MIWI-independent small RNAs (MSY-RNAs) bind to the RNA-binding protein, MSY2, in male germ cells

Role of Y-Box Binding Proteins in Ontogenesis

Y-box binding proteins (YB proteins) are multifunctional DNA/RNA-binding proteins capable of regulating gene expression at multiple levels. At present, the most studied function of these proteins is the regulation of protein synthesis. Special attention in this review has been paid to the role of YB proteins in the control of mRNA translation and stability at the earliest stages of organism formation, from fertilization to gastrulation. Furthermore, the functions of YB proteins in the formation of germ cells, in which they accumulate in large amounts, are summarized. The review then discusses the contribution of YB proteins to the regulation of gene expression during the differentiation of various types of somatic cells. Finally, future directions in the study of YB proteins and their role in ontogenesis are considered.

Noncoding RNA Roles in Pharmacogenomic Responses to Aspirin: New Molecular Mechanisms for an Old Drug

Aspirin, as one of the most frequently prescribed drugs, can have therapeutic effects on different conditions such as cardiovascular and metabolic disorders and malignancies. The effects of this common cardiovascular drug are exerted through different molecular and cellular pathways. Altered noncoding RNA (ncRNA) expression profiles during aspirin treatments indicate a close relationship between these regulatory molecules and aspirin effects through regulating gene expressions. A better understanding of the molecular networks contributing to aspirin efficacy would help optimize efficient therapies for this very popular drug. This review is aimed at discussing and highlighting the identified interactions between aspirin and ncRNAs and their targeting pathways and better understanding pharmacogenetic responses to aspirin.

Mapping of In Vivo RNA-Binding Sites by Ultraviolet (UV)-Cross-Linking Immunoprecipitation (CLIP)

RNA "CLIP" (cross-linking immunoprecipitation), the method by which RNA-protein complexes are covalently cross-linked and purified and the RNA sequenced, has attracted attention as a powerful means of developing genome-wide maps of direct, functional RNA-protein interaction sites. These maps have been used to identify points of regulation, and they hold promise for understanding the dynamics of RNA regulation in normal cell function and its dysregulation in disease.

Assessing Computational Steps for CLIP-Seq Data Analysis

RNA-binding protein (RBP) is a key player in regulating gene expression at the posttranscriptional level. CLIP-Seq, with the ability to provide a genome-wide map of protein-RNA interactions, has been increasingly used to decipher RBP-mediated posttranscriptional regulation. Generating highly reliable binding sites from CLIP-Seq requires not only stringent library preparation but also considerable computational efforts. Here we presented a first systematic evaluation of major computational steps for identifying RBP binding sites from CLIP-Seq data, including preprocessing, the choice of control samples, peak normalization, and motif discovery. We found that avoiding PCR amplification artifacts, normalizing to input RNA or mRNAseq, and defining the background model from control samples can reduce the bias introduced by RNA abundance and improve the quality of detected binding sites. Our findings can serve as a general guideline for CLIP experiments design and the comprehensive analysis of CLIP-Seq data.

Functional analysis of long noncoding RNAs in development and disease

Once viewed as part of the "dark matter" of genome, long noncoding RNAs (lncRNAs), which are mRNA-like but lack open reading frames, have emerged as an integral part of the mammalian transcriptome. Recent work demonstrated that lncRNAs play multiple structural and functional roles, and their analysis has become a new frontier in biomedical research. In this chapter, we provide an overview of different lncRNA families, describe methodologies available to study lncRNA-protein and lncRNA-DNA interactions systematically, and use well-studied lncRNAs as examples to illustrate their functional importance during normal development and in disease states.

