The brain, its development, and diseases are among the most fascinating areas of contemporary scientific research. A team led by Professor Aleksandra Pękowska from the Nencki Institute in Warsaw has discovered a new mechanism involved in the maturation of brain cells during their early development. There is much to be found in the way DNA is arranged in the cell nucleus. This may be the key to treating developmental brain diseases and cancers, including glioma.  

Professor Aleksandra Pękowska heads the Dioscuri Centre for Chromatin Biology and Epigenomics at the Nencki Institute. Her team's research focuses on gaining a deeper understanding of the evolution and development of brain cells, particularly astrocytes. The group's latest publication, which has just appeared in Nature Cell Biology, focuses on the mechanisms that control how a stem cell, which can become either a neuron or an astrocyte, ultimately follows a specific developmental path, becoming one or the other.

The way in which genetic material, i.e., the genome, is arranged in the cell nucleus is of key importance in this process. The genome is composed of chromosomes, which are long and thin strands of DNA that are easily broken, potentially leading to mutations and diseases. Furthermore, due to the size of the cell nucleus – it is only a few microns in size – the genome needs to be condensed. This is achieved through the interaction of DNA with proteins and RNA. This creates chromatin (DNA plus proteins and RNA), and the genome stiffens and packs into the limited space of the cell nucleus.

This protects the genetic material from damage. On the other hand, however, its condensation limits the access of proteins that regulate gene activity. Therefore, individual chromosomes (fragments of chromatin) are organised into a series of units called domains.  Under a microscope, these domains resemble tangles. This is the case in all types of cells. Each chromosome can therefore be imagined as a sequence of smaller and larger beads (i.e., domains). How the boundaries between these structures are regulated is one of the fundamental problems in genome biology.

- The CTCF protein establishes domain boundaries. Interestingly, both domain boundaries can also connect, creating what we call a chromatin loop in our jargon. This is the case in all cell types, says Prof. Pękowska. Research by scientists from the Nencki Institute, as well as reports from other groups, revealed a surprising phenomenon: domains and chromatin loops gradually become more pronounced during development.
‘In the case of the mouse neuronal cells we studied, this consolidation of chromatin structure lasts from the first days of embryonic development until birth. At that point, the cells lose their pluripotency (i.e., the ability to become any cell in the body) and begin to define themselves as more mature forms,’ Prof. Pękowska says.

In their latest work, her team has demonstrated that nuclear RNA-binding proteins play a key role in chromatin consolidation. CTCF significantly increases interactions with RNA-binding proteins during cell development.

“There are dozens of them. We conducted a series of experiments involving the removal of selected RNA-binding proteins and investigated the effect of these manipulations on CTCF and chromatin structure. The elimination of even one RNA-binding protein caused the domain boundaries to weaken and the chromatin to become more disordered. We wondered how it was occurring. RNA-binding proteins are present in both pluripotent and more differentiated cells. Still, CTCF interacts with them robustly but only at the more mature developmental stage", says Prof. Pękowska.

Her team's research shows that the element managing this entire process is a non-coding RNA called Pantr1.

"Non-coding RNAs are enigmatic players that influence various processes in cells. Although they do not encode proteins (hence their name), they can bind to them and thus modify their activity and functions. We have discovered that Pantr1 is active only in the precursor cell of the nervous system, where it reacts with CTCF. Its removal causes the boundaries of the domains to break down. Our data suggest that the interaction of Pantr1 with RNA-binding proteins and CTCF leads to the consolidation of chromatin structure, influencing further cell development," explains Bondita Dehingia, MSc, co-first author of the paper in Nature.

In the second part of their article, the researchers revealed that CTCF contributes to regulating the order of gene activation responsible for neural cell development.

- Brain development is spread out over time. Without CTCF and its function as a chromatin structure regulator, premature activation of neuronal genes occurs in cells. Instead of multiplying to become either a neuron or an astrocyte, a precursor cell may transform into a neuron too quickly. This would disrupt the normal course of brain development, says Małgorzata Milewska-Puchała, MSc, the second co-first author of the manuscript.

The interdisciplinary publication in Nature Cell Biology is the result of collaboration between scientists from the Nencki Institute and mathematicians from the Dioscuri Centre for Topological Data Analysis, headed by Prof. Paweł Dłotko. Prof. Jeroen Krijgsveld, an expert in proteomic analysis at the German Cancer Research Centre in Heidelberg, helped discover CTCF's protein partners. At the same time, super-resolution microscopy specialists led by Prof. Timo Zimmermann at the European Molecular Biology Laboratory, also in Heidelberg, made it possible to visualize the impact of development on the distribution of the CTCF protein in cell nuclei.

Now, Prof. Pękowska's team intends to investigate whether non-coding RNA Pantr1 and RNA-binding proteins can be used to control brain cell development. And, consequently, to treat diseases resulting from their abnormal maturation.

“Pantr1 is very active in the most aggressive brain tumour, glioblastoma. This raises the question of whether this is related to changes in chromatin structure that promote disease progression. We plan to answer this question in further research,” concludes Prof. Pękowska.

The research was carried out as part of the OPUS-17 grant awarded by the National Science Centre (2019/33/B/NZ2/02437) and the Dioscuri grant grant (a programme initiated by the Max Planck Society, jointly managed with the National Science Centre and jointly funded by the Ministry of Science and Higher Education (MNiSW) and the German Federal Ministry of Education and Research (BMBF)).

Publication text: https://pmc.ncbi.nlm.nih.gov/articles/PMC12431861/

Contact: a.pekowska@nencki.edu.pl