RNA turnover and chromatin-dependent gene silencing

The sound of silence: mechanisms and implications of HUSH complex function

The vertebrate genome is under constant threat of invasion by genetic parasites. Whether the host can immediately recognize and respond to invading elements has been unclear. The discovery of the human silencing hub (HUSH) complex, and the finding that it provides immediate protection from genome invasion by silencing products of reverse transcription, have important implications for mammalian genome evolution. In this review, we summarize recent insights into HUSH function and describe how cellular introns provide a novel means of self-nonself discrimination, allowing HUSH to recognize and transcriptionally repress a broad range of intronless genetic elements. We discuss how HUSH contributes to genome evolution, and highlight studies reporting the critical role of HUSH in development and implicating HUSH in the control of immune signaling and cancer progression.

Catalytic activities, molecular connections, and biological functions of plant RNA exosome complexes

RNA exosome complexes provide the main 3'-5'-exoribonuclease activities in eukaryotic cells and contribute to the maturation and degradation of virtually all types of RNA. RNA exosomes consist of a conserved core complex that associates with exoribonucleases and with multimeric cofactors that recruit the enzyme to its RNA targets. Despite an overall high level of structural and functional conservation, the enzymatic activities and compositions of exosome complexes and their cofactor modules differ among eukaryotes. This review highlights unique features of plant exosome complexes, such as the phosphorolytic activity of the core complex, and discusses the exosome cofactors that operate in plants and are dedicated to the maturation of ribosomal RNA, the elimination of spurious, misprocessed, and superfluous transcripts, or the removal of mRNAs cleaved by the RNA-induced silencing complex and other mRNAs prone to undergo silencing.

Genome surveillance by HUSH-mediated silencing of intronless mobile elements

All life forms defend their genome against DNA invasion. Eukaryotic cells recognize incoming DNA and limit its transcription through repressive chromatin modifications. The human silencing hub (HUSH) complex transcriptionally represses long interspersed element-1 retrotransposons (L1s) and retroviruses through histone H3 lysine 9 trimethylation (H3K9me3)1-3. How HUSH recognizes and initiates silencing of these invading genetic elements is unknown. Here we show that HUSH is able to recognize and transcriptionally repress a broad range of long, intronless transgenes. Intron insertion into HUSH-repressed transgenes counteracts repression, even in the absence of intron splicing. HUSH binds transcripts from the target locus, prior to and independent of H3K9me3 deposition, and target transcription is essential for both initiation and propagation of HUSH-mediated H3K9me3. Genomic data reveal how HUSH binds and represses a subset of endogenous intronless genes generated through retrotransposition of cellular mRNAs. Thus intronless cDNA-the hallmark of reverse transcription-provides a versatile way to distinguish invading retroelements from host genes and enables HUSH to protect the genome from 'non-self' DNA, despite there being no previous exposure to the invading element. Our findings reveal the existence of a transcription-dependent genome-surveillance system and explain how it provides immediate protection against newly acquired elements while avoiding inappropriate repression of host genes.

Feed Composition Differences Resulting from Organic and Conventional Farming Practices Affect Physiological Parameters in Wistar Rats-Results from a Factorial, Two-Generation Dietary Intervention Trial

