Cabili, M. N. et al. Integrative annotation of human massive intergenic noncoding RNAs reveals international properties and particular subclasses. Genes Dev. 25, 1915–1927 (2011).
Google ScholarÂ
Statello, L., Guo, C.-J., Chen, L.-L. & Huarte, M. Gene regulation by lengthy non-coding RNAs and its organic capabilities. Nat. Rev. Mol. Cell Biol. 22, 96–118 (2020).
Google ScholarÂ
Loda, A. & Heard, E. Xist RNA in motion: previous, current, and future. PLoS Genet. 15, e1008333 (2019).
Google ScholarÂ
Chu, C., Qu, Ok., Zhong, F. L., Artandi, S. E. & Chang, H. Y. Genomic maps of lengthy noncoding RNA occupancy reveal rules of RNA-chromatin interactions. Mol. Cell 44, 667–678 (2011).
Google ScholarÂ
Simon, M. D. et al. The genomic binding websites of a noncoding RNA. Proc. Natl Acad. Sci. USA 108, 20497–20502 (2011).
Google ScholarÂ
Engreitz, J. M. et al. The Xist lncRNA exploits three-dimensional genome structure to unfold throughout the X chromosome. Science 341, 1237973 (2013).
Google ScholarÂ
Johnson, D. S., Mortazavi, A., Myers, R. M. & Wold, B. Genome-wide mapping of in vivo protein–DNA interactions. Science 316, 1497–1502 (2007).
Google ScholarÂ
Alvarez-Dominguez, J. R., Knoll, M., Gromatzky, A. A. & Lodish, H. F. The super-enhancer-derived alncRNA-EC7/Bloodlinc potentiates crimson blood cell growth in trans. Cell Rep. 19, 2503–2514 (2017).
Google ScholarÂ
Alfeghaly, C. et al. Implication of repeat insertion domains within the trans-activity of the lengthy non-coding RNA ANRIL. Nucleic Acids Res. 49, 4954–4970 (2021).
Google ScholarÂ
Léveillé, N. et al. Genome-wide profiling of p53-regulated enhancer RNAs uncovers a subset of enhancers managed by a lncRNA. Nat. Commun. 6, 6520 (2015).
Google ScholarÂ
Simon, M. D. & Machyna, M. Rules and practices of hybridization seize experiments to check lengthy noncoding RNAs that act on chromatin. Chilly Spring Harb. Perspect. Biol. 11, a032276 (2019).
Google ScholarÂ
Iyer, N. R. et al. Modular derivation of various, regionally discrete human posterior CNS neurons allows discovery of transcriptomic patterns. Sci. Adv. 8, eabn7430 (2022).
Google ScholarÂ
Delhaye, L. et al. Stress attenuation by the adrenergic-specific lncRNA NESPR prevents cell loss of life in neuroblastoma cells. Preprint at bioRxiv (2025).
Lodrini, M. et al. Utilizing droplet digital PCR to investigate and duplicate quantity in plasma from sufferers with neuroblastoma. Oncotarget 8, 85234–85251 (2017).
Google ScholarÂ
Cazes, A. et al. Characterization of rearrangements involving the ALK gene reveals a novel truncated type related to tumor aggressiveness in neuroblastoma. Most cancers Res. 73, 195–204 (2013).
Google ScholarÂ
Heinz, S. et al. Easy combos of lineage-determining transcription components prime cis-regulatory parts required for macrophage and B cell identities. Mol. Cell 38, 576–589 (2010).
Google ScholarÂ
Bailey, T. L. STREME: correct and versatile sequence motif discovery. Bioinformatics 37, 2834–2840 (2021).
Google ScholarÂ
Niehrs, C. & Luke, B. Regulatory R-loops as facilitators of gene expression and genome stability. Nat. Rev. Mol. Cell Biol. 21, 167–178 (2020).
Google ScholarÂ
Gartlgruber, M. et al. Tremendous enhancers outline regulatory subtypes and cell id in neuroblastoma. Nat. Most cancers 2, 114–128 (2021).
Google ScholarÂ
Debruyne, D. N. et al. BORIS promotes chromatin regulatory interactions in treatment-resistant most cancers cells. Nature 572, 676–680 (2019).
Google ScholarÂ
Langmead, B., Trapnell, C., Pop, M. & Salzberg, S. L. Ultrafast and memory-efficient alignment of brief DNA sequences to the human genome. Genome Biol. 10, R25 (2009).
Google ScholarÂ
Feng, J., Liu, T., Qin, B., Zhang, Y. & Liu, X. S. Figuring out ChIP-seq enrichment utilizing MACS. Nat. Protoc. 7, 1728–1740 (2012).
