Martin-Rufino Jorge Diego, Caulier Alexis, Lee Seayoung, Castano Nicole, King Emily, Joubran Samantha, Jones Marcus, Goldman Seth R, Arora Uma P, Wahlster Lara, Lander Eric S, Sankaran Vijay G
Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
Howard Hughes Medical Institute, Boston, MA, USA.
Science. 2025 Apr 4;388(6742):52-59. doi: 10.1126/science.ads7951. Epub 2025 Apr 3.
Most phenotype-associated genetic variants map to noncoding regulatory regions of the human genome, but their mechanisms remain elusive in most cases. We developed a highly efficient strategy, Perturb-multiome, to simultaneously profile chromatin accessibility and gene expression in single cells with CRISPR-mediated perturbation of master transcription factors (TFs). We examined the connection between TFs, accessible regions, and gene expression across the genome throughout hematopoietic differentiation. We discovered that variants within TF-sensitive accessible chromatin regions in erythroid differentiation, although representing <0.3% of the genome, show a ~100-fold enrichment for blood cell phenotype heritability, which is substantially higher than that for other accessible chromatin regions. Our approach facilitates large-scale mechanistic understanding of phenotype-associated genetic variants by connecting key cis-regulatory elements and their target genes within gene regulatory networks.
大多数与表型相关的基因变异定位于人类基因组的非编码调控区域，但在大多数情况下，它们的作用机制仍不清楚。我们开发了一种高效的策略——Perturb-multiome，通过CRISPR介导的主转录因子（TFs）扰动，在单细胞中同时分析染色质可及性和基因表达。我们研究了造血分化过程中全基因组范围内TFs、可及区域和基因表达之间的联系。我们发现，在红系分化中，TF敏感的可及染色质区域内的变异，尽管只占基因组的不到0.3%，但血细胞表型遗传力却富集了约100倍，这大大高于其他可及染色质区域。我们的方法通过在基因调控网络中连接关键的顺式调控元件及其靶基因，促进了对与表型相关的基因变异的大规模机制理解。
