Project description:To investigate the interactions between FoxP3 and chromatinized templates, particularly assessing whether FoxP3 can still bind significantly to TnG-repeat DNA, we conducted FoxP3 pulldown experiments using nucleosomal DNA. Consitent with the result using naked genomic DNA, the results highlighted TnG repeats as one of the most significant motifs in these interactions.
Project description:To re-evaluate FoxP3 sequence specificity, we performed an unbiased pull-down of genomic DNA with recombinant FoxP3 protein. Use of genomic DNA, as opposed to synthetic DNA oligos, enables testing sequence specificity in the context of naturally existing repertoire of sequences. De novo motif analysis showed a strong enrichment of TnG repeats (n=2-5) by FoxP3 pull-down, using either MBP alone pull-down or input as a control.
Project description:Using a TIP-seq protocol (specifically isolating transposon insertion junctions) we determined that the Ty1 retrotransposon targets tRNA genes and, in particular, we determined that the transposon inserts into nucleosomal DNA in an asymmetric pattern. TIP-seq recovery of transposon insertion junctions in haploid and diploid yeast
Project description:Using a TIP-seq protocol (specifically isolating transposon insertion junctions) we determined that the Ty1 retrotransposon targets tRNA genes and, in particular, we determined that the transposon inserts into nucleosomal DNA in an asymmetric pattern.