Population genetics of cis-regulatory sequences that operate during embryonic development in the sea urchin Strongylocentrotus purpuratus

Population genetics of cis-regulatory sequences that operate during embryonic development in the sea urchin Strongylocentrotus purpuratus:

SUMMARY

Despite the fact that noncoding sequences comprise a substantial fraction of functional sites within all genomes, the evolutionary mechanisms that operate on genetic variation within regulatory elements remain poorly understood. In this study, we examine the population genetics of the core, upstream cis-regulatory regions of eight genes (AN, CyIIa, CyIIIa, Endo16, FoxB, HE, SM30 a, and SM50) that function during the early development of the purple sea urchin, Strongylocentrotus purpuratus. Quantitative and qualitative measures of segregating variation are not conspicuously different between cis-regulatory and closely linked “proxy neutral” noncoding regions containing no known functional sites. Length and compound mutations are common in noncoding sequences; conventional descriptive statistics ignore such mutations, under-representing true genetic variation by approximately 28% for these loci in this population. Patterns of variation in the cis-regulatory regions of six of the genes examined (CyIIa, CyIIIa, Endo16, FoxB, AN, and HE) are consistent with directional selection. Genetic variation within annotated transcription factor binding sites is comparable to, and frequently greater than, that of surrounding sequences. Comparisons of two paralog pairs (CyIIa/CyIIIa and AN/HE) suggest that distinct evolutionary processes have operated on their cis-regulatory regions following gene duplication. Together, these analyses provide a detailed view of the evolutionary mechanisms operating on noncoding sequences within a natural population, and underscore how little is known about how these processes operate on cis-regulatory sequences.

Accurate Prediction of Inducible Transcription Factor Binding Intensities In Vivo

Accurate Prediction of Inducible Transcription Factor Binding Intensities In Vivo:
by Michael J. Guertin, André L. Martins, Adam Siepel, John T. Lis

DNA sequence and local chromatin landscape act jointly to determine transcription factor (TF) binding intensity profiles. To disentangle these influences, we developed an experimental approach, called protein/DNA binding followed by high-throughput sequencing (PB–seq), that allows the binding energy landscape to be characterized genome-wide in the absence of chromatin. We applied our methods to the Drosophila Heat Shock Factor (HSF), which inducibly binds a target DNA sequence element (HSE) following heat shock stress. PB–seq involves incubating sheared naked genomic DNA with recombinant HSF, partitioning the HSF–bound and HSF–free DNA, and then detecting HSF–bound DNA by high-throughput sequencing. We compared PB–seq binding profiles with ones observed in vivo by ChIP–seq and developed statistical models to predict the observed departures from idealized binding patterns based on covariates describing the local chromatin environment. We found that DNase I hypersensitivity and tetra-acetylation of H4 were the most influential covariates in predicting changes in HSF binding affinity. We also investigated the extent to which DNA accessibility, as measured by digital DNase I footprinting data, could be predicted from MNase–seq data and the ChIP–chip profiles for many histone modifications and TFs, and found GAGA element associated factor (GAF), tetra-acetylation of H4, and H4K16 acetylation to be the most predictive covariates. Lastly, we generated an unbiased model of HSF binding sequences, which revealed distinct biophysical properties of the HSF/HSE interaction and a previously unrecognized substructure within the HSE. These findings provide new insights into the interplay between the genomic sequence and the chromatin landscape in determining transcription factor binding intensity.

Probing the Informational and Regulatory Plasticity of a Transcription Factor DNA–Binding Domain

Probing the Informational and Regulatory Plasticity of a Transcription Factor DNA–Binding Domain:
by Ryan K. Shultzaberger, Sebastian J. Maerkl, Jack F. Kirsch, Michael B. Eisen

Transcription factors have two functional constraints on their evolution: (1) their binding sites must have enough information to be distinguishable from all other sequences in the genome, and (2) they must bind these sites with an affinity that appropriately modulates the rate of transcription. Since both are determined by the biophysical properties of the DNA–binding domain, selection on one will ultimately affect the other. We were interested in understanding how plastic the informational and regulatory properties of a transcription factor are and how transcription factors evolve to balance these constraints. To study this, we developed an in vivo selection system in Escherichia coli to identify variants of the helix-turn-helix transcription factor MarA that bind different sets of binding sites with varying degrees of degeneracy. Unlike previous in vitro methods used to identify novel DNA binders and to probe the plasticity of the binding domain, our selections were done within the context of the initiation complex, selecting for both specific binding within the genome and for a physiologically significant strength of interaction to maintain function of the factor. Using MITOMI, quantitative PCR, and a binding site fitness assay, we characterized the binding, function, and fitness of some of these variants. We observed that a large range of binding preferences, information contents, and activities could be accessed with a few mutations, suggesting that transcriptional regulatory networks are highly adaptable and expandable.

The Transcription Factor Encyclopedia

The Transcription Factor Encyclopedia: Here we present the Transcription Factor Encyclopedia (TFe), a new web-based compendium of mini review articles on transcription factors (TFs) that is founded on the principles of open access and collaboration. Our consortium of over 100 researchers has collectively contributed over 130 mini review articles on pertinent human, mouse and rat TFs. Notable features of the TFe website include a high-quality PDF generator and web API for programmatic data retrieval. TFe aims to rapidly educate scientists about the TFs they encounter through the delivery of succinct summaries written and vetted by experts in the field. TFe is available at http://www.cisreg.ca/tfe.