Recent human cohort studies reported positive associations between organic food consumption and a lower incidence of obesity, cancer, and several other diseases. However, there are very few animal and human dietary intervention studies that provide supporting evidence or a mechanistic understanding of these associations. Here we report results from a two-generation, dietary intervention study with male Wistar rats to identify the effects of feeds made from organic and conventional crops on growth, hormonal, and immune system parameters that are known to affect the risk of a number of chronic, non-communicable diseases in animals and humans. A 2 × 2 factorial design was used to separate the effects of contrasting crop protection methods (use or non-use of synthetic chemical pesticides) and fertilizers (mineral nitrogen, phosphorus and potassium (NPK) fertilizers vs. manure use) applied in conventional and organic crop production. Conventional, pesticide-based crop protection resulted in significantly lower fiber, polyphenol, flavonoid, and lutein, but higher lipid, aldicarb, and diquat concentrations in animal feeds. Conventional, mineral NPK-based fertilization resulted in significantly lower polyphenol, but higher cadmium and protein concentrations in feeds. Feed composition differences resulting from the use of pesticides and/or mineral NPK-fertilizer had a significant effect on feed intake, weight gain, plasma hormone, and immunoglobulin concentrations, and lymphocyte proliferation in both generations of rats and in the second generation also on the body weight at weaning. Results suggest that relatively small changes in dietary intakes of (a) protein, lipids, and fiber, (b) toxic and/or endocrine-disrupting pesticides and metals, and (c) polyphenols and other antioxidants (resulting from pesticide and/or mineral NPK-fertilizer use) had complex and often interactive effects on endocrine, immune systems and growth parameters in rats. However, the physiological responses to contrasting feed composition/intake profiles differed substantially between the first and second generations of rats. This may indicate epigenetic programming and/or the generation of "adaptive" phenotypes and should be investigated further.

Long-term experimental evolution reveals purifying selection on piRNA-mediated control of transposable element expression

Background

Transposable elements (TEs) are an almost universal constituent of eukaryotic genomes. In animals, Piwi-interacting small RNAs (piRNAs) and repressive chromatin often play crucial roles in preventing TE transcription and thus restricting TE activity. Nevertheless, TE content varies widely across eukaryotes and the dynamics of TE activity and TE silencing across evolutionary time is poorly understood.

Results

Here, we used experimentally evolved populations of C. elegans to study the dynamics of TE expression over 409 generations. The experimental populations were evolved at population sizes of 1, 10 and 100 individuals to manipulate the efficiency of natural selection versus genetic drift. We demonstrate increased TE expression relative to the ancestral population, with the largest increases occurring in the smallest populations. We show that the transcriptional activation of TEs within active regions of the genome is associated with failure of piRNA-mediated silencing, whilst desilenced TEs in repressed chromatin domains retain small RNAs. Additionally, we find that the sequence context of the surrounding region influences the propensity of TEs to lose silencing through failure of small RNA-mediated silencing.

Conclusions

Our results show that natural selection in C. elegans is responsible for maintaining low levels of TE expression, and provide new insights into the epigenomic features responsible.

Architectural RNA in chromatin organization

RNA plays a well-established architectural role in the formation of membraneless interchromatin nuclear bodies. However, a less well-known role of RNA is in organizing chromatin, whereby specific RNAs have been found to recruit chromatin modifier proteins. Whether or not RNA can act as an architectural molecule for chromatin remains unclear, partly because dissecting the architectural role of RNA from its regulatory role remains challenging. Studies that have addressed RNA's architectural role in chromatin organization rely on in situ RNA depletion using Ribonuclease A (RNase A) and suggest that RNA plays a major direct architectural role in chromatin organization. In this review, we will discuss these findings, candidate chromatin architectural long non-coding RNAs and possible mechanisms by which RNA, along with RNA binding proteins might be mediating chromatin organization.

A Nuclear RNA Degradation Pathway Helps Silence Polycomb/H3K27me3-Marked Loci in Caenorhabditis elegans

In fission yeast and plants, RNA-processing pathways contribute to heterochromatin silencing, complementing well-characterized pathways of transcriptional repression. However, it was unclear whether this additional level of regulation occurs in metazoans. In a genetic screen, we uncovered a pathway of silencing in Caenorhabditis elegans somatic cells, whereby the highly conserved, RNA-binding complex LSM2-8 contributes to the repression of heterochromatic reporters and endogenous genes bearing the Polycomb mark H3K27me3. Importantly, the LSM2-8 complex works cooperatively with a 5'-3' exoribonuclease, XRN-2, and disruption of the pathway leads to selective mRNA stabilization. LSM2-8 complex-mediated RNA degradation does not target nor depend on H3K9me2/me3, unlike previously described pathways of heterochromatic RNA degradation. Up-regulation of lsm-8-sensitive loci coincides with a localized drop in H3K27me3 levels in the lsm-8 mutant. Put into the context of epigenetic control of gene expression, it appears that targeted RNA degradation helps repress a subset of H3K27me3-marked genes, revealing an unappreciated layer of regulation for facultative heterochromatin in animals.

