[HTML][HTML] Spatial and temporal organization of the genome: Current state and future aims of the 4D nucleome project
The four-dimensional nucleome (4DN) consortium studies the architecture of the genome
and the nucleus in space and time. We summarize progress by the consortium and highlight …
and the nucleus in space and time. We summarize progress by the consortium and highlight …
Applications of deep learning in understanding gene regulation
Gene regulation is a central topic in cell biology. Advances in omics technologies and the
accumulation of omics data have provided better opportunities for gene regulation studies …
accumulation of omics data have provided better opportunities for gene regulation studies …
[HTML][HTML] Transient naive reprogramming corrects hiPS cells functionally and epigenetically
Cells undergo a major epigenome reconfiguration when reprogrammed to human induced
pluripotent stem cells (hiPS cells). However, the epigenomes of hiPS cells and human …
pluripotent stem cells (hiPS cells). However, the epigenomes of hiPS cells and human …
DeepLoop robustly maps chromatin interactions from sparse allele-resolved or single-cell Hi-C data at kilobase resolution
Mapping chromatin loops from noisy Hi-C heatmaps remains a major challenge. Here we
present DeepLoop, which performs rigorous bias correction followed by deep-learning …
present DeepLoop, which performs rigorous bias correction followed by deep-learning …
[HTML][HTML] Single-cell multiplex chromatin and RNA interactions in ageing human brain
Dynamically organized chromatin complexes often involve multiplex chromatin interactions
and sometimes chromatin-associated RNA,–. Chromatin complex compositions change …
and sometimes chromatin-associated RNA,–. Chromatin complex compositions change …
Depletion of lamins B1 and B2 promotes chromatin mobility and induces differential gene expression by a mesoscale-motion-dependent mechanism
EM Pujadas Liwag, X Wei, N Acosta, LM Carter, J Yang… - Genome biology, 2024 - Springer
Background B-type lamins are critical nuclear envelope proteins that interact with the three-
dimensional genomic architecture. However, identifying the direct roles of B-lamins on …
dimensional genomic architecture. However, identifying the direct roles of B-lamins on …
Chemical-induced phase transition and global conformational reorganization of chromatin
T Wang, S Shi, Y Shi, P Jiang, G Hu, Q Ye, Z Shi… - Nature …, 2023 - nature.com
Chemicals or drugs can accumulate within biomolecular condensates formed through phase
separation in cells. Here, we use super-resolution imaging to search for chemicals that …
separation in cells. Here, we use super-resolution imaging to search for chemicals that …
Double-strand break toxicity is chromatin context independent
Cells respond to double-strand breaks (DSBs) by activating DNA damage response
pathways, including cell cycle arrest. We have previously shown that a single double-strand …
pathways, including cell cycle arrest. We have previously shown that a single double-strand …
Fork coupling directs DNA replication elongation and termination
DNA replication is initiated at multiple loci to ensure timely duplication of eukaryotic
genomes. Sister replication forks progress bidirectionally, and replication terminates when …
genomes. Sister replication forks progress bidirectionally, and replication terminates when …
Systematic identification of interchromosomal interaction networks supports the existence of specialized RNA factories
Most studies of genome organization have focused on intrachromosomal (cis) contacts
because they harbor key features such as DNA loops and topologically associating …
because they harbor key features such as DNA loops and topologically associating …