Loucif Remini

Thanks to my coauthors; Midas Segers, Andrea Parmeggiani and @ecarlon.bsky.social for this nice collaboration.

Taken together, our results support a scenario where interphase chromatin self-organizes into alternating α/β domains.
This spatial arrangement likely reflects the combined action of passive mechanisms (e.g. bridging interactions) and active loop extrusion processes.

This memory effect is due to looped domains which introduce periodic trajectories of the chromatin organization. The auxin treatment of cells inhibes actives processes of loop extrusion due to cohesin which leads to the disorganization of the beta phase and thus of the memory effect.

We further analyze non-Markovian effects by computing conditional distance distributions and three-point correlations.
These analyses reveal that local chromatin structure influences distal contacts over hundreds of kilobases, with stronger memory effects in WT cells compared to Auxin-treated ones.

To interpret the observed scaling and spatial heterogeneity, we introduce a heterogeneous random walk model.
Despite its simplicity, it reproduces key features of the data, including the transition between intra-loop and inter-loop regimes, and the emergent microphase-separated structure

The α phase is consistent with a crumpled globule, a metastable polymer state which is spatially compact.
The β phase has a weaker exponent, suggesting a looped organization, possibly in the form of rosette-like domains.
This interpretation is supported by experimental data and analytical modeling.

The scaling behavior of these phases is analyzed in detail.
We find consistent results across human and mouse data, with distinct exponents for the α and β phases.
This allows us to characterize different regimes of chromatin folding across multiple levels of genome organization.

We focus on the probability distributions of pairwise spatial distances between labeled genomic loci.
These distributions reveal a robust two-component structure, well described by a superposition of Gaussians.
This statistical signature points to the coexistence of two conformations α and β phases

We analyze high-resolution multiplexed FISH (m-FISH) data from human and mouse cells, covering genomic scales from 5 kb to 2 Mb.
This allows us to compare and unify chromatin structural features across species and over a wide range of genomic distances.

Inferring interphase chromosomal structure from multiplexed fluorescence in situ hybridization data: A unified picture from human and mouse cells We analyze multiplexed fluorescence in situ hybridization (m-FISH) data for human and mouse cell lines. The m-FISH technique uses fluorescently-labeled single-s

We have recently published the following article in The Journal of Chemical Physics:
“Inferring interphase chromosomal structure from multiplexed FISH data: a unified picture from human and mouse cells”

In this thread, I summarize the main findings and ideas discussed in the paper.

Congratulations @ecarlon.bsky.social !!!

I maxed out my credit card, emptied my savings account, and took out a loan to move from Alabama to Bethesda, MD. I don’t even qualify for unemployment since I’ve only worked at NIH for a month. I will be financially and medically devastated.

Seeking suggestions for anywhere that’s hiring!!

C'était hier soir

incroyable

Inferring interphase chromosomal structure from multiplexed fluorescence in situ hybridization data: A unified picture from human and mouse cells We analyze multiplexed fluorescence in situ hybridization (m-FISH) data for human and mouse cell lines. The m-FISH technique uses fluorescently-labeled single-s

Just published in J Chem Phys @aip.bsky.social special issue on "Chromatin Structure and Dynamics". I will tell more on this work in a future post. Collaboration with @lremini.bsky.social, M. Segers and A. Parmeggiani.
doi.org/10.1063/5.02...