Inside a B cell, a brief pause by a protein called NELF may leave DNA open long enough for an antibody gene to be deliberately changed. Yale School of Medicine researchers have traced how that pause helps the immune system tune its defenses against germs it has encountered.
B cells are white blood cells that make antibodies, which attach to invaders such as bacteria and viruses. After an infection, some B cells rapidly alter the DNA instructions for their antibodies. These changes, called somatic hypermutations, help produce antibodies better suited to recognize the pathogen. The mutation rate in the targeted regions is about 1 million times higher than in other parts of the genome, yet the changes are focused on a defined stretch of DNA. How the mutation-causing machinery reaches that DNA has been a long-standing question.
The Yale team, led by senior author David Schatz, chair and Waldemar Von Zedtwitz Professor of Immunobiology, identified proteins that help make the process possible. First author Lizhen Wu, an associate research scientist in Schatz’s lab, engineered a B-cell model called RASH-1C. It allowed the researchers to control and detect mutations in days rather than waiting weeks. That speed also helped them study the process before the cells became too sick to analyze.
Wu tested the role of genes by disabling them one at a time and checking what happened to hypermutation. She then focused on proteins involved in transcription, when RNA polymerase II opens DNA and copies one strand into an RNA message. The team found that NELF, or negative elongation factor, can travel with RNA polymerase II to antibody genes and make the enzyme pause. This leaves a section of DNA open, exposing a single strand.
That exposed strand is important because activation-induced deaminase, or AID, causes the mutations but needs access to single-stranded DNA. The researchers also found that two proteins, MLLT1 and MLLT3, bring AID to the right region. When either protein’s role in the process was removed, somatic hypermutation was completely abolished.
The findings, published in Nature, offer direct evidence for a molecular mechanism that scientists had proposed about 30 years ago. Schatz described the field as having been stuck, in part because experiments were hard to control: cells altered for study could die before researchers could see the mutations. RASH-1C provides a way around that problem and gives researchers a clearer view of how the process is regulated.
The work helps explain how B cells expose just the right DNA to make antibodies more responsive to pathogens, rather than simply allowing mutations to spread across the genome. Wu suspects NELF is not the only molecule that makes RNA polymerase II stall. She is now investigating other possible participants and hopes eventually to watch the process with high-resolution imaging. A clearer picture of those steps could deepen scientists’ understanding of how the immune system adapts when it meets new threats.