Project description:In normal mammalian development cytosine methylation is essential, and is directed to specific regions of the genome. Despite notable advances in mapping the genome-wide distribution, studying the direct contribution of DNA methylation to gene regulation has been limited by the lack of tools for its precise manipulation. Thus, combining the targeting capability of CRISPR/Cas9 systems with an epigenetic modifier has attracted interest in the scientific community. In contrast to profiling the genome-wide cleavage of a nuclease competent Cas9, tracing the global activity of a dead Cas9-methyltransferase is challenging within a highly modified genome. To overcome this, we utilized an engineered, methylation depleted but maintenance competent mouse ES cell line and find a surprisingly ubiquitous nuclear activity of dCas9-methyltransferases. Our results provide new insights into the targeted regulation of DNA methylation and point to an important difference between genetic and epigenetic editing tools that require unique experimental considerations.
Project description:We report the generation of CRISPR-dCas9 DNA methyltransferases to mediate targeted DNA methylation. Using the dCas9-BFP-DNMT3A and dCas9-BFP-DNMT3B methyltransferases, we have demonstrated that these two methyltransferase can mediate targeted methylation in three human genes tested: uPA, TGFBR3, and CDKN2A in human HEK293T cells. We also showed that these methyltransferases could mediate gene inhibition. five samples co-transfected with five uPA sgRNAs and each of the four dCas9 fusions, or control transfection with pUC19 plasmid
Project description:We report the generation of CRISPR-dCas9 DNA methyltransferases to mediate targeted DNA methylation. Using the dCas9-BFP-DNMT3A and dCas9-BFP-DNMT3B methyltransferases, we have demonstrated that these two methyltransferase can mediate targeted methylation in three human genes tested: uPA, TGFBR3, and CDKN2A in human HEK293T cells. We also showed that these methyltransferases could mediate gene inhibition.
Project description:Post-transcriptional gene regulation plays a significant role in the response to oxygen deprivation. Here, we utilized advances in next-generation sequencing technology to examine changes in transcriptional control, mRNA loading on to polysome, and regulation of ribosome activity during mRNA translation in 7-day-old Arabidopsis seedlings subjected to 2 hour hypoxia treatment. 14 samples, 2 conditions (2 hr hypoxia and 2 hr normoxia), 2 bioreplicates of 3 RNA pools (total mRNA, immunopurified (TRAP) polysomal mRNA, ribosome footprints), 1 bioreplicate of 1 RNA pool (immunopurified (TRAP)-ribosome footprints).