Transcription Factor Response Elements on Tip: A Sensitive Approach for Large-Scale Endogenous Transcription Factor Quantitative Identification

The ability to map endogenous transcription
factors (TFs) DNA binding activity at the proteome scale will greatly
enhance our understanding of various biological processes. Here we
report a highly sensitive, rapid, and high-throughput approach, transcription
factor response elements on tip-mass spectrometry (TOT-MS), that allows
for quantitative measurement of endogenous TFs. A total of 150 TFs
from 1 μg of nuclear extracts can be quantified with single
shot mass spectrometry detection in 1 h of machine time. Up to 755
TFs, which is comparable to the depth of RNA-seq, were identified
by TOT coupled with on-tip small size reverse-phase liquid chromatography.
We further demonstrated the capability of TOT-MS by interrogating
the dynamic change of TFs in the epidermal growth factor (EGF) signaling
pathway. This approach should find broad applications in elucidating
the TF landscape from limited amounts of biological materials.

在蛋白质组规模上解析内源性转录因子（transcription factors, TFs）的DNA结合活性，将极大深化我们对各类生物学过程的认知。本研究报道了一种高灵敏度、快速且高通量的方法——转录因子应答元件tip质谱法（transcription factor response elements on tip-mass spectrometry, TOT-MS），可实现内源性转录因子的定量检测。仅需1小时的仪器运行时长，通过单次进样质谱检测即可对1μg核提取物中的150种转录因子完成定量分析。通过TOT法结合tip微型反相液相色谱，可鉴定多达755种转录因子，其鉴定规模可与RNA测序（RNA-seq）的测序深度相匹敌。本研究进一步通过探究表皮生长因子（epidermal growth factor, EGF）信号通路中转录因子的动态变化，验证了TOT-MS的应用效能。该方法可广泛用于从微量生物样本中解析转录因子组谱。