Identification of Functional Elements in the Genome (Bing Ren)

In this episode of the Epigenetics Podcast, we caught up with Bing Ren, Ph.D., from the University of California, San Diego and the Ludwig Institute for Cancer Research to talk about his work on identifying functional elements of the genome and higher order genome structure.

 

Dr. Ren’s lab invented an approach using chromatin immunoprecipitation-based methods for the identification of transcription factor binding sites and chromatin modification status genome-wide. His group  was a major part of the ENCODE Project and the demonstration of this being an effective method for genome-wide mapping of cis-elements, has made their approach very popular among colleagues from the field.

 

His lab recently discovered Topologically associating domains (TADs), which partition the human genome into a few thousand megabase-sized domains. Interactions occur predominantly within TADs but seldom between them and are surprisingly stable during development and are evolutionarily conserved. This organisatorial pattern helps explain how enhancers, who are often located kilobases away, influence their target genes.

 

In this interview, we discuss the road of Bing Ren's scientific career, his role in the ENCODE Project and Roadmap Epigenome Consortia, and the discovery of Topologically associating domains (TADs).

 

References

• The ENCODE Project Consortium (2004) The ENCODE (ENCyclopedia Of DNA Elements) Project (Science) DOI: 10.1126/science.1105136 
• Yin Shen, Feng Yue, … Bing Ren (2012) A map of the cis -regulatory sequences in the mouse genome (Nature) DOI: 10.1038/nature11243 
• Tae Hoon Kim, Leah O. Barrera, … Bing Ren (2005) A high-resolution map of active promoters in the human genome (Nature) DOI: 10.1038/nature03877 
• Tae Hoon Kim, Ziedulla K. Abdullaev, … Bing Ren (2007) Analysis of the Vertebrate Insulator Protein CTCF-Binding Sites in the Human Genome (Cell) DOI: 10.1016/j.cell.2006.12.048 
• R. David Hawkins, Gary C. Hon, … Bing Ren (2010) Distinct Epigenomic Landscapes of Pluripotent and Lineage-Committed Human Cells (Cell Stem Cell) DOI: 10.1016/j.stem.2010.03.018 
• Jesse R. Dixon, Siddarth Selvaraj, … Bing Ren (2012) Topological domains in mammalian genomes identified by analysis of chromatin interactions (Nature) DOI: 10.1038/nature11082 
• Fulai Jin, Yan Li, … Bing Ren (2013) A high-resolution map of the three-dimensional chromatin interactome in human cells (Nature) DOI: 10.1038/nature12644

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