Signaling meets chromatin during tissue regeneration in Drosophila

Damage-responsive elements in Drosophila regeneration

One of the most important questions in regenerative biology is to unveil how and when genes change expression and trigger regeneration programs. The resetting of gene expression patterns during response to injury is governed by coordinated actions of genomic regions that control the activity of multiple sequence-specific DNA binding proteins. Using genome-wide approaches to interrogate chromatin function, we here identify the elements that regulate tissue recovery in Drosophila imaginal discs, which show a high regenerative capacity after genetically induced cell death. Our findings indicate there is global coregulation of gene expression as well as a regeneration program driven by different types of regulatory elements. Novel enhancers acting exclusively within damaged tissue cooperate with enhancers co-opted from other tissues and other developmental stages, as well as with endogenous enhancers that show increased activity after injury. Together, these enhancers host binding sites for regulatory proteins that include a core set of conserved transcription factors that control regeneration across metazoans.

A High-Density Map for Navigating the Human Polycomb Complexome

Polycomb group (PcG) proteins are major determinants of gene silencing and epigenetic memory in higher eukaryotes. Here, we systematically mapped the human PcG complexome using a robust affinity purification mass spectrometry approach. Our high-density protein interaction network uncovered a diverse range of PcG complexes. Moreover, our analysis identified PcG interactors linking them to the PcG system, thus providing insight into the molecular function of PcG complexes and mechanisms of recruitment to target genes. We identified two human PRC2 complexes and two PR-DUB deubiquitination complexes, which contain the O-linked N-acetylglucosamine transferase OGT1 and several transcription factors. Finally, genome-wide profiling of PR-DUB components indicated that the human PR-DUB and PRC1 complexes bind distinct sets of target genes, suggesting differential impact on cellular processes in mammals.

Homeotic gene regulation: a paradigm for epigenetic mechanisms underlying organismal development

The organization of eukaryotic genome into chromatin within the nucleus eventually dictates the cell type specific expression pattern of genes. This higher order of chromatin organization is established during development and dynamically maintained throughout the life span. Developmental mechanisms are conserved in bilaterians and hence they have body plan in common, which is achieved by regulatory networks controlling cell type specific gene expression. Homeotic genes are conserved in metazoans and are crucial for animal development as they specify cell type identity along the anterior-posterior body axis. Hox genes are the best studied in the context of epigenetic regulation that has led to significant understanding of the organismal development. Epigenome specific regulation is brought about by conserved chromatin modulating factors like PcG/trxG proteins during development and differentiation. Here we discuss the conserved epigenetic mechanisms relevant to homeotic gene regulation in metazoans.

Polycomb silencing of the Drosophila 4E-BP gene regulates imaginal disc cell growth

Polycomb group (PcG) proteins are best known for their role in maintaining stable, mitotically heritable silencing of the homeotic (HOX) genes during development. In addition to loss of homeotic gene silencing, some PcG mutants also have small imaginal discs. These include mutations in E(z), Su(z)12, esc and escl, which encode Polycomb repressive complex 2 (PRC2) subunits. The cause of this phenotype is not known, but the human homologs of PRC2 subunits have been shown to play a role in cell proliferation, are over-expressed in many tumors, and appear to be required for tumor proliferation. Here we show that the small imaginal disc phenotype arises, at least in part, from a cell growth defect. In homozygous E(z) mutants, imaginal disc cells are smaller than cells in normally proliferating discs. We show that the Thor gene, which encodes eIF4E-binding protein (4E-BP), the evolutionarily conserved inhibitor of cap-dependent translation and potent inhibitor of cell growth, is involved in the development of this phenotype. The Thor promoter region contains DNA binding motifs for transcription factors found in well-characterized Polycomb response elements (PREs), including PHO/PHOL, GAGA factor, and others, suggesting that Thor may be a direct target of Polycomb silencing. We present chromatin immunoprecipitation evidence that PcG proteins are bound to the Thor 5' region in vivo. The Thor gene is normally repressed in imaginal discs, but Thor mRNA and 4E-BP protein levels are elevated in imaginal discs of PRC2 subunit mutant larvae. Deletion of the Thor gene in E(z) mutants partially restores imaginal disc size toward wild-type and results in an increase in the fraction of larvae that pupariate. These results thus suggest that PcG proteins can directly modulate cell growth in Drosophila, in part by regulating Thor expression.

