7"],["dc.contributor.author","Zeidler, Sebastian"],["dc.contributor.author","Meckbach, Cornelia"],["dc.contributor.author","Tacke, Rebecca"],["dc.contributor.author","Raad, Farah S."],["dc.contributor.author","Roa, Angelica"],["dc.contributor.author","Uchida, Shizuka"],["dc.contributor.author","Zimmermann, Wolfram-Hubertus"],["dc.contributor.author","Wingender, Edgar"],["dc.contributor.author","Gültas, Mehmet"],["dc.date.accessioned","2017-09-07T11:54:27Z"],["dc.date.available","2017-09-07T11:54:27Z"],["dc.date.issued","2016"],["dc.description.abstract","Transcription factors (TFs) regulate gene expression in living organisms. In higher organisms, TFs often interact in non-random combinations with each other to control gene transcription. Understanding the interactions is key to decipher mechanisms underlying tissue development. The aim of this study was to analyze co-occurring transcription factor binding sites (TFBSs) in a time series dataset from a new cell-culture model of human heart muscle development in order to identify common as well as specific co-occurring TFBS pairs in the promoter regions of regulated genes which can be essential to enhance cardiac tissue developmental processes. To this end, we separated available RNAseq dataset into five temporally defined groups: (i) mesoderm induction stage; (ii) early cardiac specification stage; (iii) late cardiac specification stage; (iv) early cardiac maturation stage; (v) late cardiac maturation stage, where each of these stages is characterized by unique differentially expressed genes (DEGs). To identify TFBS pairs for each stage, we applied the MatrixCatch algorithm, which is a successful method to deduce experimentally described TFBS pairs in the promoters of the DEGs. Although DEGs in each stage are distinct, our results show that the TFBS pair networks predicted by MatrixCatch for all stages are quite similar. Thus, we extend the results of MatrixCatch utilizing a Markov clustering algorithm (MCL) to perform network analysis. Using our extended approach, we are able to separate the TFBS pair networks in several clusters to highlight stage-specific co-occurences between TFBSs. Our approach has revealed clusters that are either common (NFAT or HMGIY clusters) or specific (SMAD or AP-1 clusters) for the individual stages. Several of these clusters are likely to play an important role during the cardiomyogenesis. Further, we have shown that the related TFs of TFBSs in the clusters indicate potential synergistic or antagonistic interactions to switch between different stages. Additionally, our results suggest that cardiomyogenesis follows the hourglass model which was already proven for Arabidopsis and some vertebrates. This investigation helps us to get a better understanding of how each stage of cardiomyogenesis is affected by different combination of TFs. Such knowledge may help to understand basic principles of stem cell differentiation into cardiomyocytes"],["dc.identifier.doi","10.3389/fgene.2016.00033"],["dc.identifier.gro","3145188"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?gs-1/13173"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/2896"],["dc.language.iso","en"],["dc.notes.intern","Crossref Import"],["dc.notes.intern","Merged from goescholar"],["dc.notes.status","final"],["dc.publisher","Frontiers Media S.A."],["dc.relation.eissn","1664-8021"],["dc.relation.issn","1664-8021"],["dc.rights","Goescholar"],["dc.rights.uri","https://goescholar.uni-goettingen.de/licenses"],["dc.title","Computational Detection of Stage-Specific Transcription Factor Clusters during Heart Development"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","no"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.artnumber","e0216475"],["dc.bibliographiccitation.issue","5"],["dc.bibliographiccitation.journal","PLOS ONE"],["dc.bibliographiccitation.volume","14"],["dc.contributor.author","Steuernagel, Lukas"],["dc.contributor.author","Meckbach, Cornelia"],["dc.contributor.author","Heinrich, Felix"],["dc.contributor.author","Zeidler, Sebastian"],["dc.contributor.author","Schmitt, Armin O."],["dc.contributor.author","Gültas, Mehmet"],["dc.date.accessioned","2019-07-09T11:51:30Z"],["dc.date.available","2019-07-09T11:51:30Z"],["dc.date.issued","2019"],["dc.description.abstract","Transcription factors (TFs) are a special class of DNA-binding proteins that orchestrate gene transcription by recruiting other TFs, co-activators or co-repressors. Their combinatorial interplay in higher organisms maintains homeostasis and governs cell identity by finely controlling and regulating tissue-specific gene expression. Despite the rich literature on the importance of cooperative TFs for deciphering the mechanisms of individual regulatory programs that control tissue specificity in several organisms such as human, mouse, or Drosophila melanogaster, to date, there is still need for a comprehensive study to detect specific TF cooperations in regulatory processes of cattle tissues. To address the needs of knowledge about specific combinatorial gene regulation in cattle tissues, we made use of three publicly available RNA-seq datasets and obtained tissue-specific gene (TSG) sets for ten tissues (heart, lung, liver, kidney, duodenum, muscle tissue, adipose tissue, colon, spleen and testis). By analyzing these TSG-sets, tissue-specific TF cooperations of each tissue have been identified. The results reveal that similar to the combinatorial regulatory events of model organisms, TFs change their partners depending on their biological functions in different tissues. Particularly with regard to preferential partner choice of the transcription factors STAT3 and NR2C2, this phenomenon has been highlighted with their five different specific cooperation partners in multiple tissues. The information about cooperative TFs could be promising: i) to understand the molecular mechanisms of regulating processes; and ii) to extend the existing knowledge on the importance of single TFs in cattle tissues."],["dc.identifier.doi","10.1371/journal.pone.0216475"],["dc.identifier.pmid","31095599"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?gs-1/16139"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/59959"],["dc.language.iso","en"],["dc.notes.intern","Merged from goescholar"],["dc.rights","CC BY 4.0"],["dc.rights.uri","https://creativecommons.org/licenses/by/4.0"],["dc.subject.ddc","630"],["dc.title","Computational identification of tissue-specific transcription factor cooperation in ten cattle tissues"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]