Revisiting Global Gene Expression Analysis

Revisiting Global Gene Expression Analysis: Jakob Lovén, David A. Orlando, Alla A. Sigova, Charles Y. Lin, Peter B. Rahl, Christopher B. Burge, David L. Levens, Tong Ihn Lee, Richard A. Young. Gene expression analysis is a widely used and powerful method for investigating the transcriptional behavior of biological systems, for classifying cell states in disease, and for many other purpo....

Deciphering the transcriptional cis-regulatory code

Deciphering the transcriptional cis-regulatory code: J. Omar Yáñez-Cuna, Evgeny Z. Kvon, Alexander Stark. Information about developmental gene expression resides in defined regulatory elements, called enhancers, in the non-coding part of the genome. Although cells reliably utilize enhancers to orchest....

Cell type-specific genomics of Drosophila neurons

Cell type-specific genomics of Drosophila neurons:
Many tools are available to analyse genomes but are often challenging to use in a cell type–specific context. We have developed a method similar to the isolation of nuclei tagged in a specific cell type (INTACT) technique [Deal,R.B. and Henikoff,S. (2010) A simple method for gene expression and chromatin profiling of individual cell types within a tissue. Dev. Cell, 18, 1030–1040; Steiner,F.A., Talbert,P.B., Kasinathan,S., Deal,R.B. and Henikoff,S. (2012) Cell-type-specific nuclei purification from whole animals for genome-wide expression and chromatin profiling. Genome Res., doi:10.1101/gr.131748.111], first developed in plants, for use in Drosophila neurons. We profile gene expression and histone modifications in Kenyon cells and octopaminergic neurons in the adult brain. In addition to recovering known gene expression differences, we also observe significant cell type–specific chromatin modifications. In particular, a small subset of differentially expressed genes exhibits a striking anti-correlation between repressive and activating histone modifications. These genes are enriched for transcription factors, recovering those known to regulate mushroom body identity and predicting analogous regulators of octopaminergic neurons. Our results suggest that applying INTACT to specific neuronal populations can illuminate the transcriptional regulatory networks that underlie neuronal cell identity.

CTCF and the emergence of metazoan diversity [Evolution]

CTCF and the emergence of metazoan diversity [Evolution]: The great majority of metazoans belong to bilaterian phyla. They diversified during a short interval in Earth’s history known as the Cambrian explosion, ∼540 million years ago. However, the genetic basis of these events is poorly understood. Here we argue that the vertebrate genome organizer CTCF (CCCTC-binding factor) played an...

The zebrafish issue of Development [SPOTLIGHT]

The zebrafish issue of Development [SPOTLIGHT]: Christiane Nusslein-Volhard


In December 1996, a special issue of Development appeared that presented in 37 papers the results of two large screens for zebrafish mutants performed in Tübingen and Boston. The papers describe about 1500 mutations in more than 400 new genes involved in a wide range of processes that govern development and organogenesis. Up to this day, the mutants provide a rich resource for many laboratories, and the issue significantly augmented the importance of zebrafish as vertebrate model organism for the study of embryogenesis, neuronal networks, regeneration and disease. This essay relates a personal account of the history of this unique endeavor.

Regulatory Network Structure as a Dominant Determinant of Transcription Factor Evolutionary Rate

Regulatory Network Structure as a Dominant Determinant of Transcription Factor Evolutionary Rate:
by Jasmin Coulombe-Huntington, Yu Xia

The evolution of transcriptional regulatory networks has thus far mostly been studied at the level of cis-regulatory elements. To gain a complete understanding of regulatory network evolution we must also study the evolutionary role of trans-factors, such as transcription factors (TFs). Here, we systematically assess genomic and network-level determinants of TF evolutionary rate in yeast, and how they compare to those of generic proteins, while carefully controlling for differences of the TF protein set, such as expression level. We found significantly distinct trends relating TF evolutionary rate to mRNA expression level, codon adaptation index, the evolutionary rate of physical interaction partners, and, confirming previous reports, to protein-protein interaction degree and regulatory in-degree. We discovered that for TFs, the dominant determinants of evolutionary rate lie in the structure of the regulatory network, such as the median evolutionary rate of target genes and the fraction of species-specific target genes. Decomposing the regulatory network by edge sign, we found that this modular evolution of TFs and their targets is limited to activating regulatory relationships. We show that fast evolving TFs tend to regulate other TFs and niche-specific processes and that their targets show larger evolutionary expression changes than targets of other TFs. We also show that the positive trend relating TF regulatory in-degree and evolutionary rate is likely related to the species-specificity of the transcriptional regulation modules. Finally, we discuss likely causes for TFs' different evolutionary relationship to the physical interaction network, such as the prevalence of transient interactions in the TF subnetwork. This work suggests that positive and negative regulatory networks follow very different evolutionary rules, and that transcription factor evolution is best understood at a network- or systems-level.

