Fernandez Garcia Meilin, Moore Cedric D, Schulz Katharine N, Alberto Oscar, Donague Greg, Harrison Melissa M, Zhu Heng, Zaret Kenneth S
Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104-5157, USA.
Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
Mol Cell. 2019 Sep 5;75(5):921-932.e6. doi: 10.1016/j.molcel.2019.06.009. Epub 2019 Jul 11.
Fate-changing transcription factors (TFs) scan chromatin to initiate new genetic programs during cell differentiation and reprogramming. Yet the protein structure domains that allow TFs to target nucleosomal DNA remain unexplored. We screened diverse TFs for binding to nucleosomes containing motif-enriched sequences targeted by pioneer factors in vivo. FOXA1, OCT4, ASCL1/E12α, PU1, CEBPα, and ZELDA display a range of nucleosome binding affinities that correlate with their cell reprogramming potential. We further screened 593 full-length human TFs on protein microarrays against different nucleosome sequences, followed by confirmation in solution, to distinguish among factors that bound nucleosomes, such as the neuronal AP-2α/β/γ, versus factors that only bound free DNA. Structural comparisons of DNA binding domains revealed that efficient nucleosome binders use short anchoring α helices to bind DNA, whereas weak nucleosome binders use unstructured regions and/or β sheets. Thus, specific modes of DNA interaction allow nucleosome scanning that confers pioneer activity to transcription factors.
命运改变转录因子（TFs）在细胞分化和重编程过程中扫描染色质以启动新的遗传程序。然而，使TFs靶向核小体DNA的蛋白质结构域仍未被探索。我们筛选了多种TFs，使其与体内先驱因子靶向的富含基序序列的核小体结合。叉头框蛋白A1（FOXA1）、八聚体结合转录因子4（OCT4）、无翅型MMTV整合位点家族成员1/ E12α（ASCL1/E12α）、髓系锌指蛋白1（PU1）、CCAAT增强子结合蛋白α（CEBPα）和 Zelda 蛋白显示出一系列与它们的细胞重编程潜力相关的核小体结合亲和力。我们进一步在蛋白质微阵列上针对不同的核小体序列筛选了593种全长人类TFs，随后在溶液中进行确认，以区分结合核小体的因子，如神经元AP-2α/β/γ，与仅结合游离DNA的因子。DNA结合结构域的结构比较表明，有效的核小体结合剂使用短的锚定α螺旋来结合DNA，而弱的核小体结合剂使用无结构区域和/或β折叠。因此，特定的DNA相互作用模式允许核小体扫描，从而赋予转录因子先驱活性。
