New study reveals how genes switch on and off in human cells

An international team of scientists has made a significant breakthrough in understanding how gene expression is regulated across the human genome. In a recent study, researchers thoroughly examined the role of "cis-regulatory elements" (CREs)—DNA sequences that control gene transcription—revealing their influence on cell-specific gene expression and their potential links to health and disease.

CREs, such as enhancers and promoters, are critical for determining when and where genes are activated. Enhancers boost gene transcription, while promoters initiate the process. Despite their importance, large-scale studies of CRE activity have been challenging due to the complexity and vast number of CREs in the human genome. Mutations in these regions are thought to contribute significantly to human diseases and evolution, but quantifying their activity across the genome has been a difficult task.

"The human genome contains a myriad of CREs, and mutations in these regions are thought to play a major role in human diseases and evolution. However, it has been very difficult to comprehensively quantify their activity across the genome," 

Dr. Fumitaka Inoue, study co-first author from Kyoto University.

To overcome this challenge, the research team used a state-of-the-art technique they had previously developed: the lentivirus-based massively parallel reporter assay (lentiMPRA). This method employs distinct DNA barcodes to tag thousands of CREs, allowing their activity to be analyzed simultaneously. Using lentiMPRA, the researchers examined up to 680,000 candidate CREs in three widely studied cell types: induced pluripotent stem cells (artificial stem cells derived from normal body cells), lymphocytes (a type of white blood cell), and hepatocytes (liver cells).

The study revealed several key findings. About 41.7% of the analyzed CREs displayed activity across the three cell types. Promoters, which initiate gene transcription, exhibited a dependence on sequence orientation but were less cell-type specific. Enhancers, which amplify gene transcription, showed cell-type specificity and remained active regardless of sequence orientation. These observations highlight the functional differences between promoters and enhancers, shedding light on their distinct roles in the genome.

The researchers also developed machine learning models based on the experimental data to predict the regulatory activity of CREs. Among these, MPRALegNet emerged as the most accurate and efficient model, trained on the extensive lentiMPRA dataset. Its predictions closely matched experimental results, occasionally outperforming experimental replicates.

The model identified key transcription factor binding motifs—short DNA sequences critical for CRE activity—providing insight into how specific factors influence gene expression in different cell types. For example, the study highlighted the importance of GATA motifs in hepatocytes and HNF4 motifs in lymphocytes.

The findings open new doors for understanding the molecular mechanisms underlying human diseases. By precisely identifying and quantifying enhancer activity, researchers can investigate the genetic polymorphisms—DNA variations that contribute to individual differences and disease susceptibility—that affect gene regulation.

"Recently, the nearly complete human genome has been sequenced, but much of its functional regions remain unknown. Our findings link DNA sequence information with its functional roles. We hope that these results will contribute to a deeper understanding of biological phenomena, including human diseases and evolution," said Dr. Inoue.

In addition to advancing knowledge, the study has contributed a publicly accessible database of CRE activity to the ENCODE portal, providing researchers worldwide with a valuable resource. The integration of machine learning and large-scale experimental data in this research lays the foundation for future advancements in genomics and personalized medicine.

With innovative tools like lentiMPRA and MPRALegNet, scientists are now better equipped to explore the uncharted regions of the human genome and uncover the complexities of gene regulation. These advances bring us closer to understanding the genetic underpinnings of human health, evolution, and disease.