Google ScholarÂ
Luo, H. et al. HOTTIP lncRNA promotes hematopoietic stem cell self-renewal resulting in AML-like illness in mice. Most cancers Cell 36, 645–659 (2019).
Google ScholarÂ
Issler, O. et al. Intercourse-specific function for the lengthy non-coding RNA LINC00473 in melancholy. Neuron 106, 912–926.e5 (2020).
Google ScholarÂ
Powell, W. T. et al. A Prader–Willi locus lncRNA cloud modulates diurnal genes and vitality expenditure. Hum. Mol. Genet. 22, 4318–4328 (2013).
Google ScholarÂ
Li, M. A. et al. A lncRNA high-quality tunes the dynamics of a cell state transition involving Lin28, let-7 and de novo DNA methylation. eLife 6, e23468 (2017).
Google ScholarÂ
Yin, Y. et al. Opposing roles for the lncRNA Hang-out and its genomic locus in regulating HOXA gene activation throughout embryonic stem cell differentiation. Cell Stem Cell 16, 504–516 (2015).
Google ScholarÂ
Maldotti, M. et al. The acetyltransferase p300 is recruited in trans to a number of enhancer websites by lncSmad7. Nucleic Acids Res. 50, 2587–2602 (2022).
Google ScholarÂ
Chakraborty, D. et al. LncRNA Panct1 maintains mouse embryonic stem cell id by regulating TOBF1 recruitment to Oct–Sox sequences in early G1. Cell Rep. 21, 3012–3021 (2017).
Google ScholarÂ
Amemiya, H. M., Kundaje, A. & Boyle, A. P. The ENCODE Blacklist: identification of problematic areas of the genome. Sci. Rep. 9, 9354 (2019).
Google ScholarÂ
Wreczycka, Ok. et al. HOT or not: inspecting the premise of high-occupancy goal areas. Nucleic Acids Res. 47, 5735–5745 (2019).
Google ScholarÂ
Nordin, A., Zambanini, G., Pagella, P. & Cantù, C. The CUT&RUN suspect listing of problematic areas of the genome. Genome Biol. 24, 185 (2023).
Google ScholarÂ
Mittal, C., Rossi, M. J. & Pugh, B. F. Excessive similarity amongst ChEC-seq datasets. Preprint at bioRxiv (2021).
Lee, H. C. et al. A novel lengthy noncoding RNA Linc-ASEN represses mobile senescence by way of multileveled discount of p21 expression. Cell Demise Differ. 27, 1844–1861 (2020).
Google ScholarÂ
Zhang, G. et al. Complete evaluation of lengthy noncoding RNA (lncRNA)–chromatin interactions reveals lncRNA capabilities depending on binding various regulatory parts. J. Biol. Chem. 294, 15613–15622 (2019).
Google ScholarÂ
Grant, C. E., Bailey, T. L. & Noble, W. S. FIMO: scanning for occurrences of a given motif. Bioinformatics 27, 1017–1018 (2011).
Google ScholarÂ
Harkins, Ok. M. et al. A novel NGS library preparation methodology to characterize native termini of fragmented DNA. Nucleic Acids Res. 48, e47 (2020).
Google ScholarÂ
Elsner, H. I. & Lindblad, E. B. Ultrasonic degradation of DNA. DNA 8, 697–701 (1989).
Google ScholarÂ
Oh, H. J. et al. Jpx RNA regulates CTCF anchor web site choice and formation of chromosome loops. Cell 184, 6157–6173 (2021).
Google ScholarÂ
Quinodoz, S. A. et al. RNA promotes the formation of spatial compartments within the nucleus. Cell 184, 5775–5790 (2021).
Google ScholarÂ
Bonetti, A. et al. RADICL-seq identifies normal and cell type-specific rules of genome-wide RNA–chromatin interactions. Nat. Commun. 11, 1018 (2020).
Google ScholarÂ
Deforzh, E. et al. HOXDeRNA prompts a cancerous transcription program and tremendous enhancers by way of genome-wide binding. Mol. Cell 84, 3950–3966 (2024).
Google ScholarÂ
Rio, D. C., Ares, M. Jr, Hannon, G. J. & Nilsen, T. W. Elimination of DNA from RNA. Chilly Spring Harb. Protoc. 2010, pdb.prot5443 (2010).
Google ScholarÂ
Ramos, A. M. et al. Design of a excessive density SNP genotyping assay within the pig utilizing SNPs recognized and characterised by subsequent era sequencing expertise. PLoS ONE 4, e6524 (2009).
Google ScholarÂ
Zentner, G. E., Kasinathan, S., Xin, B., Rohs, R. & Henikoff, S. ChEC-seq kinetics discriminates transcription issue binding websites by DNA sequence and form in vivo. Nat. Commun. 6, 8733 (2015).
