Cabili, M. N. et al. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev. 25, 1915–1927 (2011).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Statello, L., Guo, C.-J., Chen, L.-L. & Huarte, M. Gene regulation by long non-coding RNAs and its biological functions. Nat. Rev. Mol. Cell Biol. 22, 96–118 (2020).

Article  PubMed  PubMed Central  Google Scholar 

Loda, A. & Heard, E. Xist RNA in action: past, present, and future. PLoS Genet. 15, e1008333 (2019).

Article  PubMed  PubMed Central  Google Scholar 

Chu, C., Qu, K., Zhong, F. L., Artandi, S. E. & Chang, H. Y. Genomic maps of long noncoding RNA occupancy reveal principles of RNA-chromatin interactions. Mol. Cell 44, 667–678 (2011).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Simon, M. D. et al. The genomic binding sites of a noncoding RNA. Proc. Natl Acad. Sci. USA 108, 20497–20502 (2011).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Engreitz, J. M. et al. The Xist lncRNA exploits three-dimensional genome architecture to spread across the X chromosome. Science 341, 1237973 (2013).

Article  PubMed  PubMed Central  Google Scholar 

Johnson, D. S., Mortazavi, A., Myers, R. M. & Wold, B. Genome-wide mapping of in vivo protein–DNA interactions. Science 316, 1497–1502 (2007).

Article  CAS  PubMed  Google Scholar 

Alvarez-Dominguez, J. R., Knoll, M., Gromatzky, A. A. & Lodish, H. F. The super-enhancer-derived alncRNA-EC7/Bloodlinc potentiates red blood cell development in trans. Cell Rep. 19, 2503–2514 (2017).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Alfeghaly, C. et al. Implication of repeat insertion domains in the trans-activity of the long non-coding RNA ANRIL. Nucleic Acids Res. 49, 4954–4970 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Léveillé, N. et al. Genome-wide profiling of p53-regulated enhancer RNAs uncovers a subset of enhancers controlled by a lncRNA. Nat. Commun. 6, 6520 (2015).

Article  PubMed  PubMed Central  Google Scholar 

Simon, M. D. & Machyna, M. Principles and practices of hybridization capture experiments to study long noncoding RNAs that act on chromatin. Cold Spring Harb. Perspect. Biol. 11, a032276 (2019).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Iyer, N. R. et al. Modular derivation of diverse, regionally discrete human posterior CNS neurons enables discovery of transcriptomic patterns. Sci. Adv. 8, eabn7430 (2022).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Delhaye, L. et al. Stress attenuation by the adrenergic-specific lncRNA NESPR prevents cell death in neuroblastoma cells. Preprint at bioRxiv https://doi.org/10.1101/2025.04.07.647560 (2025).

Lodrini, M. et al. Using droplet digital PCR to analyze and copy number in plasma from patients with neuroblastoma. Oncotarget 8, 85234–85251 (2017).

Article  PubMed  PubMed Central  Google Scholar 

Cazes, A. et al. Characterization of rearrangements involving the ALK gene reveals a novel truncated form associated with tumor aggressiveness in neuroblastoma. Cancer Res. 73, 195–204 (2013).

Article  CAS  PubMed  Google Scholar 

Heinz, S. et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol. Cell 38, 576–589 (2010).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bailey, T. L. STREME: accurate and versatile sequence motif discovery. Bioinformatics 37, 2834–2840 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Niehrs, C. & Luke, B. Regulatory R-loops as facilitators of gene expression and genome stability. Nat. Rev. Mol. Cell Biol. 21, 167–178 (2020).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Gartlgruber, M. et al. Super enhancers define regulatory subtypes and cell identity in neuroblastoma. Nat. Cancer 2, 114–128 (2021).

Article  CAS  PubMed  Google Scholar 

Debruyne, D. N. et al. BORIS promotes chromatin regulatory interactions in treatment-resistant cancer cells. Nature 572, 676–680 (2019).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Langmead, B., Trapnell, C., Pop, M. & Salzberg, S. L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).

Article  PubMed  PubMed Central  Google Scholar 

Feng, J., Liu, T., Qin, B., Zhang, Y. & Liu, X. S. Identifying ChIP-seq enrichment using MACS. Nat. Protoc. 7, 1728–1740 (2012).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Luo, H. et al. HOTTIP lncRNA promotes hematopoietic stem cell self-renewal leading to AML-like disease in mice. Cancer Cell 36, 645–659 (2019).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Issler, O. et al. Sex-specific role for the long non-coding RNA LINC00473 in depression. Neuron 106, 912–926.e5 (2020).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Powell, W. T. et al. A Prader–Willi locus lncRNA cloud modulates diurnal genes and energy expenditure. Hum. Mol. Genet. 22, 4318–4328 (2013).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Li, M. A. et al. A lncRNA fine tunes the dynamics of a cell state transition involving Lin28, let-7 and de novo DNA methylation. eLife 6, e23468 (2017).

Article  PubMed  PubMed Central  Google Scholar 

Yin, Y. et al. Opposing roles for the lncRNA Haunt and its genomic locus in regulating HOXA gene activation during embryonic stem cell differentiation. Cell Stem Cell 16, 504–516 (2015).

Article  CAS  PubMed  Google Scholar 

Maldotti, M. et al. The acetyltransferase p300 is recruited in trans to multiple enhancer sites by lncSmad7. Nucleic Acids Res. 50, 2587–2602 (2022).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Chakraborty, D. et al. LncRNA Panct1 maintains mouse embryonic stem cell identity by regulating TOBF1 recruitment to Oct–Sox sequences in early G1. Cell Rep. 21, 3012–3021 (2017).

Article  CAS  PubMed  Google Scholar 

Amemiya, H. M., Kundaje, A. & Boyle, A. P. The ENCODE Blacklist: identification of problematic regions of the genome. Sci. Rep. 9, 9354 (2019).

Article  PubMed  PubMed Central  Google Scholar