Biology subjects

Kind, J.

Publications and source records attributed to Kind, J..

9 recordsLinked to original sources

bioRxiv2026

Linking live-cell imaging to single-cell sequencing using genetic barcoding

Linking cellular phenotype to genotype and gene expression is a central goal in biomedical research. Live-cell imaging captures dynamic cellular phenotypes, whereas single-cell sequencing measures genome-wide molecular states, but pairing these readouts for the same cell remains challenging. Here we present Waldo, a genetically encoded single-cell barcoding strategy that can be read out by both live-cell imaging and single-cell sequencing to connect single cells across both modalities. Waldo barcodes are generated by combinatorial expression of synthetic cell-surface receptors, each detected by a cognate peptide probe coupled either to a fluorescent dye or a DNA barcode. Iterative fluorescent probe staining achieves large barcode diversity, while preserving fluorescence channels for phenotypic reporters. As a proof-of-principle, we use Waldo to link cell division phenotypes after chromosome missegregation to the karyotype and transcriptome of the same cells. Waldo provides a general strategy for connecting imaging phenotypes to genome-wide sequencing readouts in single cells.

cell biology↗

bioRxiv2025

Reconfiguration of genome-lamina interactions marks the commissioning of limb cell-fates

Diverse forms of heterochromatin block inappropriate transcription and safeguard differentiation and cell identity. Yet, how and when heterochromatin is reconfigured to facilitate changes in cell- fate remains a key open question. Here, we address this by mapping a prevalent heterochromatic feature - genome-lamina interactions - relative to transcription in single-cells during mouse embryogenesis. We find that genome-lamina interactions remain relatively uniform between germ layers following gastrulation but are extensively reconfigured in diverse tissues during later organogenesis. Focusing on limb development, we demonstrate that genome-lamina interactions are selectively released in early multipotent progenitors at key developmental genes and their surrounding regulatory domains. This "lamina-release" often precedes gene expression at later developmental stages, suggesting it primes regulatory domains for future potential activation. Conversely, lamina-release coincides with chromatin opening at sites of crucial limb transcription factor binding, and so is closely intertwined with the regulatory machinery driving limb formation. Finally, we show that the boundaries of topologically-associated domains (TADs) constrain the spread of lamina-release at a limb gene locus. This ensures independent lamina dynamics between neighbouring domains. Together, our data suggest a previously unrecognised process where genome-lamina interactions are selectively released at regulatory domains to transition loci toward more permissive chromatin states, thereby potentiating cell type specific activation. Our work thus reveals how systematic heterochromatin reorganization links to developmental multipotency, providing mechanistic insights into cell-fate decisions in vivo.

developmental biology↗

bioRxiv2023

Time-resolved and multifactorial profiling in single cells resolves the order of heterochromatin formation events during X-chromosome inactivation

The regulation of gene expression is governed at multiple levels of chromatin organization. However, how coordination is achieved remains relatively unexplored. Here we present Dam&ChIC, a method that enables time-resolved and multifactorial chromatin profiling at high resolution in single cells. Analysis of genome-lamina interactions in haploid cells reveals highly dynamic spatial repositioning of small domains during interphase and partial inheritance over mitosis. Dam&ChIC applied to study random X-inactivation uncovers that spreading of H3K27me3 on the inactive X chromosome (Xi) overlaps with remarkable genome-lamina detachment. We find that genome-lamina detachment precedes H3K27me3 accumulation on the Xi and occurs upon mitotic exit. Domains that retain genome-lamina interactions are marked by high pre-existing H3K9me3 levels. These findings imply an important role for genome-lamina interactions in regulating H3K27me3 accumulation on the Xi. We anticipate that Dam&ChIC will be instrumental in unraveling the interconnectivity and order of chromatin events underlying cell-state changes in single cells.

genomics↗

bioRxiv2023

Genome-wide profiling of DNA repair identifies higher-order coordination in single cells

Accurate repair of DNA damage is critical for maintenance of genomic integrity and cellular viability. Because damage occurs non-uniformly across the genome, single-cell resolution is required for proper interrogation, but sensitive detection has remained challenging. Here, we present a comprehensive analysis of repair protein localization in single cells using DamID and ChIC sequencing techniques. This study reports genome-wide binding profiles in response to DNA double-strand breaks induced by AsiSI, and explores variability in genomic damage locations and associated repair features in the context of spatial genome organization. By unbiasedly detecting repair factor localization, we find that repair proteins often occupy entire topologically associating domains, mimicking variability in chromatin loop anchoring. Moreover, we demonstrate the formation of multi-way chromatin hubs in response to DNA damage. Notably, larger hubs show increased coordination of repair protein binding, suggesting a preference for cooperative repair mechanisms. Together, our work offers new insights into the heterogeneous processes underlying genome stability in single cells.

genomics↗

bioRxiv2023

H3K27me3 dictates atypical genome-nuclear lamina interactions and allelic asymmetry during early embryogenesis

The very first days of mammalian embryonic development are accompanied by epigenetic reprogramming and extensive changes in nuclear organization. In particular, genomic regions located at the periphery of the nucleus, termed lamina-associated domains (LADs), undergo major rearrangements after fertilization. However, the role of LADs in regulating gene expression as well as the interplay with various chromatin marks during preimplantation development remains elusive. In this study, we obtained single-cell LAD profiles coupled with the corresponding gene expression readout throughout the first days of mouse development. We detect extensive cell-cell LAD variability at the 2-cell stage, which surprisingly does not seem to functionally affect gene expression. This suggests an unusual uncoupling between 3D-nuclear genome organization and gene expression during totipotent developmental stages. By analyzing LAD dynamics and chromatin states across early developmental stages in an allelic-specific manner, we identify genomic regions that transiently detach from the nuclear lamina and are enriched by non-canonical H3K27me3. Upon maternal knock-out of a component of the Polycomb repressive complex 2 and concomitant loss of H3K27me3 during early embryogenesis, these regions relocate to the lamina at the 2-cell stage. Our results suggest that H3K27me3 is the prime determinant in establishing the atypical distribution of the genome at the nuclear periphery during the first days of embryonic development. This study provides insight into the molecular mechanisms regulating nuclear organization of parental genomes during very early mammalian development.

