Toward a foundation model of causal cell and tissue biology with a Perturbation Cell and Tissue Atlas
JE Rood, A Hupalowska, A Regev - Cell, 2024 - cell.com
Comprehensively charting the biologically causal circuits that govern the phenotypic space
of human cells has often been viewed as an insurmountable challenge. However, in the last …
of human cells has often been viewed as an insurmountable challenge. However, in the last …
[HTML][HTML] The method in the madness: Transcriptional control from stochastic action at the single-molecule scale
PH Whitney, T Lionnet - Current Opinion in Structural Biology, 2024 - Elsevier
Cell states result from the ordered activation of gene expression by transcription factors.
Transcription factors face opposing design constraints: they need to be dynamic to trigger …
Transcription factors face opposing design constraints: they need to be dynamic to trigger …
[HTML][HTML] Rewriting regulatory DNA to dissect and reprogram gene expression
Regulatory DNA sequences within enhancers and promoters bind transcription factors to
encode cell type-specific patterns of gene expression. However, the regulatory effects and …
encode cell type-specific patterns of gene expression. However, the regulatory effects and …
Hijacked enhancer–promoter and silencer–promoter loops in cancer
X Wang, F Yue - Current Opinion in Genetics & Development, 2024 - Elsevier
Highlights•3D genome organization undergoes dramatic changes in cancer.•Oncogenes
can be ectopically activated by SV-induced enhancer hijacking.•Tumor suppressor genes …
can be ectopically activated by SV-induced enhancer hijacking.•Tumor suppressor genes …
TF-EPI: an interpretable enhancer-promoter interaction detection method based on Transformer
The detection of enhancer-promoter interactions (EPIs) is crucial for understanding gene
expression regulation, disease mechanisms, and more. In this study, we developed TF-EPI …
expression regulation, disease mechanisms, and more. In this study, we developed TF-EPI …
Linking regulatory variants to target genes by integrating single-cell multiome methods and genomic distance
ER Dorans, K Jagadeesh, K Dey, AL Price - medRxiv, 2024 - medrxiv.org
Methods that analyze single-cell paired RNA-seq and ATAC-seq multiome data have shown
great promise in linking regulatory elements to genes. However, existing methods differ in …
great promise in linking regulatory elements to genes. However, existing methods differ in …
Cross-Phenotype GWAS Supports Shared Genetic Susceptibility to Systemic Sclerosis and Primary Biliary Cholangitis
Objective An increased risk of primary biliary cholangitis (PBC) has been reported in
patients with systemic sclerosis (SSc). Our study aims to investigate the shared genetic …
patients with systemic sclerosis (SSc). Our study aims to investigate the shared genetic …
Cohesin-mediated 3D contacts tune enhancer-promoter regulation
P Guckelberger, BR Doughty, G Munson, SSP Rao… - bioRxiv, 2024 - biorxiv.org
Enhancers are key drivers of gene regulation thought to act via 3D physical interactions with
the promoters of their target genes. However, genome-wide depletions of architectural …
the promoters of their target genes. However, genome-wide depletions of architectural …
HyperCas12a enables highly-multiplexed epigenome editing screens
SM Melore, MC Hamilton, TE Reddy - bioRxiv, 2024 - biorxiv.org
Interactions between multiple genes or cis-regulatory elements (CREs) underlie a wide
range of biological processes in both health and disease. High-throughput screens using …
range of biological processes in both health and disease. High-throughput screens using …
The Role of CTCF-Mediated Chromatin Looping in Enhancer-Promoter Communication
C Logie - Epigenetics in Biological Communication, 2024 - Springer
In vertebrates, gene transcription is performed by generic eukaryotic molecular machinery
under influence of sequence-specific DNA-binding transcription factors that control gene …
under influence of sequence-specific DNA-binding transcription factors that control gene …