Study Design

• Cell Lines


• Technology for Hu13K Array
• Microarray Production
• Analysis Techniques
  
  
• Protocols
• Microarray Design and Production
• Network Motif Discovery
• Analysis of Genome-scale Location Data

Data

• Download Raw Data
• Microarray Design and Production
• Error Model
  
• Verification of Results
  
• Previous Evidence of Regulation
  

Appendices/Downloads

• Supporting Online Material (pdf)
  
• ChIP Protocol (pdf)
  

Look Lab Home Page

Despite the importance of transcription factor oncogenes such as TAL1, LYL1, LMO2, HOX11 and HOX11L2 in the pathogenesis of human T-ALL, the downstream transcriptional programs regulated by their products are largely unknown. Here, we analyze these transcriptional networks using a combination of approaches, including knockdown of oncoproteins by RNAi, gene expression profiling using microarrays and ChIP on chip analysis of transcription factors binding sites on a genome-wide scale. We used RNA interference combined with chromatin immunoprecipitation and promoter arrays (ChIP on chip) to identify direct transcriptional targets of TAL1/SCL, a bHLH transcription factor aberrantly expressed in 60% of patients with T-ALL. Our results show that knockdown of TAL1 in T-ALL cells significantly retards their growth rate without a detectable increase in cellular apoptosis, and concomitantly induces significant alterations in the expression of a large number of genes by microarray analysis. ChIP-chip analysis revealed at least 71 direct target promoters of TAL1 when the significance levels were restricted to <0.001. Interestingly, the many of these TAL1 target promoters did not appear to be significantly regulated in T-ALL cells after this RNAi-mediated knockdown of TAL1. By combining RNAi and ChIP-chip approaches, we were able to identify a small subset of genes whose regulation is likely critical for the malignant growth properties of T-ALLs overexpressing TAL1. Thus, this combination of approaches reduces the complexity of regulation that is apparent when either transcription factor binding to target promoters or the global effect on gene expression is analyzed individually. For the first time, a general strategy is available to progressively dissect oncogenic transcription factors activities, starting at the top of networks (direct target genes) and interrogating the functional significance of the genes and pathways that unfold downstream.