Position-dependent alternative splicing activity revealed by global profiling of alternative splicing events regulated by PTB

Llorian, Miriam; Schwartz, Schraga; Clark, Tyson A.; Hollander, Dror; Tan, Lit-Yeen; Spellman, Rachel; Gordon, Adele; Schweitzer, Anthony; Grange, Pierre de la; Ast, Gil; Smith, Christopher W.

doi:10.1038/nsmb.1881

Cited by 234 publications

(352 citation statements)

References 65 publications

Supporting

Mentioning

292

Contrasting

Order By: Relevance

“…Llorian et al identified splicing events in 210 genes controlled by PTBP1 in HeLa cells (Llorian et al, 2010). We could identify the Xenopus orthologues of 114 out of these 210 genes based on gene names ( Figure 3A, Table ST4).…”

Section: Compared Performances Of the Exon-centric And The Junction-cmentioning

confidence: 95%

“…We classified the 114 Xenopus genes as True Positive (TP) when at least one (Llorian et al, 2010). We classified the 114 Xenopus genes as True Positive (TP) when at least one differential exon or junction was identified in our experiments, and as False Negative (FN) when no differential exon or junction was identified.…”

Section: Figure Legends Figure 1 Comparison Of Exon-centric and Juncmentioning

confidence: 99%

“…Bed files listing differentially used junction and exon were generated for visualization in IGV. To analyze the performance of our approaches we chose an available positive dataset of genes with splicing events regulated by PTBP1 and experimentally identified in Human HeLa cells (Llorian et al, 2010). Among the 210 human genes with PTBP1-regulated splicing, 114 have identified orthologues in the Xenopus genome.…”

Section: Library Preparation Mapping and Differential Analysis Of Xementioning

confidence: 99%

“…For the 210 genes with PTBP1-controlled splicing events in HeLa cells (Llorian et al, 2010), we indicate if one orthologue exists in Xenopus laevis annotation (based on identical gene name).…”

Section: Supplemental Table 4 (Csv)mentioning

confidence: 99%

“…We analysed statistically the data with DEXSeq to identify differential junctions, differential exons, (Llorian et al, 2010). We classified the 114 Xenopus genes as True Positive (TP) when at least one (Llorian et al, 2010).…”

Section: Figure Legends Figure 1 Comparison Of Exon-centric and Juncmentioning

confidence: 99%

See 4 more Smart Citations

Robust identification of Ptbp1-dependent splicing events by a junction-centric approach in Xenopus laevis

Noiret

Méreau

Angrand

et al. 2017

Developmental Biology

View full text Add to dashboard Cite

Down-regulation of Ptbp1, a regulatory RNA-binding protein, leads to developmental skin defects in Xenopus laevis. To identify Ptbp1-dependent splicing events potentially related to the phenotype, we conducted RNAseq experiments following Ptbp1 depletion. We systematically compared exoncentric and junction-centric approaches to detect differential splicing events. We showed that the junction-centric approach performs far better than the exon-centric approach in Xenopus laevis. We carried out the same comparisons using simulated data in human, which led us to propose that the better performances of the junction-centric approach in Xenopus laevis essentially relies on an incomplete exonic annotation associated with a correct transcription unit annotation. We assessed the capacity of the exon-centric and junction-centric approaches to retrieve known and to discover new Ptbp1-dependent splicing events. Notably, the junction-centric approach identified Ptbp1-controlled exons in agfg1, itga6, actn4, and tpm4 mRNAs, which were independently confirmed.We conclude that the junction-centric approach allows for a more complete and informative description of splicing events, and we propose that this finding might hold true for other species with incomplete annotations.

show abstract

Section: Compared Performances Of the Exon-centric And The Junction-cmentioning

confidence: 95%

Section: Figure Legends Figure 1 Comparison Of Exon-centric and Juncmentioning

confidence: 99%

Section: Library Preparation Mapping and Differential Analysis Of Xementioning

confidence: 99%

Section: Supplemental Table 4 (Csv)mentioning

confidence: 99%

Section: Figure Legends Figure 1 Comparison Of Exon-centric and Juncmentioning

confidence: 99%

See 3 more Smart Citations

Robust identification of Ptbp1-dependent splicing events by a junction-centric approach in Xenopus laevis

