Tristetraprolin-RNA interaction map reveals a novel TTP-RelB regulatory network for innate immunity gene expression

Tu, Yue; Wu, Xiongfei; Yu, Fengyun; Dang, Jianzhong; Wei, Yaxun; Yu, Han; Liao, Wenbiao; Zhang, Yi; Wang, Juan

doi:10.1016/j.molimm.2020.02.004

Cited by 17 publications

(14 citation statements)

References 61 publications

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“…The primer sequences were as follows: Forward, 5′-AGCCCGGGCGGATCCGAATTCATGCCGCGCGTCTACATAGG-3′ and reverse, 5′-GTCATCCTTGTAGTCCTCGAGATCTCTGGAACTCGACCTGGACC-3′. The SRSF6-overexpressing plasmid was constructed and HeLa cells were transfected with SRSF6-overexpressing plasmid and empty plasmid as described in a previous study by our group ( 37 ).…”

Section: Methodsmentioning

confidence: 99%

SRSF6 regulates alternative splicing of genes involved in DNA damage response and DNA repair in HeLa cells

et al. 2020

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Section: Methodsmentioning

confidence: 99%

SRSF6 regulates alternative splicing of genes involved in DNA damage response and DNA repair in HeLa cells

et al. 2020

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“…Previous study provided evidence that CELF1 associated to the 5'-UTR of human p27 mRNA and suppressed expression of p27 [14]; CELF1 was also inclined to binding with 3'UTR and intron regions of mRNA and further globally changed alternative splicing and translation of multiple genes [11,28]. Recently, an investigation revealed that Tristeraprolin (TTP) peaks were enriched in CELF1 binding motifs indicating that TTP might cooperate with other RBPs to participate in multiple post-transcriptional process [41]. While, in the current study, we did not nd any obvious CELF1 peaks enriched on proteolysis-related genes.…”

Section: Discussionmentioning

confidence: 99%

CELF1 Promotes Matrix Metalloproteinases Gene Expression at Transcriptional Level in Lens Epithelial Cells

Xiao

Tian

Jin

et al. 2021

Preprint

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Background: RNA binding proteins (RBPs)-mediated regulation plays important roles in many eye diseases, including the canonical RBP CELF1 in cataract. While the definite molecular regulatory mechanisms of CELF1 on cataract still remain elusive. Methods: In this study, we overexpressed CELF1 in lens epithelial SRA01/04 cells and applied whole transcriptome sequencing (RNA-seq) method to analyze the global differences mediated by CELF1. We then analyzed public RNA-seq and CELF1-RNA interactome data to decipher the underlying mechanisms.Results: The results showed that transcriptome profile was globally changed by CELF1 overexpression (CELF1-OE). Functional analysis revealed CELF1 specifically increased the expression of genes in extracellular matrix disassembly, extracellular matrix organization, and proteolysis, which could be classified into matrix metalloproteinases (MMPs) family. This finding was also validated by RT-qPCR and public mouse early embryonic lens data. Integrating analysis with public CELF1-RNA interactome data revealed that no obvious CELF1-binding peak was found on the transcripts of these genes, indicating an indirectly regulatory role of CELF1 in lens epithelial cells. Conclusions: Our study demonstrated that CELF1-OE promotes transcriptional level of MMP genes; and this regulation may be completed by other ways except for binding to RNA targets. These results suggest that CELF1-OE is implicated in the development of lens, which is associated with cataract and expands our understanding of CELF1 regulatory roles as an RNA binding protein.

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“…‘ABLIRC’ strategy was used to identify the RNA‐binding sites for LGALS1 as previously described [23,25]. Briefly, reads with at least 1‐bp overlap were clustered as candidate peaks first.…”

Section: Methodsmentioning

confidence: 99%

“…The experiments were performed as previously described [23] (ABLife, Wuhan, China). RNAs associated with LGALS1 were isolated from the anti‐FLAG immunoprecipitates using TRIzol (Invitrogen).…”

Section: Methodsmentioning

confidence: 99%

“…We have recently developed iRIP‐seq technology to study protein–RNA interaction. UV cross‐linking of cellular protein–RNA interactions, RNase digestion of naked RNA regions, and immunoprecipitation of the protein–RNA complex were utilized in iRIP‐seq to capture the RNA–protein complex comprising direct and indirect RNA–protein interactions, followed by RNA isolation, cDNA library construction, and Illumina sequencing steps [22,23]. Results showed that galectin‐1 binds to a large population of mRNAs and pre‐mRNAs that are enriched in angiogenesis genes, including VEGFA.…”

mentioning

confidence: 99%

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Galectin‐1–RNA interaction map reveals potential regulatory roles in angiogenesis

Wei

Cheng

et al. 2021

FEBS Letters

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Hyperactive angiogenesis contributes to the immunosuppressive microenvironment important for immunotherapy. Galectin‐1, encoded by LGALS1, can trigger the vascular signaling programs and mediate the anti‐angiogenic treatment response. However, the mechanism through which galectin‐1 regulates angiogenesis is poorly understood. It has been suggested that galectin‐1 may associate with mRNAs in cells. This study applied the iRIP‐seq methodology to study the potential role of galectin‐1 as an RNA‐binding protein. We found that galectin‐1 interacts with a large number of mRNAs, with a preference for binding near stop codons and a preference for UGCA/UGGA and GAGCAG as binding motifs. Galectin‐1 binds to the mRNAs of angiogenesis‐associated genes including VEGFA, EGR1, and LAMA5, suggesting that galectin‐1 may regulate angiogenesis via its mRNA‐binding activity. We further show that shLGALS1 inhibits capillary tube formation in an in vitro angiogenesis assay and alters the expression levels of several galectin‐1‐bound angiogenesis‐associated mRNAs. These results uncover a previously unrecognized mRNA‐binding activity of galectin‐1.

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Tristetraprolin-RNA interaction map reveals a novel TTP-RelB regulatory network for innate immunity gene expression

Cited by 17 publications

References 61 publications

SRSF6 regulates alternative splicing of genes involved in DNA damage response and DNA repair in HeLa cells

SRSF6 regulates alternative splicing of genes involved in DNA damage response and DNA repair in HeLa cells

CELF1 Promotes Matrix Metalloproteinases Gene Expression at Transcriptional Level in Lens Epithelial Cells

Galectin‐1–RNA interaction map reveals potential regulatory roles in angiogenesis

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