Estimating Divergence Dates and Substitution Rates in the Drosophila Phylogeny

Estimating Divergence Dates and Substitution Rates in the Drosophila Phylogeny:
An absolute timescale for evolution is essential if we are to associate evolutionary phenomena, such as adaptation or speciation, with potential causes, such as geological activity or climatic change. Timescales in most phylogenetic studies use geologically dated fossils or phylogeographic events as calibration points, but more recently, it has also become possible to use experimentally derived estimates of the mutation rate as a proxy for substitution rates. The large radiation of drosophilid taxa endemic to the Hawaiian islands has provided multiple calibration points for the Drosophila phylogeny, thanks to the "conveyor belt" process by which this archipelago forms and is colonized by species. However, published date estimates for key nodes in the Drosophila phylogeny vary widely, and many are based on simplistic models of colonization and coalescence or on estimates of island age that are not current. In this study, we use new sequence data from seven species of Hawaiian Drosophila to examine a range of explicit coalescent models and estimate substitution rates. We use these rates, along with a published experimentally determined mutation rate, to date key events in drosophilid evolution. Surprisingly, our estimate for the date for the most recent common ancestor of the genus Drosophila based on mutation rate (25–40 Ma) is closer to being compatible with independent fossil-derived dates (20–50 Ma) than are most of the Hawaiian-calibration models and also has smaller uncertainty. We find that Hawaiian-calibrated dates are extremely sensitive to model choice and give rise to point estimates that range between 26 and 192 Ma, depending on the details of the model. Potential problems with the Hawaiian calibration may arise from systematic variation in the molecular clock due to the long generation time of Hawaiian Drosophila compared with other Drosophila and/or uncertainty in linking island formation dates with colonization dates. As either source of error will bias estimates of divergence time, we suggest mutation rate estimates be used until better models are available.

ELAV mediates 3' UTR extension in the Drosophila nervous system [Research Communications]

ELAV mediates 3' UTR extension in the Drosophila nervous system [Research Communications]:
Post-transcriptional gene regulation is prevalent in the nervous system, where multiple tiers of regulatory complexity contribute to the development and function of highly specialized cell types. Whole-genome studies in Drosophila have identified several hundred genes containing long 3' extensions in neural tissues. We show that ELAV (embryonic-lethal abnormal visual system) is a key mediator of these neural-specific extensions. Misexpression of ELAV results in the ectopic synthesis of long messenger RNAs (mRNAs) in transgenic embryos. RNA immunoprecipitation assays suggest that ELAV directly binds the proximal polyadenylation signals of many target mRNAs. Finally, ELAV is sufficient to suppress 3' end formation at a strong polyadenylation signal when tethered to a synthetic RNA. We propose that this mechanism for coordinating 3' UTR extension may be generally used in a variety of cellular processes.

Identical Genomic Organization of Two Hemichordate Hox Clusters

Identical Genomic Organization of Two Hemichordate Hox Clusters: Robert Freeman, Tetsuro Ikuta, Michael Wu, Ryo Koyanagi, Takeshi Kawashima, Kunifumi Tagawa, Tom Humphreys, Guang-Chen Fang, Asao Fujiyama, Hidetoshi Saiga, Christopher Lowe, Kim Worley, Jerry Jenkins, Jeremy Schmutz, Marc Kirschner, Daniel Rokhsar, Nori Satoh, John Gerhart. Genomic comparisons of chordates, hemichordates, and echinoderms can inform hypotheses for the evolution of these strikingly different phyla from the last common deuterostome ancestor [1–5]. Becau....