LSM2-8 and XRN-2 contribute to the silencing of H3K27me3-marked genes through targeted RNA decay

In fission yeast and plants, RNA-processing and degradation contribute to heterochromatin silencing, alongside conserved pathways of transcriptional repression. It was unknown if similar pathways exist in metazoans. Here we describe a pathway of silencing in C. elegans somatic cells, in which the highly conserved RNA binding complex LSM2-8 contributes selectively to the repression of heterochromatic reporters and endogenous genes bearing the Polycomb mark, histone H3K27me3. It acts by degrading selected transcripts through the XRN-2 exoribonuclease. Disruption of the LSM2-8 pathway leads to mRNA stabilization. Unlike previously described pathways of heterochromatic RNA degradation, LSM2-8-mediated RNA degradation does not require nor deposit H3K9 methylation. Rather, loss of this pathway coincides with a localized reduction in H3K27me3 at lsm-8-sensitive loci. Thus, we have uncovered a mechanism of RNA degradation that selectively contributes to the silencing of a subset of H3K27me3-marked genes, revealing a previously unrecognized layer of post-transcriptional control in metazoan heterochromatin.

Nuclear Ccr4-Not mediates the degradation of telomeric and transposon transcripts at chromatin in the Drosophila germline

Ccr4-Not is a highly conserved complex involved in cotranscriptional RNA surveillance pathways in yeast. In Drosophila, Ccr4-Not is linked to the translational repression of miRNA targets and the posttranscriptional control of maternal mRNAs during oogenesis and embryonic development. Here, we describe a new role for the Ccr4-Not complex in nuclear RNA metabolism in the Drosophila germline. Ccr4 depletion results in the accumulation of transposable and telomeric repeat transcripts in the fraction of chromatin-associated RNA; however, it does not affect small RNA levels or the heterochromatin state of the target loci. Nuclear targets of Ccr4 mainly comprise active full-length transposable elements (TEs) and telomeric and subtelomeric repeats. Moreover, Ccr4-Not foci localize at telomeres in a Piwi-dependent manner, suggesting a functional relationship between these pathways. Indeed, we detected interactions between the components of the Ccr4-Not complex and piRNA machinery, which indicates that these pathways cooperate in the nucleus to recognize and degrade TE transcripts at transcription sites. These data reveal a new layer of transposon control in the germline, which is critical for the maintenance of genome integrity.

Comparative cytogenetic of six species of Amazonian Peacock bass (Cichla, Cichlinae): intrachromosomal variations and genetic introgression among sympatric species

Cytogenetic data for the genus Cichla Bloch et Schneider, 1801 are still very limited, with only four karyotype descriptions to date. The sum of the available cytogenetic information for Cichla species, points to a maintenance of the diploid number of 48 acrocentric chromosomes, considered a typical ancestral feature in cichlids. In the current study, we performed molecular and classical cytogenetic analyses of the karyotype organization of six species of Cichla, the earliest-diverging genus of Neotropical cichlids. We cytogenetically analysed Cichla kelberi Kullander et Ferreira, 2006, Cichla monoculus Agassiz, 1831, Cichla piquiti Kullander et Ferreira, 2006, Cichla temensis Humboldt, 1821, Cichla vazzoleri Kullander et Ferreira, 2006 and Cichla pinima Kullander et Ferreira, 2006, including three individuals that showed mixed morphological characteristics, likely from different species, suggesting they were hybrid individuals. All individuals analysed showed 2n = 48 acrocentric chromosomes, with centromeric heterochromatic blocks on all chromosomes and a terminal heterochromatic region on the q arm of the 2^nd pair. Mapping 18S rDNA gave hybridization signals, correlated with the nucleolus organizer regions, on the 2^nd pair for all analyzed individuals. However, we found distinct patterns for 5S rDNA: interstitially at the proximal position on 6^th pair of four species (C. kelberi, C. pinima, C. piquiti and C. vazzoleri), and on the distal of the 4^th pair in two (C. monoculus and C. temensis). Accordingly, we present here new data for the genus and discuss the evolutionary trends in the karyotype of this group of fish. In addition, we provide data that supports the occurrence of hybrid individuals in the Uatumã River region, mainly based on 5S rDNA mapping.

