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# System prepended metadata

title: 参照論文

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# 参照論文
## Method, Database & Subsequent  analysis
### MARGI, 2017 
##### Systematic mapping of RNA-chromatin interactions in vivo https://www.cell.com/current-biology/fulltext/S0960-9822(17)30011-8 

### iMARGI, 2019 
##### Genome-wide co-localization of RNA-DNA interactions and fusion RNA pairs https://www.pnas.org/doi/full/10.1073/pnas.1819788116 
##### Mapping RNA–chromatin interactions by sequencing with iMARGI https://www.nature.com/articles/s41596-019-0229-4
##### Inventer: Sheng Zhong, University of California San Diego
##### Subsequent  analysis:
1) RNAs as Proximity-Labeling Media for Identifying Nuclear Speckle Positions Relative to the Genome, 2018
https://www.cell.com/iscience/fulltext/S2589-0042(18)30081-6
2) Stress-induced RNA-chromatin interactions promote endothelial dysfunction, 2020
https://www.nature.com/articles/s41467-020-18957-w
3) Regulation of nuclear transcription by mitochondrial RNA in endothelial cells, 2024
https://elifesciences.org/articles/86204
2) Genome-wide analysis of the interplay between chromatin-associated RNA and 3D genome organization in human cells, 2023/10/16 https://www.nature.com/articles/s41467-023-42274-7

### GRID-seq, 2017 
##### GRID-seq reveals the global RNA–chromatin interactome https://www.nature.com/articles/nbt.3968
##### Inventer: Xiang-Dong Fu, University of California, San Diego

##### Subsequent analysis:
1) Global profiling of RNA–chromatin interactions reveals co-regulatory gene expression networks in Arabidopsis, 2021/10/24 https://www.nature.com/articles/s41477-021-01004-x
2) Chromatin-associated RNA Dictates the ecDNA Interactome in the Nucleus,  2023/7/27 https://www.biorxiv.org/content/10.1101/2023.07.27.550855v1

### ChAR-seq, 2018 
##### Chromatin-associated RNA sequencing (ChAR-seq) maps genome-wide RNA-to-DNA contacts https://elifesciences.org/articles/27024 
##### Inventer: Aaron F Straight, Stanford University
Subsequent analysis:
1) Global mapping of RNA-chromatin contacts reveals a proximity-dominated connectivity model for ncRNA-gene interactions, 2023/9/28
https://www.nature.com/articles/s41467-023-41848-9 

### RADICL-seq, 2020 
##### RADICL-seq identifies general and cell type–specific principles of genome-wide RNA-chromatin interactions https://www.nature.com/articles/s41467-020-14337-6
##### Subsequent analysis:
1)Antisense-oligonucleotide-mediated perturbation of long non-coding RNA reveals functional features in stem cells and across cell types https://www.sciencedirect.com/science/article/pii/S2211124722017922?via%3Dihub

##### Inventer: Piero Carninci, RIKEN

### Red-C, 2020 
##### Studying RNA–DNA interactome by Red-C identifies noncoding RNAs associated with various chromatin types and reveals transcription dynamics https://academic.oup.com/nar/article/48/12/6699/5849910
##### Inventer: Andrey A Mironov, Lomonosov Moscow State University
##### Subsequent analysis:
1) RNA-Chrom: a manually curated analytical database of RNA–chromatin interactome, 2023/4/24
https://academic.oup.com/database/article/doi/10.1093/database/baad025/7176386
2) Comparative analysis of the RNA-chromatin interactions data. Completeness and accuracy 2023/9/23
https://www.biorxiv.org/content/10.1101/2023.09.21.558854v1 
3) BaRDIC: robust peak calling for RNA-DNA interaction data, 2023/9/28 https://www.biorxiv.org/content/10.1101/2023.09.21.558815v2
4) Comprehensive analysis of RNA-chromatin, RNA- and DNA-protein interactions, 2024/3/13 https://www.biorxiv.org/content/10.1101/2024.03.13.584417v1

### RD-SPRITE, 2021 
##### RNA promotes the formation of spatial compartments in the nucleus https://www.sciencedirect.com/science/article/pii/S0092867421012307?via%3Dihub
##### Inventer: Mitchell Guttman, California Institute of Technology
##### Subsequent analysis:
1) Simultaneous mapping of 3D structure and nascent RNAs argues against nuclear compartments that preclude transcription, 2022 https://www.sciencedirect.com/science/article/pii/S2211124722016084

### LnChrom
##### LnChrom: a resource of experimentally validated lncRNA–chromatin interactions in human and mouse, 2018　https://academic.oup.com/database/article/doi/10.1093/database/bay039/4999394
##### Inventer:  Yun Xiao & Xia Li, Harbin Medical University
##### Subsequent analysis:
1) Comprehensive analysis of long noncoding RNA (lncRNA)-chromatin interactions reveals lncRNA functions dependent on binding diverse regulatory elements, 2019
https://www.jbc.org/article/S0021-9258(20)30325-2/fulltext#%20
## Analysis
### AkitaR model 
Exploring the Roles of RNAs in Chromatin Architecture Using Deep Learning, 2023/10/24
https://www.biorxiv.org/content/10.1101/2023.10.22.563498v1

##### Author: Katherine S. Pollard, Gladstone Institute of Data Science and Biotechnology

## Reviews

## Interiguing Articles
Cell-type-specific prediction of 3D chromatin organization enables high-throughput in silico genetic screening (C.Origami)
https://www.nature.com/articles/s41587-022-01612-8

3D genome encoded by LINE and SINE repeats
https://www.nature.com/articles/s41422-021-00485-x

Functional identification of cis-regulatory long noncoding RNAs at controlled false discovery rates
https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkae075/7606963

Integrative modeling of lncRNA-chromatin interaction maps reveals diverse mechanisms of nuclear retention
https://link.springer.com/article/10.1186/s12864-023-09498-9