[Show abstract][Hide abstract] ABSTRACT: Identifying the interaction partners of noncoding RNAs is essential for elucidating their functions. We have developed an approach, termed microRNA crosslinking and immunoprecipitation (miR-CLIP), using pre-miRNAs modified with psoralen and biotin to capture their targets in cells. Photo-crosslinking and Argonaute 2 immunopurification followed by streptavidin affinity purification of probe-linked RNAs provided selectivity in the capture of targets, which were identified by deep sequencing. miR-CLIP with pre-miR-106a, a miR-17-5p family member, identified hundreds of putative targets in HeLa cells, many carrying conserved sequences complementary to the miRNA seed but also many that were not predicted computationally. miR-106a overexpression experiments confirmed that miR-CLIP captured functional targets, including H19, a long noncoding RNA that is expressed during skeletal muscle cell differentiation. We showed that miR-17-5p family members bind H19 in HeLa cells and myoblasts. During myoblast differentiation, levels of H19, miR-17-5p family members and mRNA targets changed in a manner suggesting that H19 acts as a 'sponge' for these miRNAs.
Full-text · Article · Dec 2014 · Nature Chemical Biology
[Show abstract][Hide abstract] ABSTRACT: The genome-wide accumulation of DNA replication errors known as microsatellite instability (MSI) is the hallmark lesion of DNA mismatch repair (MMR) deficient cancers. Although testing for MSI is widely used to guide clinical management, the contribution of MSI at distinct genic loci to the phenotype remains largely unexplored. Here we report that a mononucleotide (T/U)16 tract located in the 3' untranslated region (3'UTR) of the Ewing sarcoma breakpoint region 1 (EWSR1) gene is a novel MSI target locus that shows perfect sensitivity and specificity in detecting mismatch-repair deficient cancers in two independent populations. We further found a striking re-localization of the EWSR1 protein from nucleus to cytoplasm in MMR-deficient cancers, and that the non-protein coding MSI target locus itself has a modulatory effect on EWSR1 gene expression through alternative 3' end processing of the EWSR1 gene. Our results point to a MSI target gene-specific effect in MMR-deficient cancers.
[Show abstract][Hide abstract] ABSTRACT: To understand the function of the hundreds of RNA-binding proteins (RBPs) that are encoded in animal genomes it is important to identify their target RNAs. Although it is generally accepted that the binding specificity of an RBP is well described in terms of the nucleotide sequence of its binding sites, other factors such as the structural accessibility of binding sites or their clustering, to enable binding of RBP multimers, are also believed to play a role. Here we focus on GLD-1, a translational regulator of Caenorhabditis elegans, whose binding specificity and targets have been studied with a variety of methods such as CLIP (cross-linking and immunoprecipitation), RIP-Chip (microarray measurement of RNAs associated with an immunoprecipitated protein), profiling of polysome-associated mRNAs and biophysical determination of binding affinities of GLD-1 for short nucleotide sequences. We show that a simple biophysical model explains the binding of GLD-1 to mRNA targets to a large extent, and that taking into account the accessibility of putative target sites significantly improves the prediction of GLD-1 binding, particularly due to a more accurate prediction of binding in transcript coding regions. Relating GLD-1 binding to translational repression and stabilization of its target transcripts we find that binding sites along the entire transcripts contribute to functional responses, and that CDS-located sites contribute most to translational repression. Finally, biophysical measurements of GLD-1 affinity for a small number of oligonucleotides appear to allow an accurate reconstruction of the sequence specificity of the protein. This approach can be applied to uncover the specificity and function of other RBPs.
[Show abstract][Hide abstract] ABSTRACT: Background
In recent years, a variety of small RNAs derived from other RNAs with well-known functions such as tRNAs and snoRNAs, have been identified. The functional relevance of these RNAs is largely unknown. To gain insight into the complexity of snoRNA processing and the functional relevance of snoRNA-derived small RNAs, we sequence long and short RNAs, small RNAs that co-precipitate with the Argonaute 2 protein and RNA fragments obtained in photoreactive nucleotide-enhanced crosslinking and immunoprecipitation (PAR-CLIP) of core snoRNA-associated proteins.
