HnRNPK maintains single strand RNA through controlling double-strand RNA in mammalian cells

Although antisense transcription is a widespread event in the mammalian genome, double-stranded RNA (dsRNA) formation between sense and antisense transcripts is very rare and mechanisms that control dsRNA remain unknown. By characterizing the FGF-2 regulated transcriptome in normal and cancer cells, we identified sense and antisense transcripts IER3 and IER3-AS1 that play a critical role in FGF-2 controlled oncogenic pathways. We show that IER3 and IER3-AS1 regulate each other\u27s transcription through HnRNPK-mediated post-transcriptional regulation. HnRNPK controls the mRNA stability and colocalization of IER3 and IER3-AS1. HnRNPK interaction with IER3 and IER3-AS1 determines their oncogenic functions by maintaining them in a single-stranded form. hnRNPK depletion neutralizes their oncogenic functions through promoting dsRNA formation and cytoplasmic accumulation. Intriguingly, hnRNPK loss-of-function and gain-of-function experiments reveal its role in maintaining global single- and double-stranded RNA. Thus, our data unveil the critical role of HnRNPK in maintaining single-stranded RNAs and their physiological functions by blocking RNA-RNA interactions

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Chromatin and transcriptome-based integrative approaches to profile functional long noncoding RNAs - A computational approach

One of the major hallmarks of cancer is aberrant or uncontrollable cell division, which occurs due to a defective cell cycle process. During the synthesis phase (S-phase) of the cell cycle, before cell division or mitosis phase, the DNA in the cell makes a new copy to pass on genetic information to the daughter cells. Therefore, S-phase is one of the crucial steps for a successful cell division to occur. The DNA in the nucleus is wrapped around a set of proteins called histones, forming nucleosomes, and multiple nucleosomes give rise to the higher-order chromatin structure. This well-established chromatin structure determines which portion of DNA or gene gets activated or suppressed by switching between open or closed chromatin states. Tri- or di-methylation of lysine 4 from histone 3 (H3K4me2/3) leads to open chromatin, which in turn promotes active gene transcription. The product of gene transcription is either protein-coding mRNA that translates into protein for its function or noncoding RNA, which do not code for any protein and function as RNA. However, the human genome project has identified that protein-coding genes only constitute 2% of the genome, and the vast majority of it is noncoding. Unlike protein-coding genes, the significance of RNAs transcribed from the noncoding genome is not well-established. Apart from housekeeping noncoding RNAs (rRNA, tRNA, snRNA, and snoRNA) and microRNAs (miRNAs), most functional noncoding RNAs fall into the long noncoding RNA (lncRNA) category. In this thesis, we implemented comprehensive computational approaches to identify functionally relevant lncRNAs by analyzing chromatin and transcriptome-based sequencing datasets. In the first study (paper I), using a transcriptome approach, we profiled lncRNAs associated with the S-phase stage of the cell cycle. We demonstrated the oncogenic properties of various S-phase associated lncRNAs in multiple cancers. Earlier, studies proposed that chromatin-associated RNAs, with the help of chromatin-modifying enzymes, determines the active/open or close chromatin status to promote or suppress gene transcription. Hence, in the second study (paper II), we used chromatin-based approaches to propose a possible mechanism through which the active chromatin- associated lncRNAs may function. We show that active chromatin-associated lncRNAs regulate their partner genes in-cis by recruiting the WDR5 chromatin modifier to establish an open chromatin structure at the partner protein-coding gene promoters. In our third study (paper III), we integrated both transcriptome and chromatin-based approaches to find early development-associated lncRNAs. Here, we focused on tracing the molecular footprints of sperm lncRNAs throughout the stages of organismal development. For this purpose, we integrated datasets from gametes, preimplantation and post-implantation stages of an embryo. Interestingly, we observed distinct chromatin structures in the sperm. Also, sperm lncRNAs were active during the onset of zygotic genome activation in the preimplantation stages and in cancers. In summary, this study reveals a unique set of sperm-specific lncRNAs that are temporally activated during preimplantation stages and also aberrantly expressed in multiple cancers. Overall, the present thesis provides an extensive catalogue of functionally relevant lncRNAs that can take part in cell cycle regulation, cancer, chromatin modulation, and organism development. Our studies can serve as a comprehensive resource for future investigations on lncRNAs

Additional file 2: of GeneSCF: a real-time based functional enrichment tool with support for multiple organisms

The list of organisms supported by GeneSCF for Gene ontology functional database. (XLS 9 kb

Additional file 6: of Global DNA methylation profiling reveals new insights into epigenetically deregulated protein coding and long noncoding RNAs in CLL

Additonal data 5. (XLS 5827 kb

Additional file 3: of Global DNA methylation profiling reveals new insights into epigenetically deregulated protein coding and long noncoding RNAs in CLL

Additonal data 2. (XLS 172 kb

Subcellular Distribution of p53 by the p53-Responsive lncRNA NBAT1 Determines Chemotherapeutic Response in Neuroblastoma

Neuroblastoma has a low mutation rate for the p53 gene. Alternative ways of p53 inactivation have been proposed in neuroblastoma, such as abnormal cytoplasmic accumulation of wildtype p53. However, mechanisms leading to p53 inactivation via cytoplasmic accumulation are not well investigated. Here we show that the neuroblastoma risk-associated locus 6p22.3-derived tumor suppressor NBAT1 is a p53-responsive lncRNA that regulates p53 subcellular levels. Low expression of NBAT1 provided resistance to genotoxic drugs by promoting p53 accumulation in cytoplasm and loss from mitochondrial and nuclear compartments. Depletion of NBAT1 altered CRM1 function and contributed to the loss of p53-dependent nuclear gene expression during genotoxic drug treatment. CRM1 inhibition rescued p53-dependent nuclear functions and sensitized NBAT1-depleted cells to genotoxic drugs. Combined inhibition of CRM1 and MDM2 was even more effective in sensitizing aggressive neuroblastoma cells with p53 cytoplasmic accumulation. Thus, our mechanistic studies uncover an NBAT1-dependent CRM1/MDM2-based potential combination therapy for patients with high-risk neuroblastoma. Significance: This study shows how a p53-responsive lncRNA mediates chemotherapeutic response by modulating nuclear p53 pathways and identifies a potential treatment strategy for patients with high-risk neuroblastoma

The Risk-Associated Long Noncoding RNA NBAT-1 Controls Neuroblastoma Progression by Regulating Cell Proliferation and Neuronal Differentiation

Neuroblastoma is an embryonal tumor of the sympathetic nervous system and the most common extracranial tumor of childhood. By sequencing transcriptonnes of low- and high-risk neuroblastomas, we detected differentially expressed annotated and nonannotated long noncoding RNAs (lncRNAs). We identified a lncRNA neuroblastoma associated transcript-1 (NBAT-1) as a biomarker significantly predicting clinical outcome of neuroblastoma. CpG methylation and a high-risk neuroblastoma associated SNP on chromosome 6p22 functionally contribute to NBAT-1 differential expression. Loss of NBAT-1 increases cellular proliferation and invasion. It controls these processes via epigenetic silencing of target genes. NBAT-1 loss affects neuronal differentiation through activation of the neuronal-specific transcription factor NRSF/REST. Thus, loss of NBAT-1 contributes to aggressive neuroblastoma by increasing proliferation and impairing differentiation of neuronal precursors