Interaction-seq

Computational Method

I. RNA-RNA

2025 Nature communications biology - Cellular dsRNA interactome captured by K1 antibody reveals the regulatory map of exogenous RNA sensing
✅ [review] 2024 Molecular Cell - Technological advancements in deciphering RNA-RNA interactions
✅ 2024 Cell - snoRNA-facilitated protein secretion revealed by transcriptome-wide snoRNA target identification
✅ 2024 Nature Biotechnology - KARR-seq reveals cellular higher-order RNA structures and RNA–RNA interactions
2023 Nature - Complementary Alu sequences mediate enhancer–promoter selectivity
[review] 2022 Current Opinion in Genetics & Development - Architecture of RNA–RNA interactions
✅ 2020 Nature - RIC-seq for global in situ profiling of RNA–RNA spatial interactions
✅ 2020 Nature - RIC-seq for global in situ profiling of RNA–RNA spatial interactions.

✅ MUSIC-seq: 2024 Nature - Single-cell multiplex chromatin and RNA interactions in ageing human brain
2024 Nature Leukemia - The landscape of RNA-chromatin interaction reveals samll non-coding RNAs as essential mediators of leukemia maintenance
2022 Nature Protocols - SPRITE: a genome-wide method for mapping higher-order 3D interactions in the nucleus using combinatorial split-and-pool barcoding
2017 Nature Biotech. - GRID-seq reveals the global RNA–chromatin interactome

2024 Nature Biotechnology - Pooled CRISPR screens with joint single-nucleus chromatin accessibility and transcriptome profiling

2024 Nat. Biotech. - Tracking-seq reveals the heterogeneity of off-target effects in CRISPR–Cas9-mediated genome editing
2023 Nat. Methods - Improving the sensitivity of in vivo CRISPR off-target detection with DISCOVER-Seq+
2019 Science - Unbiased detection of CRISPR off-targets in vivo using DISCOVER-Seq