Genomic maps of long noncoding RNA occupancy reveal principles of RNA-chromatin interactions

Long noncoding RNAs (lncRNAs) are key regulators of chromatin state, yet the nature and sites of RNA-chromatin interaction are mostly unknown. Here we introduce Chromatin Isolation by RNA Purification (ChIRP), where tiling oligonucleotides retrieve specific lncRNAs with bound protein and DNA sequences, which are enumerated by deep sequencing. ChIRP-seq of three lncRNAs reveal that RNA occupancy sites in the genome are focal, sequence-specific, and numerous. Drosophila roX2 RNA occupies male X-linked gene bodies with increasing tendency toward the 3' end, peaking at CES sites. Human telomerase RNA TERC occupies telomeres and Wnt pathway genes. HOTAIR lncRNA preferentially occupies a GA-rich DNA motif to nucleate broad domains of Polycomb occupancy and histone H3 lysine 27 trimethylation. HOTAIR occupancy occurs independently of EZH2, suggesting the order of RNA guidance of Polycomb occupancy. ChIRP-seq is generally applicable to illuminate the intersection of RNA and chromatin with newfound precision genome wide.     

RNA quality control in the nucleus: The Angels' share of RNA

Biological processes are not exempt from errors and RNA production is not an exception to this rule. Errors can arise stochastically or be genetically fixed and systematically appear in the biochemical or cellular phenotype. In any case, quality control mechanisms are essential to minimize the potentially toxic effects of faulty RNA production or processing. Although many RNA molecules express their functional potential in the cytoplasm, as messengers, adaptors or operators of gene expression pathways, a large share of quality control occurs in the nucleus. This is likely because the early timing of occurrence and the subcellular partition make the control more efficient, at least as long as the defects can be detected ahead of the cytoplasmic phase of the RNA life cycle. One crucial point in discussing RNA quality control resides in its definition. A stringent take would imply the existence of specific mechanisms to recognize the error and the consequent repair or elimination of the faulty molecule. One example in the RNA field could be the recognition of a premature stop codon by the nonsense-mediated decay pathway, discussed elsewhere in this issue. A more relaxed view posits that the thermodynamic or kinetic aftermath of a mistake (e.g. a blockage or a delay in processing) by itself constitutes the recognition event, which triggers downstream quality control. Because whether inappropriate molecules are specifically recognized remains unclear in many cases, we will adopt the more relaxed definition of RNA quality control. RNA repair remains episodic and the degradative elimination of crippled molecules appears to be the rule. Therefore we will briefly describe the actors of RNA degradation in the nucleus. Detailed analyses of the mechanism of action of these enzymes can be found in several excellent and recent reviews, including in this issue. Finally, we will restrict our analysis to the yeast model, which is used in the majority of RNA quality control studies, but examples exist in the literature indicating that many of the principles of RNA quality control described in yeast also apply to other eukaryotes. This article is part of a Special Issue entitled: RNA Decay mechanisms.     

Presence of RNA in the sperm nucleus

The RNase-colloidal gold procedure for the ultrastructural localization of RNA was used for rat testis. Along with other structures, it was found that the testicular sperm nucleus was well stained. Similar labelling was observed in the nucleus of rat epididymal sperm and human sperm. The RNA was extracted from sperm and analyzed by electrophoresis on 10% polyacrylamide gel and 7 M urea. The electrophoretic profile revealed a complex set of bands ranging in size from tRNA to high molecular weight components. On the average, a content of about 0.1 pg of RNA per rat or human sperm was found.     

时序调控小分子RNA的研究进展

长期以来,RNA被认为在细胞中只传递信息和氨基酸,但现在因其多功能而颇受瞩目.小分子RNA能够关闭一种线虫的基因,相似于植物中的"基因沉默",基因功能研究因此又向前迈进了一步.主要对时序调控小分子RNA在基因表达调控中的作用,即其对发育时间机制的控制进行了论述.     

Transfer RNA biogenesis: A visa to leave the nucleus

Only correctly folded and mature tRNAs can leave the nucleus and enter the cytoplasm. Surprisingly, tRNA-aminoacylation has been found to occur, not only in the cytosol, but also inside the nucleus, where it may act as an additional proofreading step and facilitate the export of 'ready-to-function' aminoacyl-tRNAs.     

Small nucleolar RNA

The review considers small nucleolar RNAs (snoRNAs), an abundant group of non-protein-coding RNAs. In association with proteins, snoRNAs determine the two most common nucleotide modifications in rRNA and some other cell RNAs: 2′-O-methylation of ribose and pseudouridylation. In addition, snoRNAs are involved in pre-mRNA cleavage and the telomerase function. Almost all snoRNAs fall into two families, C/D and H/ACA, distinguished by conserved sequence boxes. Although the proteins of C/D and H/ACA snoRNPs have homologous regions, these snoRNPs are assembled differently. The RNA components of RNases P and MRP are also classed with snoRNAs. Another problem considered is the structure and function of small RNAs from Cajal bodies (small organelles associated with the nucleoli), which are similar to snoRNAs.     

