Large-scale sequencing projects have great potential to provide a wealth of knowledge to scientists and the public. Perhaps the most celebrated project of this nature is the Human Genome Project (HGP) which was completed in 2003. For many, the multi-billion endeavor was considered a “moonshot” for biology, but with its successful completion (99% of the euchromatic genome sequenced with 99.99% accuracy) came the launch of many other large-scale sequencing projects such as the Cancer Genome Atlas (2005) or more recently, the Earth Bio-genome Project (2018). The introduction of large-scale quantitative methods, such as next-generation sequencing, have also made these projects feasible.
The G1/S cell cycle checkpoints control whether eukaryotic cells enter the S phase (synthesis phase) of DNA synthesis through the G1 phase. Two cell cycle kinase complexes, CDK4/6-Cyclin D and CDK2- Cyclin E, work together to relieve the inhibition of dynamic transcriptional complexes containing retinoblastoma protein (Rb) and E2F. In cells undefined during the G1 phase, hypophosphorylated Rb binds to the E2F-DP1 transcription factor and forms an inhibitory complex with HDAC, thereby inhibiting downstream key transcriptional activities. Clear entry into the S phase is achieved by continuous phosphorylation of Rb by Cyclin D-CDK4/6 and Cyclin E-CDK2, which separates the transcription factor E2F from the inhibitory complex and allows transcription of the gene required for DNA replication. After the growth factor disappears, the expression level of cylin D is down-regulated by down-regulation of protein expression and phosphorylation-dependent degradation.
Proteins known as transcription factors play a crucial role in gene regulation by activating, enhancing, and even silencing a gene’s expression. Many textbooks and resources compare transcription factors (TFs) to something like an on/off switch for gene transcription. However, it is a bit more complicated than just turning gene expression on or off. Various properties (e.g. binding affinity, specificity, and genetic variance of binding sites) impact the binding of TFs to DNA, thereby altering gene expression. To study transcription and how it is regulated, scientists study TF-DNA interactions on a genome-wide level.