A human haploid gene trap collection to study lncRNAs with unusual RNA biology

<p>Many thousand long non-coding (lnc) RNAs are mapped in the human genome. Time consuming studies using reverse genetic approaches by post-transcriptional knock-down or genetic modification of the locus demonstrated diverse biological functions for a few of these transcripts. The Human Gene Trap Mutant Collection in haploid KBM7 cells is a ready-to-use tool for studying protein-coding gene function. As lncRNAs show remarkable differences in RNA biology compared to protein-coding genes, it is unclear if this gene trap collection is useful for functional analysis of lncRNAs. Here we use the uncharacterized <i>LOC100288798</i> lncRNA as a model to answer this question. Using public RNA-seq data we show that <i>LOC100288798</i> is ubiquitously expressed, but inefficiently spliced. The minor spliced <i>LOC100288798</i> isoforms are exported to the cytoplasm, whereas the major unspliced isoform is nuclear localized. This shows that <i>LOC100288798</i> RNA biology differs markedly from typical mRNAs. <i>De novo</i> assembly from RNA-seq data suggests that <i>LOC100288798</i> extends 289kb beyond its annotated 3' end and overlaps the downstream <i>SLC38A4</i> gene. Three cell lines with independent gene trap insertions in <i>LOC100288798</i> were available from the KBM7 gene trap collection. RT-qPCR and RNA-seq confirmed successful lncRNA truncation and its extended length. Expression analysis from RNA-seq data shows significant deregulation of 41 protein-coding genes upon <i>LOC100288798</i> truncation. Our data shows that gene trap collections in human haploid cell lines are useful tools to study lncRNAs, and identifies the previously uncharacterized <i>LOC100288798</i> as a potential gene regulator.</p

Uni- and multivariable analyses of 299 subjects with transfers resulting in live births.

<p>*Adjusted odds ratios (AORs) for a fully adjusted logistic regression model.</p><p>Uni- and multivariable analyses of 299 subjects with transfers resulting in live births.</p

Increasing Live Birth Rate by Preimplantation Genetic Screening of Pooled Polar Bodies Using Array Comparative Genomic Hybridization - Fig 2

<p>(A) Number of chromosomal aberrations in aneuploid oocytes. In total, the polar bodies of 530 oocytes were tested by aCGH, and 359 were found to have a chromosomal aberration. Approximately 65% of aneuploid oocytes had two or more aneuploidies. (B) Distribution of chromosome errors in aneuploid oocytes. All chromosomes were found to be involved in aneuploidies. Aneuploidy of chromosome 4 was observed in only 10% of oocytes, while chromosome 19 aberrations were most frequently detected in up to 30% of oocytes.</p

Characteristics of the total study population.

<p>The data are expressed as the mean ± standard deviation as well as the median (IQR) and counts (%).</p><p>* p-value based on the Wilcoxon rank sum test.</p><p>Characteristics of the total study population.</p