The Many Landscapes of Recombination in Drosophila melanogaster

The Many Landscapes of Recombination in Drosophila melanogaster:
by Josep M. Comeron, Ramesh Ratnappan, Samuel Bailin

Recombination is a fundamental biological process with profound evolutionary implications. Theory predicts that recombination increases the effectiveness of selection in natural populations. Yet, direct tests of this prediction have been restricted to qualitative trends due to the lack of detailed characterization of recombination rate variation across genomes and within species. The use of imprecise recombination rates can also skew population genetic analyses designed to assess the presence and mode of selection across genomes. Here we report the first integrated high-resolution description of genomic and population variation in recombination, which also distinguishes between the two outcomes of meiotic recombination: crossing over (CO) and gene conversion (GC). We characterized the products of 5,860 female meioses in Drosophila melanogaster by genotyping a total of 139 million informative SNPs and mapped 106,964 recombination events at a resolution down to 2 kilobases. This approach allowed us to generate whole-genome CO and GC maps as well as a detailed description of variation in recombination among individuals of this species. We describe many levels of variation in recombination rates. At a large-scale (100 kb), CO rates exhibit extreme and highly punctuated variation along chromosomes, with hot and coldspots. We also show extensive intra-specific variation in CO landscapes that is associated with hotspots at low frequency in our sample. GC rates are more uniformly distributed across the genome than CO rates and detectable in regions with reduced or absent CO. At a local scale, recombination events are associated with numerous sequence motifs and tend to occur within transcript regions, thus suggesting that chromatin accessibility favors double-strand breaks. All these non-independent layers of variation in recombination across genomes and among individuals need to be taken into account in order to obtain relevant estimates of recombination rates, and should be included in a new generation of population genetic models of the interaction between selection and linkage.

Complex brain and optic lobes in an early Cambrian arthropod

Complex brain and optic lobes in an early Cambrian arthropod:
Complex brain and optic lobes in an early Cambrian arthropod

Nature 490, 7419 (2012). doi:10.1038/nature11495

Authors: Xiaoya Ma, Xianguang Hou, Gregory D. Edgecombe & Nicholas J. Strausfeld
The nervous system provides a fundamental source of data for understanding the evolutionary relationships between major arthropod groups. Fossil arthropods rarely preserve neural tissue. As a result, inferring sensory and motor attributes of Cambrian taxa has been limited to interpreting external features, such as compound eyes or sensilla decorating appendages, and early-diverging arthropods have scarcely been analysed in the context of nervous system evolution. Here we report exceptional preservation of the brain and optic lobes of a stem-group arthropod from 520 million years ago (Myr ago), Fuxianhuia protensa, exhibiting the most compelling neuroanatomy known from the Cambrian. The protocerebrum of Fuxianhuia is supplied by optic lobes evidencing traces of three nested optic centres serving forward-viewing eyes. Nerves from uniramous antennae define the deutocerebrum, and a stout pair of more caudal nerves indicates a contiguous tritocerebral component. Fuxianhuia shares a tripartite pre-stomodeal brain and nested optic neuropils with extant Malacostraca and Insecta, demonstrating that these characters were present in some of the earliest derived arthropods. The brain of Fuxianhuia impacts molecular analyses that advocate either a branchiopod-like ancestor of Hexapoda or remipedes and possibly cephalocarids as sister groups of Hexapoda. Resolving arguments about whether the simple brain of a branchiopod approximates an ancestral insect brain or whether it is the result of secondary simplification has until now been hindered by lack of fossil evidence. The complex brain of Fuxianhuia accords with cladistic analyses on the basis of neural characters, suggesting that Branchiopoda derive from a malacostracan-like ancestor but underwent evolutionary reduction and character reversal of brain centres that are common to hexapods and malacostracans. The early origin of sophisticated brains provides a probable driver for versatile visual behaviours, a view that accords with compound eyes from the early Cambrian that were, in size and resolution, equal to those of modern insects and malacostracans.