Thermodynamic State Ensemble Models of cis-Regulation

Thermodynamic State Ensemble Models of cis-Regulation:
by Marc S. Sherman, Barak A. Cohen

A major goal in computational biology is to develop models that accurately predict a gene's expression from its surrounding regulatory DNA. Here we present one class of such models, thermodynamic state ensemble models. We describe the biochemical derivation of the thermodynamic framework in simple terms, and lay out the mathematical components that comprise each model. These components include (1) the possible states of a promoter, where a state is defined as a particular arrangement of transcription factors bound to a DNA promoter, (2) the binding constants that describe the affinity of the protein–protein and protein–DNA interactions that occur in each state, and (3) whether each state is capable of transcribing. Using these components, we demonstrate how to compute a cis-regulatory function that encodes the probability of a promoter being active. Our intention is to provide enough detail so that readers with little background in thermodynamics can compose their own cis-regulatory functions. To facilitate this goal, we also describe a matrix form of the model that can be easily coded in any programming language. This formalism has great flexibility, which we show by illustrating how phenomena such as competition between transcription factors and cooperativity are readily incorporated into these models. Using this framework, we also demonstrate that Michaelis-like functions, another class of cis-regulatory models, are a subset of the thermodynamic framework with specific assumptions. By recasting Michaelis-like functions as thermodynamic functions, we emphasize the relationship between these models and delineate the specific circumstances representable by each approach. Application of thermodynamic state ensemble models is likely to be an important tool in unraveling the physical basis of combinatorial cis-regulation and in generating formalisms that accurately predict gene expression from DNA sequence.

Controlling gene expression with the Q repressible binary expression system in Caenorhabditis elegans

Controlling gene expression with the Q repressible binary expression system in Caenorhabditis elegans:
Controlling gene expression with the Q repressible binary expression system in Caenorhabditis elegans

Nature Methods 9, 391 (2012).
doi:10.1038/nmeth.1929

Authors: Xing Wei, Christopher J Potter, Liqun Luo & Kang Shen

Chromatin-modifying enzymes as modulators of reprogramming

Chromatin-modifying enzymes as modulators of reprogramming:
Chromatin-modifying enzymes as modulators of reprogramming

Nature 483, 7391 (2012). doi:10.1038/nature10953

Authors: Tamer T. Onder, Nergis Kara, Anne Cherry, Amit U. Sinha, Nan Zhu, Kathrin M. Bernt, Patrick Cahan, B. Ogan Marcarci, Juli Unternaehrer, Piyush B. Gupta, Eric S. Lander, Scott A. Armstrong & George Q. Daley
Generation of induced pluripotent stem cells (iPSCs) by somatic cell reprogramming involves global epigenetic remodelling. Whereas several proteins are known to regulate chromatin marks associated with the distinct epigenetic states of cells before and after reprogramming, the role of specific chromatin-modifying enzymes in reprogramming remains to be determined. To address how chromatin-modifying proteins influence reprogramming, we used short hairpin RNAs (shRNAs) to target genes in DNA and histone methylation pathways, and identified positive and negative modulators of iPSC generation. Whereas inhibition of the core components of the polycomb repressive complex 1 and 2, including the histone 3 lysine 27 methyltransferase EZH2, reduced reprogramming efficiency, suppression of SUV39H1, YY1 and DOT1L enhanced reprogramming. Specifically, inhibition of the H3K79 histone methyltransferase DOT1L by shRNA or a small molecule accelerated reprogramming, significantly increased the yield of iPSC colonies, and substituted for KLF4 and c-Myc (also known as MYC). Inhibition of DOT1L early in the reprogramming process is associated with a marked increase in two alternative factors, NANOG and LIN28, which play essential functional roles in the enhancement of reprogramming. Genome-wide analysis of H3K79me2 distribution revealed that fibroblast-specific genes associated with the epithelial to mesenchymal transition lose H3K79me2 in the initial phases of reprogramming. DOT1L inhibition facilitates the loss of this mark from genes that are fated to be repressed in the pluripotent state. These findings implicate specific chromatin-modifying enzymes as barriers to or facilitators of reprogramming, and demonstrate how modulation of chromatin-modifying enzymes can be exploited to more efficiently generate iPSCs with fewer exogenous transcription factors.

