Trans- and cis-acting effects of Firre on epigenetic features of the inactive X chromosome

He, Fang; Bonora, Giancarlo; Lewandowski, Jordan P.; Thakur, Jitendra; Filippova, Galina N.; Henikoff, Steven; Shendure, Jay; Duan, Zhijun; Rinn, John L.; Deng, Xinxian; Noble, William Stafford; Distèche, Christine M.

doi:10.1038/s41467-020-19879-3

Cited by 42 publications

(31 citation statements)

References 100 publications

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“…Their dynamic chromatin enrichment patterns might be associated with their roles in regulating gene expression during the cell fate transition. For example, chromatin associated lncRNA XIST in cis regulates X chromosome inactivity over long genomic distance; and chromatin associated lncRNA FIRRE has both trans - and cis -acting effects on epigenetic features [ 54 ]. In addition, the dissociation of lncRNAs from chromatin is also important for their regulatory roles, such as lncRNA A-ROD was shown to enhance its upstream gene DKK1 transcription at its release from chromatin [ 55 ].…”

Section: Discussionmentioning

confidence: 99%

Genome-wide analysis and functional annotation of chromatin-enriched noncoding RNAs in rice during somatic cell regeneration

et al. 2022

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Background Plants have the remarkable ability to generate callus, a pluripotent cell mass that acquires competence for subsequent tissue regeneration. Global chromatin remodeling is required for this cell fate transition, but how the process is regulated is not fully understood. Chromatin-enriched noncoding RNAs (cheRNAs) are thought to play important roles in maintaining chromatin state. However, whether cheRNAs participate in somatic cell regeneration in plants has not yet been clarified. Results To uncover the characteristics and functions of cheRNAs during somatic cell reprogramming in plants, we systematically investigate cheRNAs during callus induction, proliferation and regeneration in rice. We identify 2284 cheRNAs, most of which are novel long non-coding RNAs or small nucleolar RNAs. These cheRNAs, which are highly conserved across plant species, shuttle between chromatin and the nucleoplasm during somatic cell regeneration. They positively regulate the expression of neighboring genes via specific RNA motifs, which may interact with DNA motifs around cheRNA loci. Large-scale mutant analysis shows that cheRNAs are associated with plant size and seed morphology. Further detailed functional investigation of two che-lncRNAs demonstrates that their loss of function impairs cell dedifferentiation and plant regeneration, highlighting the functions of cheRNAs in regulating the expression of neighboring genes via specific motifs. These findings support cis- regulatory roles of cheRNAs in influencing a variety of rice traits. Conclusions cheRNAs are a distinct subclass of regulatory non-coding RNAs that are required for somatic cell regeneration and regulate rice traits. Targeting cheRNAs has great potential for crop trait improvement and breeding in future.

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Section: Discussionmentioning

confidence: 99%

Genome-wide analysis and functional annotation of chromatin-enriched noncoding RNAs in rice during somatic cell regeneration

et al. 2022

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“…[18][19][20][21] Cis-regulation has been extensively studied in the regulatory function of lncRNAs on nearby genes to govern cell fate. [22][23][24] Therefore, we explored the nearest PCG, ARRDC3, which was 54 kilobytes away from LUCAT1. However, ARRDC3 expression had no change when LUCAT1 was knocked down or overexpressed (Figures S6E-S6H), which suggested that LU-CAT1 might not regulate the expression of apoptosis-related proteins through the cis-pathway.…”

Section: Lucat1 Regulates Foxq1 Expression In a Jmjd6-dependent Mannermentioning

confidence: 99%

Long noncoding RNA LUCAT1 enhances the survival and therapeutic effects of mesenchymal stromal cells post-myocardial infarction

