Novel full-length transcriptome analysis workflow ‘Nexons’ to uncover the regulation of poison exons in splicing factors in human germinal centre B cells


Özge Gizlenci

Ozge Gizlenci received her B.Sc. degree in Molecular Biology and Genetics from Middle East Technical University in Turkey. Following her graduation in 2015, she continued her M.Sc. degree in Molecular Biosciences with a major in Cancer Biology from the University of Heidelberg. During the Master’s program, she took a semester abroad to start a joint project in her specialized interests, gene editing and stem cells, in the laboratory of Dr. Christian Brendel and Dr. David A. Williams at Dana-Farber/Boston Children’s Cancer and Blood Disorders Center where she returned to her work with Dr. Christian Brendel as a researcher prior to her graduate studies. At Dana-Farber, she used the base editing method to correct a disease-causing mutation in Schwachman-Diamond Syndrome disease and later to apply it to gene therapy approaches. In October 2018, she started her PhD position funded by the Marie Skłodowska-Curie Actions of the European Union’s Horizon 2020 research and innovation programme of COSMIC consortium in the Immunology Programme at the Babraham Institute. Her PhD project with Dr. Martin Turner is focused on understanding the changes in gene expression and alternative splicing in B cells in response to positive selection signals in the germinal centre using long-read next-generation sequencing technologies (e.g. Oxford Nanopore Technology). She aims to investigate the relationship between alternative splicing and abnormally functioning adaptive immune cells in B cell malignancy and Rheumatoid Arthritis using both computational and molecular biology approaches.


Alternative splicing (AS) plays a major role in the differentiation of immune cells during an immune response as 29% of AS genes are specific to the immune system. Although the role of AS is extensively investigated in T cells, its role in B cell activation is less characterised. We sought to develop a long-read technology, Oxford Nanopore Technologies (ONT), workflow to understand post-transcriptional regulation at both gene and isoform levels of human germinal centre B cells. As one of the challenges of ONT is the accurate computational analysis of isoforms, we developed the ‘Nexons’ pipeline to identify differentially spliced transcript variants using long-read sequencing. An in-depth analysis of splicing regulators with Nexons revealed that poison exons of splicing factors (e.g. SRSF3) were preferentially spliced out upon activation whereas naïve B cells expressed isoforms carrying poison exon, leading to nonsense-mediated mRNA decay. Moreover, we identified novel spliced variants of these genes, which were difficult to deconvolute using short-read data due to the limitations of short-read technology. Altogether, our findings validate the combination of Nexons with ONT cDNA-PCR sequencing as a suitable method for the identification and quantification of complex isoforms.

Date: May 20th, 2022 – 10:30 AM (GMT+3)

Language: English

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