Periodic Reporting for period 4 - 3DEpi (Transgenerational epigenetic inheritance of chromatin states : the role of Polycomb and 3D chromosome architecture)
Periodo di rendicontazione: 2023-05-01 al 2024-10-31
It has long been known that DNA is the primary carrier of heritable information in biological organisms. While this “genetic” information is contained within the DNA sequence, there exists another layer of information on top of it, the “epigenetic” information. Although the definition of epigenetic may vary, it is generally agreed to include such elements as chemical modification of DNA and the histone proteins that package DNA as well as some RNA molecules. Epigenetic factors have long been known to regulate gene expression and are the primary reason that cells within an organism differ from each other.Furthermore some of this epigenetic information can be passed on to the next generation.
The 3DEpi project focused on Epigenetic Inheritance of chromatin states, with a special focus on how transmission can pass through cell division and, when derailed, can lead to disease, and how epigenetics can transmit information from one generation to the next and be maintained across multiple generations – a phenomenon called transgenerational epigenetic inheritance (TEI). The project had three main goals:
Aim 1: Analysis of the molecular mechanisms regulating Polycomb-mediated epigenetic inheritance.
Aim 2: Role of 3D genome organization in the regulation of TEI.
Aim 3: Identification of a broader role of TEI during development.
Knowledge in these fields is critical for a deeper understanding of life and evolution. Furthermore, it has a deep impact in biomedical science since epigenetic inheritance is frequently derailed in disease.
The 3DEpi project focused on Epigenetic Inheritance of chromatin states, with a special focus on how transmission can pass through cell division and, when derailed, can lead to disease, and how epigenetics can transmit information from one generation to the next and be maintained across multiple generations – a phenomenon called transgenerational epigenetic inheritance (TEI). The project had three main goals:
Aim 1: Analysis of the molecular mechanisms regulating Polycomb-mediated epigenetic inheritance.
Aim 2: Role of 3D genome organization in the regulation of TEI.
Aim 3: Identification of a broader role of TEI during development.
Knowledge in these fields is critical for a deeper understanding of life and evolution. Furthermore, it has a deep impact in biomedical science since epigenetic inheritance is frequently derailed in disease.
Our research provided ground breaking information on each of the aims of the project. The main discoveries from the 3DEpi project are as follows:
Aim 1a). The Drosophila fruit fly can carry transgenerational epigenetic inheritance (TEI) of chromatin states thanks to the modulation of its three-dimensional (3D) nuclear organization. In the past, we had exploited a system of transgenic flies that can lead to TEI. In the 3DEpi project, we mutated transcription factor binding sites within the Fab-7 element. The data demonstrate the importance of two DNA binding proteins in the establishment and maintenance of TEI. This work has been published recently (see paper 1).
Aim 1b). In a second endeavour, we investigated whether memory of chromatin states can be perturbed by transient impairment of Polycomb function. Thanks to the 3DEpi project, we could show that epithelial cells with an identical genome could be committed to a tumor phenotype by transiently reducing the activity of the PRC1 complex during development. These tumors are therefore completely epigenetic in nature (see paper 2).
Aim 2a). In order to directly address whether 3D genome organization changes can lead to TEI, we have designed a synthetic biological system called “Three-Dimensional Contact Induction System” or “3D-CIS”. This system can artificially induce chromatin contacts. Our results showed that the activation of the 3D-CIS system was able to establish TEI. These results demonstrate that chromatin contacts alone, in the absence of any genetic perturbation, are sufficient to induce TEI in Drosophila (see paper 1).
Aim 2b). In parallel, we used super-resolution microscopy in order to understand the physical nature of chromatin domains in single cells and to understand whether challenges to mammalian cells can translate into modification of this physical state. Our analysis provided fundamental information for the folding of individual chromosomes at the nanoscale (see paper 3) and it is being used as a basis for further studies aimed at understanding the role or 3D architecture in epigenetic inheritance.
Aim 3). Here, we explored whether TEI could play a more general role in natural populations and conditions. We concentrated on the Waddington assimilation of an acquired character experiment (see PMID: 13666847). We could demonstrate that the assimilation of this trait is driven by the selection of regulatory alleles already present in the ancestral populations, rather than stress-induced genetic or epigenetic variation, drives the evolution of ectopic veins in natural fly populations (see paper 4).
1) Fitz-James, M. H., Sabaris, G., Sarkies, P., Bantignies, F. & Cavalli, G. Interchromosomal contacts between regulatory regions trigger stable transgenerational epigenetic inheritance in Drosophila. Molecular Cell (2024), DOI: 10.1016/j.molcel.2024.11.021.
2) Parreno, V. et al. Transient loss of Polycomb components induces an epigenetic cancer fate. Nature 629, 688-696 (2024). https://doi.org:10.1038/s41586-024-07328-w.
3) Szabo, Q. et al. Regulation of single-cell genome organization into TADs and chromatin nanodomains. Nature Genetics 52, 1151-1157 (2020).
4) Sabaris, G. et al. A mechanistic basis of genetic assimilation in natural fly populations. Proc Natl Acad Sci U S A in press, (2025).
Aim 1a). The Drosophila fruit fly can carry transgenerational epigenetic inheritance (TEI) of chromatin states thanks to the modulation of its three-dimensional (3D) nuclear organization. In the past, we had exploited a system of transgenic flies that can lead to TEI. In the 3DEpi project, we mutated transcription factor binding sites within the Fab-7 element. The data demonstrate the importance of two DNA binding proteins in the establishment and maintenance of TEI. This work has been published recently (see paper 1).