Molecular mechanisms of epigenetic inheritance: Possible evolutionary implications

Recently interest in multi-generational epigenetic phenomena have been fuelled by highly reproducible intergenerational and transgenerational inheritance paradigms in several model organisms. Such paradigms are essential in order to begin to use genetics to unpick the mechanistic bases of how epigenetic information may be transmitted between generations; indeed great strides have been made towards understanding these mechanisms. Far less well understood is the relationship between epigenetic inheritance, ecology and evolution. In this review I focus on potential connections between laboratory studies of transgenerational epigenetic inheritance phenomena and evolutionary processes that occur in natural populations. In the first section, I consider whether transgenerational epigenetic inheritance might provide an advantage to organisms over the short term in adapting to their environment. Second, I consider whether epigenetic changes can contribute to the evolution of species by contributing to stable phenotypic variation within a population. Finally I discuss whether epigenetic changes could influence evolution by either directly or indirectly promoting DNA sequence changes that could impact phenotypic divergence. Additionally, I will discuss how epigenetic changes could influence the evolution of human cancer and thus be directly relevant for the development of this disease.

Genomic Organization Under Different Environmental Conditions: Hoplosternum Littorale as a Model

The Amazon has abundant rivers, streams, and floodplains in both polluted and nonpolluted environments, which show great adaptability. Thus, the goal of this study was to map repetitive DNA sequences in both mitotic chromosomes and erythrocyte micronuclei of tamoatás from polluted and nonpolluted environments and to assess the possible genotoxic effects of these environments. Individuals were collected in Manaus, Amazonas (AM), and submitted to classical and molecular cytogenetic techniques, as well as to a blood micronucleus test. Diploid number equal to 60 chromosomes are present in all individuals, with 18S ribosomal DNA sites present in one chromosome pair and no interstitial telomeric sites on chromosomes. The micronucleus test showed no significant differences in pairwise comparisons between environments or collection sites, but the Rex3 retroelement was dispersed on the chromosomes of individuals from unpolluted environments and compartmentalized in individuals from polluted environments. Divergent numbers of 5S rDNA sites are present in individuals from unpolluted and polluted environments. The mapping of repetitive sequences revealed that micronuclei have different compositions both intra- and interindividually that suggests different regions are lost in the formation of micronuclei, and no single fragile region undergoes breaks, although repetitive DNA elements are involved in this process.

Differential repetitive DNA composition in the centromeric region of chromosomes of Amazonian lizard species in the family Teiidae

Differences in heterochromatin distribution patterns and its composition were observed in Amazonian teiid species. Studies have shown repetitive DNA harbors heterochromatic blocks which are located in centromeric and telomeric regions in Ameiva ameiva (Linnaeus, 1758), Kentropyx calcarata (Spix, 1825), Kentropyx pelviceps (Cope, 1868), and Tupinambis teguixin (Linnaeus, 1758). In Cnemidophorus sp.1, repetitive DNA has multiple signals along all chromosomes. The aim of this study was to characterize moderately and highly repetitive DNA sequences by C ot1-DNA from Ameiva ameiva and Cnemidophorus sp.1 genomes through cloning and DNA sequencing, as well as mapping them chromosomally to better understand its organization and genome dynamics. The results of sequencing of DNA libraries obtained by C ot1-DNA showed that different microsatellites, transposons, retrotransposons, and some gene families also comprise the fraction of repetitive DNA in the teiid species. FISH using C ot1-DNA probes isolated from both Ameiva ameiva and Cnemidophorus sp.1 showed these sequences mainly located in heterochromatic centromeric, and telomeric regions in Ameiva ameiva, Kentropyx calcarata, Kentropyx pelviceps, and Tupinambis teguixin chromosomes, indicating they play structural and functional roles in the genome of these species. In Cnemidophorus sp.1, C ot1-DNA probe isolated from Ameiva ameiva had multiple interstitial signals on chromosomes, whereas mapping of C ot1-DNA isolated from the Ameiva ameiva and Cnemidophorus sp.1 highlighted centromeric regions of some chromosomes. Thus, the data obtained showed that many repetitive DNA classes are part of the genome of Ameiva ameiva, Cnemidophorus sp.1, Kentroyx calcarata, Kentropyx pelviceps, and Tupinambis teguixin, and these sequences are shared among the analyzed teiid species, but they were not always allocated at the same chromosome position.