Mediator Acts Upstream of the Transcriptional Activator Gal4

Mediator Acts Upstream of the Transcriptional Activator Gal4:
by Keven Ang, Gary Ee, Edwin Ang, Elvin Koh, Wee Leng Siew, Yu Mun Chan, Sabrina Nur, Yee Sun Tan, Norbert Lehming

The proteasome inhibitor MG132 had been shown to prevent galactose induction of the S. cerevisiae GAL1 gene, demonstrating that ubiquitin proteasome-dependent degradation of transcription factors plays an important role in the regulation of gene expression. The deletion of the gene encoding the F-box protein Mdm30 had been reported to stabilize the transcriptional activator Gal4 under inducing conditions and to lead to defects in galactose utilization, suggesting that recycling of Gal4 is required for its function. Subsequently, however, it was argued that Gal4 remains stably bound to the enhancer under inducing conditions, suggesting that proteolytic turnover of Gal4 might not be required for its function. We have performed an alanine-scanning mutagenesis of ubiquitin and isolated a galactose utilization-defective ubiquitin mutant. We have used it for an unbiased suppressor screen and identified the inhibitor Gal80 as a suppressor of the transcriptional defects of the ubiquitin mutant, indicating that the protein degradation of the inhibitor Gal80, and not of the activator Gal4, is required for galactose induction of the GAL genes. We also show that in the absence of Gal80, Mdm30 is not required for Gal4 function, strongly supporting this hypothesis. Furthermore, we have found that Mediator controls the galactose-induced protein degradation of Gal80, which places Mediator genetically upstream of the activator Gal4. Mediator had originally been isolated by its ability to respond to transcriptional activators, and here we have discovered a leading role for Mediator in the process of transcription. The protein kinase Snf1 senses the inducing conditions and transduces the signal to Mediator, which initiates the degradation of the inhibitor Gal80 with the help of the E3 ubiquitin ligase SCF^Mdm30. The ability of Mediator to control the protein degradation of transcriptional inhibitors indicates that Mediator is actually able to direct its own recruitment to gene promoters.

Spider Antp has a role in leg repression [Developmental Biology]

Spider Antp has a role in leg repression [Developmental Biology]: Evolution often results in morphologically similar solutions in different organisms, a phenomenon known as convergence. However, there is little knowledge of the processes that lead to convergence at the genetic level. The genes of the Hox cluster control morphology in animals. They may also be central to the convergence of morphological traits, but whether morphological similarities also require similar changes in Hox gene function is disputed. In arthropods, body subdivision into a region with locomotory appendages (“thorax”) and a region with reduced appendages (“abdomen”) has evolved convergently in several groups, e.g., spiders and insects. In insects, legs develop in the expression domain of the Hox gene Antennapedia (Antp), whereas the Hox genes Ultrabithorax (Ubx) and abdominal-A mediate leg repression in the abdomen. Here, we show that, unlike Antp in insects, the Antp gene in the spider Achaearanea tepidariorum represses legs in the first segment of the abdomen (opisthosoma), and that Antp and Ubx are redundant in the following segment. The down-regulation of Antp in A. tepidariorum leads to a striking 10-legged phenotype. We present evidence from ectopic expression of the spider Antp gene in Drosophila embryos and imaginal tissue that this unique function of Antp is not due to changes in the Antp protein, but likely due to divergent evolution of cofactors, Hox collaborators or target genes in spiders and flies. Our results illustrate an interesting example of convergent evolution of abdominal leg repression in arthropods by altering the role of distinct Hox genes at different levels of their action.

Free Extracellular Diffusion Creates the Dpp Morphogen Gradient of the Drosophila Wing Disc

Free Extracellular Diffusion Creates the Dpp Morphogen Gradient of the Drosophila Wing Disc: Shaohua Zhou, Wing-Cheong Lo, Jeffrey L. Suhalim, Michelle A. Digman, Enrico Gratton, Qing Nie, Arthur D. Lander. BackgroundHow morphogen gradients form has long been a subject of controversy. The strongest support for the view that morphogens do not simply spread by free diffusion has come from a variety of ....

Widespread Site-Dependent Buffering of Human Regulatory Polymorphism

Widespread Site-Dependent Buffering of Human Regulatory Polymorphism:
by Matthew T. Maurano, Hao Wang, Tanya Kutyavin, John A. Stamatoyannopoulos

The average individual is expected to harbor thousands of variants within non-coding genomic regions involved in gene regulation. However, it is currently not possible to interpret reliably the functional consequences of genetic variation within any given transcription factor recognition sequence. To address this, we comprehensively analyzed heritable genome-wide binding patterns of a major sequence-specific regulator (CTCF) in relation to genetic variability in binding site sequences across a multi-generational pedigree. We localized and quantified CTCF occupancy by ChIP-seq in 12 related and unrelated individuals spanning three generations, followed by comprehensive targeted resequencing of the entire CTCF–binding landscape across all individuals. We identified hundreds of variants with reproducible quantitative effects on CTCF occupancy (both positive and negative). While these effects paralleled protein–DNA recognition energetics when averaged, they were extensively buffered by striking local context dependencies. In the significant majority of cases buffering was complete, resulting in silent variants spanning every position within the DNA recognition interface irrespective of level of binding energy or evolutionary constraint. The prevalence of complex partial or complete buffering effects severely constrained the ability to predict reliably the impact of variation within any given binding site instance. Surprisingly, 40% of variants that increased CTCF occupancy occurred at positions of human–chimp divergence, challenging the expectation that the vast majority of functional regulatory variants should be deleterious. Our results suggest that, even in the presence of “perfect” genetic information afforded by resequencing and parallel studies in multiple related individuals, genomic site-specific prediction of the consequences of individual variation in regulatory DNA will require systematic coupling with empirical functional genomic measurements.

