Altered expression of the FMR1 splicing variants landscape in premutation carriers

Tseng, Elizabeth; Tang, Han; AlOlaby, Reem Rafik; Hickey, Luke; Tassone, Flora

doi:10.1016/j.bbagrm.2017.08.007

Cited by 30 publications

(36 citation statements)

References 47 publications

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“…Mutations in this gene can cause Fragile X Syndrome and predispose carriers to premature menopause. Women with an increased risk of giving birth to a son with Fragile X show different expression levels of some of these isoforms (5). …”

Section: Delving Into Rnamentioning

confidence: 99%

Going Long and Direct

Webb¹

2018

BioTechniques

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Biologist Chris Vollmers of the University of California, Santa Cruz relies on RNA sequencing to study the rich and unique biology of B cells, where each cell lineage recombines its genome to produce specific antibodies. As these cells modulate their response to immune challenges, they can further mutate and produce diverse transcripts, even within the same individuals. To study these cells, short-read RNA sequencing, the current gold standard, fell short.After reverse transcription, Vollmers' team produced fulllength cDNA that they then chopped into short sequences of roughly 200 bases in length. "You have this beautiful full-length isoform information that you then lose completely because of the technology in the library preparation," Vollmers said. The resulting data was cumbersome to assemble, limiting his ability to study transcriptional isoforms and the coding regions for antibodies.So in a recent study (1), his team tried a long-read strategy. They took advantage of the full-length cDNA and used Oxford Nanopore's MinION sequencer to examine whole sequences in a single read. They soon realized that there was far more going on in B cells than they could see with short-read data. "You think you have a homogenous population, but really, cells make totally different isoforms, which may do totally different things," he said.Vollmer's work is just one example of researchers fueling sequencing innovations for mining the rich biology of RNA. Scientists are also using sequencing to find and study chemical modifications to transcripts. Routine direct RNA sequencing is

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Section: Delving Into Rnamentioning

confidence: 99%

Going Long and Direct

Webb¹

2018

BioTechniques

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“…Previously, we and others reported a novel 140 bp exon when detecting alternatively spliced transcripts from FMR1 gene [12,13] . This 140 bp sequence comes from intron 9 of human FMR1 gene and introduces a premature stop codon in the resulting mRNAs.…”

Section: Introductionmentioning

confidence: 99%

Further identification of a 140bp sequence from amid intron 9 of human FMR1 gene as a new exon

Yang

Yan

et al. 2020

Preprint

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Background: the disease gene of fragile X syndrome, FMR1 gene, encodes fragile X mental retardation protein (FMRP). The alternative splicing (AS) of FMR1 can affect the structure and function of FMRP. However, the biological functions of alternatively spliced isoforms remain elusive. In a previous study, we identified a new 140 bp exon from the intron 9 of human FMR1 gene. In this study, we further examined the biological functions of this new exon and its underlying signaling pathways. Results: qRT-PCR results showed that this novel exon is commonly expressed in the peripheral blood of normal individuals. Comparative genomics showed that sequences paralogous to the 140 bp sequence only exist in the genomes of primates. To explore the biological functions of the new transcript, we constructed recombinant eukaryotic expression vectors and lentiviral overexpression vectors. Results showed that the spliced transcript encoded a truncated protein which was expressed mainly in the cell nucleus. Additionally, several genes, including the BEX1 gene involved in mGluR-LTP or mGluR-LTD signaling pathways were significantly influenced when the truncated FMRP was overexpressed. Conclusions: our work identified a new exon from amid intron 9 of human FMR1 gene with wide expression in normal healthy individuals, which emphasizes the notion that the AS of FMR1 gene is complex and may in a large part account for the multiple functions of FMRP.

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“…The availability of third generation long read technologies provides an unprecedented and nearly complete picture of isoform structures. However, existing long read transcript sequencing for human disease genes have used an amplicon-based approach (Treutlein et al 2014;Tseng et al 2017;Kohli 2017). While this approach has been successful in identifying complex alternative splicing in human disease genes, it is limited to the PCR primer design and will not uncover alternative start and end sites.…”

Section: Introductionmentioning

confidence: 99%

The landscape of SNCA transcripts across synucleinopathies: New insights from long reads sequencing analysis

Tseng

Rowell

Omolara-Chinue

et al. 2019

Preprint

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Dysregulation of alpha-synuclein expression has been implicated in the pathogenesis of synucleinopathies, in particular Parkinson's Disease (PD) and Dementia with Lewy bodies (DLB). Previous studies have shown that the alternatively spliced isoforms of the SNCA gene are differentially expressed in different parts of the brain for PD and DLB patients. Similarly, SNCA isoforms with skipped exons can have a functional impact on the protein domains. The large intronic region of the SNCA gene was also shown to harbor structural variants that affect transcriptional levels. Here we apply the first study of using long read sequencing with targeted capture of both the gDNA and cDNA of the SNCA gene in brain tissues of PD, DLB, and control samples using the PacBio Sequel system. The targeted full-length cDNA (Iso-Seq) data confirmed complex usage of known alternative start sites and variable 3' UTR lengths, as well as novel 5' starts and 3' ends not previously described. The targeted gDNA data allowed phasing of up to 81% of the ~114kb SNCA region, with the longest phased block excedding 54 kb. We demonstrate that long gDNA and cDNA reads have the potential to reveal long-range information not previously accessible using traditional sequencing methods. This approach has a potential impact in studying disease risk genes such as SNCA, providing new insights into the genetic etiologies, including perturbations to the landscape the gene transcripts, of human complex diseases such as synucleinopathies.

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Altered expression of the FMR1 splicing variants landscape in premutation carriers

Cited by 30 publications

References 47 publications

Going Long and Direct

Going Long and Direct

Further identification of a 140bp sequence from amid intron 9 of human FMR1 gene as a new exon

The landscape of SNCA transcripts across synucleinopathies: New insights from long reads sequencing analysis

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