Small RNA in rice genome

Rice has many characteristics of a model plant. The recent completion of the draft of the rice genome represents an important advance in our knowledge of plant biology and also has an important contribution to the understanding of general genomic evolution. Besides the rice genome finishing map, the next urgent step for rice researchers is to annotate the genes and noncoding functional sequences. The recent work shows that noncoding RNAs (ncRNAs) play significant roles in biological systems. We have explored all the known small RNAs (a kind of ncRNA) within rice genome and other six species sequences, including Arabidopsis, maize, yeast, worm, mouse and pig. As a result we find 160 out of 552 small RNAs (sRNAs) in database have homologs in 108 rice scaffolds, and almost all of them (99.41%) locate in intron regions of rice by gene predication. 19 sRNAs only appear in rice. More importantly, we find two special LJ14 sRNAs: one is located in a set of sRNA ZMU14SNR9(s) which only appears in three plants, 86% sequences of them can be compared as the same sequence in rice, Arabidopsis and maize; the other conserved sRNA XLHS7CU14 has a segment which appears in almost all these species from plants to animals. All these results indicate that sRNA do not have evident borderline between plants and animals.     

Small RNA in rice genome

Rice has many characteristics of a model plant. The recent completion of the draft of the rice genome represents an important advance in our knowledge of plant biology and also has an important contribution to the understanding of general genomic evolution. Besides the rice genome finishing map, the next urgent step for rice researchers is to annotate the genes and non-coding functional sequences. The recent work shows that noncoding RNAs (ncRNAs) play significant roles in biological systems. We have explored all the known small RNAs (a kind of ncRNA) within rice genome and other six species sequences, including Arabidopsis, maize, yeast, worm, mouse and pig. As a result we find 160 out of 552 small RNAs (sRNAs) in database have ho-mologs in 108 rice scaffolds, and almost all of them (99.41 %) locate in intron regions of rice by gene predication. 19 sRNAs only appear in rice. More importantly, we find two special U14 sRNAs: one is located in a set of sRNA ZMU14SNR9(s) which only appears in three plants,     

Small worlds in RNA structures

I consider conformational spaces of tRNA^phe defined by sets of suboptimal structures from the perspective of small-world networks. Herein, the influence of modifications on typical small-world network properties and the shape of energy landscapes is discussed. Results indicate that natural modifications influence the degree of local clustering and mean path lengths far more than random or no modifications. High frequencies in the thermodynamic ensemble coincide with high numbers of neighboring structures that one conformation can adopt by one elementary move. Conformation spaces indicate the existence of modular substructures. It can be shown that modifications leave the nature of small-world topology untouched albeit natural modifications have a reasonable enhancing and streamlining effect on the degree of clustering and therefore on the substructures of the conformational space.     

Protein and RNA export from the nucleus

The presence of the nuclear envelope necessitates the movement of proteins and RNAs between the nucleus and the cytoplasm. Elaborate cellular machinery exists to promote the nuclear transport of macromolecules. Recent advances in the field have illuminated our comprehension of both nuclear import and export as powerful means of gene regulation. As our appreciation of the importance of the process has grown, its study has matured, moving beyond the single cell to the entire organism. This review discusses basic mechanisms and regulation of protein, mRNA, and ribosome export with an emphasis on developmental examples.     

Small RNA sorting: matchmaking for Argonautes

Small RNAs directly or indirectly impact nearly every biological process in eukaryotic cells. To perform their myriad roles, not only must precise small RNA species be generated, but they must also be loaded into specific effector complexes called RNA-induced silencing complexes (RISCs). Argonaute proteins form the core of RISCs and different members of this large family have specific expression patterns, protein binding partners and biochemical capabilities. In this Review, we explore the mechanisms that pair specific small RNA strands with their partner proteins, with an eye towards the substantial progress that has been recently made in understanding the sorting of the major small RNA classes - microRNAs (miRNAs) and small interfering RNAs (siRNAs) - in plants and animals.     

The exosome and RNA quality control in the nucleus

To control the quality of RNA biogenesis in the nucleus, cells use sophisticated molecular machines. These machines recognize and degrade not only RNA trimmings--the leftovers of RNA processing--but also incorrectly processed RNAs that contain defects. By using this mechanism, cells ensure that only high-quality RNAs are engaged in protein synthesis and other cellular processes. The exosome--a complex of several exoribonucleolytic and RNA-binding proteins--is the central 3'-end RNA degradation and processing factor in this surveillance apparatus. The exosome operates with auxiliary factors that stimulate its activity and recruit its RNA substrates in the crowded cellular environment. In this review, we discuss recent structural and functional data related to the nuclear quality-control apparatus, including the long-awaited structure of the human exosome and its activity.     

新型非编码小RNA——Piwi-interacting RNA(piRNA)

piRNA(Piwi-interacting RNA)是最近从哺乳动物睾丸组织中发现的一类能与PIWI蛋白质相互作用,且长度分布在26～31nt的新型小分子单链RNA,主要综述piRNA的相关研究进展.     

RNA promotes the formation of spatial compartments in the nucleus

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