Google ScholarÂ
Kaya-Okur, H. S. et al. CUT&Tag for environment friendly epigenomic profiling of small samples and single cells. Nat. Commun. 10, 1930 (2019).
Google ScholarÂ
Skene, P. J. & Henikoff, S. An environment friendly focused nuclease technique for high-resolution mapping of DNA binding websites. eLife 6, e21856 (2017).
Google ScholarÂ
Yan, Z. et al. Genome-wide colocalization of RNA–DNA interactions and fusion RNA pairs. Proc. Natl Acad. Sci. USA 116, 3328–3337 (2019).
Google ScholarÂ
Li, X. et al. GRID-seq reveals the worldwide RNA–chromatin interactome. Nat. Biotechnol. 35, 940–950 (2017).
Google ScholarÂ
Bell, J. C. et al. Chromatin-associated RNA sequencing (ChAR-seq) maps genome-wide RNA-to-DNA contacts. eLife 7, e27024 (2018).
Google ScholarÂ
Gavrilov, A. A. et al. Learning RNA–DNA interactome by Pink-C identifies noncoding RNAs related to numerous chromatin varieties and divulges transcription dynamics. Nucleic Acids Res. 48, 6699–6714 (2020).
Google ScholarÂ
Tsue, A. F. et al. Multiomic characterization of RNA microenvironments by oligonucleotide-mediated proximity-interactome mapping. Nat. Strategies 21, 2058–2071 (2024).
Google ScholarÂ
Yap, Ok., Chung, T. H. & Makeyev, E. V. Hybridization-proximity labeling reveals spatially ordered interactions of nuclear RNA compartments. Mol. Cell 82, 463–478.e11 (2022).
Google ScholarÂ
Trupej, A. et al. HCR-Proxy resolves site-specific proximal RNA microenvironments at subcompartmental decision. Nucleic Acids Res. 54, gkag086 (2026).
Google ScholarÂ
Koziol, M. J. & Rinn, J. L. RNA site visitors management of chromatin complexes. Curr. Opin. Genet. Dev. 20, 142–148 (2010).
Google ScholarÂ
Guo, J. Ok. et al. Denaturing purifications exhibit that PRC2 and different extensively reported chromatin proteins don’t seem to bind on to RNA in vivo. Mol. Cell 84, 1271–1289 (2024).
Google ScholarÂ
Davidovich, C., Zheng, L., Goodrich, Ok. J. & Cech, T. R. Promiscuous RNA binding by Polycomb repressive advanced 2. Nat. Struct. Mol. Biol. 20, 1250–1257 (2013).
Google ScholarÂ
Nielsen, M. & Ulitksy, I. The hyperlinks are nonetheless lacking: revisiting the function of RNA as a information for chromatin-associated proteins. Mol. Cell 84, 1178–1179 (2024).
Google ScholarÂ
Corridor Hickman, A. & Jenner, R. G. Obvious RNA bridging between PRC2 and chromatin is an artifact of non-specific chromatin precipitation upon RNA degradation. Cell Rep. 43, 113856 (2024).
Google ScholarÂ
Healy, E. et al. The obvious lack of PRC2 chromatin occupancy as an artifact of RNA depletion. Cell Rep. 43, 113858 (2024).
Google ScholarÂ
Lee, Y. et al. Re-analysis of CLAP knowledge affirms PRC2 as an RNA binding protein. Preprint at bioRxiv (2024).
Guo, J. Ok., Blanco, M. R. & Guttman, M. Failing to account for RNA amount inflates background and results in the deceptive look that PRC2 and GFP bind to RNA in vivo. Preprint at bioRxiv (2024).
Cai, D. et al. Mixed depletion of cell cycle and transcriptional cyclin-dependent kinase actions induces apoptosis in most cancers cells. Most cancers Res. 66, 9270–9280 (2006).
Chu, C., Quinn, J. & Chang, H. Y. Chromatin isolation by RNA purification (ChIRP). J. Vis. Exp. (61), e3912.
Kuhn, R. M., Haussler, D. & Kent, W. J. The UCSC Genome Browser and related instruments. Transient. Bioinform. 14, 144–161 (2013).
Google ScholarÂ
Langmead, B. & Salzberg, S. L. Quick gapped-read alignment with Bowtie 2. Nat. Strategies 9, 357–359 (2012).
Google ScholarÂ
Quinlan, A. R. & Corridor, I. M. BEDTools: a versatile suite of utilities for evaluating genomic options. Bioinformatics 26, 841–842 (2010).
Google ScholarÂ
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