Ian K. Quigley
PostdocSalk Institute for Biological Studies
Molecular Neurobiology Lab - Kintner
10010 North Torrey Pines Road
La Jolla, California
How DNA sequence, transcription factors, epigenetic marks, and 3D chromosomal conformation integrate to promote discrete transcriptional programs is largely unknown. Moreover, the majority of work addressing this question employs cell lines, which are removed from their tissue context. I use multiciliated cells in X. laevis pluripotent progenitors (animal caps) to understand how these disparate genomic elements contribute to transcription. Multiciliated cells are normally found in the skin, and I use a variety of manipulations to change their numbers or character in their native tissue. While cells in developing X. laevis skin have enormous advantages for examining transcriptional and cellular processes, until recently there were few resources or methods to interrogate them genome-wide. To address this, I incorporated or developed both wet (molecular biology) and dry (bioinformatics) methods to examine X. laevis transcriptomes (RNAseq), epigenetic marks (histone modification ChIPseq), transcription factor binding (tagged TF ChIPseq), chromatin accessibility (ATACseq), 3D chromosomal conformation (HiC), and nascent transcription (global run-on sequencing or GROseq) across the genome. As a whole, this work supports a model wherein genes requiring complex regulation, such as developmental transcription factors, are influenced by numerous flanking enhancers. Moreover, it hints that these enhancers are recruited to their target genes in DNA loops using specific sequences and factors, such as rfx proteins, for targeting or stabilization. Finally, these data show that such interactions occur within larger genomic structures of some 200 kb, termed topological domains, that clump together.