CELF1 preferentially binds to exon-intron boundary and regulates alternative splicing in HeLa cells

Xia, Heng; Chen, Dong; Wu, Qinghua; Wu, Gang; Zhou, Yanhong; Zhang, Yi; Zhang, Libin

doi:10.1016/j.bbagrm.2017.07.004

Cited by 119 publications

(121 citation statements)

References 61 publications

Supporting

Mentioning

121

Contrasting

Order By: Relevance

“…After we aligned reads onto the genome, only uniquely mapped reads were applied for the following analysis. “ABLIRC” strategy was applied to identify the binding regions of TTP on genome ( Xia et al, 2017 ). At least 1 bp overlapped reads were clustered as peaks.…”

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

IGF2BP3 May Contributes to Lung Tumorigenesis by Regulating the Alternative Splicing of PKM

Huang

Zhang

Jiang

et al. 2020

Front. Bioeng. Biotechnol.

View full text Add to dashboard Cite

RNA binding proteins (RBPs) play a key role in genome regulation. Here we report the post-transcript regulation of IGF2BP3, which belongs to the insulin-like growth factor 2 mRNA binding protein family. We used iRIP-seq and RNA-seq to analyze the transcript regulation and alternative splicing on IGF2BP3 treated with overexpression cells and control. Overexpressed IGF2BP3 has broadly increased genes expression which involved in G-protein coupled receptor signaling pathway, positive regulation of cell proliferation, and signal transduction. IGF2BP3 regulated alternative splicing of multiple genes mainly clustered at response to hypoxia, negative regulation of transcription, and embryonic development. This study first provides alternative splicing analysis on transcription level of IGF2BP3 regulation, which laid the foundation for later research on IGF2BP3 critical functions.

show abstract

Section: Methodsmentioning

confidence: 99%

“…As described previously, the ABLas pipeline ( Jin et al, 2017 ; Xia et al, 2017 ) was used to define and quantify the ASEs (alternative splicing events) and RASEs (regulated alternative splicing events) between the samples. In short, detection of seven types of canonical ASEs in each sample was on the basis of the splice junction reads.…”

Section: Methodsmentioning

confidence: 99%

IGF2BP3 May Contributes to Lung Tumorigenesis by Regulating the Alternative Splicing of PKM

Huang

Zhang

Jiang

et al. 2020

Front. Bioeng. Biotechnol.

View full text Add to dashboard Cite

show abstract

“…AS analysis. The AS analysis was performed using the ABLas pipeline, as previously described (21,22). ABLas detects 10 types of alternative splicing events (ASEs) based on the splice junction reads and uniquely mapped reads.…”

Section: Rna-seq and Differentially Expressed Gene (Deg) Analysismentioning

confidence: 99%

Filamin B extensively regulates transcription and alternative splicing, and is associated with apoptosis in HeLa cells

Cao

Wang

et al. 2020

Oncol Rep

View full text Add to dashboard Cite

Post-transcriptional mechanisms are an important approach in the treatment of cancer, and may also be hijacked by tumor cells to help adapt to the local microenvironment. Filamin B (FLNB), an actin-binding protein that provides crucial scaffolds for cell motility and signaling, has also been identified as an RNA-binding protein. Recent studies demonstrated that FLNB might play an important role, not only in skeletal development, but also in regulating tumorigenesis; however, the effects of dysregulated expression of FLNB at the molecular level are not clear. In the present study, RNA-sequencing was performed to analyze changes in overall transcriptional and alternative splicing between the knocked-down FLNB and the control in HeLa cells. Decreased FLNB levels resulted in significantly lower apoptosis compared with control cells. FLNB knockdown extensively regulated the expression of genes in cell apoptosis, tumorigenesis, metastases, transmembrane transport and cartilage development. Moreover, FLNB regulated alternative splicing of a large number of genes involved in 'cell death' and the 'apoptotic process'. Some genes and alternative splicing related to skeletal development were enriched and regulated by FLNB. Reverse transcription-quantitative-PCR identified FLNB-regulated transcription and alternative splicing of genes, such as NLR family apoptosis inhibitory protein, interleukin 23 subunit α, metastasis associated lung adenocarcinoma transcript 1, phosphofurin acidic cluster sorting protein 2, bone morphogenetic protein 7, matrix metallopeptidase 13, collagen type II α 1 chain, fibroblast growth factor receptor 2 and vitamin D receptor. The present study is the first study, to the best of the authors' knowledge, to provide transcriptome-wide analysis of differential gene expression and alternative splicing upon FLNB silencing. The present results suggested that FLNB may play an important regulatory role in cervical cancer cell apoptosis via regulation of transcription and alternative splicing, which provide insight for the current understanding of the mechanisms of FLNB-mediated gene regulation.

show abstract

“…It is involved in energy homeostasis transition in adipose tissue [34]. Controls alternative splicing in human cells [35]. Participates in microRNA destabilization [36].…”

Section: Resultsmentioning

confidence: 99%

Untitled

2017

Biopolym. Cell

View full text Add to dashboard Cite

To identify novel protein partners of translation factor eEF1Bβ in nucleus of human lung carcinoma cells. Methods. Protein partners of eEF1Bβ in the nuclear fraction of A549 cells were identified by co-immunoprecipitation (co-IP) combined with liquid chromatographytandem mass spectrometry (LC-MS/MS). Specific protein partners of eEF1Bβ were further selected by using the results of previously published global, quantitative and dynamic mapping of protein subcellular localization with help of "Mapofthecell" program. Results. 104 highscored proteins interacting with eEF1Bβ in the nuclear fraction of A549 cells have been identified by mass-spectrometry. Among these proteins, 9 partners of eEF1Bβ were confirmed by the co-fractionation approach. Functional analysis of the partners has divided them on the pro-oncogenic (lung-cancer related) and neutral/anti-oncogenic moieties. These two groups are estimated to be spatially separated in human cancer cells. Conclusions. The position of eEF1Bβ as a link between the oncogenic and neutral/tumor-suppressor moieties of its protein partners in nucleus of lung cancer cells is suggested. Deciphering of a possible role of the eEF1Bβ distribution between the pro-cancer or anti-cancer communities of its protein partners can be a subject of further research.

show abstract

CELF1 preferentially binds to exon-intron boundary and regulates alternative splicing in HeLa cells

Cited by 119 publications

References 61 publications

IGF2BP3 May Contributes to Lung Tumorigenesis by Regulating the Alternative Splicing of PKM

IGF2BP3 May Contributes to Lung Tumorigenesis by Regulating the Alternative Splicing of PKM

Filamin B extensively regulates transcription and alternative splicing, and is associated with apoptosis in HeLa cells

Untitled

Contact Info

Product

Resources

About