Selective Functions of Individual Zinc Fingers Within the DNA-Binding Domain of Ikaros (RNA-seq: sorted DP thymocytes)

The C2H2 zinc finger is the most prevalent DNA-binding motif in the mammalian proteome, with DNA-binding domains usually containing more tandem fingers than are needed for stable sequence-specific DNA recognition. To examine the reason for the frequent presence of multiple zinc fingers, we generated mice lacking finger 1 or finger 4 of the 4-finger DNA-binding domain of Ikaros, a critical regulator of lymphopoiesis and leukemogenesis. Each mutant strain exhibited a specific subset of the phenotypes observed with Ikaros null mice. Of particular relevance, fingers 1 and 4 contributed to distinct stages of B- and T-cell development and finger 4 was selectively required for tumor suppression in thymocytes and in a new model of BCR-ABL+ acute lymphoblastic leukemia. These results, combined with transcriptome profiling (this GEO submission: RNA-Seg of whole thymus from wt and the two ZnF mutants), reveal that different subsets of fingers within multi-finger transcription factors can regulate distinct target genes and biological functions, and they demonstrate that selective mutagenesis can facilitate efforts to elucidate the functions and mechanisms of action of this prevalent class of factors. Ikaros RNA-Seq from double positive thymocytes comparing wt (n=2), Ikaros-ZnF1-/- mutant (n=2) and Ikaros-ZnF4-/- mutant (n=2)C2H2型锌指（C2H2 zinc finger）是哺乳动物蛋白质组中最为普遍的DNA结合基序，其DNA结合结构域通常包含的串联锌指数量，超出了实现稳定序列特异性DNA识别所需的数目。为探究多锌指结构频繁存在的原因，我们构建了缺失艾克罗司（Ikaros）4指DNA结合结构域第1指或第4指的小鼠——艾克罗司是调控淋巴细胞生成与白血病发生的关键转录因子。各突变株均呈现出Ikaros敲除小鼠表型的特定子集。尤为关键的是，第1指与第4指分别参与B细胞和T细胞发育的不同阶段，且第4指是胸腺细胞及一种新型BCR-ABL阳性急性淋巴细胞白血病模型中肿瘤抑制所选择性必需的。 本研究的转录组分析（transcriptome profiling）数据已提交至GEO数据库，相关数据为野生型与两种锌指突变小鼠的全胸腺RNA测序（RNA-Seq）结果。结合上述实验结果，本研究揭示：多锌指转录因子内的不同锌指子集可调控不同的靶基因与生物学功能；同时证实，选择性诱变策略可助力阐明这类广泛存在的转录因子家族的功能与作用机制。 本次数据集包含双阳性胸腺细胞中的Ikaros RNA测序数据，比对组别为野生型（n=2）、Ikaros-ZnF1敲除突变型（n=2）及Ikaros-ZnF4敲除突变型（n=2）小鼠。