Biology subjects

Lando, D.

Publications and source records attributed to Lando, D..

7 recordsLinked to original sources

bioRxiv2026

Tissue-specific chromatin accessibility and co-factor availability together define ASCL1-dependent neural reprogrammability across germ layers during embryogenesis

The proneural transcription factor ASCL1 is well established as a pioneering neuronal reprogramming factor in several contexts. However, the extent to which distinct tissue types adopt a similar or divergent response to the same ASCL1 fate challenge is unclear. By expressing ASCL1 across germ layers and tissues of the developing Xenopus neurula embryo, we reveal widespread but largely distinct transcriptomic and chromatin responses to ASCL1. Ectopic ASCL1 can access partially open chromatin sites across all tissues, but it is able to further open those sites specifically in neuroectoderm. Using motif enrichment and accessibility analyses we identify Sox transcription factor motifs as enriched and preferentially accessible at ASCL1-bound regions in neuroectoderm. We show that co-expression of Sox3 and ASCL1 can enable the activation of otherwise refractory ASCL1 target genes in mesoderm and epidermal skin. Our findings reveal how the chromatin landscape and co-factor availability work together to modulate the response to transcription factor-driven fate challenge during development. Summary statementSingle-cell multi-omics reveals how chromatin accessibility and cofactor availability constrains ASCL1-driven neuronal reprogramming across tissues in the developing Xenopus embryo.

developmental biology↗

bioRxiv2026

Hierarchical TBX6-FOXC Regulatory Logic Controls Human Trunk Mesoderm Diversification

Mesoderm forms during gastrulation and diversifies to generate many embryonic tissues, yet the regulatory logic governing early human mesodermal lineage decisions remains poorly defined. We use human iPSC-derived 3D trunk-like structures (hTLS) to model lineage specification during early post-gastrulation development, a stage experimentally inaccessible in humans. Developing hTLS generate neural and mesodermal lineages and recapitulate progressive mesodermal diversification into paraxial (somitic) and intermediate (renal) identities. Using genetic perturbations and temporally controlled transcription factor activation, we identify duration-dependent TBX6 activity as a critical determinant of mesodermal diversification. Downstream, the forkhead box transcription factors FOXC1 and FOXC2 stabilise somitic identity and are required for sclerotome differentiation. These findings reveal a duration-dependent hierarchical regulatory logic in early human mesoderm, in which competence for diversification is established before downstream lineage identities are stabilised, positioning hTLS as a powerful platform to experimentally dissect human developmental programs. HighlightsO_LIHuman trunk-like structures model mesodermal diversification during early post-gastrulation human trunk development C_LIO_LITBX6 duration acts as a temporal gate controlling mesodermal fate potential C_LIO_LIFOXC1/2 function downstream of TBX6 to lock in somitic identity and restrict alternative fates C_LIO_LIDegTrace enables lineage tracing following transient transcription factor activation C_LI

developmental biology↗

bioRxiv2025

HP1β and densely packed chromatin form separate microdomains in mouse ES cells, which are reconfigured upon exit from naive pluripotency

Heterochromatin proteins play a key role in establishing local chromatin structure to control the transcription of target genes. Here we uncover a surprising segregation between regions of high DNA- and high heterochromatin protein 1{beta} (HP1{beta})-density in mouse ES cells. DNA-low/HP1{beta}-high foci retain freely diffusing HP1{beta}, and form via condensation through a multitude of weak interactions on top of HP1{beta} that is bound stably to chromatin. DNA-high/HP1{beta}-low foci exclude freely diffusing HP1{beta} and display reduced chromatin mobility, suggesting a higher degree of chromatin self-interaction and a more repressive environment. Finally, the two types of environments are intertwined in DNA-high/HP1{beta}-high foci, where HP1{beta} maintains heterochromatin in a more compact yet dynamic chromatin state. During the exit from naive pluripotency HP1{beta} is lost from regions of high DNA density as cells transition through the formative state, which might facilitate the reconfiguration of genome structure accompanying a change in cell state that we observed previously. Subsequently, as cells enter primed pluripotency, canonical heterochromatin is established.

molecular biology↗

bioRxiv2023

High changing curvature regions detect chromatin enrichment in single cell data

Chromatin organization is nowadays accessible from population and single cell Hi-C data in the form of large contact matrices. Yet reconstructing the three-dimensional chromatin structure remains challenging and relies on polymer models and numerical simulations to account for these Hi-C data. Here we propose a novel optimization algorithm to identify cross-linker ensemble reproducing the experimental contact matrix. Furthermore, based on the polymer configurations extracted from the optimization procedure, we identify high changing curvature (HCC) regions in the chromatin, detected both in population and in single cell Hi-C, that we also compare to Topological Associated Domains (TADs). We report here that the HCC regions correlate with gene expression and CTCF high density distribution. Interestingly, the HCC region locations are heterogeneous across one cell repeats, revealing cell-to-cell variability. To conclude, HCC regions appear both in single and population Hi-C polymer reconstruction and can provide a possible unit for gene regulation.

