Unraveling the secrets of the H1 protein, the guardian of genome stability

Histones are proteins that regulate the organization of DNA throughout the cell cycle and their modifications determine the degree of compaction of the genetic material and the expression of its genes, in what is known as epigenetics. The histone H1 protein is considered the guardian of genome stability because it ensures that regions of the genome that should not be expressed are silenced.

7 years ago, a team from the Institute of Molecular Biology of Barcelona (IBMB), dependent on the Higher Council for Scientific Research (CSIC) in Spain, discovered this regulatory role of H1 in heterochromatin, which is found in the nucleus of cells. . What the researchers did not know was how this regulatory mechanism develops.

Part of that is what they reveal in a new work, directed by Jordi Bernués and Fernando Azorín, both IBMB scientists. The results show that the deletion of histone H1 leads to several effects on chromatin, among which the greatest accessibility of chromatin, an increase in chromatin RNA (cRNA) and the disappearance of two proteins, hrp36 and hrp48, which under normal conditions cover the cRNA and prevent the formation of RNA:DNA hybrids, called R-loops.

H1 maintains genome stability

Chromatin is the form in which DNA is packaged inside the nucleus of cells and consists of two parts: euchromatin (accessible and containing normally expressed genes) and heterochromatin. “Heterochromatin,” the researchers explain, “is the most compacted part of the DNA, the least rich in genes and the most silenced and least accessible: in general, its genes are not expressed nor are they expected to be expressed.”

As revealed in previous work by the same IBMB team, when they reduced the content of H1 by half, intense genomic damage was triggered in the heterochromatin and the expression of genes and retrotransposons (DNA sequences of viral origin) that, in normal conditions, they should not be expressed.

All of this led to genomic instability, and compromised the survival of the organism (Drosophila fly embryos with 50% H1 in all their cells could not survive). When the reduction of H1 only occurred in one organ (in the wing), malformations and general degeneration of the organ appeared.

As they observed then, the DNA damage, genomic instability and cell death induced by the absence of H1 were directly related to the formation of RNA:DNA hybrids, called R-loops. These are structures that are formed when a newly formed RNA strand hybridizes again with the template DNA strand, leaving the untranscribed DNA strand loose, unhybridized. Although they are produced naturally in cells under normal conditions, excess R-loops are very harmful.

Structure of Drosophila histone H1 (prediction from the artificial intelligence program, AlphaFold). (Image: IBMB)

Two protective RNA proteins

The results now obtained by the team, which includes Paula Bujosa from the IBMB and the Barcelona Biomedicine Research Institute (IRB Barcelona), reveal that the deletion of H1 leads to an increase in the accessibility of chromatin, the presence of RNA polymerase II and transcription, as well as the disappearance of at least the two major proteins, hrp36 and hrp48, which under normal conditions cover the chromatin RNA (cRNA).

The hrp36 and hrp38 proteins, among others, are responsible for protecting and transporting the nascent RNA. Without them, the RNA is exposed and accessible, which facilitates the formation of RNA:DNA hybrids, destabilizes the structure of heterochromatin and increases the expression of sequences that should not be expressed.

The finding may help understand the mechanisms involved in genomic instability and hyperrecombination in some types of cancer. In fact, years ago it had been seen that in some cancer cell lines there is a decrease in H1.

It will also help understand how gene expression is controlled, in this case, how H1 represses non-coding areas. And there is a large part of the DNA of eukaryotic living beings, including humans, that does not code for any gene: almost all of that non-coding DNA is in the heterochromatin, the most compact part and least rich in genes but which, Paradoxically, it is highly conserved, and whose stability depends largely on histone H1.

The study, which also had the collaboration of the CRG (Center for Genomic Regulation) of Barcelona, ​​is titled “Linker histone H1 regulates homeostasis of heterochromatin-associated cRNAs”. And it has been published in the academic journal Cell Reports. (Source: CSIC)