Analysis of these data sets reveals that many loci in the human genome reproducibly give rise to C/D box-like snoRNAs, whose expression and evolutionary conservation are typically less pronounced relative to the snoRNAs that are currently cataloged. We further find that virtually all C/D box snoRNAs are specifically processed inside the regions of terminal complementarity, retaining in the mature form only 4-5 nucleotides upstream of the C box and 2-5 nucleotides downstream of the D box. Sequencing of the total and Argonaute 2-associated populations of small RNAs reveals that despite their cellular abundance, C/D box-derived small RNAs are not efficiently incorporated into the Ago2 protein.
We conclude that the human genome encodes a large number of snoRNAs that are processed along the canonical pathway and expressed at relatively low levels. Generation of snoRNA-derived processing products with alternative, particularly miRNA-like, functions appears to be uncommon.
[Show abstract][Hide abstract] ABSTRACT: Cross-linking and immunoprecipitation (CLIP) is increasingly used to map transcriptome-wide binding sites of RNA-binding proteins. We developed a method for CLIP data analysis, and applied it to compare CLIP with photoactivatable ribonucleoside-enhanced CLIP (PAR-CLIP) and to uncover how differences in cross-linking and ribonuclease digestion affect the identified sites. We found only small differences in accuracies of these methods in identifying binding sites of HuR, which binds low-complexity sequences, and Argonaute 2, which has a complex binding specificity. We found that cross-link-induced mutations led to single-nucleotide resolution for both PAR-CLIP and CLIP. Our results confirm the expectation from original CLIP publications that RNA-binding proteins do not protect their binding sites sufficiently under the denaturing conditions used during the CLIP procedure, and we show that extensive digestion with sequence-specific RNases strongly biases the recovered binding sites. This bias can be substantially reduced by milder nuclease digestion conditions.
[Show abstract][Hide abstract] ABSTRACT: Eukaryotic cells express a large variety of ribonucleic acid-(RNA)-binding proteins (RBPs) with diverse affinity and specificity
towards target RNAs that play a crucial role in almost every aspect of RNA metabolism. In addition, specific domains in RBPs
impart catalytic activity or mediate protein–protein interactions, making RBPs versatile regulators of gene expression. In
this review, we elaborate on recent experimental and computational approaches that have increased our understanding of RNA–protein
interactions and their role in cellular function. We review aspects of gene expression that are modulated post-transcriptionally
by RBPs, namely the stability of polymerase II-derived mRNA transcripts and their rate of translation into proteins. We further
highlight the extensive regulatory networks of RBPs that implement a combinatorial control of gene expression. Taking cues
from the recent development in the field, we argue that understanding spatio-temporal RNA–protein association on a transcriptome
level will provide invaluable and unexpected insights into the regulatory codes that define growth, differentiation and disease.
Full-text · Article · Dec 2010 · Briefings in functional genomics
[Show abstract][Hide abstract] ABSTRACT: The 5-HT2C receptor (5-HT2CR) belongs to the family of seven transmembrane-containing G-protein-coupled receptors (GPCRs) and is located on the human
X chromosome band q24. The pre-mRNA generated from this gene undergoes extensive RNA processing. Due to RNA editing and alternative
splicing, the gene could generate at least 288 different isoforms. Under physiological conditions, the RNA processing is tightly
regulated. Deviations from the normal processing patterns that disturb the balance between the mRNA isoforms lead to diseases.
Here we describe the regulation of alternative splicing of exon Vb of the 5-HT2C receptor. This exon encodes the second intracellular loop that is important for signaling. The exon is regulated by a splicing
silencer that can be modified by RNA editing. The inclusion of the nonedited exon Vb is promoted by a small nucleolar RNA
(snoRNA), HBII-52/SNORD115 and its processed isoforms. The regulation of this exon appears to be altered in the Prader–Willi
[Show abstract][Hide abstract] ABSTRACT: Alternative splicing is one of the most important post-transcriptional processing steps that enhances genomic information
by generating multiple RNA isoforms from a single gene. Recently, microarrays have been developed that can detect changes
in splice site selection. Currently, the biggest challenge for the analysis of alternative splicing with microarrays is the
bioinformatics analysis of array data and their low reproducibility by RT-PCR. Despite these problems, microarrays revealed
an unexpected number of expressed RNAs, showed changes of alternative splicing in diseases and indicated that a splicing factor
regulates a biologically meaningful set of genes.