Molecular functions of small regulatory noncoding RNA

Recently, using large-scale genomic sequencing, a great number of small noncoding RNAs (ncRNA) has been discovered. Short ncRNAs can be classified into three major classes--small interfering RNA (siRNA), microRNA (miRNA), and piwi-interacting RNA (piRNA). These short ncRNAs ranging from 20 to 300 nt in size are now recognized as a new paradigm of gene regulation for controlling many biological processes. In this paper, we review the biogenesis and recent research on the functions of small regulatory non-coding RNAs and aim at understanding their important functions in living organisms.

Tdrkh is essential for spermatogenesis and participates in primary piRNA biogenesis in the germline

Piwi proteins and Piwi-interacting RNAs (piRNAs) repress transposition, regulate translation, and guide epigenetic programming in the germline. Here, we show that an evolutionarily conserved Tudor and KH domain-containing protein, Tdrkh (a.k.a. Tdrd2), is required for spermatogenesis and involved in piRNA biogenesis. Tdrkh partners with Miwi and Miwi2 via symmetrically dimethylated arginine residues in Miwi and Miwi2. Tdrkh is a mitochondrial protein often juxtaposed to pi-bodies and piP-bodies and is required for Tdrd1 cytoplasmic localization and Miwi2 nuclear localization. Tdrkh mutants display meiotic arrest at the zygotene stage, attenuate methylation of Line1 DNA, and upregulate Line1 RNA and protein, without inducing apoptosis. Furthermore, Tdrkh mutants have severely reduced levels of mature piRNAs but accumulate a distinct population of 1'U-containing, 2'O-methylated 31-37 nt RNAs that largely complement the missing mature piRNAs. Our results demonstrate that the primary piRNA biogenesis pathway involves 3'→5' processing of 31-37 nt intermediates and that Tdrkh promotes this final step of piRNA biogenesis but not the ping-pong cycle. These results shed light on mechanisms underlying primary piRNA biogenesis, an area in which information is conspicuously absent.

Bioinformatic identification of novel elements potentially involved in messenger RNA fate control during spermatogenesis

In eukaryotic cells, 3' untranslated regions (3' UTRs) of mRNA transcripts contain conserved sequence elements (motifs), which, once bound by RNA-binding proteins, can affect mRNA stability and translational efficacy. Despite abundant sequences contained within the 3' UTRs, only a limited number of motifs are known to interact with RNA-binding proteins and have a role in mRNA fate control. Spermatogenesis represents an excellent in vivo model for studying posttranscriptional regulation of gene expression because numerous mRNAs are transcribed in late pachytene spermatocytes and/or round spermatids, but their translation will not occur until many hours or even days later, when they have developed into elongated spermatids, in which transcription has long been shut off because of the increasingly condensed chromatin. Translationally suppressed mRNAs are sequestered and confined to ribonuclear protein particles, and their loading onto the ribosomes marks their translation. By bioinformatic sequence analyses of the 3' UTRs of translationally suppressed mRNAs during spermatogenesis, we identified numerous novel sequence elements overrepresented in the transcripts subject to posttranscriptional regulation than in the unregulated transcripts. These include AU(U/A)(U/A)UGAGU and (A/U)AUUA(U/C/G) for genes translationally upregulated in early spermiogenesis, and (G/A)GUACG(U/C/A)(A/U)(A/U) and UGUAGC for genes translationally upregulated in late spermiogenesis. The bioinformatic approach reported in this study can be adapted for rapid discovery of novel regulatory elements involved in mRNA fate control in a wide range of tissues or organs.

