Related Links
Our research focus is the development of tools to promote successful use of transplanted neural stem cells to repair spinal cord injury. Projects include the role of microRNAs in neural stem cell differentiation and the identification of regeneration-promoting genes in brain neurons. As part of the W.M. Keck Center for Collaborative Neuroscience and the Rutgers Stem Cell Research Center, we share several collaborative projects with our colleagues.
Recent work from our laboratory identified 146 new microRNAs in human embryonic stem cells (hESC). We sequenced more than 107 unique small RNA sequences using ultra-deep SOLiD sequencing technology, aligned these with genome in "colorspace" using SHRiMP (Rumble, 2009), and fit results to a model of Microprocessor cleavage (miRDeep, Friedlander, 2008). This produced 818 candidate genomic loci matching the basic structure of a microRNA precursor and aligning with observed RNA sequences. This list was filtered for small RNAs that were immunoprecipitated with anti-Ago2 antibody, reasoning that functional microRNAs should be associated with RISC complexes. 146 of the predicted microRNAs were identified in Ago2 IP samples. Among these new microRNAs, 30% share seed sequences with previously-known microRNAs, suggesting that many are new members of existing microRNA families. Sequence conservation analysis shows that most new microRNAs are conserved across several mammalian species but are not broadly conserved across animals, consistent with a recent evoluationary appearance. These new microRNAs are regulated during hESC differentiation in patterns similar to other microRNAs. This work was published in PLoSOne at this address: http://dx.plos.org/10.1371/journal.pone.0007192. Also read an article in Epigenie covering this work!
Supplemental links for Goff et al. (2009):
- Complete set of supplemental figures (1.2 Mb PDF, opens in a new window)
- UCSC Genome Browser BED file of 818 computed microRNA-encoding genes (right-click and select "Copy Shortcut" and paste link into Genome Browser's "add custom tracks" form.)
- UCSC Genome Browser BED file of 146 Ago2-immunoprecipitated microRNA genes (right-click and select "Copy Shortcut" and paste link into Genome Browser's "add custom tracks" form.)
- GEO dataset for microarrays used in Fig. 1
- SRA dataset for SOLiD results of H1 ESC and NSC listed as experiment 1 in Supplemental Table 1
