Development of the central nervous system requires the precise coordination of intrinsic genetic programs to instruct cell fate, synaptic connectivity and function. The MEF2 family of transcription factors (TFs) plays many essential roles in neural development; however, the mechanisms of gene regulation by MEF2 in neurons remain unclear. This dissertation focuses on the molecular mechanisms by which MEF2 binds to the genome, activates enhancers, and regulates gene expression within the developing nervous system. We find that one MEF2 family member in particular, MEF2D, is an essential regulator of the development and function of retinal photoreceptors, the primary sensory neurons responsible for vision. Despite being expressed broadly across many tissues, in the retina MEF2D binds to retina-specific enhancers and regulates photoreceptor-specific transcripts, including critical retinal disease genes. Functional genome-wide analyses demonstrate that MEF2D achieves tissue-specific binding and action through cooperation with a retina-specific TF, CRX. CRX recruits MEF2D away from canonical MEF2 binding sites by promoting MEF2D binding to retina-specific enhancers that lack a strong consensus MEF2 binding sequence. MEF2D and CRX then synergistically co-activate these enhancers to regulate a cohort of genes critical for normal photoreceptor development. These findings demonstrate that MEF2D, a broadly expressed TF, contributes to retina-specific gene expression in photoreceptor development by binding to and activating tissue-specific enhancers cooperatively with CRX, a tissue-specific co-factor. A major unresolved feature of MEF2D function in the retina is that the number of MEF2D binding sites significantly exceeds the number of genes that are dependent on MEF2D for expression. We investigated causes of this discrepancy in an unbiased manner by characterizing the activity of MEF2D-bound enhancers genome-wide. We find that many MEF2D-bound enhancers are inactive. Furthermore, less than half of active MEF2D-bound enhancers require MEF2D for activity, suggesting that significant redundancies exist for TF function within enhancers. These findings demonstrate that observed TF binding significantly overestimates direct TF regulation of gene expression. Taken together, our results suggest that the broadly expressed TF MEF2D achieves tissue specificity through competitive recruitment to enhancers by tissue-specific TFs and activates a small subset of enhancers to regulate genes.

Huntingtons sjukdom (HD) är ett neurodegenerativt tillstånd som orsakas av mutationer i huntingtin gen (Htt), och resulterar till upprepade glutamin (polyQ) i Htt-proteinet. Muterad Htt kan inte vika sig ordentligt och börjar därför aggregera i celler. I detta projekt undersöktes molekylära mekanismerna bakom HD genom att analysera genuttryck hos musvävnader och jämföra detta med biomarkörer identifierats hos HD-patienter. För närvarande finns det ingen behandling för att stoppa utveckling av HD. Därför behövs det mer kunskap om sjukdomen. Projektets mål var att öka vår förståelse på regulatoriska mekanismer som ligger bakom den neurodegenerativa sjukdomen och identifiera potentiella diagnostiska biomarkörer. För denna studie användes mRNA-seq-data från 11 distinkta vävnader från Q175 HD-möss. Vävnader som analyserades inkluderar hjärnstammen, cerebellum, corpus callosum, hippocampus och thalamus/hypothalamus, fettvävnader (brun, vit nära gonad och vit nära tarm) och andra vävnader så som hjärta, hud och gastrocnemius muskel. Efter en grundlig genomgång av HD-litteraturen valdes biomarkörer som sedan undersöktes för mRNA-uttryck hos Q175-möss via Gene Set Enrichment Analysis (GSEA). Genuttrycksförändringar hos HD-möss visade sig vara vävnadsspecifika, med betydande effekter på hud och fettvävnader, men mindre effekter hos hjärnvävnader. Även om gemensamma mRNA-förändringar inte hittas bland de olika vävnader, uppvisade relaterade vävnader förändringar i samma pathways. Immunsvar och ribosomal dysfunktion var utbredd, men varje hjärnregion visade unika förändringar relaterade till sömn, synaptisk signalering och energiprocesser. Muskel- och fettvävnader uppvisar också distinkta mönstrar. Detta understryker vikten av vävnadsspecifik biomarkörforskning för neurodegenerativa sjukdomar. / Huntington's disease (HD) is a neurodegenerative condition caused by a mutation in the Huntingtin (Htt) gene which results in glutamine repeats (polyQ) and a longer Htt-protein. The mutated Htt-protein cannot fold properly and thus, is prone to aggregate in cells. There is currently no treatment available to stop the progression of HD. Therefore, there is a need for more knowledge regarding the disease. This project investigates the molecular mechanisms underlying HD by analysing gene expression program in wild type (Wt) and HD mice. The objective is to investigate changes in gene regulatory mechanisms underlying the neurodegenerative disease and identify potential diagnostic markers. For this study, mRNA-seq data from 11 distinct tissues from Q175 HD model mouse were analysed. These tissues included brainstem, cerebellum, corpus callosum, hippocampus, and thalamus/hypothalamus, adipose tissues (brown, white near gonad and white near intestine), heart, skin and gastrocnemius muscle. Following a thorough literature review, biomarkers of HD were chosen, and their expression investigated in the HD mouse using Gene Set Enrichment Analysis (GSEA). Gene expression changes in HD mouse were specific to different tissues, with significant changes identified in skin and adipose tissues, while smaller changes were detected in the brain tissues. While common changes across the 11 tissues were not found, related tissues exhibited alterations in the same pathways. Changes in immune response and ribosomal dysfunction were widespread across tissues. Moreover, each brain region showed unique changes related to sleep, synaptic signalling, and energy processes. Muscle and adipose tissues displayed distinctive patterns. These results underscore the importance of tissue-specific biomarker research for neurodegenerative diseases.

The present study focuses on the biological functions of the transcription factor EMA/E2F-6, a member of the E2F-family of transcription factors that play an import role in cell cycle progression, differentiation and apoptosis. EMA/E2F-6 functions as a transcriptional repressor by recruiting a large protein complex, that includes polycomb group proteins, to specific target genes in order to silence their expression. To identify the biological functions of EMA/E2F-6 mice lacking this factor were developed and subsequently analysed. EMA/E2F6-/- mice are born with the expected frequency, are fertile and develop normally up to 18 months of age. Then about 25 % of these mice develop a paralysis of the hind limbs and present with a severe primary myelination defect of the spinal cord (and in part of peripheral nerves, too) that is accompanied by a massive infiltration of macrophages. Importantly, the histological findings were also detected in EMA/E2F-6-/- mice lacking clinical symptoms albeit to a lesser extend. With respect to EMA/E2F-6 association with polycomb group (Pc-G) proteins there were no significant findings such as skeletal transformations. In addition, only a mild proliferation defect of T-lymphocytes was observed that, in a more severe form, is typical for Pc-G mutations in the mice. Surprisingly, embryonic fibroblasts from EMA/E2F-6-/- mice have no obvious cell cycle defects. Accordingly, gene expression profiles showed that classical E2F target genes were normally regulated in these cells. However, EMA/E2F-6-/- fibroblasts ubiquitously express genes like alpha-tubulin-3 and -7 that are normally expressed in a strictly testis-specific manner. All EMA/E2F-6-dependent target genes identified contain a conserved E2F-binding site in their promoters that is required both for EMA/E2F-6 binding and regulation.