and deposited in the ENCODE data repository has empowered thousands of researchers worldwide to make discoveries in human diseases, from cardio- vascular disease to bipolar disease. ENCODE also produced numerous protocols for genome-wide functional analysis that have become standards in the field. The project led to the identification of more than a million DNA switches and made significant head- way into understanding the 1,600 or so DNA-binding proteins called transcription factors, better under- standing how they turn genes on or off or determine the levels of gene expression in different cell types and at different times during development. Throughout the ENCODE Project, Myers and his lab, in collaboration with Dr. Eric Mendenhall at HudsonAlpha and Dr. Barbara Wold at Caltech, conducted the largest study of transcription factors expressed at normal levels to date. They generated hundreds of genome-wide datasets that measure transcription factor binding sites in the human genome, identified RNA transcripts in mouse and human cells, and identified DNA methylation sites throughout the human genome. By expanding the catalog of known transcription factors and their functions, Myers and his lab helped unlock new ave- nues for medical innovation, enabling researchers to navigate the complexities of human biology and identify potential therapeutic targets.
lab has been its pivotal role in the Encyclopedia of DNA Elements (ENCODE) Project . This ambitious international effort aimed to characterize all of the functional elements within the human genome, in- cluding both protein-coding genes and non-coding elements that regulate gene activity. It also sought to understand how these components interact in biological processes. The ENCODE Consortium, funded by the National Human Genome Research Institute (NHGRI) , spanned two decades and included more than 30 institutions and 500 scientists worldwide. It made monumental strides in advancing our knowledge of the human genome, maintaining the large-scale, open-access data release championed by the Human Genome Project. The wealth of pub- licly accessible data generated by the Consortium
BEYOND ENCODE: SEARCHING FOR BRAIN-SPECIFIC TRANSCRIPTION FACTORS
The ENCODE Project’s legacy will live on for de- cades as researchers utilize the vast amounts of data generated by the Consortium. For their part, Myers and his lab are just getting started. In late 2023, they published a comprehensive analysis of the binding of 680 human transcription factors and how they regulate gene expression patterns in HepG2 cells, a type of human liver cancer cell with extensive ENCODE data 1 . Transcription factors play a crucial role in gene regulation by binding to cis-regulatory elements (CREs), short stretches of DNA near the genes they regulate. ChIP-seq is a powerful technique that
BrainTF, a comprehensive resource that maps the binding sites of more than 100 transcription factors in human postmortem brain tissue.
HUDSONALPHA INSTITUTE FOR BIOTECHNOLOGY
10
Made with FlippingBook - Online magazine maker