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 …

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 …

Genome organization around nuclear speckles drives mRNA splicing efficiency

P Bhat, A Chow, B Emert, O Ettlin, SA Quinodoz… - Nature, 2024 - nature.com
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 …

Simultaneous mapping of 3D structure and nascent RNAs argues against nuclear compartments that preclude transcription

IN Goronzy, SA Quinodoz, JW Jachowicz, N Ollikainen… - Cell reports, 2022 - cell.com
Mammalian genomes are organized into three-dimensional DNA structures called A/B
compartments that are associated with transcriptional activity/inactivity. However, whether …

Deciphering multi-way interactions in the human genome

GA Dotson, C Chen, S Lindsly, A Cicalo… - Nature …, 2022 - nature.com
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 …

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 …

ChIP-DIP maps binding of hundreds of proteins to DNA simultaneously and identifies diverse gene regulatory elements

AA Perez, IN Goronzy, MR Blanco, BT Yeh, JK Guo… - Nature Genetics, 2024 - nature.com
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 …

Systematic identification of interchromosomal interaction networks supports the existence of specialized RNA factories

BH Hristov, WS Noble, A Bertero - Genome Research, 2024 - genome.cshlp.org
Most studies of genome organization have focused on intrachromosomal (cis) contacts
because they harbor key features such as DNA loops and topologically associating …

HAT: Hypergraph analysis toolbox

J Pickard, C Chen, R Salman, C Stansbury… - PLOS Computational …, 2023 - journals.plos.org
Recent advances in biological technologies, such as multi-way chromosome conformation
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

R Hamamoto, K Takasawa, N Shinkai… - Briefings in …, 2023 - academic.oup.com
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 …