Aim 1b). In a second endeavour, we investigated whether memory of chromatin states can be perturbed by transient impairment of Polycomb function. Thanks to the 3DEpi project, we could show that epithelial cells with an identical genome could be committed to a tumor phenotype by transiently reducing the activity of the PRC1 complex during development. These tumors are therefore completely epigenetic in nature (see paper 2).
Aim 2a). In order to directly address whether 3D genome organization changes can lead to TEI, we have designed a synthetic biological system called “Three-Dimensional Contact Induction System” or “3D-CIS”. This system can artificially induce chromatin contacts. Our results showed that the activation of the 3D-CIS system was able to establish TEI. These results demonstrate that chromatin contacts alone, in the absence of any genetic perturbation, are sufficient to induce TEI in Drosophila (see paper 1).
Aim 2b). In parallel, we used super-resolution microscopy in order to understand the physical nature of chromatin domains in single cells and to understand whether challenges to mammalian cells can translate into modification of this physical state. Our analysis provided fundamental information for the folding of individual chromosomes at the nanoscale (see paper 3) and it is being used as a basis for further studies aimed at understanding the role or 3D architecture in epigenetic inheritance.
Aim 3). Here, we explored whether TEI could play a more general role in natural populations and conditions. We concentrated on the Waddington assimilation of an acquired character experiment (see PMID: 13666847). We could demonstrate that the assimilation of this trait is driven by the selection of regulatory alleles already present in the ancestral populations, rather than stress-induced genetic or epigenetic variation, drives the evolution of ectopic veins in natural fly populations (see paper 4).
1) Fitz-James, M. H., Sabaris, G., Sarkies, P., Bantignies, F. & Cavalli, G. Interchromosomal contacts between regulatory regions trigger stable transgenerational epigenetic inheritance in Drosophila. Molecular Cell (2024), DOI: 10.1016/j.molcel.2024.11.021.
2) Parreno, V. et al. Transient loss of Polycomb components induces an epigenetic cancer fate. Nature 629, 688-696 (2024). https://doi.org:10.1038/s41586-024-07328-w.
3) Szabo, Q. et al. Regulation of single-cell genome organization into TADs and chromatin nanodomains. Nature Genetics 52, 1151-1157 (2020).
4) Sabaris, G. et al. A mechanistic basis of genetic assimilation in natural fly populations. Proc Natl Acad Sci U S A in press, (2025).
We believe that our results represent significant progress beyond the state of the art in multiple ways:
The work published in paper 1 (see above) is a breakthrough because it shows that the perturbation of chromosome architecture is in itself capable to induce a plasticity in chromatin states that can lead to subsequent fixation of alternative phenotypes in a fly population, in the absence of changes in DNA sequence. Paper 2 challenges the dominant model in cancer biology, which postulates that the genesis of a tumor depends on a predominantly genetic process with the appearance and accumulation of mutations in somatic cells which will gradually acquire and evolve towards an increasingly aggressive tumor phenotype (the “Somatic Mutation Theory”). Instead, our work demonstrates that a tumor can have a purely epigenetic origin by keeping a tumor program in memory, this well after the signal that causes it is turned off. These studies are very exciting for the field of cancer biology and are being followed up by ourselves and many other investigators. Paper 3 advanced the research field of 3D chromosome organization beyond the state of the art because, by combining fluorescent DNA labeling with super-resolution microscopy in mouse embryonic cells, this research has provided a new understanding of the 3D architecture of genomic domains in metazoans. Finally, paper 4 elucidates the genetic and molecular mechanisms underlying the evolution of an acquired trait, the ectopic veins phenotype, in natural populations. Our results support a model in which trait assimilation results from selection on pre-existing alleles within the ancestral population. While Waddington is often quoted to be “the father of epigenetics”, in the particular case we studies it is genetics which is at the root of the information required for the acquisition of the trait that he studied. This will prompt future investigations in order to understand how much epigenetics can effect the evolution of natural characters.
The work published in paper 1 (see above) is a breakthrough because it shows that the perturbation of chromosome architecture is in itself capable to induce a plasticity in chromatin states that can lead to subsequent fixation of alternative phenotypes in a fly population, in the absence of changes in DNA sequence. Paper 2 challenges the dominant model in cancer biology, which postulates that the genesis of a tumor depends on a predominantly genetic process with the appearance and accumulation of mutations in somatic cells which will gradually acquire and evolve towards an increasingly aggressive tumor phenotype (the “Somatic Mutation Theory”). Instead, our work demonstrates that a tumor can have a purely epigenetic origin by keeping a tumor program in memory, this well after the signal that causes it is turned off. These studies are very exciting for the field of cancer biology and are being followed up by ourselves and many other investigators. Paper 3 advanced the research field of 3D chromosome organization beyond the state of the art because, by combining fluorescent DNA labeling with super-resolution microscopy in mouse embryonic cells, this research has provided a new understanding of the 3D architecture of genomic domains in metazoans. Finally, paper 4 elucidates the genetic and molecular mechanisms underlying the evolution of an acquired trait, the ectopic veins phenotype, in natural populations. Our results support a model in which trait assimilation results from selection on pre-existing alleles within the ancestral population. While Waddington is often quoted to be “the father of epigenetics”, in the particular case we studies it is genetics which is at the root of the information required for the acquisition of the trait that he studied. This will prompt future investigations in order to understand how much epigenetics can effect the evolution of natural characters.