Mammalian DNA methylation is a critical epigenetic mechanism orchestrating gene expression networks in many biological processes. However, investigation of the functions of specific methylation events remains challenging. Here, we demonstrate that fusion of Tet1 or Dnmt3a with a catalytically inactive Cas9 (dCas9) enables targeted DNA methylation editing. Targeting of the dCas9-Tet1 or -Dnmt3a fusion protein to methylated or unmethylated promoter sequences caused activation or silencing, respectively, of an endogenous reporter. Targeted demethylation of the BDNF promoter IV or the MyoD distal enhancer by dCas9-Tet1 induced BDNF expression in post-mitotic neurons or activated MyoD facilitating reprogramming of fibroblasts into myoblasts, respectively. Targeted de novo methylation of a CTCF loop anchor site by dCas9-Dnmt3a blocked CTCF binding and interfered with DNA looping, causing altered gene expression in the neighboring loop. Finally, we show that these tools can edit DNA methylation in mice, demonstrating their wide utility for functional studies of epigenetic regulation.
An algorithm for identifying transcript factor binding sites. MACS captures the influence of genome complexity to evaluate the significance of enriched ChIP regions, and MACS improves the spatial resolution of binding sites through combining the information of both sequencing tag position and orientation. MACS can be easily used for ChIP-Seq data alone, or with control sample with the increase of specificity.
It is an open source image processing Java program designed for scientific multidimensional images. This open platform for scientific image analysis is used in life sciences.
Image J has been transformed to ImageJ2 application.
This new application improves ImageJ data engine to be sufficient to analyze modern datasets and makes the addition of new functionality possible and provides a framework for interoperability between a plethora of external image visualization and analysis programs.
ImageJ2 strengthens ImageJ’s utility by: 1) generalizing the ImageJ data model; 2) introducing a robust architecture instrumental in building bridges across a range of other image processing tools; 3) remaining open source and cross-platform with permissive licensing, enabling continued widespread adoption and extension; 4) building on the huge collection of existing ImageJ plugins while enabling the creation of new plugins with more powerful features; and 5) leveraging a correspondingly large and diverse community to foster a collaborative and interdisciplinary project that facilitates the collective advancement of science.
An image processing package described as a distribution of ImageJ (and ImageJ2) together with Java, Java3D and a lot of plugins organized into a coherent menu structure. The main focus of Fiji is to assist research in life sciences.
SciCrunch is a data sharing and display platform. Anyone can create a custom portal where they can select searchable subsets of hundreds of data sources, brand their web pages and create their community. SciCrunch will push data updates automatically to all portals on a weekly basis. User communities can also add their own data to SciCrunch, however this is not currently a free service.