Laura Benítez Montalvo
Laura, a junior studying Biomedical Sciences at the Pontifical Catholic University of Puerto Rico – Ponce Campus, identified unique regions of accessible chromatin by profiling multiple cell states while differentiating a 15-donor pool of Human Induced Pluripotent Stem Cells.
Genome-Wide Association Studies (GWAS) have identified that 90% of disease-associated common variants lie in non-coding genome regions. While it is known that these regions can act as cell-type specific regulatory elements (REs), it is still being determined how the presence of genomic variants impacts different cell types. Calling myself a BSRP alum is one of my greatest accomplishments as a student, scientist, and person. This summer has been the most enriching, inspiring, and collaborative learning experience I’ve had in scientific research, and I’m thankful to all of those who made it possible. At the Broad Institute, I recognized that I belong in this field and can’t wait to return to do more amazing, impactful research. Mapping chromatin accessibility genome-wide provides a catalog of potential REs that can influence cell-type-specific gene expression. Here, we used an Assay for Transposase Accessible Chromatin Sequencing (ATAC-seq) to profile chromatin accessibility across the differentiation of human induced pluripotent stem cells (iPSCs) towards Hepatic Progenitor Cells (HPCs). To further examine changes among the four cell states observed, we performed Chromatin Immunoprecipitation Sequencing (ChIP-seq), specifically targeting genomic regions bound by the CTCF transcription factor. We analyzed the sequencing results to generate genome-wide maps representing accessible chromatin and CTCF-bound regions for each differentiation day. We compared these maps across cell states for each assay, highlighting regions unique to or shared among observed cell states. In terms of chromatin accessibility, we observed that 51% of identified regions among all cell states were shared, suggesting an important role in the regulation of housekeeping genes. On the other hand, 10-23% of identified regions were uniquely present in a given cell state, possibly alluding to the impact of REs controlling cell-state-specific gene expression programs. We performed these differentiations with an iPSC pool of 15 human donors to identify known genomic variants within these candidate regulatory regions. Ultimately, this allows us to determine the impact of known variants on chromatin accessibility and CTCF binding.
Project: Profiling Chromatin State in Pools of Human-Induced Pluripotent Stem Cells
Mentors: Elisa Donnard
PI: Lander Lab