Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy.
PLoS Comput Biol. 2020 Dec 28;16(12):e1008488. doi: 10.1371/journal.pcbi.1008488. eCollection 2020 Dec.
NF-Y is a trimeric Transcription Factor -TF- which binds with high selectivity to the conserved CCAAT element. Individual ChIP-seq analysis as well as ENCODE have progressively identified locations shared by other TFs. Here, we have analyzed data introduced by ENCODE over the last five years in K562, HeLa-S3 and GM12878, including several chromatin features, as well RNA-seq profiling of HeLa cells after NF-Y inactivation. We double the number of sequence-specific TFs and co-factors reported. We catalogue them in 4 classes based on co-association criteria, infer target genes categorizations, identify positional bias of binding sites and gene expression changes. Larger and novel co-associations emerge, specifically concerning subunits of repressive complexes as well as RNA-binding proteins. On the one hand, these data better define NF-Y association with single members of major classes of TFs, on the other, they suggest that it might have a wider role in the control of mRNA production.
NF-Y 是一种三聚体转录因子（TF），能与保守的 CCAAT 元件高度特异性结合。个别 ChIP-seq 分析以及 ENCODE 已经逐步确定了其他 TF 共享的位置。在这里，我们分析了过去五年中 ENCODE 在 K562、HeLa-S3 和 GM12878 中引入的数据，包括几种染色质特征，以及 NF-Y 失活后 HeLa 细胞的 RNA-seq 分析。我们将报告的序列特异性 TF 和共因子的数量增加了一倍。我们根据共关联标准将它们分类为 4 类，推断靶基因分类，确定结合位点和基因表达变化的位置偏向。更大和新的共关联出现，特别是与抑制复合物的亚基以及 RNA 结合蛋白有关。一方面，这些数据更好地定义了 NF-Y 与主要 TF 类别的单个成员的关联，另一方面，它们表明它可能在控制 mRNA 产生方面发挥更广泛的作用。
