Computational characterisation of transcription factor complexes regulating erythroid differentiation

Sumić, Sara (2011) Computational characterisation of transcription factor complexes regulating erythroid differentiation. Diploma thesis, Faculty of Science > Department of Biology.

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Transcription factors (TFs) interact with each other and DNA to form multiprotein complexes that modulate transcription rate of target genes during differentiation of erythroid progenitors into mature erythrocytes. Chromatin immunoprecipitation (ChIP), followed by high-throughput sequencing (ChIP-seq) allows the DNA binding locations of individual TFs to be mapped genome-wide, and the co-occurence of the binding locations of different TFs and transcriptional cofactors indicates their involment in a TF complex. Computational approach to the analysis of ChIP-seq datasets presented in this work was used to characterize the composition of TF complexes genome-wide, formed by 14 TFs before and after differentiation of MEL cells - a model system for erythroid differentiation. Genome locations of the identified complexes were associated with gene expression profiles during differentiation of MEL cells, obtained by computational analysis of RNA-seq datasets, and enabled identification of potential target genes. I was able to confirm the known functional types of TF complexes among the 14 TFs, and also discover new types of complexes and suggest their regulatory roles in erythroid differentiation.

Item Type: Thesis (Diploma thesis)
Keywords: transcription factor complexes, transcription regulation, erythroid differentiation, ChIP-seq technology, computational analysis methods
Supervisor: Lenhard, Boris
Date: 2011
Number of Pages: 45
Subjects: NATURAL SCIENCES > Biology
Divisions: Faculty of Science > Department of Biology
Depositing User: Grozdana Sirotic
Date Deposited: 07 Jul 2014 11:51
Last Modified: 18 Sep 2014 11:05

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