KeywordsAlternative splicing-Microarrays-RNA isoforms-Experimental validation-Exon-intron
[Show abstract][Hide abstract] ABSTRACT: Almost all human protein-coding transcripts undergo pre-mRNA splicing and a majority of them is alternatively spliced. The most common technique used to analyze the regulation of an alternative exon is through reporter minigene constructs. However, their construction is time-consuming and is often complicated by the limited availability of appropriate restriction sites. Here, we report a fast and simple recombination-based method to generate splicing reporter genes, using a new vector, pSpliceExpress. The system allows generation of minigenes within one week. Minigenes generated with pSpliceExpress show the same regulation as displayed by conventionally cloned reporter constructs and provide an alternate avenue to study splice site selection in vivo.
[Show abstract][Hide abstract] ABSTRACT: We previously found the soluble interleukin 4 receptor (sIL4R) to be differently expressed in allergic asthma patients compared to healthy individuals. Here we present data demonstrating the involvement of the sequence variations, c.912-1003A > G, c.912-833T > C, c. 912-630A > G, and c.912-577A > G, in the expressional regulation of IL4R splice variants. By using an IL4R minigene construct, genomic DNA and mRNA from asthma patients and nonasthmatic individuals, we analyzed the function of four highly-linked SNPs, flanking the alternatively-spliced exon in the IL4R gene. Results from the minigene assay showed that the form containing the minor alleles significantly decreased the expression of the soluble IL4R (exon 8+) variant, a decrease that could only be seen in the major construct after increasing amounts of either the splicing factor SRp20, or YT521-B. Analysis of mRNA expression in our human material confirmed the results, demonstrating lower expression of the sIL4R in patients and controls carrying the minor alleles. Together these results show sequence variations as a possible way of altering alternative splicing selection of IL4R in vivo.
[Show abstract][Hide abstract] ABSTRACT: The SNURF-SNRPN locus located on chromosome 15 is maternally imprinted and generates a large transcript containing at least 148 exons. Loss of the paternal allele causes Prader-Willi syndrome (PWS). The 3' end of the transcript harbors several evolutionarily conserved C/D box small nucleolar RNAs (snoRNAs) that are tissue-specifically expressed. With the exception of 47 copies of HBII-52 snoRNAs, none of the snoRNAs exhibit complementarity to known RNAs. Due to an 18-nucleotide sequence complementarity, HBII-52 can bind to the alternatively spliced exon Vb of the serotonin receptor 2C pre-mRNA, where it masks a splicing silencer, which results in alternative exon usage. This silencer can also be destroyed by RNA editing, which changes the amino acid sequence and appears to be independent of HBII-52. Lack of HBII-52 expression in individuals with PWS causes most likely a lack of the high-efficacy serotonin receptor, which could contribute to the disease. It is therefore possible that snoRNAs could act as versatile modulators of gene expression by modulating alternative splicing.
Preview · Article · Feb 2006 · Cold Spring Harbor Symposia on Quantitative Biology
[Show abstract][Hide abstract] ABSTRACT: The Prader-Willi syndrome is a congenital disease that is caused by the loss of paternal gene expression from a maternally
imprinted region on chromosome 15. This region contains a small nucleolar RNA (snoRNA), HBII-52, that exhibits sequence complementarity
to the alternatively spliced exon Vb of the serotonin receptor 5-HT2CR. We found that HBII-52 regulates alternative splicing of 5-HT2CR by binding to a silencing element in exon Vb. Prader-Willi syndrome patients do not express HBII-52. They have different
5-HT2CR messenger RNA (mRNA) isoforms than healthy individuals. Our results show that a snoRNA regulates the processing of an mRNA
expressed from a gene located on a different chromosome, and the results indicate that a defect in pre-mRNA processing contributes
to the Prader-Willi syndrome.