Cis-acting element localizes mRNA to synapses [Neuroscience]

Cis-acting element localizes mRNA to synapses [Neuroscience]: Messenger RNA (mRNA) localization and regulated translation can spatially restrict gene expression to each of the thousands of synaptic compartments formed by a single neuron. Although cis-acting RNA elements have been shown to direct localization of mRNAs from the soma into neuronal processes, less is known about signals that target transcripts specifically to synapses. In Aplysia sensory-motor neuronal cultures, synapse formation rapidly redistributes the mRNA encoding the peptide neurotransmitter sensorin from neuritic shafts into synapses. We find that the export of sensorin mRNA from soma to neurite and the localization to synapse are controlled by distinct signals. The 3′ UTR is sufficient for export into distal neurites, whereas the 5′ UTR is required for concentration of reporter mRNA at synapses. We have identified a 66-nt element in the 5′ UTR of sensorin that is necessary and sufficient for synaptic mRNA localization. Mutational and chemical probing analyses are consistent with a role for secondary structure in this process.

On a fundamental structure of gene networks in living cells [Chemistry]

On a fundamental structure of gene networks in living cells [Chemistry]: Computers are organized into hardware and software. Using a theoretical approach to identify patterns in gene expression in a variety of species, organs, and cell types, we found that biological systems similarly are comprised of a relatively unchanging hardware-like gene pattern. Orthogonal patterns of software-like transcripts vary greatly, even among tumors of the same type from different individuals. Two distinguishable classes could be identified within the hardware-like component: those transcripts that are highly expressed and stable and an adaptable subset with lower expression that respond to external stimuli. Importantly, we demonstrate that this structure is conserved across organisms. Deletions of transcripts from the highly stable core are predicted to result in cell mortality. The approach provides a conceptual thermodynamic-like framework for the analysis of gene-expression levels and networks and their variations in diseased cells.

Differential regulation of mesodermal gene expression by Drosophila cell type-specific Forkhead transcription factors [RESEARCH ARTICLES]

Differential regulation of mesodermal gene expression by Drosophila cell type-specific Forkhead transcription factors [RESEARCH ARTICLES]: Xianmin Zhu, Shaad M. Ahmad, Anton Aboukhalil, Brian W. Busser, Yongsok Kim, Terese R. Tansey, Adrian Haimovich, Neal Jeffries, Martha L. Bulyk, and Alan M. Michelson


A common theme in developmental biology is the repeated use of the same gene in diverse spatial and temporal domains, a process that generally involves transcriptional regulation mediated by multiple separate enhancers, each with its own arrangement of transcription factor (TF)-binding sites and associated activities. Here, by contrast, we show that the expression of the Drosophila Nidogen (Ndg) gene at different embryonic stages and in four mesodermal cell types is governed by the binding of multiple cell-specific Forkhead (Fkh) TFs – including Biniou (Bin), Checkpoint suppressor homologue (CHES-1-like) and Jumeau (Jumu) – to three functionally distinguishable Fkh-binding sites in the same enhancer. Whereas Bin activates the Ndg enhancer in the late visceral musculature, CHES-1-like cooperates with Jumu to repress this enhancer in the heart. CHES-1-like also represses the Ndg enhancer in a subset of somatic myoblasts prior to their fusion to form multinucleated myotubes. Moreover, different combinations of Fkh sites, corresponding to two different sequence specificities, mediate the particular functions of each TF. A genome-wide scan for the occurrence of both classes of Fkh domain recognition sites in association with binding sites for known cardiac TFs showed an enrichment of combinations containing the two Fkh motifs in putative enhancers found within the noncoding regions of genes having heart expression. Collectively, our results establish that different cell-specific members of a TF family regulate the activity of a single enhancer in distinct spatiotemporal domains, and demonstrate how individual binding motifs for a TF class can differentially influence gene expression.

Regulated Noise in the Epigenetic Landscape of Development and Disease

Regulated Noise in the Epigenetic Landscape of Development and Disease: Elisabet Pujadas, Andrew P. Feinberg. In this Perspective, we synthesize past and present observations in the field of epigenetics to propose a model in which the epigenome can modulate cellular plasticity in development and disease b....

Promoter Nucleosome Organization Shapes the Evolution of Gene Expression

Promoter Nucleosome Organization Shapes the Evolution of Gene Expression:
by Dalia Rosin, Gil Hornung, Itay Tirosh, Ariel Gispan, Naama Barkai

Understanding why genes evolve at different rates is fundamental to evolutionary thinking. In species of the budding yeast, the rate at which genes diverge in expression correlates with the organization of their promoter nucleosomes: genes lacking a nucleosome-free region (denoted OPN for “Occupied Proximal Nucleosomes”) vary widely between the species, while the expression of those containing NFR (denoted DPN for “Depleted Proximal Nucleosomes”) remains largely conserved. To examine if early evolutionary dynamics contributes to this difference in divergence, we artificially selected for high expression of GFP–fused proteins. Surprisingly, selection was equally successful for OPN and DPN genes, with ∼80% of genes in each group stably increasing in expression by a similar amount. Notably, the two groups adapted by distinct mechanisms: DPN–selected strains duplicated large genomic regions, while OPN–selected strains favored trans mutations not involving duplications. When selection was removed, DPN (but not OPN) genes reverted rapidly to wild-type expression levels, consistent with their lower diversity between species. Our results suggest that promoter organization constrains the early evolutionary dynamics and in this way biases the path of long-term evolution.