H3K9 methylation extends across natural boundaries of heterochromatin in the absence of an HP1 protein

Proteins of the conserved HP1 family are elementary components of heterochromatin and are generally assumed to play a central role in the creation of a rigid, densely packed heterochromatic network that is inaccessible to the transcription machinery. Here, we demonstrate that the fission yeast HP1 protein Swi6 exists as a single highly dynamic population that rapidly exchanges in cis and in trans between different heterochromatic regions. Binding to methylated H3K9 or to heterochromatic RNA decelerates Swi6 mobility. We further show that Swi6 is largely dispensable to the maintenance of heterochromatin domains. In the absence of Swi6, H3K9 methylation levels are maintained by a mechanism that depends on polymeric self‐association properties of Tas3, a subunit of the RNA‐induced transcriptional silencing complex. Our results disclose a surprising role for Swi6 dimerization in demarcating constitutive heterochromatin from neighboring euchromatin. Thus, rather than promoting maintenance and spreading of heterochromatin, Swi6 appears to limit these processes and appropriately confine heterochromatin.

mRNA quality control goes transcriptional

Eukaryotic mRNAs are extensively processed to generate functional transcripts, which are 5′ capped, spliced and 3′ polyadenylated. Accumulation of unprocessed (aberrant) mRNAs can be deleterious for the cell, hence processing fidelity is closely monitored by QC (quality control) mechanisms that identify erroneous transcripts and initiate their selective removal. Nucleases including Xrn2/Rat1 and the nuclear exosome have been shown to play an important role in the turnover of aberrant mRNAs. Recently, with the growing appreciation that mRNA processing occurs concomitantly with polII (RNA polymerase II) transcription, it has become evident that QC acts at the transcriptional level in addition to degrading aberrant RNAs. In the present review, we discuss mechanisms that allow cells to co-transcriptionally initiate the removal of RNAs as well as down-regulate transcription of transcripts where processing repeatedly fails.

Chromatin-associated ncRNA activities

RNA transcripts that do not code for proteins have been long known to lie at the heart of many biological processes, such as splicing and translation. Yet their full potential has only been appreciated recently and non-coding RNAs (ncRNAs) are now attracting increasing attention. Pioneering work in yeast and plant systems has revealed that non-coding RNAs can have a major influence on the deposition of histone and DNA modifications. This can introduce heritable variation into gene expression and, thus, be the basis of epigenetic phenomena. Mechanistically, such processes have been studied extensively in the fission yeast Schizosaccharomyces pombe, providing an important conceptual framework for possible modes of action of ncRNAs also in other organisms. In this review, we highlight mechanistic insights into chromatin-associated ncRNA activities gained from work with fission yeast, and we draw parallels to studies in other eukaryotes that indicate evolutionary conservation.

Heterochromatic gene silencing by activator interference and a transcription elongation barrier

Heterochromatin silences transcription, contributing to development, differentiation, and genome stability in eukaryotic organisms. Budding yeast heterochromatic silencing is strictly dependent on the silent information regulator (SIR) complex composed of the Sir2 histone deacetylase and the chromatin-interacting proteins Sir3 and Sir4. We use reconstituted SIR heterochromatin to characterize the steps in transcription that are disrupted to achieve silencing. Transcriptional activator binding is permitted before and after heterochromatin assembly. A comprehensive proteomic approach identified heterochromatin-mediated disruption of activator interactions with coactivator complexes. We also find that if RNA polymerase II (Pol II) is allowed to initiate transcription, the SIR complex blocks elongation on chromatin while maintaining Pol II in a halted conformation. This Pol II elongation barrier functions for even one nucleosome, is more effective when assembled with multiple nucleosomes, and is sensitive to a histone mutation that is known to disrupt silencing. This dual mechanism of silencing suggests a conserved principle of heterochromatin in assembling a specific structure that targets multiple steps to achieve repression.

