Back-spliced RNA from retrotransposon binds to centromere and regulates centromeric chromatin loops in maize [PDF]
PLoS Biology, 2020 In most plants, centromeric DNA contains highly repetitive sequences, including tandem repeats and retrotransposons; however, the roles of these sequences in the structure and function of the centromere are unclear.
Yalin Liu, Handong Su, Fangpu Han
exaly +3 more sources
SnapFISH: a computational pipeline to identify chromatin loops from multiplexed DNA FISH data [PDF]
Nature Communications, 2023 Multiplexed DNA fluorescence in situ hybridization (FISH) imaging technologies have been developed to map the folding of chromatin fibers at tens of nanometers and up to several kilobases in resolution in single cells.
Lindsay Lee +14 more
doaj +2 more sources
CapsNetYY1: identifying YY1-mediated chromatin loops based on a capsule network architecture [PDF]
BMC Genomics, 2023 Background Previous studies have identified that chromosome structure plays a very important role in gene control. The transcription factor Yin Yang 1 (YY1), a multifunctional DNA binding protein, could form a dimer to mediate chromatin loops and active ...
Zhimin Zhang +3 more
doaj +2 more sources
Hi-TrAC reveals division of labor of transcription factors in organizing chromatin loops [PDF]
Nature Communications, 2022 The three-dimensional genomic structure plays a critical role in gene expression, cellular differentiation, and pathological conditions. It is pivotal to elucidate fine-scale chromatin architectures, especially interactions of regulatory elements, to ...
Shuai Liu +4 more
doaj +2 more sources
DLoopCaller: A deep learning approach for predicting genome-wide chromatin loops by integrating accessible chromatin landscapes. [PDF]
PLoS Computational Biology, 2022 In recent years, major advances have been made in various chromosome conformation capture technologies to further satisfy the needs of researchers for high-quality, high-resolution contact interactions.
Siguo Wang +6 more
doaj +2 more sources
CellLoop: Identifying single-cell 3D genome chromatin loops [PDF]
Nature CommunicationsSingle-cell 3D genome technologies provide unprecedented views of chromatin architecture, but the extreme sparsity and noise of contact maps limit robust detection of chromatin loops at the individual cell level. Here we present CellLoop, a computational
Yusen Ye +8 more
doaj +2 more sources
A Bioconductor/R Workflow for the Detection and Visualization of Differential Chromatin Loops [version 1; peer review: 2 approved] [PDF]
F1000ResearchBackground Chromatin loops play a critical role in gene regulation by connecting regulatory loci and gene promoters. The identification of changes in chromatin looping between cell types or biological conditions is an important task for understanding ...
Eric Davis +4 more
doaj +2 more sources
CLAMP: predicting specific protein-mediated chromatin loops in diverse species with a chromatin accessibility language model [PDF]
Genome BiologyEmerging DNA language models provide powerful tools to address the challenge of accurately predicting chromatin loops, fundamental structures governing 3D genome organization and gene regulation.
Zhijie He +7 more
doaj +2 more sources
ESCO1 and CTCF enable formation of long chromatin loops by protecting cohesinSTAG1 from WAPL [PDF]
eLife, 2020 Eukaryotic genomes are folded into loops. It is thought that these are formed by cohesin complexes via extrusion, either until loop expansion is arrested by CTCF or until cohesin is removed from DNA by WAPL.
Gordana Wutz +19 more
doaj +2 more sources
The anatomy of transcriptionally active chromatin loops in Drosophila primary spermatocytes using super-resolution microscopy. [PDF]
PLoS Genetics, 2023 While the biochemistry of gene transcription has been well studied, our understanding of how this process is organised in 3D within the intact nucleus is less well understood.
Madeleine L Ball +5 more
doaj +2 more sources