Selective Sweep of a cis-Regulatory Sequence in a Non-African Population of Drosophila melanogaster

Selective Sweep of a cis-Regulatory Sequence in a Non-African Population of Drosophila melanogaster:
Although it is thought that changes in gene expression play an important role in adaptation, the identification of gene-regulatory sequences that have been targets of positive selection has proved difficult. Here, we identify a cis-regulatory element of the Drosophila melanogaster CG9509 gene that is associated with a selective sweep in a derived non-African population of the species. Expression analyses indicate that CG9509 consistently shows greater expression in non-African than in African strains of D. melanogaster. We find that a 1.8 kb region located just upstream of the CG9509 coding region is devoid of DNA sequence polymorphism in a European population sample and that this is best explained by the recent action of positive selection (within the past 4,000–10,000 years). Using a reporter gene construct and phiC31-mediated site-specific integration, we show that the European version of the CG9509 upstream region drives 2–3 times greater expression than the African version in an otherwise identical genetic background. This expression difference corresponds well to that of the native gene and indicates that sequence variation within the CG9509 upstream region can completely account for its high expression in the European population. Selection appears to have favored a quantitative increase in gene expression in the Malphigian tubule, the tissue where CG9509 is predominantly expressed.

Molecular Evolution in Nonrecombining Regions of the Drosophila melanogaster Genome

Molecular Evolution in Nonrecombining Regions of the Drosophila melanogaster Genome:
We study the evolutionary effects of reduced recombination on the Drosophila melanogaster genome, analyzing more than 200 new genes that lack crossing-over and employing a novel orthology search among species of the melanogaster subgroup. These genes are located in the heterochromatin of chromosomes other than the dot (fourth) chromosome. Noncrossover regions of the genome all exhibited an elevated level of evolutionary divergence from D. yakuba at nonsynonymous sites, lower codon usage bias, lower GC content in coding and noncoding regions, and longer introns. Levels of gene expression are similar for genes in regions with and without crossing-over, which rules out the possibility that the reduced level of adaptation that we detect is caused by relaxed selection due to lower levels of gene expression in the heterochromatin. The patterns observed are consistent with a reduction in the efficacy of selection in all regions of the genome of D. melanogaster that lack crossing-over, as a result of the effects of enhanced Hill–Robertson interference. However, we also detected differences among nonrecombining locations: The X chromosome seems to exhibit the weakest effects, whereas the fourth chromosome and the heterochromatic genes on the autosomes located most proximal to the centromere showed the largest effects. However, signatures of selection on both nonsynonymous mutations and on codon usage persist in all heterochromatic regions.

Genome-wide structure and organization of eukaryotic pre-initiation complexes

Genome-wide structure and organization of eukaryotic pre-initiation complexes:
Genome-wide structure and organization of eukaryotic pre-initiation complexes

Nature 483, 7389 (2012). doi:10.1038/nature10799

Authors: Ho Sung Rhee & B. Franklin Pugh
Transcription and regulation of genes originate from transcription pre-initiation complexes (PICs). Their structural and positional organization across eukaryotic genomes is unknown. Here we applied lambda exonuclease to chromatin immunoprecipitates (termed ChIP-exo) to examine the precise location of 6,045 PICs in Saccharomyces. PICs, including RNA

Stringent Analysis of Gene Function and Protein-Protein Interactions Using Fluorescently Tagged Genes [Methods, Technology, and Resources]

Stringent Analysis of Gene Function and Protein-Protein Interactions Using Fluorescently Tagged Genes [Methods, Technology, and Resources]:
In Drosophila collections of green fluorescent protein (GFP) trap lines have been used to probe the endogenous expression patterns of trapped genes or the subcellular localization of their protein products. Here, we describe a method, based on nonoverlapping, highly specific, shRNA transgenes directed against GFP, that extends the utility of these collections to loss-of-function studies. Furthermore, we used a MiMIC transposon to generate GFP traps in Drosophila cell lines with distinct subcellular localization patterns, which will permit high-throughput screens using fluorescently tagged proteins. Finally, we show that fluorescent traps, paired with recombinant nanobodies and mass spectrometry, allow the study of endogenous protein complexes in Drosophila.

