Felipe Karam Teixeira

Assessing the impact of transgenerational epigenetic variation on complex traits.

Loss or gain of DNA methylation can affect gene expression and is sometimes transmitted across generations. Such epigenetic alterations are thus a possible source of heritable phenotypic variation in the absence of DNA sequence change. However, attempts to assess the prevalence of stable epigenetic variation in natural and experimental populations and to quantify its impact on complex traits have been hampered by the confounding effects of DNA sequence polymorphisms. To overcome this problem as much as possible, two parents with little DNA sequence differences, but contrasting DNA methylation profiles, were used to derive a panel of epigenetic Recombinant Inbred Lines (epiRILs) in the reference plant Arabidopsis thaliana. The epiRILs showed variation and high heritability for flowering time and plant height (∼30%), as well as stable inheritance of multiple parental DNA methylation variants (epialleles) over at least eight generations. These findings provide a first rationale to identify epiallelic variants that contribute to heritable variation in complex traits using linkage or association studies. More generally, the demonstration that numerous epialleles across the genome can be stable over many generations in the absence of selection or extensive DNA sequence variation highlights the need to integrate epigenetic information into population genetics studies.

A Role for RNAi in the Selective Correction of DNA Methylation Defects

DNA methylation is essential for silencing transposable elements and some genes in higher eukaryotes, which suggests that this modification must be tightly controlled. However, accidental changes in DNA methylation can be transmitted through mitosis (as in cancer) or meiosis, leading to epiallelic variation. We demonstrated the existence of an efficient mechanism that protects against transgenerational loss of DNA methylation in Arabidopsis. Remethylation is specific to the subset of heavily methylated repeats that are targeted by the RNA interference (RNAi) machinery. This process does not spread into flanking regions, is usually progressive over several generations, and faithfully restores wild-type methylation over target sequences in an RNAi-dependent manner. Our findings suggest an important role for RNAi in protecting genomes against long-term epigenetic defects.

Chromatin indexing in Arabidopsis: an epigenomic tale of tails and more.

Packaging DNA into chromatin is pivotal for the regulation of genome activity in eukaryotes. This chromatin-level control relies on a range of histone modifications and variants, chromatin-remodeling proteins and DNA methylation in plants and mammals. High-resolution maps have recently been obtained for several chromatin modifications in Arabidopsis, which provide a first glimpse at the organization of plant epigenomes. These maps suggest a pervasive involvement of transcriptional activity in indexing chromatin with reference to the underlying DNA sequence. However, to assess the contribution of chromatin dynamics to plant development and phenotypic plasticity, it will be necessary to shift from a static to a dynamic view of the Arabidopsis epigenome.

Cytosolic APx knockdown indicates an ambiguous redox responses in rice

Ascorbate peroxidases (APX, EC 1.1.11.1) are class I heme-peroxidases, which catalyze the conversion of H(2)O(2) into H(2)O, using ascorbate as a specific electron donor. Previously, the presence of eight Apx genes was identified in the nuclear genome of rice (Oryza sativa), encoding isoforms that are located in different sub-cellular compartments. Herein, the generation of rice transgenic plants silenced for either both or each one of the cytosolic Apx1 and Apx2 genes was carried out in order to investigate the importance of cytosolic Apx isoforms on plant development and on plant stress responses. Transgenic double Apx1/2-silenced plants exhibited normal development, even though these plants showed a global reduction of Apx activity which strongly impacts the whole antioxidant system regulation. Apx1/2-silenced plants also showed increased H(2)O(2) accumulation under control and stress situations and presented higher tolerance to toxic concentration of aluminum when compared to wild type plants. On the other hand, silencing OsApx1 and OsApx2 genes individually resulted in strong effect on plant development producing semi-dwarf phenotype. These results suggested that the double silencing of cytosolic OsApx genes induced compensatory antioxidant mechanisms in rice while single knockdown of these genes did not, which resulted in the impairing of normal plant development.

Regulation of Ribosome Biogenesis and Protein Synthesis Controls Germline Stem Cell Differentiation

Complex regulatory networks regulate stem cell behavior and contributions to tissue growth, repair, and homeostasis. A full understanding of the networks controlling stem cell self-renewal and differentiation, however, has not yet been realized. To systematically dissect these networks and identify their components, we performed an unbiased, transcriptome-wide in vivo RNAi screen in female Drosophila germline stem cells (GSCs). Based on characterized cellular defects, we classified 646 identified genes into phenotypic and functional groups and unveiled a comprehensive set of networks regulating GSC maintenance, survival, and differentiation. This analysis revealed an unexpected role for ribosomal assembly factors in controlling stem cell cytokinesis. Moreover, our data show that the transition from self-renewal to differentiation relies on enhanced ribosome biogenesis accompanied by increased protein synthesis. Collectively, these results detail the extensive genetic networks that control stem cell homeostasis and highlight the intricate regulation of protein synthesis during differentiation.

Gene body DNA methylation in plants: a means to an end or an end to a means?

