Gene regulatory network inference in the era of single-cell multi-omics
The interplay between chromatin, transcription factors and genes generates complex
regulatory circuits that can be represented as gene regulatory networks (GRNs). The study …
regulatory circuits that can be represented as gene regulatory networks (GRNs). The study …
3D enhancer-promoter interactions and multi-connected hubs: Organizational principles and functional roles
The spatiotemporal control of gene expression is dependent on the activity of cis-acting
regulatory sequences, called enhancers, which regulate target genes over variable genomic …
regulatory sequences, called enhancers, which regulate target genes over variable genomic …
Super-resolution chromatin tracing reveals domains and cooperative interactions in single cells
INTRODUCTION Chromatin adopts an intricate three-dimensional (3D) organization in the
nucleus that is critical for many genome processes, from gene regulation to genome …
nucleus that is critical for many genome processes, from gene regulation to genome …
Promoter-proximal CTCF binding promotes distal enhancer-dependent gene activation
N Kubo, H Ishii, X **ong, S Bianco… - Nature structural & …, 2021 - nature.com
The CCCTC-binding factor (CTCF) works together with the cohesin complex to drive the
formation of chromatin loops and topologically associating domains, but its role in gene …
formation of chromatin loops and topologically associating domains, but its role in gene …
Joint profiling of histone modifications and transcriptome in single cells from mouse brain
Genome-wide profiling of histone modifications can reveal not only the location and activity
state of regulatory elements, but also the regulatory mechanisms involved in cell-type …
state of regulatory elements, but also the regulatory mechanisms involved in cell-type …
Mitochondrial base editor induces substantial nuclear off-target mutations
DddA-derived cytosine base editors (DdCBEs)—which are fusions of split DddA halves and
transcription activator-like effector (TALE) array proteins from bacteria—enable targeted C• …
transcription activator-like effector (TALE) array proteins from bacteria—enable targeted C• …
A compendium of promoter-centered long-range chromatin interactions in the human genome
A large number of putative cis-regulatory sequences have been annotated in the human
genome, but the genes they control remain poorly defined. To bridge this gap, we generate …
genome, but the genes they control remain poorly defined. To bridge this gap, we generate …
An ultra high-throughput method for single-cell joint analysis of open chromatin and transcriptome
Simultaneous profiling of transcriptome and chromatin accessibility within single cells is a
powerful approach to dissect gene regulatory programs in complex tissues. However …
powerful approach to dissect gene regulatory programs in complex tissues. However …
Transcriptionally active HERV-H retrotransposons demarcate topologically associating domains in human pluripotent stem cells
Chromatin architecture has been implicated in cell type-specific gene regulatory programs,
yet how chromatin remodels during development remains to be fully elucidated. Here, by …
yet how chromatin remodels during development remains to be fully elucidated. Here, by …
Structural variants drive context-dependent oncogene activation in cancer
Higher-order chromatin structure is important for the regulation of genes by distal regulatory
sequences,. Structural variants (SVs) that alter three-dimensional (3D) genome organization …
sequences,. Structural variants (SVs) that alter three-dimensional (3D) genome organization …