将转录因子丰度与染色质可及性整合到人类红系谱系的定向分化中。

Integrating transcription-factor abundance with chromatin accessibility in human erythroid lineage commitment.

机构信息

Department of Pathology, Stanford University, Stanford, CA 94305, USA.

Cancer Biology Program, Stanford University, Stanford, CA 94305, USA.

出版信息

Cell Rep Methods. 2022 Mar 28;2(3). doi: 10.1016/j.crmeth.2022.100188. Epub 2022 Mar 21.

Master transcription factors (TFs) directly regulate present and future cell states by binding DNA regulatory elements and driving gene-expression programs. Their abundance influences epigenetic priming to different cell fates at the chromatin level, especially in the context of differentiation. In order to link TF protein abundance to changes in TF motif accessibility and open chromatin, we developed InTAC-seq, a method for simultaneous quantification of genome-wide chromatin accessibility and intracellular protein abundance in fixed cells. Our method produces high-quality data and is a cost-effective alternative to single-cell techniques. We showcase our method by purifying bone marrow (BM) progenitor cells based on GATA-1 protein levels and establish high GATA-1-expressing BM cells as both epigenetically and functionally similar to erythroid-committed progenitors.

主转录因子（TFs）通过结合 DNA 调控元件并驱动基因表达程序，直接调节当前和未来的细胞状态。它们的丰度影响染色质水平上不同细胞命运的表观遗传启动，特别是在分化的背景下。为了将 TF 蛋白丰度与 TF 基序可及性和开放染色质的变化联系起来，我们开发了 InTAC-seq 方法，用于同时定量固定细胞中的全基因组染色质可及性和细胞内蛋白丰度。我们的方法产生高质量的数据，是单细胞技术的一种具有成本效益的替代方法。我们通过基于 GATA-1 蛋白水平来纯化骨髓（BM）祖细胞，并确定高表达 GATA-1 的 BM 细胞在表观遗传和功能上都与红细胞定向祖细胞相似，展示了我们的方法。