Transcriptional and structural outcomes of genome-wide CTCF depletion in B cells
Author
Rodríguez Ronchel, AnaEntity
UAM. Departamento de Ingeniería InformáticaDate
2021-02Subjects
CTCF; B cell; DNA loops; InformáticaNote
Trabajo Fin de Máster en Bioinformática y Biología ComputacionalEsta obra está bajo una licencia de Creative Commons Reconocimiento-NoComercial-SinObraDerivada 4.0 Internacional.
Abstract
CTCF is involved in establishing long-range interactions that define chromatin architecture and
regulate transcriptional programs. In B cells, CTCF participates during VDJ recombination
and class switch recombination, both critical processes for the immune response. However, to
date, the relationship between CTCF-mediated contacts and their transcriptional implications
in mature B cells is not completely understood. Here we used a conditional mouse model where
CTCF is eliminated specifically in mature B cells and found a subset of CTCF-binding sites
that are resistant to protein depletion. These "retained" CTCF sites have a higher proportion
of consensus like CTCF motifs and are preferentially localized at topologically associating domains (TADs) boundaries. In addition, we found that CTCF deletion causes few transcriptional
changes in mature B cells. To link CTCF differential binding with changes in gene expression we
studied CTCF binding to promoter regions and the formation of CTCF-mediated loops. With
that aim, we developed an algorithm that identifies regions that can be transcriptionally regulated by CTCF-dependent loops. We consider that this approach represents a step forward in
the understanding of transcriptional regulation mediated by CTCF loops, which will be further
strengthen with the experimental validation of the regions identified in our study.
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Google Scholar:Rodríguez Ronchel, Ana
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