Identification of RNA-protein interaction networks using PAR-CLIP

All mRNA molecules are subject to some degree of post-transcriptional gene regulation (PTGR) involving sequence-dependent modulation of splicing, cleavage and polyadenylation, editing, transport, stability, and translation. The recent introduction of deep-sequencing technologies enabled the development of new methods for broadly mapping interaction sites between RNA-binding proteins (RBPs) and their RNA target sites. In this article, we review crosslinking and immunoprecipitation (CLIP) methods adapted for large-scale identification of target RNA-binding sites and the respective RNA recognition elements. CLIP methods have the potential to detect hundreds of thousands of binding sites in single experiments although the separation of signal from noise can be challenging. As a consequence, each CLIP method has developed different strategies to distinguish true targets from background. We focus on photoactivatable ribonucleoside-enhanced CLIP, which relies on the intracellular incorporation of photoactivatable ribonucleoside analogs into nascent transcripts, and yields characteristic sequence changes upon crosslinking that facilitate the separation of signal from noise. The precise knowledge of the position and distribution of binding sites across mature and primary mRNA transcripts allows critical insights into cellular localization and regulatory function of the examined RBP. When coupled with other systems-wide approaches measuring transcript and protein abundance, the generation of high-resolution RBP-binding site maps across the transcriptome will broaden our understanding of PTGR and thereby lead to new strategies for therapeutic treatment of genetic diseases perturbing these processes.

Control of messenger RNA fate by RNA-binding proteins: an emphasis on mammalian spermatogenesis

Posttranscriptional status of messenger RNAs (mRNA) can be affected by many factors, most of which are RNA-binding proteins (RBP) that either bind mRNA in a nonspecific manner or through specific motifs, usually located in the 3' untranslated regions. RBPs can also be recruited by small noncoding RNAs (sncRNA), which have been shown to be involved in posttranscriptional regulations and transposon repression (eg, microRNAs or P-element-induced wimpy testis-interacting RNA) as components of the sncRNA effector complex. Non-sncRNA-binding RBPs have much more diverse effects on their target mRNAs. Some can cause degradation of their target transcripts and/or repression of translation, whereas others can stabilize and/or activate translation. The splicing and exportation of transcripts from the nucleus to the cytoplasm are often mediated by sequence-specific RBPs. The mechanisms by which RBPs regulate mRNA transcripts involve manipulating the 3' poly(A) tail, targeting the transcript to polysomes or to other ribonuclear protein particles, recruiting regulatory proteins, or competing with other RBPs. Here, we briefly review the known mechanisms of posttranscriptional regulation mediated by RBPs, with an emphasis on how these mechanisms might control spermatogenesis in general.

Widespread expression of piRNA-like molecules in somatic tissues

Piwi-interacting RNA (piRNA) are small RNA abundant in the germline across animal species. In fruit flies and mice, piRNA have been implicated in maintenance of genomic integrity by transposable elements silencing. Outside of the germline, piRNA have only been found in fruit fly ovarian follicle cells. Previous studies have further reported presence of multiple piRNA-like small RNA (pilRNA) in fly heads and a small number of pilRNA have been reported in mouse tissues and in human NK cells. Here, we analyze high-throughput small RNA sequencing data in more than 130 fruit fly, mouse and rhesus macaque samples. The results show widespread presence of pilRNA, displaying all known characteristics of piRNA in multiple somatic tissues of these three species. In mouse pancreas and macaque epididymis, pilRNA abundance was compatible with piRNA abundance in the germline. Using in situ hybridizations, we further demonstrate pilRNA co-localization with mRNA expression of Piwi-family genes in all macaque tissues. Further, using western blot, we have shown the expression of Miwi protein in mouse pancreas. These findings indicate that piRNA-like molecules might play important roles outside of the germline.

RNA-protein interactions in human health and disease

It is now clear that the genomes of many organisms encode thousands of large and small non-coding (nc)RNAs. However, relative to the discovery of ncRNAs the functions and mechanisms of ncRNAs remain disproportionately understood. One intriguing observation is that many ncRNAs are found to be associated with protein complexes including those involved in transcription regulation, post-transcriptional silencing, and epigentic regulation. These observations suggest that the functions and mechanisms of many of these ncRNAs may depend on their interactions with various protein complexes within the cell. In this review we discuss well known examples as well as newly emerging evidence of a widespread RNA-protein interactions in distinct biological processes in a wide range of organisms, and highlight the importance of developing new technologies to dissect these interactions. Finally, we propose that mis-regulation of ncRNAs interactions with their protein partners may contribute to human disease, and open up a novel approach to therapeutic interventions.

