IGD: A resource for intronless genes in the human genome

Louhichi, Amel; Fourati, A; Rebaï, Ahmed

doi:10.1016/j.gene.2011.08.013

Cited by 53 publications

(52 citation statements)

References 17 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Validating our RIP assay, immunoprecipitation of both SRSF1 or SRSF1-m4 led to specific co-precipitation of SMN , a known SRSF1-binder55, but not of JUN , an intronless control transcript not expected to be bound by SRSF1 (ref. 56), in N2A cells expressing either sense (Fig. 6c) or antisense (Fig.…”

Section: Resultsmentioning

confidence: 95%

SRSF1-dependent nuclear export inhibition of C9ORF72 repeat transcripts prevents neurodegeneration and associated motor deficits

et al. 2017

View full text Add to dashboard Cite

Hexanucleotide repeat expansions in the C9ORF72 gene are the commonest known genetic cause of amyotrophic lateral sclerosis and frontotemporal dementia. Expression of repeat transcripts and dipeptide repeat proteins trigger multiple mechanisms of neurotoxicity. How repeat transcripts get exported from the nucleus is unknown. Here, we show that depletion of the nuclear export adaptor SRSF1 prevents neurodegeneration and locomotor deficits in a Drosophila model of C9ORF72-related disease. This intervention suppresses cell death of patient-derived motor neuron and astrocytic-mediated neurotoxicity in co-culture assays. We further demonstrate that either depleting SRSF1 or preventing its interaction with NXF1 specifically inhibits the nuclear export of pathological C9ORF72 transcripts, the production of dipeptide-repeat proteins and alleviates neurotoxicity in Drosophila, patient-derived neurons and neuronal cell models. Taken together, we show that repeat RNA-sequestration of SRSF1 triggers the NXF1-dependent nuclear export of C9ORF72 transcripts retaining expanded hexanucleotide repeats and reveal a novel promising therapeutic target for neuroprotection.

show abstract

Section: Resultsmentioning

confidence: 95%

SRSF1-dependent nuclear export inhibition of C9ORF72 repeat transcripts prevents neurodegeneration and associated motor deficits

et al. 2017

View full text Add to dashboard Cite

show abstract

“…Intronless genes are not uncommon in metazoans (e.g. Sakharkar et al, 2006;Louhichi et al, 2011), but a continuous ORF may impose difficulties in transcription, leading to erroneous mRNA formation (Berget, 1995). In several fungal species, intron gain followed acquisition of bacterial α-amylases (Da Lage et al, 2013).…”

Section: Domestication Of Prokaryotic-origin Genesmentioning

confidence: 99%

Multiple horizontally acquired genes from fungal and prokaryotic donors encode cellulolytic enzymes in the bdelloid rotifer Adineta ricciae

Szydłowski

Boschetti

Crisp

et al. 2015

Gene

View full text Add to dashboard Cite

“…This carefully-selected dataset contains 1000 genes: 500 of them are human intronless genes which are randomly chosen from Intronless Gene Database [25], and the other 500 are intron-containing genes which are randomly chosen from Genbank database (release 170). Here we must emphasize that all the 1000 genes are from eukaryotic organisms.…”

Section: Resultsmentioning

confidence: 99%

“…Similarly, the 600 intron-containing genes also include 200 human genes, 200 drosophila genes, and 200 yeast genes. These genes are chosen from Intronless Gene Database [25], Berkeley Drosophila Genome Project [26], and Saccharomyces Genome Database [27]. We partition the 1200 sequences into 5 parts; each part contains 240 sequences (120 intronless genes and 120 intron-containing genes).…”

Section: Resultsmentioning

confidence: 99%

DFA7, a New Method to Distinguish between Intron-Containing and Intronless Genes

Deng²,

Zheng

et al. 2014

PLoS ONE

View full text Add to dashboard Cite

Intron-containing and intronless genes have different biological properties and statistical characteristics. Here we propose a new computational method to distinguish between intron-containing and intronless gene sequences. Seven feature parameters , , , , , , and based on detrended fluctuation analysis (DFA) are fully used, and thus we can compute a 7-dimensional feature vector for any given gene sequence to be discriminated. Furthermore, support vector machine (SVM) classifier with Gaussian radial basis kernel function is performed on this feature space to classify the genes into intron-containing and intronless. We investigate the performance of the proposed method in comparison with other state-of-the-art algorithms on biological datasets. The experimental results show that our new method significantly improves the accuracy over those existing techniques.

show abstract

IGD: A resource for intronless genes in the human genome

Cited by 53 publications

References 17 publications

SRSF1-dependent nuclear export inhibition of C9ORF72 repeat transcripts prevents neurodegeneration and associated motor deficits

SRSF1-dependent nuclear export inhibition of C9ORF72 repeat transcripts prevents neurodegeneration and associated motor deficits

Multiple horizontally acquired genes from fungal and prokaryotic donors encode cellulolytic enzymes in the bdelloid rotifer Adineta ricciae

DFA7, a New Method to Distinguish between Intron-Containing and Intronless Genes

Contact Info

Product

Resources

About