HP1(Swi6) mediates the recognition and destruction of heterochromatic RNA transcripts

HP1 proteins are major components of heterochromatin, which is generally perceived to be an inert and transcriptionally inactive chromatin structure. Yet, HP1 binding to chromatin is highly dynamic and robust silencing of heterochromatic genes can involve RNA processing. Here, we demonstrate by a combination of in vivo and in vitro experiments that the fission yeast HP1(Swi6) protein guarantees tight repression of heterochromatic genes through RNA sequestration and degradation. Stimulated by positively charged residues in the hinge region, RNA competes with methylated histone H3K9 for binding to the chromodomain of HP1(Swi6). Hence, HP1(Swi6) binding to RNA is incompatible with stable heterochromatin association. We propose a model in which an ensemble of HP1(Swi6) proteins functions as a heterochromatin-specific checkpoint, capturing and priming heterochromatic RNAs for the RNA degradation machinery. Sustaining a functional checkpoint requires continuous exchange of HP1(Swi6) within heterochromatin, which explains the dynamic localization of HP1 proteins on heterochromatin.

Long noncoding RNA: unveiling hidden layer of gene regulatory networks

Long noncoding RNAs (lncRNAs) are increasingly recognized as functional regulatory components in eukaryotic gene regulation. Distinct classes of lncRNAs have been identified in eukaryotes and they play roles in various regulatory networks. Previously characterized lncRNAs include primary transcripts for small regulatory RNAs. In the era of deep sequencing, new classes of lncRNAs have emerged as potent regulatory components in gene regulation. Recent studies showed that many lncRNAs are potent cis- and trans-regulators of gene activity and they can function as scaffolds for chromatin-modifying complexes. Furthermore, differential expressions of lncRNAs suggest that transcription of lncRNAs can modulate gene activity during development and in response to external stimuli. Here, we summarize our current understanding on potential roles of lncRNAs in plants.

Dicer associates with chromatin to repress genome activity in Schizosaccharomyces pombe

In the fission yeast S. pombe, the RNA interference (RNAi) pathway is required to generate small interfering RNAs (siRNAs) that mediate heterochromatic silencing of centromeric repeats. Here, we demonstrate that RNAi also functions to repress genomic elements other than constitutive heterochromatin. Using DNA adenine methyltransferase identification (DamID), we show that the RNAi proteins Dcr1 and Rdp1 physically associate with some euchromatic genes, noncoding RNA genes and retrotransposon long terminal repeats, and that this association is independent of the Clr4 histone methyltransferase. Physical association of RNAi with chromatin is sufficient to trigger a silencing response but not to assemble heterochromatin. The mode of silencing at the newly identified RNAi targets is consistent with a co-transcriptional gene silencing model, as proposed earlier, and functions with trace amounts of siRNAs. We anticipate that similar mechanisms could also be operational in other eukaryotes.

Wisely chosen paths--regulation of rRNA synthesis: delivered on 30 June 2010 at the 35th FEBS Congress in Gothenburg, Sweden

All cells, from prokaryotes to vertebrates, synthesize enormous amounts of rRNA to produce 1-2 million ribosomes per cell cycle, which are required to maintain the protein synthesis capacity of the daughter cells. In recent years, considerable progress has been made in the elucidation of the basic principles of transcriptional regulation and the pathways that adapt cellular rRNA synthesis to metabolic activity, a process that is essential for understanding the link between nucleolar activity, cell growth, proliferation, and apoptosis. I will survey our present knowledge of the highly coordinated networks that regulate transcription by RNA polymerase I, coordinating rRNA gene transcription and ribosome production with environmental cues. Moreover, I will discuss the epigenetic mechanisms that control the chromatin structure and transcriptional activity of rRNA genes, in particular the role of noncoding RNA in DNA methylation and transcriptional silencing.