Polycomb proteins in mammalian cell differentiation and plasticity

During development cell differentiation is accompanied by progressive restriction of the developmental potential and increased structural and functional specialization of cells. In this context, mechanisms of cell memory guarantee that cells maintain different identities previously determined by the integrated action of signalling and specific sets of transcription factors. Unraveling the molecular basis by which cells build and maintain their memory represents one of the most fascinating problems in biology. PcG proteins were originally identified as part of an epigenetic cellular memory system that controls gene silencing via chromatin structure. However, recent reports suggest that they are also involved in controlling dynamics and plasticity of gene regulation, particularly during differentiation, by interacting with other components of the transcriptional apparatus. In this review, we discuss the role of PcG proteins in pluripotent ES cells and in well known mammalian cell differentiation systems including skeletal muscle, epidermal, neuronal differentiation. The emerging picture suggests that indeed, plasticity and not rigidity is a fundamental aspect of PcG physiology and cell memory function.

Developmental gene regulation in the era of genomics

Genetic experiments over the last few decades have identified many developmental control genes critical for pattern formation and cell fate specification during the development of multicellular organisms. A large fraction of these genes encode transcription factors and signaling molecules, show highly dynamic expression patterns during development, and are deeply evolutionarily conserved and deregulated in various human diseases such as cancer. Because of their importance in development, evolution, and disease, a fundamental question in biology is how these developmental control genes are regulated in such an extensive and precise fashion. Using genomics methods, it has become clear that developmental control genes are a distinct group of genes with special regulatory characteristics. However, a systematic analysis of these characteristics has not been presented. Here we review how developmental control genes were discovered, evaluate their genome-wide regulation and gene structure, discuss emerging evidence for their mode of regulation, and estimate their overall abundance in the genome. Understanding the global regulation of developmental control genes may provide a new perspective on development in the era genomics.

Creating reference datasets for systems biology applications using text mining

High-throughput experimental techniques are generating large data collections with the aim of identifying novel entities involved in fundamental cellular processes as well as drawing a systematic picture of the relationships between individual components. Determining the accuracy of the resulting data and the selection of a subset of targets for more careful characterizations often requires relying on information provided by manually annotated data repositories. These repositories are incomplete and cover only a small fraction of the knowledge contained in the literature. We propose in this paper the use of text-mining technologies to extract, organize, and present information relevant for a particular biological topic. The aims of the resulting approach are (1) to enable topic-centric biological literature navigation, (2) to assist in the construction of manually revised data repositories, (3) to provide prioritization of biological entities for experimental studies, and (4) to enable human interpretation of large-scale experiments by providing direct links of bio-entities to relevant descriptions in the literature.

Genetic and systems level analysis of Drosophila sticky/citron kinase and dFmr1 mutants reveals common regulation of genetic networks

Background

In Drosophila, the genes sticky and dFmr1 have both been shown to regulate cytoskeletal dynamics and chromatin structure. These genes also genetically interact with Argonaute family microRNA regulators. Furthermore, in mammalian systems, both genes have been implicated in neuronal development. Given these genetic and functional similarities, we tested Drosophila sticky and dFmr1 for a genetic interaction and measured whole genome expression in both mutants to assess similarities in gene regulation.

Results

We found that sticky mutations can dominantly suppress a dFmr1 gain-of-function phenotype in the developing eye, while phenotypes produced by RNAi knock-down of sticky were enhanced by dFmr1 RNAi and a dFmr1 loss-of-function mutation. We also identified a large number of transcripts that were misexpressed in both mutants suggesting that sticky and dFmr1 gene products similarly regulate gene expression. By integrating gene expression data with a protein-protein interaction network, we found that mutations in sticky and dFmr1 resulted in misexpression of common gene networks, and consequently predicted additional specific phenotypes previously not known to be associated with either gene. Further phenotypic analyses validated these predictions.

Conclusion

These findings establish a functional link between two previously unrelated genes. Microarray analysis indicates that sticky and dFmr1 are both required for regulation of many developmental genes in a variety of cell types. The diversity of transcripts regulated by these two genes suggests a clear cause of the pleiotropy that sticky and dFmr1 mutants display and provides many novel, testable hypotheses about the functions of these genes. As both of these genes are implicated in the development and function of the mammalian brain, these results have relevance to human health as well as to understanding more general biological processes.

