Ultrasensitive quantification of multiplexed mRNA variants via splice-junction anchored DNA probes and SplintR ligase-initiated PCR

Yuting Jia; Jun Han; Hui Wang; Weixiang Hong; Honghong Wang; Mai Zhang; Zhengping Li

doi:10.1039/d1cc03033g

Ultrasensitive quantification of multiplexed mRNA variants via splice-junction anchored DNA probes and SplintR ligase-initiated PCR

Chemical Communications ◽

10.1039/d1cc03033g ◽

2021 ◽

Vol 57 (78) ◽

pp. 10011-10014

Author(s):

Yuting Jia ◽

Jun Han ◽

Hui Wang ◽

Weixiang Hong ◽

Honghong Wang ◽

...

Keyword(s):

Splice Junction ◽

Dna Probes ◽

Mrna Splicing ◽

Mrna Variants ◽

Splicing Variants

A method was developed for multiplexed quantification of mRNA splicing variants via splice-junction anchored DNA probes and SplintR ligase-initiated PCR.

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Correction: Dynamic visualization of mRNA splicing variants with a transactivating reporter

Chemical Communications ◽

10.1039/d1cc90324a ◽

2021 ◽

Vol 57 (75) ◽

pp. 9626-9626

Author(s):

Si Chen ◽

Wenjie Shu ◽

Haifeng Zheng ◽

Zhe Ma ◽

Miao Li ◽

...

Keyword(s):

Mrna Splicing ◽

Dynamic Visualization ◽

Splicing Variants

Correction for ‘Dynamic visualization of mRNA splicing variants with a transactivating reporter’ by Si Chen et al., Chem. Commun., 2021, DOI: 10.1039/d1cc02439f.

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NEIL1 mRNA Splicing Variants are Expressed in Normal Mouse Organs

Journal of Radiation Research ◽

10.1269/jrr.11029 ◽

2012 ◽

Vol 53 (2) ◽

pp. 234-241 ◽

Cited By ~ 2

Author(s):

Ryohei YAMAMOTO ◽

Mizuki YAMAMOTO ◽

Hiroyuki KUSAKA ◽

Hideaki MASATSUGU ◽

Satoshi MATSUYAMA ◽

...

Keyword(s):

Normal Mouse ◽

Mrna Splicing ◽

Splicing Variants

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SpliceRCA: in Situ Single-Cell Analysis of mRNA Splicing Variants

ACS Central Science ◽

10.1021/acscentsci.8b00081 ◽

2018 ◽

Vol 4 (6) ◽

pp. 680-687 ◽

Cited By ~ 13

Author(s):

Xiaojun Ren ◽

Ruijie Deng ◽

Kaixiang Zhang ◽

Yupeng Sun ◽

Xucong Teng ◽

...

Keyword(s):

Single Cell ◽

Single Cell Analysis ◽

Mrna Splicing ◽

Cell Analysis ◽

Splicing Variants

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Real-time detection of mRNA splicing variants with specifically designed reverse-transcription loop-mediated isothermal amplification

RSC Advances ◽

10.1039/d0ra00591f ◽

2020 ◽

Vol 10 (11) ◽

pp. 6271-6276

Author(s):

Fengxia Su ◽

Guanhao Wang ◽

Jianing Ji ◽

Pengbo Zhang ◽

Fangfang Wang ◽

...

Keyword(s):

Real Time ◽

Reverse Transcription ◽

Mrna Splicing ◽

Isothermal Amplification ◽

Loop Mediated Isothermal Amplification ◽

Splicing Variant ◽

Splicing Variants ◽

Real Time Detection

A novel splicing variant assay is developed based on specifically designed reverse-transcription (RT) loop-mediated isothermal amplification.

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Validation of predicted mRNA splicing mutations using high-throughput transcriptome data

F1000Research ◽

10.12688/f1000research.3-8.v1 ◽

2014 ◽

Vol 3 ◽

pp. 8

Author(s):

Coby Viner ◽

Stephanie N. Dorman ◽

Ben C. Shirley ◽

Peter K. Rogan

Keyword(s):

Exon Skipping ◽

Mrna Splicing ◽

Cryptic Splice Site ◽

Sequencing Data ◽

Manual Inspection ◽

Large Numbers ◽

Splicing Variants ◽

Complete Genomes ◽

Site Use ◽

Splicing Patterns

Interpretation of variants present in complete genomes or exomes reveals numerous sequence changes, only a fraction of which are likely to be pathogenic. Mutations have been traditionally inferred from allele frequencies and inheritance patterns in such data. Variants predicted to alter mRNA splicing can be validated by manual inspection of transcriptome sequencing data, however this approach is intractable for large datasets. These abnormal mRNA splicing patterns are characterized by reads demonstrating either exon skipping, cryptic splice site use, and high levels of intron inclusion, or combinations of these properties. We present, Veridical, anin silicomethod for the automatic validation of DNA sequencing variants that alter mRNA splicing. Veridical performs statistically valid comparisons of the normalized read counts of abnormal RNA species in mutant versus non-mutant tissues. This leverages large numbers of control samples to corroborate the consequences of predicted splicing variants in complete genomes and exomes.

