ArticleNature communications2024
Exploring the roles of RNAs in chromatin architecture using deep learning.
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers, 1 of them a synthesis that pooled it.
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Who cites it
21 citing papers in PubMed, 1 synthesis or guideline pooled it.
- The role of R-loops-mediated epigenetic regulation in genome stability maintenance and disease pathogenesis: a systematic review.Epigenetics · 2026Pooled it
- Scoparone protects against acetaminophen-induced acute liver injury: Insights from In vivo experiments and RNA sequencing.Biochemistry and biophysics reports · 2026Article
- Machine learning reveals sequence and genomic context features underlyingbioRxiv : the preprint server for biology · 2026Article
- Foundation model reveals the shared organization of transcription and topologically associating domains.Cell systems · 2026Article
- mNature reviews. Neuroscience · 2026Review
- R-loops and D-loops: a delicate balance in genomic stability and instability.Cell communication and signaling : CCS · 2026Review
- Improved RNA-DNA interaction calling suggests RNA-based gene regulation of phenotypic transitions.Nucleic acids research · 2026Article
- HNRNPU and architectural lncRNAs as nuclear tethers of epithelial state stability.EMBO molecular medicine · 2026Review
- GraphChIAr: genome-wide super-resolution reconstruction of protein-mediated remote chromatin interactions by augmenting hi-C interaction maps with multiple ChIP-seq profiles.Briefings in bioinformatics · 2026Article
- Direct roles of long non-coding RNAs in transcription activation.Nature structural & molecular biology · 2026Review
- Dissecting the contribution of transposable elements to interphase chromosome structure.Genome biology · 2026Article
- The METTL3-YTHDC1 axis mediates architectural RNA mMolecular cancer · 2025Article
- Isoformic: a workflow for transcript-level RNA-seq interpretation.NAR genomics and bioinformatics · 2025Article
- Recent advances in single-cell bioinformatics for inferring higher-order chromatin contact maps.BMB reports · 2025Review
- Role of RNA in genome folding: It's all about affinity.Current opinion in structural biology · 2025Review
- Simultaneous Capture of Chromatin-Associated RNA and Global RNA-RNA Interactions With Reduced Input Requirements.Bio-protocol · 2025Article
- Recipes and ingredients for deep learning models of 3D genome folding.Current opinion in genetics & development · 2025Review
- A Joint Analysis of RNA-DNA and DNA-DNA Interactomes Reveals Their Strong Association.International journal of molecular sciences · 2025Article
- Exploring the roles of RNAs in chromatin architecture using deep learning.Nature communications · 2024Article
- SuPreMo: a computational tool for streamlining in silico perturbation using sequence-based predictive models.Bioinformatics (Oxford, England) · 2024Article
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Abstract
Recent studies have highlighted the impact of both transcription and transcripts on 3D genome organization, particularly its dynamics. Here, we propose a deep learning framework, called AkitaR, that leverages both genome sequences and genome-wide RNA-DNA interactions to investigate the roles of chromatin-associated RNAs (caRNAs) on genome folding in HFFc6 cells. In order to disentangle the cis- and trans-regulatory roles of caRNAs, we have compared models with nascent transcripts, trans-located caRNAs, open chromatin data, or DNA sequence alone. Both nascent transcripts and trans-located caRNAs improve the models' predictions, especially at cell-type-specific genomic regions. Analyses of feature importance scores reveal the contribution of caRNAs at TAD boundaries, chromatin loops and nuclear sub-structures such as nuclear speckles and nucleoli to the models' predictions. Furthermore, we identify non-coding RNAs (ncRNAs) known to regulate chromatin structures, such as MALAT1 and NEAT1, as well as several new RNAs, RNY5, RPPH1, POLG-DT and THBS1-IT1, that might modulate chromatin architecture through trans-interactions in HFFc6. Our modeling also suggests that transcripts from Alus and other repetitive elements may facilitate chromatin interactions through trans R-loop formation. Our findings provide insights and generate testable hypotheses about the roles of caRNAs in shaping chromatin organization.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.