Yue

Liu

et al. 2022

Molecular Therapy - Nucleic Acids

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Mesenchymal stromal cell (MSC) transplantation has been a promising therapeutic strategy for repairing heart tissues post-myocardial infarction (MI). Nevertheless, its therapeutic efficacy remains low, which is mainly ascribed to the low viability of transplanted MSCs. Recently, long noncoding RNAs (lncRNAs) have been reported to participate in diverse physiological and pathological processes, but little is known about their role in MSC survival. Using unbiased transcriptome profiling of hypoxia-preconditioned MSCs (HP-MSCs) and normoxic MSCs (N-MSCs), we identified a lncRNA named lung cancer-associated transcript 1 (LUCAT1) under hypoxia. LUCAT1 knockdown reduced the survival of engrafted MSCs and decreased the MSC-based therapeutic potency, as shown by impaired cardiac function, reduced cardiomyocyte survival, and increased fibrosis post-MI. Conversely, LUCAT1 overexpression had the opposite results. Mechanistically, LUCAT1 bound with and recruited jumonji domain-containing 6 (JMJD6) to the promoter of forkhead box Q1 (FOXQ1), which demethylated FOXQ1 at H4R3me 2(s) and H3R2me 2(a) , thus downregulating Bax expression and upregulating Bcl-2 expression to attenuate MSC apoptosis. Therefore, our findings revealed the protective effects of LUCAT1 on MSC apoptosis and demonstrated that the LUCAT1-mediated JMJD6-FOXQ1 pathway might represent a novel target to potentiate the therapeutic effect of MSC-based therapy for ischemic cardiovascular diseases.

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“…FIRRE forms “RNA clouds” in the nucleus, binds the nuclear matrix protein HNRNPU (heterogeneous nuclear ribonucleoprotein U), and serves as a platform for trans-chromosomal associations [ 63 ]. FIRRE is transcribed from the active X chromosome and acts in trans and cis to maintain X chromosome inactivation [ 64 ]. No reports of FIRRE/LNC01200 in BC were located in PubMed.…”

Section: Resultsmentioning

confidence: 99%

Identification and Roles of miR-29b-1-3p and miR29a-3p-Regulated and Non-Regulated lncRNAs in Endocrine-Sensitive and Resistant Breast Cancer Cells

Muluhngwi

Klinge

2021

Cancers

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Despite improvements in the treatment of endocrine-resistant metastatic disease using combination therapies in patients with estrogen receptor α (ERα) primary tumors, the mechanisms underlying endocrine resistance remain to be elucidated. Non-coding RNAs (ncRNAs), including microRNAs (miRNA) and long non-coding RNAs (lncRNA), are targets and regulators of cell signaling pathways and their exosomal transport may contribute to metastasis. Previous studies have shown that a low expression of miR-29a-3p and miR-29b-3p is associated with lower overall breast cancer survival before 150 mos. Transient, modest overexpression of miR-29b1-3p or miR-29a-3p inhibited MCF-7 tamoxifen-sensitive and LCC9 tamoxifen-resistant cell proliferation. Here, we identify miR-29b-1/a-regulated and non-regulated differentially expressed lncRNAs in MCF-7 and LCC9 cells using next-generation RNA seq. More lncRNAs were miR-29b-1/a-regulated in LCC9 cells than in MCF-7 cells, including DANCR, GAS5, DSCAM-AS1, SNHG5, and CRND. We examined the roles of miR-29-regulated and differentially expressed lncRNAs in endocrine-resistant breast cancer, including putative and proven targets and expression patterns in survival analysis using the KM Plotter and TCGA databases. This study provides new insights into lncRNAs in endocrine-resistant breast cancer.

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Trans- and cis-acting effects of Firre on epigenetic features of the inactive X chromosome

Cited by 42 publications

References 100 publications

Genome-wide analysis and functional annotation of chromatin-enriched noncoding RNAs in rice during somatic cell regeneration

Genome-wide analysis and functional annotation of chromatin-enriched noncoding RNAs in rice during somatic cell regeneration

Long noncoding RNA LUCAT1 enhances the survival and therapeutic effects of mesenchymal stromal cells post-myocardial infarction

Identification and Roles of miR-29b-1-3p and miR29a-3p-Regulated and Non-Regulated lncRNAs in Endocrine-Sensitive and Resistant Breast Cancer Cells

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