genomics↗

bioRxiv2023

Enhancer-promoter interactions are reconfigured through the formation of long-range multiway chromatin hubs as mouse ES cells exit pluripotency

Enhancers are genomic DNA sequences that bind transcription factors, chromatin regulators and non-coding transcripts to modulate the expression of target genes. They have been found to act from different locations relative to a gene and to modulate the activity of promoters up to [~]1 Mb away. Here we report the first 3D genome structures of single mouse ES cells as they are induced to exit pluripotency, transition through a formative stage and undergo neuroectodermal differentiation. In order to directly study how interactions between enhancers and promoters are reconfigured genome wide we have determined 3D structures of haploid cells using single cell Hi-C, where we can unambiguously map the contacts to particular chromosomes. We find that there is a remarkable reorganisation of 3D genome structure where inter-chromosomal intermingling increases dramatically in the formative state. This intermingling is associated with the formation of a large number of multiway hubs that bring together enhancers and promoters with similar chromatin states from typically 5-8 distant chromosomal sites that are often separated by many Mb from each other. Genes important for pluripotency exit establish contacts with emerging enhancers within multiway chromatin hubs as cells enter the formative state, consistent with these structural changes playing an important role in establishing new cell identities. Furthermore, we find that different multiway chromatin hubs, and thus different enhancer-promoter interactions, are formed in different individual cells. Our results suggest that studying genome structure in single cells will be important to identify key changes in enhancer-promoter interactions that occur as cells undergo developmental transitions.

developmental biology↗

bioRxiv2021

Unraveling the kinetochore nanostructure in Schizosaccharomyces pombe using multi-color single-molecule localization microscopy

The key to ensuring proper chromosome segregation during mitosis is the kinetochore complex. This large and tightly regulated multi-protein complex links the centromeric chromatin to the microtubules attached to the spindle pole body and as such leads the segregation process. Understanding the architecture, function and regulation of this vital complex is therefore essential. However, due to its complexity and dynamics, only its individual subcomplexes could be studied in high-resolution structural detail so far. In this study we construct a nanometer-precise in situ map of the human-like regional kinetochore of Schizosaccharomyces pombe (S. pombe) using multi-color single-molecule localization microscopy (SMLM). We measure each kinetochore protein of interest (POI) in conjunction with two reference proteins, cnp1CENP-A at the centromere and sad1 at the spindle pole. This arrangement allows us to determine the cell cycle and in particularly the mitotic plane, and to visualize individual centromere regions separately. From these data, we determine protein distances within the complex using Bayesian inference, establish the stoichiometry of each POI for individual chromosomes and, consequently, build an in situ kinetochore model for S.pombe with so-far unprecedented precision. Being able to quantify the kinetochore proteins within the full in situ kinetochore structure, we provide valuable new insights in the S.pombe kinetochore architecture.

microbiology↗

bioRxiv2020

Live-cell 3D single-molecule tracking reveals how NuRD modulates enhancer dynamics

Enhancer-promoter dynamics are crucial for the spatiotemporal control of gene expression, but it remains unclear whether these dynamics are controlled by chromatin regulators, such as the nucleosome remodelling and deacetylase (NuRD) complex. The NuRD complex binds to all active enhancers to modulate transcription and here we use Hi-C experiments to show that it blurs TAD boundaries and increases the proximity of intermediate-range (~1 Mb) genomic sequences and enhancer-promoter interactions. To understand whether NuRD alters the dynamics of 3D genome structure, we developed an approach to segment and extract key biophysical parameters from 3D single-molecule trajectories of the NuRD complex determined using live-cell imaging. Unexpectedly, this revealed that the intact NuRD complex decompacts chromatin structure and makes NuRD-bound enhancers move faster, increasing the overall volume of the nucleus that these key regulatory regions explore. Interestingly, we also uncovered a rare fast-diffusing state of NuRD bound enhancers that exhibits directed motion. The NuRD complex reduces the amount of time that enhancers remain in this fast-diffusing state, which we propose might otherwise re-organise enhancer-promoter proximity. Thus, we uncover an intimate connection between a chromatin remodeller and the spatial dynamics of the local regions of the genome to which it binds.

cell biology↗