Higher-order regulatory interactions between enhancer elements and target gene promoters have been implicated in the coordination and regulation of transcription in a spatio-temporal manner. Within development, the graded activity of enhancers controls transcriptional programs necessary to establish cell fates and tissue patterning. How enhancer promoter interactions form and dynamically change throughout development remains largely unknown. The aim of this thesis is to further characterise BMP enhancers during development. Using ChIP data, an enrichment of architectural binding proteins (ABPs) with enhancers regulated by the BMP pathway was identified. Analysis of chromatin signatures revealed a correlation with the active histone marks, H3K27ac and H3K36me3, over BMP enhancers enriched for the ABP BEAF32. BEAF32 mutants show disrupted expression of BMP target genes and altered tissue fates defined by the BMP pathway. Consequently, the role of BEAF32 genome-wide was considered, revealing interactions with factors associated with enhancers and promoters, in addition to a correlation with RNA Polymerase II (RNAPII) pausing at promoter regions. This suggests a possible role for BEAF32 in bridging enhancer promoter interactions and releasing paused RNAPII. Based on the prevalence of BEAF32 at some enhancer sites and interaction with CBP, eRNAs were identified within the Drosophila embryo, utilising available GRO-seq data and GroHMM. eRNA expression correlates to accessible enhancer states regardless of chromatin composition, with transcribed enhancers revealing interactions with active promoters, supporting correlations to transcriptional activation. Chromatin architecture of BMP targets were lastly considered using Capture-C against BMP regulated promoters, revealing multiple regulatory interactions including contacts with enhancers regulated along the Dorso-ventral (DV) axis and additional BMP promoters, with dynamic interactions between enhancers and promoters. Overall the presented data suggest that BMP promoters are dynamically regulated by distal enhancers, with a plausible role for BEAF32 in mediating enhancer promoter interactions, to co-ordinate transcription programs used to pattern dorsal tissues in the Drosophila embryo.

Trippelnegativ bröstcancer (TNBC) är den mest maligna formen av bröstcancer utan någon framträdande behandlingsbar biomarkör. Således har den djupa återfallsfrekvensen och bristen på behandlingsalternativ öppnat behovet av att förstå TNBC: s etiopatogenes och molekylära mekanism. Huvudsyftet är att kartlägga det genomomfattande differentiella uttrycket av den förmodade cancergenen (en prenyleringsgen) och dess betydelse vid trippelnegativ bröstcancer. Hi-Cap (Capture Hi-C) är en teknik som genererar högupplösta promotor-förstärkare interak- tioner med nästan en-förstärkare upplösning.Vi arbetade med cancercellinjer, MDA-MB_231, med och utan den förmodade genen. Hi-C-tekniken optimerades i enlighet därmed för cancer- cellinjen för att generera en högupplöst berikad region. Resultaten kan vidare användas för att utföra biblioteksförberedelser och bioinformatikanalys. Dessa fynd kommer att ägnas åt att upptäcka nya vägar involverade i prenylering och TNBC. / Triple-negative Breast cancer (TNBC) is the most malignant form of breast cancer with no prominent treatable biomarker. The profound recurrence rate and lack of treatment options have opened the need to understand the etiopathogenesis and molecular mechanism of TNBC. The main objective of this study is to map the genome-wide differential expression of the putative cancer gene (a prenylation gene) and its importance in Triple-Negative Breast cancer. Hi-Cap (Capture Hi-C) is a technique which generates high-resolution promoter-enhancer interactions with almost single-enhancer resolution. We worked with cancer cell lines, MDA-MB_231, with and without the putative gene. The Hi-C technique was optimized accordingly for the cancer cell line to generate a high-resolution enriched region. The results can be further used to perform library prep and bioinformatics analysis. These findings will devote to discovering novel pathways involved with prenylation and TNBC.