FIONA: Functional Imaging Of Nuclear Architecture
Our group studies the physical mechanisms governing
the dynamics organization of chromatin and proteins in vivo. The nucleus
contains one of the most intriguing molecule, DNA, as well as millions of
proteins. Far from being structures with a static organization inside living
cells, these molecular assemblies are constantly formed and unraveled according
to their functional needs. How our genome fits into a nucleus around 200 000
times smaller than unwrapped DNA? How millions of proteins diffuse, find their
target and assemble into condensates to perform their biological function
within the proper time and space window? Our research focuses on these exciting
questions using a multi-scale approaches combining super-resolution microscopy,
advanced image analysis, genetics, micro-fluidic.
Our research is organized into
3 themes :
Dynamics organization of
chromatin upon DNA damage
Dynamics organization of the
nucleus in cells under pressure
Phase separation as an nuclear
organizer
Experimental approaches :
We use single molecule microscopy
(PALM - Photo Activable Localization Microscopy, STORM – Stochastic Optical
Reconstruction Microscopy and Single Particle Tracking – SPT) to visualize and
quantify the behavior of individual molecules in vivo. We use budding
yeast as a model system allowing powerful genetic manipulation, as well as
human cells.
Dynamics organization of
chromatin upon DNA damage
Chromatin mobility
is strongly altered in response to DNA damage in budding yeast and in some mammalian
cells. The figure summarizes the different effects of DSB on chromatin dynamics
(figure from Miné-Hattab & Chiolo 2020, art by Olga Markova):
I) damaged loci explore a larger nuclear volume during HR in
diploid budding yeast, likely facilitating homology search;
II) undamaged
chromatin also becomes more dynamic during DSB repair, albeit to a lesser
extent than repair sites. Such global change shows that increased chromatin
mobility is a general response following DSBs, and not only an intrinsic property of homologous pairing,
III) multiple repair sites cluster
IV) DSBs relocalize
to specific sub-nuclear compartment when the lesion occus in DNA regions that
are difficult to repair.
We study the mechanisms
governing these changes in chromatin mobility upon DNA damage, and their consequences.
Dynamics organization of the nucleus in cells under pressure
Most of the studies addressing nuclear organization have been conducted in exponentially growing cell cultures, and cell imaging is then performed on cells grown or arranged as a monolayer. In these conditions, there is still some growingspace available and there is no particular mechanical stress. However, in nature, cells often have to proliferate in a confined environment. External mechanical stress can dramatically alter essential functions of the cell. In this research axis, we investigate how nuclear organization is altered by compressive stress and what are the consequences for genome integrity.
Phase separation as an nuclear
organizer

The cell nucleus contains membrane-less condensates
inside which specific proteins are more highly concentrated than elsewhere in
the nucleus. This enhanced concentration is hypothesized to help the proteins
coordinate and collectively perform their function. The formation of such foci
at the right place in the nucleus, and within the proper time window, is
essential for the functioning of the cell. However, how such membrane-less
sub-compartments are formed, maintained or disassembled remains unclear. Importantly,
the (de)regulation of these sub-compartments is tightly linked with the
formation of protein aggregates related to the outbreak of neurological
diseases. Several models are intensively debated in the literature to
understand the physical nature of sub-compartments (figure from Miné-Hattab & Taddei 2019, art by Olga Markova). Among them, an
attractive hypothesis is that membrane-less compartments arise from liquid
phase separation and form droplets. Although some biochemical and wide field
microscopy data support this hypothesis, these observations are at the limit of
the optical resolution. In this research axis, we use single molecule
microscopy approaches to distinguish between several models of condensates.
contact: judith.mine-hattab@sorbonne-universite.fr