Noiret

Méreau

Angrand

et al. 2017

Developmental Biology

View full text Add to dashboard Cite

show abstract

Transcriptomic profile analysis of mouse neural tube development by RNA‐Seq

Guo

et al. 2017

IUBMB Life

View full text Add to dashboard Cite

The neural tube is the primordium of the central nervous system (CNS) in which its development is not entirely clear. Understanding the cellular and molecular basis of neural tube development could, therefore, provide vital clues to the mechanism of neural tube defects (NTDs). Here, we investigated the gene expression profiles of three different time points (embryonic day (E) 8.5, 9.5 and 10.5) of mouse neural tube by using RNA-seq approach. About 391 differentially expressed genes (DEGs) were screened during mouse neural tube development, including 45 DEGs involved in CNS development, among which Bmp2, Ascl1, Olig2, Lhx1, Wnt7b and Eomes might play the important roles. Of 45 DEGs, Foxp2, Eomes, Hoxb3, Gpr56, Hap1, Nkx2-1, Sez6l2, Wnt7b, Tbx20, Nfib, Cntn1 and Dcx had different isoforms, and the opposite expression pattern of different isoforms was observed for Gpr56, Nkx2-1 and Sez6l2. In addition, alternative splicing, such as mutually exclusive exon, retained intron, skipped exon and alternative 3' splice site was identified in 10 neural related differentially splicing genes, including Ngrn, Ddr1, Dctn1, Dnmt3b, Ect2, Map2, Mbnl1, Meis2, Vcan and App. Moreover, seven neural splicing factors, such as Nova1/2, nSR100/Srrm4, Elavl3/4, Celf3 and Rbfox1 were differentially expressed during mouse neural tube development. Interestingly, nine DEGs identified above were dysregulated in retinoic acid-induced NTDs model, indicating the possible important role of these genes in NTDs. Taken together, our study provides more comprehensive information on mouse neural tube development, which might provide new insights on NTDs occurrence. © 2017 IUBMB Life, 69(9):706-719, 2017.

show abstract

PTBP1 promotes the growth of breast cancer cells through the PTEN/Akt pathway and autophagy

Wang

Yang

Fan

et al. 2018

Journal Cellular Physiology

View full text Add to dashboard Cite

Invasion and migration is the hallmark of malignant tumors as well as the major cause for breast cancer death. The polypyrimidine tract binding, PTB, protein serves as an important model for understanding how RNA binding proteins affect proliferation and invasion and how changes in the expression of these proteins can control complex programs of tumorigenesis. We have investigated some roles of polypyrimidine tract binding protein 1 (PTBP1) in human breast cancer. We found that PTBP1 was upregulated in breast cancer tissues compared with normal tissues and the same result was confirmed in breast cancer cell lines. Knockdown of PTBP1 substantially inhibited tumor cell growth, migration, and invasion. These results suggest that PTBP1 is associated with breast tumorigenesis and appears to be required for tumor cell growth and maintenance of metastasis. We further analyzed the relationship between PTBP1 and clinicopathological parameters and found that PTBP1 was correlated with her‐2 expression, lymph node metastasis, and pathological stage. This will be a novel target for her‐2(+) breast cancer. PTBP1 exerts these effects, in part, by regulating the phosphatase and tensin homolog‐phosphatidylinositol‐4,5‐bisphosphate 3‐kinase/protein kinase B (PTEN‐PI3K/Akt) pathway and autophagy, and consequently alters cell growth and contributes to the invasion and metastasis.

show abstract

Position-dependent alternative splicing activity revealed by global profiling of alternative splicing events regulated by PTB

Cited by 234 publications

References 65 publications

Robust identification of Ptbp1-dependent splicing events by a junction-centric approach in Xenopus laevis

Robust identification of Ptbp1-dependent splicing events by a junction-centric approach in Xenopus laevis

Transcriptomic profile analysis of mouse neural tube development by RNA‐Seq

PTBP1 promotes the growth of breast cancer cells through the PTEN/Akt pathway and autophagy

Contact Info

Product

Resources

About