HIRA, a new factor in the genome’s 3D organizational assembly chain

At the heart of every cell, vital information is “written” on the DNA, a long molecular ribbon almost one meter long bundled inside the nucleus of the cell. For the DNA to fit inside this small space, it is rolled up like a ball of yarn in a highly organized structure called chromatin. Beyond its purely structural role, the spatial organization of DNA is essential to the basic processes of a cell’s life because it provides information that is added to that contributed by the genetic code. This ball-like structure, which protects the DNA, plays an important role in all the functions of our genome, most notably in the modulation of the genes’ expression.

At the Institute Curie, CNRS (1) researchers collaborating with a team from the Institute Gustave-Roussy, recently announced the discovery of a new factor that helps regulate the spatial organization of DNA: a protein called HIRA. This assembly factor plays a key role since any disorganization of the genome could compromise its function and, in certain cases, lead to pathologies such as cancer.

The work of the researchers on this new DNA “assembler” was published in the May 24th issue of the journal Molecular Cell.

Each of our cells possesses all the information necessary for the proper function of our body. All the essential information required for the synthesis of proteins are inscribed within the DNA in a genetic code. This book is composed of about 3 billion cryptograms – but its complexity doesn’t stop there: the spatial organization of the genetic code within the nucleus is no coincidence. The 3D scaffolding of the genetic material provides information that is added to that contained by the genetic code. Hence, DNA can be read at several levels.

DNA’s assembly chain

Within the nucleus, DNA is assembled in a highly organized structure called chromatin* which not only tightly compacts the genetic material, but also spatially organizes it.

• DNA’s double helix (with a diameter of 2 nanometers) is initially rolled up around “compacting” proteins called histones (see inset), to form a string of beads. This is the nucleosome* which forms the basic universal structure of eucaryotes (see diagram enclosed).
• The string of beads (composed of a series of nucleosomes) then binds together by curling up in such a way as to form a fiber.
• This chromatin fiber can be further compacted. The end result of this compacting can be observed at the chromosomal level during cell division.
  The slightest error in this highly sophisticated structure could lead to a disorganization of the genome, modifications in gene expression, and eventually, cellular dysfunctions.

Winding up and unraveling chromatin

To ensure the proper function of a cell, the DNA’s information must be readily accessible for consultation, which necessitates highly dynamic and plastic qualities of chromatin.
Depending on the needs of the cell, chromatin employs varying levels of compaction:

• At the point of replication, when the cell is about to divide, chromatin condenses to a maximum in the form of chromosomes;
• When a gene must be expressed or repaired, chromatin locally rearranges itself to facilitate access to the proteins involved in these operations; hence, in the context of the production of these proteins, the degree of compaction will modulate the reading of the DNA by the transcription factors (2) thus dictating the degree of expression of the genes.

HIRA: the core of a new DNA assembly chain

At present, only one means of DNA nucleosome assembly is known. It employs the CAF1 protein* which is active during replication or reparation processes.

The “Chromatin Dynamic” team, under the direction of Genevieve Almouzni (UMR 218 CNRS/Institut Curie) (3), has studied the spatial organization of chromatin and its restructuring during the various phases of a cell’s life.
In addition to its research on CAF1, the team is working on identifying other proteins that also play a role in the assembly of genetic material.
The scientists are currently studying the HIRA protein* (named after its similarity to yeast proteins, hir for histone regulating protein) which is known to interact with the histones.

Certainties…

First, the researchers combined HIRA protein with histones and a fragment of DNA. The result: the DNA formed nucleosomes in vitro! This was the first indication that HIRA protein played a role in the formation of nucleosomes.
Then, the researchers studied the assembly of the nucleosomes on a fragment of DNA, but this time with extracts of Xenopus eggs (see inset).

Although nucleosomes form under these conditions, once the HIRA protein is removed from the cellular extracts, only newly synthesized DNA (either replicated or repaired) is capable of assembly.

HIRA protein is thus one of the factors necessary for the assembly of DNA into nucleosomes, but it acts in a manner entirely independent of CAF1.

…and hypotheses

Thus, Institute Curie researchers have discovered a new means of chromatic DNA assembly. At least two distinct processes coexist within the cell to ensure the formation of chromatin and play a role in maintaining the functional integrity of the genome.

The researchers, who must now try to better understand the role of HIRA protein, have put forward a number of hypotheses:

Does HIRA act as the “quality controller” for CAF1?
Somewhat like a “finished works inspector,” HIRA may intervene once the DNA has been assembled by means of CAF1 to perform a quality control check. By preventing the occurrence of errors subsequent to the many DNA “winding and unwinding” operations, HIRA acts to preserve the integrity of cell’s functions.

…or is it CAF1’s “coworker”?
The HIRA protein may also act as a watchman, standing guard to ensure the spatial organization of certain regions of DNA is strictly maintained throughout the cellular cycle – which, for example, is akin to the role played by telomeres* and centromeres.*

With the discovery of this new genetic material assembly factor, Curie Institute researchers have taken a significant step forward in the understanding of chromatin’s highly sophisticated organization.

This research may one day provide a greater insight into the dysfunctions that occur in the spatial organization of the genome, particularly in genetic instability syndromes.
Eventually, this insight may have spin-off applications in a variety of diseases linked to genetic alterations, particularly in the field of cancerology.

Notes :

* Words followed by an asterisk * are explained in the glossary
(1) CNRS Life Sciences Department
(2) Proteins that decrypt the genetic code to convert it into a RNA molecule that will later provide the basis for protein synthesis.
(3) The UMR 218 (“Dynamique nucleaire et plasticite du genome” – CNRS/Institut Curie) is led by Genevieve Almouzni.

Reference :

HIRA is critical for a nucleosome assembly pathway independent of DNA synthesis
Dominique Ray-Gallet1, Jean-Pierre Quivy1, Christine Scamps2, Emmanuelle M.-D. Martini1, Marc Lipinski2 et Geneviève Almouzni1
Molecular Cell, may 24, 2002
1 Laboratoire ” Dynamique nucléaire et plasticité du génome “, UMR 218 CNRS/Institut Curie
2 Interactions moléculaires et cancer, UMR 1598, Institut Gustave Roussy

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Chromatin glossary :

Centromeres: Regions of the chromosomes that ensure the segregation of the newly duplicated chromosomes to generated daughter cells.

Chromatin: The basic structure of chromosomes, primarily made up of DNA and histones, and situated within the nucleus.

Histones: Proteins around which DNA is wound to form the nucleosome.

Nucleosome: Basic component of chromatin resembling a string of beads composed of a short length of DNA wrapped around a protein core composed of histones.

CAF1 Protein (Chromatin Assembly Factor 1): A protein that plays a role in the assembly of DNA during cellular replication or reparation.

Telomeres: Regions situated at the ends of the chromosomes and made up of a number of repeated sequences. Telomeres help prevent the loss of genetic material during repeated cellular division.