Interaction of noncoding RNA with the rDNA promoter mediates recruitment of DNMT3b and silencing of rRNA genes

Noncoding RNAs are important components of regulatory networks controlling the epigenetic state of chromatin. We analyzed the role of pRNA (promoter-associated RNA), a noncoding RNA that is complementary to the rDNA promoter, in mediating de novo CpG methylation of rRNA genes (rDNA). We show that pRNA interacts with the target site of the transcription factor TTF-I, forming a DNA:RNA triplex that is specifically recognized by the DNA methyltransferase DNMT3b. The results reveal a compelling new mechanism of RNA-dependent DNA methylation, suggesting that recruitment of DNMT3b by DNA:RNA triplexes may be a common and generally used pathway in epigenetic regulation.

Non-protein-coding RNAs and their interacting RNA-binding proteins in the plant cell nucleus

The complex responses of eukaryotic cells to external factors are governed by several transcriptional and post-transcriptional processes. Several of them occur in the nucleus and have been linked to the action of non-protein-coding RNAs (or npcRNAs), both long and small npcRNAs, that recently emerged as major regulators of gene expression. Regulatory npcRNAs acting in the nucleus include silencing-related RNAs, intergenic npcRNAs, natural antisense RNAs, and other aberrant RNAs resulting from the interplay between global transcription and RNA processing activities (such as Dicers and RNA-dependent polymerases). Generally, the resulting npcRNAs exert their regulatory effects through interactions with RNA-binding proteins (or RBPs) within ribonucleoprotein particles (or RNPs). A large group of RBPs are implicated in the silencing machinery through small interfering RNAs (siRNAs) and their localization suggests that several act in the nucleus to trigger epigenetic and chromatin changes at a whole-genome scale. Other nuclear RBPs interact with npcRNAs and change their localization. In the fission yeast, the RNA-binding Mei2p protein, playing pivotal roles in meiosis, interact with a meiotic npcRNA involved in its nuclear re-localization. Related processes have been identified in plants and the ENOD40 npcRNA was shown to re-localize a nuclear-speckle RBP from the nucleus to the cytoplasm in Medicago truncatula. Plant RBPs have been also implicated in RNA-mediated chromatin silencing in the FLC locus through interaction with specific antisense transcripts. In this review, we discuss the interactions between RBPs and npcRNAs in the context of nuclear-related processes and their implication in plant development and stress responses. We propose that these interactions may add a regulatory layer that modulates the interactions between the nuclear genome and the environment and, consequently, control plant developmental plasticity.

Proteomic and functional analysis of the noncanonical poly(A) polymerase Cid14

The fission yeast Cid14 protein belongs to a family of noncanonical poly(A) polymerases which have been implicated in a broad range of biological functions. Here we describe an extensive Cid14 protein-protein interaction network and its biochemical dissection. Cid14 most stably interacts with the zinc-knuckle protein Air1 to form the Cid14-Air1 complex (CAC). Providing a link to ribosomal RNA processing, Cid14 sediments with 60S ribosomal subunits and copurifies with 60S assembly factors. In contrast, no physical link to chromatin has been identified, although gene expression profiling revealed that efficient silencing of a few heterochromatic genes depends on Cid14 and/or Air1.

Long intronic GAA repeats causing Friedreich ataxia impede transcription elongation

Friedreich ataxia is a degenerative disease caused by deficiency of the protein frataxin (FXN). An intronic expansion of GAA triplets in the FXN-encoding gene, FXN, causes gene silencing and thus reduced FXN protein levels. Although it is widely assumed that GAA repeats block transcription via the assembly of an inaccessible chromatin structure marked by methylated H3K9, direct proof for this is lacking. In this study, we analysed different histone modification patterns along the human FXN gene in FRDA patient-derived lymphoblastoid cell lines. We show that FXN mRNA synthesis, but not turnover rates are affected by an expanded GAA repeat tract. Importantly, rather than preventing transcription initiation, long GAA repeat tracts affect transcription at the elongation step and this can occur independently of H3K9 methylation. Our data demonstrate that finding novel strategies to overcome the transcription elongation problem may develop into promising new treatments for FRDA.

