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. 2023 Feb 7;22:27. doi: 10.1186/s12943-023-01724-y

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© The Author(s) 2023

Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

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Fig. 2 — The mechanisms of chromatin-associated noncoding RNAs in gene regulation. A and B Chromatin-associated lncRNAs directly interact with DNA. A Antisense lncRNA TARID directly binds to the TCF21 promoter and is recognized by GADD45A and subsequent TET1, which results in DNA demethylation and TCF21 expression. B LncRNA TERRA with a specific sequence forms R-loops in telomeres and is recognized by RAD51, leading to telomere fragility. C-E Chromatin-associated lncRNAs indirectly interact with DNA or chromatin. C LncRNAs bind U1 snRNP to form a complex, which regulates transcription through RNA Pol II both in cis and trans. D LncRNA Rewind can recruit G9a to Wnt7b chromatin, leading to H3K9me2 deposition and gene repression. E Xist can bind many proteins, such as SPEN, hnRNP K, PRC1 and PRC2, to mediate transcriptional silencing, which is involved in the initiation, construction and spread of X-chromosome inactivation. F and G Chromatin-associated circRNAs directly or indirectly interact with DNA. F EIciRNAs within specific sequences interact with U1 snRNP at promoters and increase gene expression in cis. G CircRNA ci-ankrd52 forms R-loops by directly inserting DNA double strands, which will inhibit transcription, while RNase H1 can resolve R-loops and disarm the transcriptional inhibition effect. TCF21, transcription Factor 21; GADD45A, growth arrest and DNA damage inducible alpha; TET1, tet methylcytosine dioxygenase 1; TCF21, transcription factor 21; hnRNP K, heterogeneous nuclear ribonucleoprotein K