• A
  • A
  • A
  • ABC
  • ABC
  • ABC
  • А
  • А
  • А
  • А
  • А
Regular version of the site

Structure of Transcription Factor Footprints in Chromatin Accessibility Profiles

Student: Sakharova Ekaterina

Faculty: Faculty of Computer Science

Educational Programme: Data Analysis for Biology and Medicine (Master)

Year of Graduation: 2018

Mechanisms of gene regulation are among the key questions of molecular biology and bioinformatics. The transcription factors binding specific DNA sites in the regulatory genomic regions play a crucial role in the transcriptional regulation. This study is focused on the local structure of chromatin accessibility profiles in the vicinity of transcription factor binding sites in different cell types. The chromatin accessibility data, for example, obtained by from genome-wide endonuclease cleavage patterns (DNase-Seq), allows inferring the so-called footprints, the profile heterogeneities resulting from DNA sites bound by the transcription factors and protected from cleavage. We used the data from the DREAM-ENCODE challenge on genome-wide prediction of transcription factor binding sites. For selected transcription factors and cell types, the structure of footprints was studied both using the initial DNase-accessibility profiles and the profiles smoothed by the Bayesian segmentation. We show that footprints indeed have a specific structure that can be captured by different machine learning approaches. The resulting footprint models are portable between cell types and homologous transcription factors. Thus, the computational description of footprints is a good invariant feature that can be used in practical analyses such as genome-wide prediction of binding sites.

Student Theses at HSE must be completed in accordance with the University Rules and regulations specified by each educational programme.

Summaries of all theses must be published and made freely available on the HSE website.

The full text of a thesis can be published in open access on the HSE website only if the authoring student (copyright holder) agrees, or, if the thesis was written by a team of students, if all the co-authors (copyright holders) agree. After a thesis is published on the HSE website, it obtains the status of an online publication.

Student theses are objects of copyright and their use is subject to limitations in accordance with the Russian Federation’s law on intellectual property.

In the event that a thesis is quoted or otherwise used, reference to the author’s name and the source of quotation is required.

Search all student theses