Variability of 18S rDNA locus among Symphysodon fishes: chromosomal rearrangements

Three species of cichlids belonging to the genus Symphysodon have demonstrated interspecific and intraspecific variation in nucleolus organizer regions (NOR) detected with silver nitrate. In order to understand the evolution of this marker in the genus, the structural variability of these sequences in mitotic chromosomes from Symphysodon aequifasciatus, Symphysodon discus and Symphysodon haraldi was investigated using both silver nitrate impregnation and hybridization of the 18S rRNA gene probe. For the three species, the two markers were intraspecifically and interspecifically variable both in the number and in the size of the sites. This polymorphism may stem from duplications and translocations, which suggests that structural chromosome rearrangements effectively act in the karyoevolution of wild Symphysodon species and may have favoured the adaptability of these fishes to diverse aquatic environments in the Amazon.

Life without RNAi: noncoding RNAs and their functions in Saccharomyces cerevisiae

There are a number of well-characterized and fundamental roles for noncoding RNAs (ncRNAs) in gene regulation in all kingdoms of life. ncRNAs, such as ribosomal RNAs, transfer RNAs, small nuclear RNAs, small nucleolar RNAs, and small interfering RNAs, can serve catalytic and scaffolding functions in transcription, messenger RNA processing, translation, and RNA degradation. Recently, our understanding of gene expression has been dramatically challenged by the identification of large and diverse populations of novel ncRNAs in the eukaryotic genomes surveyed thus far. Studies carried out using the budding yeast Saccharomyces cerevisiae indicate that at least some coding genes are regulated by these novel ncRNAs. S. cerevisiae lacks RNA interference (RNAi) and, thus, provides an ideal system for studying the RNAi-independent mechanisms of ncRNA-based gene regulation. The current picture of gene regulation is one of great unknowns, in which the transcriptional environment surrounding a given locus may have as much to do with its regulation as its DNA sequence or local chromatin structure. Drawing on the recent research in S. cerevisiae and other organisms, this review will discuss the identification of ncRNAs, their origins and processing, and several models that incorporate ncRNAs into the regulation of gene expression and chromatin structure.

Epigenome manipulation as a pathway to new natural product scaffolds and their congeners

The covalent modification of chromatin is an important control mechanism used by fungi to modulate the transcription of genes involved in secondary metabolite production. To date, both molecular-based and chemical approaches targeting histone and DNA posttranslational processes have shown great potential for rationally directing the activation and/or suppression of natural-product-encoding gene clusters. In this Highlight, the organization of the fungal epigenome is summarized and strategies for manipulating chromatin-related targets are presented. Applications of these techniques are illustrated using several recently published accounts in which chemical-epigenetic methods and mutant studies were successfully employed for the de novo or enhanced production of structurally diverse fungal natural products (e.g., anthraquinones, cladochromes, lunalides, mycotoxins, and nygerones).

Silent chromatin at the middle and ends: lessons from yeasts

Eukaryotic centromeres and telomeres are specialized chromosomal regions that share one common characteristic: their underlying DNA sequences are assembled into heritably repressed chromatin. Silent chromatin in budding and fission yeast is composed of fundamentally divergent proteins tat assemble very different chromatin structures. However, the ultimate behaviour of silent chromatin and the pathways that assemble it seem strikingly similar among Saccharomyces cerevisiae (S. cerevisiae), Schizosaccharomyces pombe (S. pombe) and other eukaryotes. Thus, studies in both yeasts have been instrumental in dissecting the mechanisms that establish and maintain silent chromatin in eukaryotes, contributing substantially to our understanding of epigenetic processes. In this review, we discuss current models for the generation of heterochromatic domains at centromeres and telomeres in the two yeast species.