Epigenetic regulation of transcription and cellular development

Epigenetic machinery can regulate different biological processes via different mechanisms. In this thesis, we explore the effects of the epigenetic system on transcription and how it can differ during cellular development in different human cell lines models, with focus on hematopoiesis.

Paper I, aimed to identify new roles for different epigenetic regulators in myeloid differentiation. We performed a CRISPR-Cas9 screen that targeted 1092 epigenetic factors in a model for myeloid differentiation, with the objective to uncover novel roles for regulatory factors that are important for differentiation in hematopoiesis. In our analysis, the chromodomain helicase DNA-binding 2 (CHD2) showed a crucial impact on megakaryocytic differentiation in the K-562 cell line model. In paper II, our aim was to identify the roles of different PHC subunits in Polycomb repressive complex 1 during hematopoiesis. Data mining from publicly available datasets showed opposite expression pattern between each PHC subunit. PHC1 is higher expressed in early stages of myelopoiesis that is opposite to PHC2, and PHC3, which expression increasing with differentiation. PHC1-3 was knocked down individually, using siRNA in the myeloblast cell line KG-1. RNA-sequencing analysis after knock down for each specific PHC subunit, showed how PHC1, 2 and 3 play different roles during development and myeloid differentiation. In paper III, we used the FANTOM5 database for transcription start sites (TSS) in a wide variety of primary cells. The study mapped the usage of alternative TSS that leads to exclusion of coding sequence, and exclusion of annotated protein domains. We demonstrated a dynamic usage of alternative TSS and their potential regulatory roles in different cell lineages and development stages. We investigated the role of alternative TSSs for KDM2B in the Jurkat T-cell lineage and their potential functional consequences. In paper IV, our aim was to study the dynamics of 3D chromatin structure in relation to the circadian rhythm. We demonstrated that chromosomal fiber interactions are organized by PARP1-CTCF activity. We showed how the 3D genome structure can influence circadian rhythm machinery and how the transcription activation and silencing are under oscillation.

List of scientific papers

I. A regulator role for CHD2 in myelopoiesis. Shahin Varnoosfaderani F, Palau A, Dong W, Persson J, Durand-Dubief M, Svensson JP, Lennartsson A. Epigenetics. 2020 Jan;1-13.
https://doi.org/10.1080/15592294.2019.1710913

II. Distinct roles for Polycomb repressive complex 1 subunits PHC1, PHC2 and PHC3 in myeloid differentiation. Anna Palau, Farzaneh Shahin Varnoosfaderani and Andreas Lennartsson. [Manuscript]

III. Investigation of protein coding sequence exclusion by alternative transcription start site usage across the human body. Wenbo Dong*, Berit Lilje*, Farzaneh Shahin Varnoosfaderani, Erik Arner, The FANTOM consortium, Andreas Lennartsson*, Albin Sandelin*. *Authors contributed equally to this study. [Manuscript]

IV. PARP1- and CTCF-Mediated Interactions between Active and Repressed Chromatin at the Lamina Promote Oscillating Transcription. Zhao H*, Sifakis EG*, Sumida N*, Millán-Ariño L*, Scholz BA, Svensson JP, Chen X, Ronnegren AL, Mallet de Lima CD, Varnoosfaderani FS, Shi C, Loseva O, Yammine S, Israelsson M, Rathje LS, Németi B, Fredlund E, Helleday T, Imreh MP, Göndör A. Mol Cell. 2015;59(6):984-97. *Authors contributed equally to this study.
https://doi.org/10.1016/j.molcel.2015.07.019