Combinatorial Activation and Repression by Seven Transcription Factors Specify Drosophila Odorant Receptor Expression

Combinatorial Activation and Repression by Seven Transcription Factors Specify Drosophila Odorant Receptor Expression:
by Shadi Jafari, Liza Alkhori, Alexander Schleiffer, Anna Brochtrup, Thomas Hummel, Mattias Alenius

The mechanism that specifies olfactory sensory neurons to express only one odorant receptor (OR) from a large repertoire is critical for odor discrimination but poorly understood. Here, we describe the first comprehensive analysis of OR expression regulation in Drosophila. A systematic, RNAi-mediated knock down of most of the predicted transcription factors identified an essential function of acj6, E93, Fer1, onecut, sim, xbp1, and zf30c in the regulation of more than 30 ORs. These regulatory factors are differentially expressed in antennal sensory neuron classes and specifically required for the adult expression of ORs. A systematic analysis reveals not only that combinations of these seven factors are necessary for receptor gene expression but also a prominent role for transcriptional repression in preventing ectopic receptor expression. Such regulation is supported by bioinformatics and OR promoter analyses, which uncovered a common promoter structure with distal repressive and proximal activating regions. Thus, our data provide insight into how combinatorial activation and repression can allow a small number of transcription factors to specify a large repertoire of neuron classes in the olfactory system.

GENETIC SIGNATURE OF ADAPTIVE PEAK SHIFT IN THREESPINE STICKLEBACK

GENETIC SIGNATURE OF ADAPTIVE PEAK SHIFT IN THREESPINE STICKLEBACK:

ABSTRACT

Transition of an evolving population to a new adaptive optimum is predicted to leave a signature in the distribution of effect sizes of fixed mutations. If they affect many traits (are pleiotropic), large effect mutations should contribute more when a population evolves to a farther adaptive peak than to a nearer peak. We tested this prediction in wild threespine stickleback fish (Gasterosteus aculeatus) by comparing the estimated frequency of large effect genetic changes underlying evolution as the same ancestor adapted to two lake types since the end of the ice age. A higher frequency of large effect genetic changes (quantitative trait loci) contributed to adaptive evolution in populations that adapted to lakes representing a more distant optimum than to lakes in which the optimum phenotype was nearer to the ancestral state. Our results also indicate that pleiotropy, not just optimum overshoot, contributes to this difference. These results suggest that a series of adaptive improvements to a new environment leaves a detectable mark in the genome of wild populations. Although not all assumptions of the theory are likely met in natural systems, the prediction may be robust enough to the complexities of natural environments to be useful when forecasting adaptive responses to large environmental changes.

2012 The Author(s). Journal compilation © 2012 The Society for the Study of Evolution

Multiple exposures to drought 'train' transcriptional responses in Arabidopsis

Multiple exposures to drought 'train' transcriptional responses in Arabidopsis:
Multiple exposures to drought 'train' transcriptional responses in Arabidopsis

Nature Communications 3, 740 (2012). doi:10.1038/ncomms1732

Authors: Yong Ding, Michael Fromm & Zoya Avramova

Identification of co-occurring transcription factor binding sites from DNA sequence using clustered position weight matrices

Identification of co-occurring transcription factor binding sites from DNA sequence using clustered position weight matrices:
Accurate prediction of transcription factor binding sites (TFBSs) is a prerequisite for identifying cis-regulatory modules that underlie transcriptional regulatory circuits encoded in the genome. Here, we present a computational framework for detecting TFBSs, when multiple position weight matrices (PWMs) for a transcription factor are available. Grouping multiple PWMs of a transcription factor (TF) based on their sequence similarity improves the specificity of TFBS prediction, which was evaluated using multiple genome-wide ChIP-Seq data sets from 26 TFs. The Z-scores of the area under a receiver operating characteristic curve (AUC) values of 368 TFs were calculated and used to statistically identify co-occurring regulatory motifs in the TF bound ChIP loci. Motifs that are co-occurring along with the empirical bindings of E2F, JUN or MYC have been evaluated, in the basal or stimulated condition. Results prove our method can be useful to systematically identify the co-occurring motifs of the TF for the given conditions.

[Perspective] Retrospective: Roy J. Britten (1919–2012)

[Perspective] Retrospective: Roy J. Britten (1919–2012): A molecular biologist founded fundamental concepts in DNA sequence organization and gene expression that underlie modern genomics and genome evolution.

Author: Eric H. Davidson

Insights into hominid evolution from the gorilla genome sequence

Insights into hominid evolution from the gorilla genome sequence:
Insights into hominid evolution from the gorilla genome sequence

Nature 483, 7388 (2012). doi:10.1038/nature10842

Authors: Aylwyn Scally, Julien Y. Dutheil, LaDeana W. Hillier, Gregory E. Jordan, Ian Goodhead, Javier Herrero, Asger Hobolth, Tuuli Lappalainen, Thomas Mailund, Tomas Marques-Bonet, Shane McCarthy, Stephen H. Montgomery, Petra C. Schwalie, Y. Amy Tang, Michelle C. Ward, Yali Xue, Bryndis Yngvadottir, Can Alkan, Lars N. Andersen, Qasim Ayub, Edward V. Ball, Kathryn Beal, Brenda J. Bradley, Yuan Chen, Chris M. Clee, Stephen Fitzgerald, Tina A. Graves, Yong Gu, Paul Heath, Andreas Heger, Emre Karakoc, Anja Kolb-Kokocinski, Gavin K. Laird, Gerton Lunter, Stephen Meader, Matthew Mort, James C. Mullikin, Kasper Munch, Timothy D. O’Connor, Andrew D. Phillips, Javier Prado-Martinez, Anthony S. Rogers, Saba Sajjadian, Dominic Schmidt, Katy Shaw, Jared T. Simpson, Peter D. Stenson, Daniel J. Turner, Linda Vigilant, Albert J. Vilella, Weldon Whitener, Baoli Zhu, David N. Cooper, Pieter de Jong, Emmanouil T. Dermitzakis, Evan E. Eichler, Paul Flicek, Nick Goldman, Nicholas I. Mundy, Zemin Ning, Duncan T. Odom, Chris P. Ponting, Michael A. Quail, Oliver A. Ryder, Stephen M. Searle, Wesley C. Warren, Richard K. Wilson, Mikkel H. Schierup, Jane Rogers, Chris Tyler-Smith & Richard Durbin
Gorillas are humans’ closest living relatives after chimpanzees, and are of comparable importance for the study of human origins and evolution. Here we present the assembly and analysis of a genome sequence for the western lowland gorilla, and compare the whole genomes of all extant