Salt stress-induced cell reprogramming, cell fate switch and adaptive plasticity during root hair development in Arabidopsis

Developmental plasticity defines an adaptive mechanism, which plays a fundamental role in plant development and survival. How intrinsic or extrinsic factors are integrated to specify cell fates and subsequent organ and body building of a plant is still poorly understood. By studying developmental plasticity of Arabidopsis root hair in response to salt stress, we have begun to understand more about the basis of cellular plasticity. This paper summarizes our recent paper in which it described salt stress induced plasticity of root epidermis and root hair development in Arabidopsis. Analysis of gene expression of the homeobox transcription factor GLABRA2 (GL2), which determines hair/non-hair cell fate, showed that salt stress modulates root epidermal cell proliferation and changes the cell fate decisions. Furthermore, by analyzing the salt overly sensitive (sos) mutants, we showed that salt-induced root hair plastic response is caused by ion disequilibrium and it appears to be adaptive mechanism. Based on the most recent discoveries, we propose here that chromatin remodeling and epigenetic control may be the basis for cell fate changes and the ultimately adaptive plasticity in response to transient changes of environmental conditions.

Drosophila sticky/citron kinase is a regulator of cell-cycle progression, genetically interacts with Argonaute 1 and modulates epigenetic gene silencing

The sticky/citron kinase protein is a conserved regulator of cell-cycle progression from invertebrates to humans. While this kinase is essential for completion of cytokinesis, sticky/citron kinase phenotypes disrupting neurogenesis and cell differentiation suggest additional non-cell-cycle functions. However, it is not known whether these phenotypes are an indirect consequence of sticky mutant cell-cycle defects or whether they define a novel function for this kinase. We have isolated a temperature-sensitive allele of the Drosophila sticky gene and we show that sticky/citron kinase is required for histone H3-K9 methylation, HP1 localization, and heterochromatin-mediated gene silencing. sticky genetically interacts with Argonaute 1 and sticky mutants exhibit context-dependent Su(var) and E(var) activity. These observations indicate that sticky/citron kinase functions to regulate both actin-myosin-mediated cytokinesis and epigenetic gene silencing, possibly linking cell-cycle progression to heterochromatin assembly and inheritance of gene expression states.

Disruption of tumor cell adhesion promotes angiogenic switch and progression to micrometastasis in RAF-driven murine lung cancer

Progression of non-small-cell lung cancer (NSCLC) to metastasis is poorly understood. Two genetic approaches were used to evaluate the role of adherens junctions in a C-RAF driven mouse model for NSCLC: conditional ablation of the cdh1 gene and expression of dominant-negative (dn) E-cadherin. Disruption of E-cadherin caused massive formation of intratumoral vessels that was reversible in the early phase of induction. Vascularized tumors grew more rapidly, developed invasive fronts, and gave rise to micrometastasis. beta-catenin was identified as a critical effector of E-cadherin disruption leading to upregulation of VEGF-A and VEGF-C. In vivo, lung tumor cells with disrupted E-cadherin expressed beta-catenin target genes normally found in other endodermal lineages suggesting that reprogramming may be involved in metastatic progression.

Polycomb comes of age: genome-wide profiling of target sites

The Polycomb group proteins are best known for their role as epigenetic regulators of the fly homeotic (Hox) gene clusters, but it has long been clear that these well conserved proteins have many other targets. For example, they are vital for maintaining both the pluripotency of stem cells and the identity of differentiated cells. However, a comprehensive list of experimentally defined targets has been lacking. Six new studies use genome wide profiling techniques to map Polycomb targets in stem cells and differentiated cells in vertebrates and flies. The findings of these studies demand that we rethink some of our current assumptions about Polycomb function.

Genetic and epigenetic regulators of pluripotency

Genetic and epigenetic mechanisms regulate the transition from the totipotent zygote to pluripotent primitive ectoderm cells in the inner cell mass of mouse blastocysts. These pluripotent cells can be propagated indefinitely in vitro, underpinned by a unique epigenetic state. Following implantation of the blastocyst, diverse epigenetic modifiers control differentiation of pluripotent epiblast cells into somatic cells, while specification of germ cells requires repression of the somatic program. Regenerating totipotency during development of germ cells entails re-expression of pluripotency-specific genes and extensive erasure of epigenetic modifications. Increasing knowledge of key underlying mechanisms heightens prospects for creating pluripotent cells directly from adult somatic cells.