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Pan-cancer repository of validated natural and cryptic mRNA splicing mutations

F1000Research ◽

10.12688/f1000research.17204.2 ◽

2019 ◽

Vol 7 ◽

pp. 1908 ◽

Cited By ~ 1

Author(s):

Ben C. Shirley ◽

Eliseos J. Mucaki ◽

Peter K. Rogan

Keyword(s):

Splice Junction ◽

Cancer Genome ◽

Mrna Splicing ◽

The Cancer Genome Atlas ◽

Splice Sites ◽

Global Alliance ◽

Multiple Tumor ◽

Link Type ◽

Splicing Mutations ◽

Single Nucleotide Polymorphism Database

We present a major public resource of mRNA splicing mutations validated according to multiple lines of evidence of abnormal gene expression. Likely mutations present in all tumor types reported in the Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC) were identified based on the comparative strengths of splice sites in tumor versus normal genomes, and then validated by respectively comparing counts of splice junction spanning and abundance of transcript reads in RNA-Seq data from matched tissues and tumors lacking these mutations. The comprehensive resource features 341,486 of these validated mutations, the majority of which (69.9%) are not present in the Single Nucleotide Polymorphism Database (dbSNP 150). There are 131,347 unique mutations which weaken or abolish natural splice sites, and 222,071 mutations which strengthen cryptic splice sites (11,932 affect both simultaneously). 28,812 novel or rare flagged variants (with <1% population frequency in dbSNP) were observed in multiple tumor tissue types. Single variants or chromosome ranges can be queried using a Global Alliance for Genomics and Health (GA4GH)-compliant, web-based Beacon “Validated Splicing Mutations” either separately or in aggregate alongside other Beacons through the public Beacon Network, as well as through our website.

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Comprehensive quantitative analysis of alternative splicing variants reveals the HNF1B mRNA splicing pattern in various tumour and non-tumour tissues

Scientific Reports ◽

10.1038/s41598-021-03989-z ◽

2022 ◽

Vol 12 (1) ◽

Author(s):

Jan Hojny ◽

Romana Michalkova ◽

Eva Krkavcova ◽

Quang Hiep Bui ◽

Michaela Bartu ◽

...

Keyword(s):

Alternative Splicing ◽

Mrna Expression ◽

Large Intestine ◽

Digital Pcr ◽

Splicing Pattern ◽

Mrna Variants ◽

Splicing Variants ◽

Quantitative Changes ◽

Nuclear Factor 1 ◽

Regulatory Functions

AbstractHepatocyte nuclear factor-1-beta (HNF1B) is a transcription factor and putative biomarker of solid tumours. Recently, we have revealed a variety of HNF1B mRNA alternative splicing variants (ASVs) with unknown, but potentially regulatory, functions. The aim of our work was to quantify the most common variants and compare their expression in tumour and non-tumour tissues of the large intestine, prostate, and kidney. The HNF1B mRNA variants 3p, Δ7, Δ7–8, and Δ8 were expressed across all the analysed tissues in 28.2–33.5%, 1.5–2%, 0.8–1.7%, and 2.3–6.9% of overall HNF1B mRNA expression, respectively, and occurred individually or in combination. The quantitative changes of ASVs between tumour and non-tumour tissue were observed for the large intestine (3p, Δ7–8), prostate (3p), and kidney samples (Δ7). Decreased expression of the overall HNF1B mRNA in the large intestine and prostate cancer samples compared with the corresponding non-tumour samples was observed (p = 0.019 and p = 0.047, respectively). The decreased mRNA expression correlated with decreased protein expression in large intestine carcinomas (p < 0.001). The qualitative and quantitative pattern of the ASVs studied by droplet digital PCR was confirmed by next-generation sequencing, which suggests the significance of the NGS approach for further massive evaluation of the splicing patterns in a variety of genes.

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Corepressors: Custom Tailoring and Alterations While you Wait

Nuclear Receptor Signaling ◽

10.1621/nrs.03003 ◽

2005 ◽

Vol 3 (1) ◽

pp. nrs.03003 ◽

Cited By ~ 40

Author(s):

Michael Goodson ◽

Brian A. Jonas ◽

Martin A. Privalsky

Keyword(s):

Transcription Factor ◽

Transcriptional Repression ◽

Developmental Stages ◽

Thyroid Hormone Receptor ◽

Protein Complexes ◽

Biological Properties ◽

Mrna Splicing ◽

Alternative Mrna Splicing ◽

Splicing Variants ◽

Protein Variants

A diverse cadre of metazoan transcription factors mediate repression by recruiting protein complexes containing the SMRT (silencing mediator of retinoid and thyroid hormone receptor) or N-CoR (nuclear receptor corepressor) corepressors. SMRT and N-CoR nucleate the assembly of still larger corepressor complexes that perform the specific molecular incantations necessary to confer transcriptional repression. Although SMRT and N-CoR are paralogs and possess similar molecular architectures and mechanistic strategies, they nonetheless exhibit distinct molecular and biological properties. It is now clear that the functions of both SMRT and N-CoR are further diversified through alternative mRNA splicing, yielding a series of corepressor protein variants that participate in distinctive transcription factor partnerships and display distinguishable repression properties. This review will discuss what is known about the structure and actions of SMRT, N-CoR, and their splicing variants, and how alternative splicing may allow the functions of these corepressors to be adapted and tailored to different cells and to different developmental stages.

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