Study highlights the interaction between single-stranded DNA and the linker histone H1

Human DNA is neatly locked in place around a central disc in the tight quarters of the cell nucleus by H1 linker histone that helps shepherd DNA into the tidy chromatin fibers that make up chromosomes. The linker histone, on the other hand, is much more than a protein clip.

Study highlights the interaction between single-stranded DNA and the linker histone H1
An artistic representation of the interaction between single-stranded DNA and linker histone H1, featured on the cover of the journal in which the new findings were reported. Image Credit: Gabriella Chua.

When there is not enough H1, gene transcription slows down, and the delicate dance of DNA repair comes to a standstill. The simple linker histone, perched unassumingly atop the nucleosomes, appears to be involved in several activities critical to genome maintenance.

According to a recent study published in Nature Structural and Molecular Biology, linker histone can tell the difference between different types of nucleic acids, preferring to form condensates with single-stranded DNA than double-stranded DNA. This distinguishing trait adds to the growing body of evidence showing that H1’s function extends far beyond chromatin compaction and may explain the protein’s participation in DNA repair and a variety of human disorders.

This changes the paradigm of H1 function in the cell, and provides a new perspective in understanding different H1 variants and disease-associated mutations.”

Shixin Liu, Laboratory Head, Nanoscale Biophysics and Biochemistry, Rockefeller University

Linker histone has long been considered to have a function in a variety of genomic processes. Aside from evidence that H1 is involved in DNA repair and transcription, the presence of several forms of linker histone in human cells suggests that the protein has a broader function.

We wouldn’t need 11 different subtypes of linker histone if its role was purely structural.”

Rachel Leicher, Study Co-Author and Former Graduate Student, Liu’s Lab, Rockefeller University

Leicher and Gabriella Chua, one of Liu’s current graduate students, conducted a study.

Motivated by their suspicions, Liu, Leicher, and Chua created a partnership with a team from Memorial Sloan Kettering Cancer Center headed by Yael David, the pioneer of recombinant linker histone protein purification. To explore how H1 interacts with DNA up close, researchers used the laboratory’s area of expertise, single-molecule detection, and manipulation.

Liu and colleagues stretched a sample by pushing double-stranded DNA between concentrated laser beams called optical tweezers till portions of it dissolved into single-stranded DNA. To their astonishment, linker histone filled the single-stranded area.

H1 and single-stranded DNA form a thick, gel-like droplet, as opposed to the more fluid droplet formed when H1 gradually coalesces around double-stranded DNA, according to further research. The Liu lab’s in vitro findings were supported by computer simulations conducted by Bin Zhang’s lab at MIT, and also cellular imaging of how linker histone functions in the nucleus conducted by the David lab.

We did not go in with this hypothesis—our assumption was that H1 would only interact with double-stranded DNA and nucleosomes. But when we stretched DNA, we fortuitously observed the accumulation of H1 around the portions of the molecule that had popped into single strands. That was when we realized that H1 not only binds single-stranded DNA, but likes it better than double-stranded DNA.”

Rachel Leicher, Study Co-Author and Former Graduate Student, Liu’s Lab, Rockefeller University

The findings fit very neatly with H1’s suggested involvement in DNA repair since one hallmark of DNA damage is the breaking of double strands into frayed single strands. If H1 is involved in the response to DNA damage, it should have a special affinity for single-stranded DNA.

The current study focused on a single H1 subtype, which is also one of the most common. Future research will look at how the other linker histone subtypes interface with damaged DNA, building on the optical tweezer approach, which has allowed the researchers to explore the material characteristics of molecular condensates in ways that standard methods have not been able to.

In the long run, a better knowledge of linker histone might help researchers better comprehend a variety of cancers linked to H1 mutations.

Our work opens up a new way to think about the function of linker histone. It’s not purely an architectural factor, but a protein that plays a diverse and dynamic role. And since we know that H1 mutations can drive some cancers, we’re particularly interested in studying how linker histone impacts genome stability and gene expression,” Liu concluded.

Source:
Journal reference:

Leicher, R., et al. (2022) Single-stranded nucleic acid binding and coacervation by linker histone H1. Nature Structural & Molecular Biology. doi.org/10.1038/s41594-022-00760-4.

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