Enhancer–promoter specificity in gene transcription: molecular mechanisms and disease associations
MJ Friedman, T Wagner, H Lee… - … & Molecular Medicine, 2024 - nature.com
Although often located at a distance from their target gene promoters, enhancers are the
primary genomic determinants of temporal and spatial transcriptional specificity in …
primary genomic determinants of temporal and spatial transcriptional specificity in …
Following the Birth, Life, and Death of mRNAs in Single Cells
BT Eichenberger, E Griesbach… - Annual Review of …, 2023 - annualreviews.org
Recent advances in single-molecule imaging of mRNAs in fixed and living cells have
enabled the lives of mRNAs to be studied with unprecedented spatial and temporal detail …
enabled the lives of mRNAs to be studied with unprecedented spatial and temporal detail …
Genome organization around nuclear speckles drives mRNA splicing efficiency
The nucleus is highly organized, such that factors involved in the transcription and
processing of distinct classes of RNA are confined within specific nuclear bodies,. One …
processing of distinct classes of RNA are confined within specific nuclear bodies,. One …
Simultaneous mapping of 3D structure and nascent RNAs argues against nuclear compartments that preclude transcription
Mammalian genomes are organized into three-dimensional DNA structures called A/B
compartments that are associated with transcriptional activity/inactivity. However, whether …
compartments that are associated with transcriptional activity/inactivity. However, whether …
Deciphering multi-way interactions in the human genome
Chromatin architecture, a key regulator of gene expression, can be inferred using chromatin
contact data from chromosome conformation capture, or Hi-C. However, classical Hi-C does …
contact data from chromosome conformation capture, or Hi-C. However, classical Hi-C does …
Emerging toolkits for decoding the co-occurrence of modified histones and chromatin proteins
AS Pepin, R Schneider - EMBO reports, 2024 - embopress.org
In eukaryotes, DNA is packaged into chromatin with the help of highly conserved histone
proteins. Together with DNA-binding proteins, posttranslational modifications (PTMs) on …
proteins. Together with DNA-binding proteins, posttranslational modifications (PTMs) on …
ChIP-DIP maps binding of hundreds of proteins to DNA simultaneously and identifies diverse gene regulatory elements
Gene expression is controlled by dynamic localization of thousands of regulatory proteins to
precise genomic regions. Understanding this cell type-specific process has been a …
precise genomic regions. Understanding this cell type-specific process has been a …
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 …
HAT: Hypergraph analysis toolbox
Recent advances in biological technologies, such as multi-way chromosome conformation
capture (3C), require development of methods for analysis of multi-way interactions …
capture (3C), require development of methods for analysis of multi-way interactions …
Analysis of super-enhancer using machine learning and its application to medical biology
The analysis of super-enhancers (SEs) has recently attracted attention in elucidating the
molecular mechanisms of cancer and other diseases. SEs are genomic structures that …
molecular mechanisms of cancer and other diseases. SEs are genomic structures that …