Project description:4C was performed to identify genomic loci interacting with the 9P21 locus. Subsequently, the effect on cell transformation was furhter investigated upon knockdown/overexpression of the selected candidate targets.
Project description:To characterize enhancer elements regulating the MEF2C gene during neurodevelopment, we performed among others Circularized Chromosome Conformation Capture (4C) sequencing in a neuronal cell line, SH-SY5Y, and a non-neuronal control, HEK. We found that, in a neuronal cell line, the MEF2C promoter interacts with several putative enhancer elements in its upstream region, forming a complex interaction network. Moreover, these interactions are completely absent in HEK cells.
Project description:RNA sequencing was performed to identify mRNAs that are dysregulated upon loss of 9p21. Subsequently, the effect on cell transformation was investigated upon knockdown/overexpression of the candidate targets found from the RNA sequencing analysis .
Project description:Cebpa is a critical transcription factor gene for adipocyte differentiation and adipose tissue development. However, mechanisms controlling Cebpa expression during adipogenic differentiation remain largely unknown. Here, we generated the high-resolution chromatin interaction maps of Cebpa in 3T3-L1 preadipocytes (3T3-L1) and 3T3-L1 adipocytes (3T3-L1-AD) using circularized chromosome conformation capture coupled with next-generation sequencing (4C-seq), and characterized differences in their chromatin interactomes and chromatin status of the interaction sites during adipogenic differentiation. We performed a 4C-seq experiment on inguinal white adipose tissue (iWAT) to evaluate whether chromatin interaction between Cebpa-L1-AD-En2 and Cebpa promoters in 3T3-L1 adipocytes also exists in mouse adipose tissue.
Project description:4C procedure was used for analysis of genomic contacts of rDNA units in HEK 293T cells. The primers for 4C were selected downstream from EcoRI site at coordinate 30487 in rDNA sequence with Accession number U13369.1.
Project description:4C-rDNA procedure was used for analysis of genomic contacts of rDNA units in HEK 293T cells. The primers for 4C were selected downstream from EcoRI site at coordinate 30487 in rDNA sequence with Accession number U13369.1.
Project description:To test if there is a physical interaction between the IRF8 promoter and the rs2280381-containing region, we conducted circular chromatin conformation capture assay in the U937 cell. For the IRF8 viewpoint group, we used CSP6I as the first digested enzyme and NlaIII as the second enzyme. For the rs2280381-containing region, we used MboI as the first digested enzyme and NlaIII as the second enzyme. We use 4C-PCR primer to construct IRF8 point view and rs2280381-containing region 4C library.
Project description:To test the chromatin interaction landscape of the miR-146a promoter region, we performed 4C-seq in JURKAT and RAJI cell lines based on the miR-146a promoter viewpoint. (First digestion enzyme MboI, second digestion enzyme NlaIII)