The chromatin-associated RNAs in gene regulation and cancer

Abstract

Eukaryotic genomes are prevalently transcribed into many types of RNAs that translate into proteins or execute gene regulatory functions. Many RNAs associate with chromatin directly or indirectly and are called chromatin-associated RNAs (caRNAs). To date, caRNAs have been found to be involved in gene and transcriptional regulation through multiple mechanisms and have important roles in different types of cancers. In this review, we first present different categories of caRNAs and the modes of interaction between caRNAs and chromatin. We then detail the mechanisms of chromatin-associated nascent RNAs, chromatin-associated noncoding RNAs and emerging m⁶A on caRNAs in transcription and gene regulation. Finally, we discuss the roles of caRNAs in cancer as well as epigenetic and epitranscriptomic mechanisms contributing to cancer, which could provide insights into the relationship between different caRNAs and cancer, as well as tumor treatment and intervention.

Keywords: CaRNAs; Cancer; Gene regulation; R-loops; RNA modification; ncRNAs.

Fig. 1

Chromatin-associated nascent RNAs in transcriptional regulation. A Nascent caRNAs can form R-loops at promoter, enhancer and termination regions, especially with G4 structures. The promoter region R-loops and terminator region R-loops can contribute to transcription pausing and termination in cis, respectively. R-loop formation facilitates antisense lncRNA transcription. Nascent eRNAs can act in trans to participate in promoter R-loop formation and gene regulation. B Nascent caRNAs can cooperate with epigenetic factors to regulate gene expression. Nascent caRNAs recruit PCR2 to inactive gene regions and promote H3K27me3 spreading, while in active gene regions, nascent caRNAs can continuously evict PRC2 from chromatin. CaRNAs, Chromatin-associated RNAs; G4, G-quadruplex; PRC2, Polycomb repressive complex 2

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

Fig. 3

m⁶A on caRNAs regulates transcription and gene expression. A The m⁶A methyltransferase complex can recognize m⁶A on nascent RNAs (nascent eRNAs, upstream promoter RNAs, etc.) to ensure mRNA transcription while inhibiting premature termination by the integrator complex. Moreover, Xist-mediated X chromosome gene silencing requires m⁶A modification and YTHDC1 reorganization. B m⁶A on caRNAs crosstalk with epigenetics in gene regulation. m6A on carRNAs such as eRNAs and repeat RNAs can be recognized by YTHDC1 and NEXT, resulting in carRNA degradation, while demethylated carRNAs recruit histone modifiers and the TF YY1 to activate transcription. The m⁶A eraser FTO and reader YTHDC1 both play important roles in repeat RNA LINE1-mediated gene repression, and FTO depletion causes higher m⁶A levels of LINE1 and leads to recruitment of YTHDC1, which not only recruits the NEXT complex to accelerate LINE1 decay but also recruits SETDB1 and cooperating proteins to deposit the repressive histone mark H3K9me3. However, YTHDC1-recruited KDM3B can decrease the H3K9me2 level to promote gene expression. m6A, N6-methyladenosine; YTHDC1, YTH domain containing 1; CarRNAs, Chromatin-associated regulatory RNAs; NEXT, Nuclear exosome targeting; LINE1, Long interspersed nuclear elements 1; ERNAs Enhancer RNAs; YY1, Yin Yang 1; SETDB1, SET domain bifurcated histone lysine methyltransferase 1

Fig. 4

CaRNAs form R-loops and the m⁶A modification on caRNAs in cancer. A The accumulation of R-loops resulted in genomic instability, and DNA damage has dual roles in cancer. The deletion of the DNA damage response protein RNF168 or transcription coactivator BRD4 blocks the unwinding of DNA and RNA heterozygous strands on the genome, leading to the accumulation of R-loops on the cancer cell genome and tumor repression. The BRD4 inhibitor JQ1 can also lead to similar accumulation of R-loops. Mutation of the tumor suppressor DDX41 causes aberrant R-loop accumulation, and genomic instability stimulates the inflammatory response and AML progression. Similarly, lncRNA HOTTIP-formed R-loops can recruit the CTCF/cohesin complex at TAD boundaries, which promotes Wnt/β-catenin transcription and accelerates leukemogenesis as well as AML development. B ALKBH5 can specifically decrease the level of m⁶A in the 3’UTR of FOXM1 pre-mRNA, while As-FOXM1 promotes the interaction between ALKBH5 and FOXM1 pre-mRNA, which increases FOXM1 expression as well as GSC self-renewal and tumorigenesis. Similarly, As-ARHGAP5 can not only promote the transcription of ARHGAP5 but also induce METTL3 to deposit m⁶A modifications on ARHGAP5 mRNA, increasing the stability of ARHGAP5 mRNA in the cytoplasm and promoting the chemotherapy resistance of gastric cancer. Notably, HuR is involved in mRNA regulation in both the nucleus and cytoplasm. Another lncRNA, LCAT3, can be directly recognized by METTL3 and modified by m⁶A to increase stability and be upregulated, then it can bind to the far upstream elements of MYC together with FUBP1, leading to MYC activation and proliferation, invasion and metastasis of lung cancer cells. RNF168, Ring Finger Protein 168; BRD4, Bromodomain Containing 4; ELAVL1/HuR, ELAV Like RNA Binding Protein 1; DDX41, Dead box helicase 41; AML, Acute myeloid leukemia; TAD, Topologically associated domain; ALKBH5, AlkB Homolog 5; METTL3, Methyltransferase like 3; FOXM1, Forkhead Box M1; ARHGAP5, Rho GTPase Activating Protein 5; LCAT3, Lung Cancer Associated Transcript 3; FUBP1, Far Upstream Element Binding Protein 1