The roles of the DAZ family in spermatogenesis: More than just translation?

The DAZ family of genes are important fertility factors in animals, including humans. The family consists of Y-linked DAZ, and autosomal homologs Boule and Dazl. All three genes encode RNA-binding proteins that are nearly exclusively expressed in germ cells. The DAZ family is highly conserved, with ancestral Boule present in sea anemones through humans, Dazl conserved among vertebrates, and DAZ present only in higher primates. Here we review studies on DAZ family genes from multiple organisms, and summarize the common features of each DAZ gene and their roles during spermatogenesis in animals. DAZ family proteins are thought to activate the translation of RNA targets, but recent work has uncovered additional functions. Boule, Dazl, and DAZ likely function through similar mechanisms, and we present known functions of the DAZ family in spermatogenesis, and discuss possible mechanisms in addition to translation activation.

Polypyrimidine tract-binding protein 2 binds to selective, intronic messenger RNA and microRNA targets in the mouse testis

Here we use an in vivo cross-linking and immunoprecipitation procedure to detect RNA targets of the multifunctional RNA-binding protein polypyrimidine tract-binding protein (PTBP) 2 in mouse testis. Eleven known mRNAs, including Ptbp2 mRNA, 28 RNAs matching intron sequences, and 12 small RNAs and repeat sequences are identified. The specificity of interaction between PTBP2 and its target RNAs was confirmed using RNA interference with mouse N2A cells. Reduction of PTBP2 levels led to decreases in 7 of 10 of the mRNAs, to the repression of alternative splicing of introns, and to reductions in specific miRNAs.

RNA regulation in neurologic disease and cancer

The paraneoplastic neurologic diseases (PNDs) are brain degenerations that develop in the setting of clinically inapparent cancers. PNDs arise when common cancers express brain proteins, triggering an anti-tumor immune response and tumor immunity. Research on these brain-cancer proteins has revealed a new world of neuron-specific RNA binding proteins whose functions may be aberrantly used by tumor cells. Efforts to gain insight into their function has led to the development of new methods and strategies to understand RNA protein regulation in living tissues.

HITS-CLIP: panoramic views of protein-RNA regulation in living cells

The study of gene regulation in cells has recently begun to shift from a period dominated by the study of transcription factor-DNA interactions to a new focus on RNA regulation. This was sparked by the still-emerging recognition of the central role for RNA in cellular complexity emanating from the RNA World hypothesis, and has been facilitated by technologic advances, in particular high throughput RNA sequencing and crosslinking methods (RNA-Seq, CLIP, and HITS-CLIP). This study will place these advances in context, and, focusing on CLIP, will explain the method, what it can be used for, and how to approach using it. Examples of the successes, limitations, and future of the technique will be discussed.

Non-coding RNAs: regulators of disease

For 50 years the term 'gene' has been synonymous with regions of the genome encoding mRNAs that are translated into protein. However, recent genome-wide studies have shown that the human genome is pervasively transcribed and produces many thousands of regulatory non-protein-coding RNAs (ncRNAs), including microRNAs, small interfering RNAs, PIWI-interacting RNAs and various classes of long ncRNAs. It is now clear that these RNAs fulfil critical roles as transcriptional and post-transcriptional regulators and as guides of chromatin-modifying complexes. Here we review the biology of ncRNAs, focusing on the fundamental mechanisms by which ncRNAs facilitate normal development and physiology and, when dysfunctional, underpin disease. We also discuss evidence that intergenic regions associated with complex diseases express ncRNAs, as well as the potential use of ncRNAs as diagnostic markers and therapeutic targets. Taken together, these observations emphasize the need to move beyond the confines of protein-coding genes and highlight the fact that continued investigation of ncRNA biogenesis and function will be necessary for a comprehensive understanding of human disease.