A cell-based splicing reporter system to identify regulators of cis-splicing between adjacent genes

Chwalenia, Katarzyna; Qin, Fujun; Singh, Sandeep

doi:10.1093/nar/gky1288

Cited by 18 publications

(18 citation statements)

References 62 publications

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“…RNA extraction and quantitative reverse transcription polymerase chain reaction (qRT-PCR) were performed as described previously [33]. Primers are listed in Table S3.…”

Section: Rna Extraction and Qrt-pcrmentioning

confidence: 99%

Functional heritage: the evolution of chimeric RNA into a gene

Singh

Shi

et al. 2019

RNA Biology

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Once believed to be unique features of neoplasia, chimeric RNAs are now being discovered in normal physiology. We speculated that some chimeric RNAs may be functional precursors of genes, and that forming chimeric RNA at the transcriptional level may be a 'trial' mechanism before the functional element is fixed into the genome. Supporting this idea, we identified a chimeric RNA, HNRNPA1L2-SUGT1 (H-S), whose sequence is highly similar to that of a 'pseudogene' MRPS31P5. Sequence analysis revealed that MRPS31P5 transcript is more similar to H-S chimeric RNA than its 'parent' gene, MRPS31. Evolutionarily, H-S precedes MRPS31P5, as it can be detected bioinformatically and experimentally in marmosets, which do not yet possess MRPS31P5 in their genome. Conversely, H-S is minimally expressed in humans, while instead, MRPS31P5 is abundantly expressed. Silencing H-S in marmoset cells resulted in similar phenotype as silencing MRPS31P5 in human cells. In addition, whole transcriptome analysis and candidate downstream target validation revealed common signalling pathways shared by the two transcripts. Interestingly, H-S failed to rescue the phenotype caused by silencing MPRS31P5 in human and rhesus cells, whereas MRPS31P5 can at least partially rescue the phenotype caused by silencing H-S in marmoset cells, suggesting that MRPS31P5 may have further evolved into a distinct entity. Thus, multiple lines of evidence support that MRPS31P5 is not truly a pseudogene of MRPS31, but a likely functional descendent of H-S chimera. Instead being a gene fusion product, H-S is a product of cissplicing between adjacent genes, while MRPS31P5 is likely produced by genome rearrangement.

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“…RNA extraction and quantitative reverse transcription polymerase chain reaction (qRT-PCR) were performed as described previously [33]. Primers are listed in Table S3.…”

Section: Rna Extraction and Qrt-pcrmentioning

confidence: 99%

Functional heritage: the evolution of chimeric RNA into a gene

Singh

Shi

et al. 2019

RNA Biology

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“…In this work, we have demonstrated the presence of fusion transcripts in various neural cell types in the developing human cortex and performed functional analysis on a human-specific fusion CTNNBIP1-CLSTN1 (CTCL), which has been shown to be generated by cis-splicing fusion of the first 5 exons of CTNNBIP1 (b-Catenin-interacting protein1) and the last 17 exons of CLSTN1 (Calsyntenin 1) (Babiceanu et al, 2016;Chwalenia et al, 2019). Given the recurrent detection of CTCL in normal human tissues and cells but not in mice (Babiceanu et al, 2016) and the enrichment of CTCL in oRGs, we analyzed the role of CTCL in human cortex development using cultured human cerebral organoids as the model system.…”

Section: Introductionmentioning

confidence: 99%

The CTNNBIP1-CLSTN1 fusion transcript regulates human neocortical development

Xiao

et al. 2021

Cell Reports

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The CTNNBIP1-CLSTN1 fusion transcript regulates human neocortical development Graphical abstract Highlights d Fusion transcripts occur in developing human cortex in celltype-specific manner. d The CTCL fusion transcript is expressed in human cortical neural progenitors. d CTCL tightly controls neural progenitor proliferation and neuronal differentiation. d CTCL fine-tunes Wnt/b-catenin signaling in human cortical neural progenitors.

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“…However, there has been increasing evidence of chimeric RNAs in non-cancer tissues and cells [ 18 , 20 , 31 , 41 ]. Recent work on RNA trans-splicing [ 18 , 32 ] and cis-splicing between adjacent genes [ 8 , 9 , 42 ] have defined a new exemplification for alternative splicing mechanisms, which can also generate chimeric RNAs.…”

Section: Discussionmentioning

confidence: 99%

Landscape of Chimeric RNAs in Non-Cancerous Cells

Chen

Haddox

Tang

et al. 2021

Genes

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Gene fusions and their products (RNA and protein) have been traditionally recognized as unique features of cancer cells and are used as ideal biomarkers and drug targets for multiple cancer types. However, recent studies have demonstrated that chimeric RNAs generated by intergenic alternative splicing can also be found in normal cells and tissues. In this study, we aim to identify chimeric RNAs in different non-neoplastic cell lines and investigate the landscape and expression of these novel candidate chimeric RNAs. To do so, we used HEK-293T, HUVEC, and LO2 cell lines as models, performed paired-end RNA sequencing, and conducted analyses for chimeric RNA profiles. Several filtering criteria were applied, and the landscape of chimeric RNAs was characterized at multiple levels and from various angles. Further, we experimentally validated 17 chimeric RNAs from different classifications. Finally, we examined a number of validated chimeric RNAs in different cancer and non-cancer cells, including blood from healthy donors, and demonstrated their ubiquitous expression pattern.

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A cell-based splicing reporter system to identify regulators of cis-splicing between adjacent genes

Cited by 18 publications

References 62 publications

Functional heritage: the evolution of chimeric RNA into a gene

Functional heritage: the evolution of chimeric RNA into a gene

The CTNNBIP1-CLSTN1 fusion transcript regulates human neocortical development

Landscape of Chimeric RNAs in Non-Cancerous Cells

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