Fig. 5

Chromatin-associated noncoding RNAs in cancer. ncRNAs have dual roles in cancer by interacting with intranuclear TFs, epigenetic regulators, transcriptional coactivators and DNA/RNA helicases on chromatin. A Chromatin-associated ncRNAs contribute to tumor progression. LncRNA MaTAR2 recruits the transcriptional coactivator PURB at the Tensin1 promoter to promote transcription and BC proliferation, invasion and migration. LncRNA BlackMamba can bind and recruit LSH to the promoter regions of tumor migration-related genes such as Regulator of G Protein Signaling 1 (RGS1), Thymus and activation-regulated chemokine (TARC), P21 (RAC1) Activated Kinase 2 (PAK2) and Potassium Calcium-Activated Channel Subfamily M Alpha 1 (KCNMA1) to promote transcription and ultimately maintain the ALCL phenotype and growth. CircIPO11 recruits TOP1 to the GLI1 promoter to activate transcription and promotes the self-renewal of liver CSCs. At the chromatin level, lncRNA LINC00839 recruits the transcriptional activator Ruvb1/KAT5 complex to the NRF1 promoter to deposit activating histone marks H4K5ac and H4K8ac and promote OXPHOS and CRC processes. Some caRNAs can also recruit repressive histone marks. lncRNA FOXD2-AS1 can induce EZH2 to the CDKN1B promoter and construct H3K27me3 to silence CDKN1B, leading to HCC proliferation. Similarly, lncRNA Linc-ASEN can interact with the UPF1-PRC1/PRC2 complex to silence p21 and delay tumor cell senescence. B Chromatin-associated ncRNAs inhibit tumor progression. LINC-PINT recruits PRC2 to the EGR1 and ITGA3 gene loci and induces their silencing, which ultimately inhibits tumor migration. CircMRPS35 recruits KAT7 to the FOXO1 and FOXO3a promoters, leading to upregulation of p21 and p27 and downregulation of Twist1 and E-cadherin, thereby inhibiting GC proliferation and invasion. CircGSK3B can directly bind EZH2 to block its deposition on the RORA promoter, which causes the upregulation of RORA and finally inhibits GC progression. CircNCOR1 recruits hnRNPL to the SMAD7 promoter, promoting SMAD7 transcription and inhibiting the TGFβ/SMAD signaling pathway, which ultimately inhibits BC growth and lymph node metastasis. However, the SUMOylated DDX39B-mediated abnormal export of circNCOR1 from the nucleus to the cytoplasm weakens the tumor-inhibiting effect of circNCOR1. PURB, Purine rich element binding protein B; NRF1, Nuclear Respiratory Factor 1; CRC, Colorectal cancer; OXPHOS, Oxidative phosphorylation; RGS1, Regulator of G Protein Signaling 1; CCL17, Thymus and activation-regulated chemokine, TARC; PAK2, P21 (RAC1) Activated Kinase 2; KCNMA1, Potassium Calcium-Activated Channel Subfamily M Alpha 1; ALCL, Anaplastic large cell lymphoma; LSH, ymphoid-specific helicase; EZH2, Enhancer of zeste homolog 2; CDKN1B, Cyclin Dependent Kinase Inhibitor 1B; EGR1, Early Growth Response 1; ITGA3, Integrin alpha 3; TOP1, Topoisomerase 1; GLI1, GLI Family Zinc Finger 1; CSCs, Cancer stem cells; HCC, Hepatocellular carcinoma; KAT7, Lysine Acetyltransferase 7; Twist1, Twist Family BHLH Transcription Factor 1; GC, Gastric cancer