Genomic logic processing functions in development [Developmental Biology]

Genomic logic processing functions in development [Developmental Biology]: Gene regulatory networks (GRNs) control the dynamic spatial patterns of regulatory gene expression in development. Thus, in principle, GRN models may provide system-level, causal explanations of developmental process. To test this assertion, we have transformed a relatively well-established GRN model into a predictive, dynamic Boolean computational model. This Boolean model...

Combinatorial Assembly of Developmental Stage-Specific Enhancers Controls Gene Expression Programs during Human Erythropoiesis

Combinatorial Assembly of Developmental Stage-Specific Enhancers Controls Gene Expression Programs during Human Erythropoiesis: Jian Xu, Zhen Shao, Kimberly Glass, Daniel E. Bauer, Luca Pinello, Ben Van Handel, Serena Hou, John A. Stamatoyannopoulos, Hanna K.A. Mikkola, Guo-Cheng Yuan, Stuart H. Orkin. Gene-distal enhancers are critical for tissue-specific gene expression, but their genomic determinants within a specific lineage at different stages of development are unknown. Here we profile chr....

Uncovering cis-regulatory sequence requirements for context-specific transcription factor binding [METHOD]

Uncovering cis-regulatory sequence requirements for context-specific transcription factor binding [METHOD]:

The regulation of gene expression is mediated at the transcriptional level by enhancer regions that are bound by sequence-specific transcription factors (TFs). Recent studies have shown that the in vivo binding sites of single TFs differ between developmental or cellular contexts. How this context-specific binding is encoded in the cis-regulatory DNA sequence has, however, remained unclear. We computationally dissect context-specific TF binding sites in Drosophila, Caenorhabditis elegans, mouse, and human and find distinct combinations of sequence motifs for partner factors, which are predictive and reveal specific motif requirements of individual binding sites. We predict that TF binding in the early Drosophila embryo depends on motifs for the early zygotic TFs Vielfaltig (also known as Zelda) and Tramtrack. We validate experimentally that the activity of Twist-bound enhancers and Twist binding itself depend on Vielfaltig motifs, suggesting that Vielfaltig is more generally important for early transcription. Our finding that the motif content can predict context-specific binding and that the predictions work across different Drosophila species suggests that characteristic motif combinations are shared between sites, revealing context-specific motif codes (cis-regulatory signatures), which appear to be conserved during evolution. Taken together, this study establishes a novel approach to derive predictive cis-regulatory motif requirements for individual TF binding sites and enhancers. Importantly, the method is generally applicable across different cell types and organisms to elucidate cis-regulatory sequence determinants and the corresponding trans-acting factors from the increasing number of tissue- and cell-type-specific TF binding studies.

Polygenic cis-regulatory adaptation in the evolution of yeast pathogenicity [RESEARCH]

Polygenic cis-regulatory adaptation in the evolution of yeast pathogenicity [RESEARCH]:
The acquisition of new genes, via horizontal transfer or gene duplication/diversification, has been the dominant mechanism thus far implicated in the evolution of microbial pathogenicity. In contrast, the role of many other modes of evolution—such as changes in gene expression regulation—remains unknown. A transition to a pathogenic lifestyle has recently taken place in some lineages of the budding yeast Saccharomyces cerevisiae. Here we identify a module of physically interacting proteins involved in endocytosis that has experienced selective sweeps for multiple cis-regulatory mutations that down-regulate gene expression levels in a pathogenic yeast. To test if these adaptations affect virulence, we created a panel of single-allele knockout strains whose hemizygous state mimics the genes' adaptive down-regulations, and measured their virulence in a mammalian host. Despite having no growth advantage in standard laboratory conditions, nearly all of the strains were more virulent than their wild-type progenitor, suggesting that these adaptations likely played a role in the evolution of pathogenicity. Furthermore, genetic variants at these loci were associated with clinical origin across 88 diverse yeast strains, suggesting the adaptations may have contributed to the virulence of a wide range of clinical isolates. We also detected pleiotropic effects of these adaptations on a wide range of morphological traits, which appear to have been mitigated by compensatory mutations at other loci. These results suggest that cis-regulatory adaptation can occur at the level of physically interacting modules and that one such polygenic adaptation led to increased virulence during the evolution of a pathogenic yeast.