Cytosine methylation is widely known for its role in silencing transposable elements and some genes in plants and mammals. However, whereas methylation of promoter sequences can lead to transcriptional repression, the function of gene body methylation remains elusive. This situation is particularly perplexing in the plant Arabidopsis, where many genes are methylated, specifically, over their body. A new study in this issue of The EMBO Journal shows that gene body methylation results from two conflicting activities, one imposing it at CG sites, and one preventing its extension to CHG sites (where H=A,T or C). Importantly, the latter activity is not targeted towards silent transposable elements and is likely coupled to transcription elongation, suggesting that CHG methylation hinders this step.

piRNA-mediated regulation of transposon alternative splicing in the soma and germ line

Transposable elements can drive genome evolution, but their enhanced activity is detrimental to the host and therefore must be tightly regulated. The Piwi-interacting small RNA (piRNA) pathway is vital for the regulation of transposable elements, by inducing transcriptional silencing or post-transcriptional decay of mRNAs. Here we show that piRNAs and piRNA biogenesis components regulate precursor mRNA splicing of P-transposable element transcripts in vivo, leading to the production of the non-transposase-encoding mature mRNA isoform in Drosophila germ cells. Unexpectedly, we show that the piRNA pathway components do not act to reduce transcript levels of the P-element transposon during P–M hybrid dysgenesis, a syndrome that affects germline development in Drosophila. Instead, splicing regulation is mechanistically achieved together with piRNA-mediated changes to repressive chromatin states, and relies on the function of the Piwi–piRNA complex proteins Asterix (also known as Gtsf1) and Panoramix (Silencio), as well as Heterochromatin protein 1a (HP1a; encoded by Su(var)205). Furthermore, we show that this machinery, together with the piRNA Flamenco cluster, not only controls the accumulation of Gypsy retrotransposon transcripts but also regulates the splicing of Gypsy mRNAs in cultured ovarian somatic cells, a process required for the production of infectious particles that can lead to heritable transposition events. Our findings identify splicing regulation as a new role and essential function for the Piwi pathway in protecting the genome against transposon mobility, and provide a model system for studying the role of chromatin structure in modulating alternative splicing during development.

The cellular basis of hybrid dysgenesis and Stellate regulation in Drosophila.

During normal tissue development, the accumulation of unrepaired cellular and genomic damage can impair growth and ultimately leads to death. To preserve cellular integrity, cells employ a number of defense mechanisms including molecular checkpoints, during which development is halted while dedicated pathways attempt repair. This process is most critical in germline tissues where cellular damage directly threatens an organisms reproductive capacity and offspring viability. In the fruit fly, Drosophila melanogaster, germline development has been extensively studied for over a century and the breadth of our knowledge has flourished in the genomics age. Intriguingly, several peculiar phenomena that trigger catastrophic germline damage described decades ago, still endure only a partial understanding of the underlying molecular causes. A deeper reexamination using new molecular and genetic tools may greatly benefit our understanding of host system biology. Among these, and the focus of this concise review, are hybrid dysgenesis and an intragenomic conflict that pits the X and Y sex chromosomes against each other.

Ultrastructural Analysis of Drosophila Ovaries by Electron Microscopy.

The Drosophila melanogaster ovary is a powerful, genetically tractable system through which one can elucidate the principles underlying cellular function and organogenesis in vivo. In order to understand the intricate process of oogenesis at the subcellular level, microscopic analysis with the highest possible resolution is required. In this chapter, we describe the preparation of ovaries for ultrastructural analysis using transmission electron microscopy and focused ion beam scanning electron microscopy. We discuss and provide protocols for chemical fixation of Drosophila ovaries that facilitate optimal imaging with particular attention paid to preserving and resolving mitochondrial membrane morphology and structure.

L(3)mbt safeguards tissue identity by maintaining transcriptional integrity at head-to-head genes

Maintenance of cellular identity is essential for development and homeostasis and problems in such control can have dire consequences such as organ malformation or cancer. At the molecular level, cell identity is determined by the coordinated activation and repression of defined sets of genes. The tumor suppressor L(3)mbt was shown to secure cellular identity in Drosophila larval brains by repressing germline specific genes, although the mechanisms remain elusive. Here we show that L(3)mbt safeguards the integrity of the somatic and germline tissues forming the Drosophila ovary. L(3)mbt mutation causes multiple developmental defects and simultaneous expression of original identity markers and new tissue-specific misexpression signatures. We demonstrate that the ovarian developmental defects are largely due to the ectopic expression of nanos, a key regulator of germline fate in the somatic cells of the ovary, rather than to the loss of cellular identity. Importantly, using genome-wide analysis we found that L(3)mbt exerts boundary activity between differentially regulated genes by binding to high occupancy insulator sites enriched at the borders of topological domains. Using nanos as an example, we propose that L(3)mbt maintains cell fate and specific gene expression programs by locally insulating repressed genes from closely apposed transcribed neighbors.Maintenance of cellular identity is essential for tissue development and homeostasis. At the molecular level, cell identity is determined by the coordinated activation and repression of defined sets of genes. Defects in the maintenance of the genetic programs required for identity can have dire consequences such as organ malformation and cancer. The tumor suppressor L(3)mbt was shown to secure cellular identity in Drosophila larval brains by repressing germline-specific genes. Here we interrogate the temporal and spatial requirements for L(3)mbt in the Drosophila ovary, and show that it safeguards the integrity of both somatic and germline tissues. L(3)mbt mutant ovaries exhibit multiple developmental defects, which we find to be largely caused by the inappropriate expression of a single gene, nanos, a key regulator of germline fate, in the somatic cells of the ovary. In the female germline, we find that L(3)mbt represses testis-specific and neuronal genes. Molecularly, we show that L(3)mbt function in the ovary is mediated through its cofactor Lint1 but independent of the dREAM complex. Together, our work uncovers a more complex role for L(3)mbt than previously understood and demonstrates that L(3)mbt secures tissue identity by preventing the simultaneous expression of original identity markers and tissue-specific misexpression signatures.