Single-Cell Exome Sequencing and Monoclonal Evolution of a JAK2-Negative Myeloproliferative Neoplasm

Single-Cell Exome Sequencing and Monoclonal Evolution of a JAK2-Negative Myeloproliferative Neoplasm:

Yong Hou, Luting Song, Ping Zhu, Bo Zhang, Ye Tao, Xun Xu, Fuqiang Li, Kui Wu, Jie Liang, Di Shao, Hanjie Wu, Xiaofei Ye, Chen Ye, Renhua Wu, Min Jian, Yan Chen, Wei Xie, Ruren Zhang, Lei Chen, Xin Liu, Xiaotian Yao, Hancheng Zheng, Chang Yu, Qibin Li, Zhuolin Gong, Mao Mao, Xu Yang, Lin Yang, Jingxiang Li, Wen Wang, Zuhong Lu, Ning Gu, Goodman Laurie, Lars Bolund, Karsten Kristiansen, Jian Wang, Huanming Yang, Yingrui Li, Xiuqing Zhang, Jun Wang. Tumor heterogeneity presents a challenge for inferring clonal evolution and driver gene identification. Here, we describe a method for analyzing the cancer genome at a single-cell nucleotide level....

Single-Cell Exome Sequencing Reveals Single-Nucleotide Mutation Characteristics of a Kidney Tumor

Single-Cell Exome Sequencing Reveals Single-Nucleotide Mutation Characteristics of a Kidney Tumor:

Xun Xu, Yong Hou, Xuyang Yin, Li Bao, Aifa Tang, Luting Song, Fuqiang Li, Shirley Tsang, Kui Wu, Hanjie Wu, Weiming He, Liang Zeng, Manjie Xing, Renhua Wu, Hui Jiang, Xiao Liu, Dandan Cao, Guangwu Guo, Xueda Hu, Yaoting Gui, Zesong Li, Wenyue Xie, Xiaojuan Sun, Min Shi, Zhiming Cai, Bin Wang, Meiming Zhong, Jingxiang Li, Zuhong Lu, Ning Gu, Xiuqing Zhang, Laurie Goodman, Lars Bolund, Jian Wang, Huanming Yang, Karsten Kristiansen, Michael Dean, Yingrui Li, Jun Wang. Clear cell renal cell carcinoma (ccRCC) is the most common kidney cancer and has very few mutations that are shared between different patients. To better understand the intratumoral genetics under....

Akirin Links Twist-Regulated Transcription with the Brahma Chromatin Remodeling Complex during Embryogenesis

Akirin Links Twist-Regulated Transcription with the Brahma Chromatin Remodeling Complex during Embryogenesis:
by Scott J. Nowak, Hitoshi Aihara, Katie Gonzalez, Yutaka Nibu, Mary K. Baylies

The activities of developmentally critical transcription factors are regulated via interactions with cofactors. Such interactions influence transcription factor activity either directly through protein–protein interactions or indirectly by altering the local chromatin environment. Using a yeast double-interaction screen, we identified a highly conserved nuclear protein, Akirin, as a novel cofactor of the key Drosophila melanogaster mesoderm and muscle transcription factor Twist. We find that Akirin interacts genetically and physically with Twist to facilitate expression of some, but not all, Twist-regulated genes during embryonic myogenesis. akirin mutant embryos have muscle defects consistent with altered regulation of a subset of Twist-regulated genes. To regulate transcription, Akirin colocalizes and genetically interacts with subunits of the Brahma SWI/SNF-class chromatin remodeling complex. Our results suggest that, mechanistically, Akirin mediates a novel connection between Twist and a chromatin remodeling complex to facilitate changes in the chromatin environment, leading to the optimal expression of some Twist-regulated genes during Drosophila myogenesis. We propose that this Akirin-mediated link between transcription factors and the Brahma complex represents a novel paradigm for providing tissue and target specificity for transcription factor interactions with the chromatin remodeling machinery.

[Report] Condition-Dependent Transcriptome Reveals High-Level Regulatory Architecture in Bacillus subtilis

[Report] Condition-Dependent Transcriptome Reveals High-Level Regulatory Architecture in Bacillus subtilis: A horizontal analysis reveals the breadth of genes turned on and off as nutrients change.

