Although often located at a distance from their target gene promoters, enhancers are the
primary genomic determinants of temporal and spatial transcriptional specificity in …

R-loops are three-stranded nucleic acid structures that are abundant and widespread across
the genome and that have important physiological roles in many nuclear processes. Their …

Nuclear compartments are prominent features of 3D chromatin organization, but sequencing
depth limitations have impeded investigation at ultra fine-scale. CTCF loops are generally …

CTCF is a critical regulator of genome architecture and gene expression that binds
thousands of sites on chromatin. CTCF genomic localization is controlled by the recognition …

Recent studies have highlighted the impact of both transcription and transcripts on 3D
genome organization, particularly its dynamics. Here, we propose a deep learning …

Simple Summary The human genome produces various types of RNA molecules. A
significant portion of these are long non-coding RNAs (lncRNAs) exceeding 200 nts without …

A longstanding enigma in molecular biology is the lack of scaling of protein-coding genes
with developmental complexity, referred to as the g-value paradox. On the other hand, a …

Simulating chromatin is crucial for predicting genome organization and dynamics. Although
coarse-grained bead-spring polymer models are commonly used to describe chromatin, the …

Topologically associated domains (TADs) restrict promoter-enhancer interactions, thereby
maintaining the spatiotemporal pattern of gene activity. However, rearrangements of the …

Histone modifications, known as histone marks, are pivotal in regulating gene expression
within cells. The vast array of potential combinations of histone marks presents a …