genomics↗

bioRxiv2023

Combinatorial single-cell profiling of all major chromatin types with MAbID

Gene expression programs result from the collective activity of many regulatory factors. To obtain insight into the mechanisms that govern gene regulation, it is imperative to study their combined mode of action and interconnectivity. However, it has been challenging to simultaneously measure a combination of these factors within one sample. Here, we introduce MAbID, a method that combines genomic profiling of many histone modifications and chromatin-binding proteins in a single reaction. MAbID employs antibody-DNA conjugates to enable genomic barcoding of chromatin at sites of epitope occupancy. This barcoding strategy allows for the combined incubation of multiple antibodies in a single sample to reveal the genomic distributions of many epigenetic states simultaneously. We used MAbID to profile both active and inactive chromatin types in human cell lines and multiplexed measurements in the same sample without loss of data quality. Moreover, we obtained joint measurements of six epitopes covering all major chromatin types in single cells during mouse in vitro neural differentiation and captured associated changes in multifactorial chromatin states. Thus, MAbID holds the potential to gain unique insights into the interplay between gene regulatory mechanisms, especially in settings with limited sample material and in single cells.

genomics↗

bioRxiv2021

Single-cell profiling of transcriptome and histone modifications with EpiDamID

Recent advances in single-cell sequencing technologies have enabled simultaneous measurement of multiple cellular modalities, including various combinations of transcriptome, genome and epigenome. However, comprehensive profiling of the histone post-translational modifications that influence gene expression at single-cell resolution has remained limited. Here, we introduce EpiDamID, an experimental approach to target a diverse set of chromatin types by leveraging the binding specificities of genetically engineered proteins. By fusing Dam to single-chain variable fragment antibodies, engineered chromatin reader domains, or endogenous chromatin-binding proteins, we render the DamID technology and all its implementations compatible with the genome-wide identification of histone post-translational modifications. Importantly, this enables the joint analysis of chromatin marks and transcriptome in a variety of biological systems at the single-cell level. In this study, we use EpiDamID to profile single-cell Polycomb occupancy in mouse embryoid bodies and provide evidence for hierarchical gene regulatory networks. We further demonstrate the applicability of this method to in vivo systems by mapping H3K9me3 in early zebrafish embryogenesis, and detect striking heterochromatic regions specifically in the notochord. Overall, EpiDamID is a new addition to a vast existing toolbox for obtaining systematic insights into the role of chromatin states during dynamic cellular processes.

genomics↗

bioRxiv2019

Self-organization of post-implantation-like embryonic tissues from blastoids

The early mammalian embryo (blastocyst) contains three co-developing types of stem cells. Two supporting extraembryonic types - the trophectoderm and the primitive endoderm - encase and guide the pluripotent epiblast that eventually forms all body tissues. Unlike embryos, stem cell-based models of the embryo can be generated in large numbers and subjected to high-content screens as a basis for basic and biomedical discoveries (Rivron et al., 2018a; Vrij et al., 2016b). Here, we show that aggregates of naive Embryonic stem cells cultured in chemically-defined conditions and exposed to combinatorial screens of signaling molecules, rapidly (48 hours) and efficiently (80%) set apart PrE-like cells. These cells produce a basal lamina, generate progenitors resembling both visceral and parietal endoderm, and polarize co-developing Epiblast cells to form a proamniotic cavity. In blastoids, stem cell-based models of the early blastocyst (Rivron et al., 2018b), this combination of signals increases the ratio and number of Gata6+/Nanog+ cells and promotes the survival, growth and morphogenesis of a post-implantation-like Epiblast in vitro. Modeling early embryonic development in chemically-defined in vitro conditions shows that the primitive endoderm forms via a specific combination of signaling pathways and sufficient to drive the development of the Epiblast.

developmental biology↗

bioRxiv2018

Modeling of DNA methylation in cis reveals principles of chromatin folding in vivo in the absence of crosslinking and ligation

Mammalian chromosomes are folded into an intricate hierarchy of structural domains, within which topologically associating domains (TADs) and CTCF-associated loops partition the physical interactions between regulatory sequences. Current understanding of chromosome folding largely relies on chromosome conformation capture (3C)-based experiments, where chromosomal interactions are detected as ligation products after crosslinking of chromatin. To measure chromosome structure in vivo, quantitatively and without relying on crosslinking and ligation, we have implemented a new method named damC. DamC combines DNA-methylation based detection of chromosomal interactions with next-generation sequencing and a biophysical model of methylation kinetics. DamC performed in mouse embryonic stem cells provides the first in vivo validation of the existence of TADs and CTCF loops, confirms 3C-based measurements of the scaling of contact probabilities within TADs, and provides evidence that mammalian chromatin in vivo is essentially rigid below 5 kilobases. Combining damC with transposon-mediated genomic engineering shows that new loops can be formed between ectopically introduced and endogenous CTCF sites, which alters the partitioning of physical interactions within TADs. This establishes damC as a crosslinking-and ligation-free framework to measure and modify chromosome interactions combined with a solid theoretical background for rigorous data interpretation. This orthogonal approach to 3C validates the existence of key structural features of mammalian chromosomes and provides novel insights into how chromosome structure within TADs can be manipulated.

genomics↗