Project description:The aim of this study was to identify genes/DNA sequences which serum-derived and internalized C3 might interact with in the human B lymphoblastoma cell line, Raji. The project involved analysis of the proteins’ uptake from the serum, the verification of its nuclear entry and identification of the potential interacting nucleic acid sequences by ChIPsequencing.
Project description:Mitochondrial genomes are separated from the nuclear genome for most of the cell cycle by the nuclear double membrane, intervening cytoplasm and the mitochondrial double membrane. Despite these physical barriers we show that somatically acquired mitochondrial-nuclear genome fusion sequences are present in cancer cells. Most occur in conjunction with intranuclear genomic rearrangements and the features of the fusion fragments indicate that non-homologous end joining and/or replication-dependent DNA double strand break repair are the dominant mechanism involved. This study includes 12 pairs of whole-genome sequences (tumour and paired-normal), which present somatic mitochondrial DNA integrations in tumour genomes. Reference: Young Seok Ju et al., Frequent somatic transfer of mitochondrial DNA into the nuclear genome of human cancer cells, Genome Research (2015).
Project description:RNA-directed DNA methylation (RdDM) is a de novo DNA methylation mechanism in plants that plays a fundamental role in plant defence against invasive DNA and in maintaining genome stability by silencing transposons and repetitive sequences. Using nuclear RNA immunoprecipitation, we constructed a highly enriched library and obtained sequences of ncRNAs specifically associated with Argonaute 4 (AGO4), a key component of RNA-directed DNA methylation. A negative immunoprecipation (IP) library was prepared using IP RNA from tissues that don't express the target protein. A nuclear RNA library was also prepared using nuclei isolated RNA.
Project description:RNA-directed DNA methylation (RdDM) is a de novo DNA methylation mechanism in plants that plays a fundamental role in plant defence against invasive DNA and in maintaining genome stability by silencing transposons and repetitive sequences. Using nuclear RNA immunoprecipitation, we constructed a highly enriched library and obtained sequences of ncRNAs specifically associated with Argonaute 4 (AGO4), a key component of RNA-directed DNA methylation. A negative immunoprecipation (IP) library was prepared using IP RNA from tissues that don't express the target protein. A nuclear RNA library was also prepared using nuclei isolated RNA. Three libraries (1X FLAGAGO4 IP, 1X negative IP, 1X nuclear RNA). RNA-IP or nuclear RNA seq cDNA libraries were prepared using the template-switch cDNA library preparation method derived from Zhao et al (2010), and subjected to Illumina GAIIx single end sequencing (100bp)