Authors: Pierre Nicolas, Ulrike Mäder, Etienne Dervyn, Tatiana Rochat, Aurélie Leduc, Nathalie Pigeonneau, Elena Bidnenko, Elodie Marchadier, Mark Hoebeke, Stéphane Aymerich, Dörte Becher, Paola Bisicchia, Eric Botella, Olivier Delumeau, Geoff Doherty, Emma L. Denham, Mark J. Fogg, Vincent Fromion, Anne Goelzer, Annette Hansen, Elisabeth Härtig, Colin R. Harwood, Georg Homuth, Hanne Jarmer, Matthieu Jules, Edda Klipp, Ludovic Le Chat, François Lecointe, Peter Lewis, Wolfram Liebermeister, Anika March, Ruben A. T. Mars, Priyanka Nannapaneni, David Noone, Susanne Pohl, Bernd Rinn, Frank Rügheimer, Praveen K. Sappa, Franck Samson, Marc Schaffer, Benno Schwikowski, Leif Steil, Jörg Stülke, Thomas Wiegert, Kevin M. Devine, Anthony J. Wilkinson, Jan Maarten van Dijl, Michael Hecker, Uwe Völker, Philippe Bessières, Philippe Noirot

[Report] Global Network Reorganization During Dynamic Adaptations of Bacillus subtilis Metabolism

[Report] Global Network Reorganization During Dynamic Adaptations of Bacillus subtilis Metabolism: A vertical analysis reveals that a simple switch of one food for another evokes changes at many levels.

Authors: Joerg Martin Buescher, Wolfram Liebermeister, Matthieu Jules, Markus Uhr, Jan Muntel, Eric Botella, Bernd Hessling, Roelco Jacobus Kleijn, Ludovic Le Chat, François Lecointe, Ulrike Mäder, Pierre Nicolas, Sjouke Piersma, Frank Rügheimer, Dörte Becher, Philippe Bessieres, Elena Bidnenko, Emma L. Denham, Etienne Dervyn, Kevin M. Devine, Geoff Doherty, Samuel Drulhe, Liza Felicori, Mark J. Fogg, Anne Goelzer, Annette Hansen, Colin R. Harwood, Michael Hecker, Sebastian Hubner, Claus Hultschig, Hanne Jarmer, Edda Klipp, Aurélie Leduc, Peter Lewis, Frank Molina, Philippe Noirot, Sabine Peres, Nathalie Pigeonneau, Susanne Pohl, Simon Rasmussen, Bernd Rinn, Marc Schaffer, Julian Schnidder, Benno Schwikowski, Jan Maarten Van Dijl, Patrick Veiga, Sean Walsh, Anthony J. Wilkinson, Jörg Stelling, Stéphane Aymerich, Uwe Sauer

Promoter architecture of mouse olfactory receptor genes [RESEARCH]

Promoter architecture of mouse olfactory receptor genes [RESEARCH]:

Odorous chemicals are detected by the mouse main olfactory epithelium (MOE) by about 1100 types of olfactory receptors (OR) expressed by olfactory sensory neurons (OSNs). Each mature OSN is thought to express only one allele of a single OR gene. Major impediments to understand the transcriptional control of OR gene expression are the lack of a proper characterization of OR transcription start sites (TSSs) and promoters, and of regulatory transcripts at OR loci. We have applied the nanoCAGE technology to profile the transcriptome and the active promoters in the MOE. nanoCAGE analysis revealed the map and architecture of promoters for 87.5% of the mouse OR genes, as well as the expression of many novel noncoding RNAs including antisense transcripts. We identified candidate transcription factors for OR gene expression and among them confirmed by chromatin immunoprecipitation the binding of TBP, EBF1 (OLF1), and MEF2A to OR promoters. Finally, we showed that a short genomic fragment flanking the major TSS of the OR gene Olfr160 (M72) can drive OSN-specific expression in transgenic mice.

Sequence shortening in the rodent ancestor [RESEARCH]

Sequence shortening in the rodent ancestor [RESEARCH]:
Insertions and deletions (indels), together with nucleotide substitutions, are major drivers of sequence evolution. An excess of deletions over insertions in genomic sequences—the so-called deletional bias—has been reported in a wide range of species, including mammals. However, this bias has not been found in the coding sequences of some mammalian species, such as human and mouse. To determine the strength of the deletional bias in mammals, and the influence of mutation and selection, we have quantified indels in both neutrally evolving noncoding sequences and protein-coding sequences, in six mammalian branches: human, macaque, ancestral primate, mouse, rat, and ancestral rodent. The results obtained with an improved algorithm for the placement of insertions in multiple alignments, Prank_+F, indicate that contrary to previous results, the only mammalian branch with a strong deletional bias is the rodent ancestral branch. We estimate that such a bias has resulted in an ~2.5% sequence loss of mammalian syntenic region in the ancestor of the mouse and rat. Further, a comparison of coding and noncoding sequences shows that negative selection is acting more strongly against mutations generating amino acid insertions than against mutations resulting in amino acid deletions. The strength of selection against indels is found to be higher in the rodent branches than in the primate branches, consistent with the larger effective population sizes of the rodents.