Accurate Quantification of DNA Recognition and Methylation Readout by Transcription Factors
Event details
| Date | 23.05.2017 |
| Hour | 12:15 › 13:15 |
| Speaker | Prof. Harmen J. Bussemaker, Columbia University, NYC, NY (USA) |
| Location | |
| Category | Conferences - Seminars |
BIOENGINEERING SEMINAR
Abstract:
Mutations in non-coding DNA are increasingly found to be associated with human disease, yet we currently lack robust methods for predicting transcription factor (TF) binding from sequence, especially at lower affinities. We developed a versatile maximum likelihood framework named No Read Left Behind (NRLB) that fits a biophysical model of protein-DNA recognition to sequencing-based in vitro TF binding data, across the full affinity range. NRLB predicts human Max homodimer binding in near-perfect agreement with existing low-throughput measurements. The model captures the specificity of p53 tetrameric binding sites and discovers multiple binding modes in a single sample. Additionally, we confirm that newly-identified low-affinity enhancer binding sites are functional in vivo, and that their contribution to gene expression matches their predicted affinity. We will also describe EpiSELEX-seq, our method for quantifying the sensitivity of TF binding to cytosine methylation in a context-specific manner, and its application to Hox and bZIP complexes as well as p53. Finally, we will discuss our efforts to decipher the autonomous rules of transcriptional control in human cells using a massively parallel reporter assay named Survey of Regulatory Elements (SuRE), coupled with statistical analysis using generalized linear models.
Bio:
Experience
Associate Professor
Columbia University, NYC, NY (USA)
Professor, Departments of Biological Sciences and Systems Biology
Columbia University, NYC, NY (USA)
2014 – Present
Education
Utrecht University (NL)
Doctor of Philosophy (Ph.D.), Physics
1991 – 1995
Utrecht University (NL)
Master's degree, Physics
1989 – 1991
Utrecht University (NL)
Bachelor's degree, Physics
1986 – 1989
Abstract:
Mutations in non-coding DNA are increasingly found to be associated with human disease, yet we currently lack robust methods for predicting transcription factor (TF) binding from sequence, especially at lower affinities. We developed a versatile maximum likelihood framework named No Read Left Behind (NRLB) that fits a biophysical model of protein-DNA recognition to sequencing-based in vitro TF binding data, across the full affinity range. NRLB predicts human Max homodimer binding in near-perfect agreement with existing low-throughput measurements. The model captures the specificity of p53 tetrameric binding sites and discovers multiple binding modes in a single sample. Additionally, we confirm that newly-identified low-affinity enhancer binding sites are functional in vivo, and that their contribution to gene expression matches their predicted affinity. We will also describe EpiSELEX-seq, our method for quantifying the sensitivity of TF binding to cytosine methylation in a context-specific manner, and its application to Hox and bZIP complexes as well as p53. Finally, we will discuss our efforts to decipher the autonomous rules of transcriptional control in human cells using a massively parallel reporter assay named Survey of Regulatory Elements (SuRE), coupled with statistical analysis using generalized linear models.
Bio:
Experience
Associate Professor
Columbia University, NYC, NY (USA)
Professor, Departments of Biological Sciences and Systems Biology
Columbia University, NYC, NY (USA)
2014 – Present
Education
Utrecht University (NL)
Doctor of Philosophy (Ph.D.), Physics
1991 – 1995
Utrecht University (NL)
Master's degree, Physics
1989 – 1991
Utrecht University (NL)
Bachelor's degree, Physics
1986 – 1989
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