Variable motif utilization in homeotic selector (Hox)-cofactor complex formation controls specificity [Developmental Biology]

Variable motif utilization in homeotic selector (Hox)-cofactor complex formation controls specificity [Developmental Biology]: Homeotic selector (Hox) proteins often bind DNA cooperatively with cofactors such as Extradenticle (Exd) and Homothorax (Hth) to achieve functional specificity in vivo. Previous studies identified the Hox YPWM motif as an important Exd interaction motif. Using a comparative approach, we characterize the contribution of this and additional conserved sequence motifs to the regulation of specific target genes for three Drosophila Hox proteins. We find that Sex combs reduced (Scr) uses a simple interaction mechanism, where a single tryptophan-containing motif is necessary for Exd-dependent DNA-binding and in vivo functions. Abdominal-A (AbdA) is more complex, using multiple conserved motifs in a context-dependent manner. Lastly, Ultrabithorax (Ubx) is the most flexible, in that it uses multiple conserved motifs that function in parallel to regulate target genes in vivo. We propose that using different binding mechanisms with the same cofactor may be one strategy to achieve functional specificity in vivo.

[Report] From Flat Foot to Fat Foot: Structure, Ontogeny, Function, and Evolution of Elephant “Sixth Toes”

[Report] From Flat Foot to Fat Foot: Structure, Ontogeny, Function, and Evolution of Elephant “Sixth Toes”: Elephants have an extra bone in their feet that can be traced through their fossil record to reveal a transition from flat to raised feet.

Authors: John R. Hutchinson, Cyrille Delmer, Charlotte E. Miller, Thomas Hildebrandt, Andrew A. Pitsillides, Alan Boyde

[Report] Fossilized Nuclei and Germination Structures Identify Ediacaran “Animal Embryos” as Encysting Protists

[Report] Fossilized Nuclei and Germination Structures Identify Ediacaran “Animal Embryos” as Encysting Protists: High-resolution imaging of 570-million-year-old fossils suggests that they were not remnants of early animals.

Authors: Therese Huldtgren, John A. Cunningham, Chongyu Yin, Marco Stampanoni, Federica Marone, Philip C. J. Donoghue, Stefan Bengtson

A Genome-wide SNP Genotyping Array Reveals Patterns of Global and Repeated Species-Pair Divergence in Sticklebacks

A Genome-wide SNP Genotyping Array Reveals Patterns of Global and Repeated Species-Pair Divergence in Sticklebacks: Felicity C. Jones, Yingguang Frank Chan, Jeremy Schmutz, Jane Grimwood, Shannon D. Brady, Audrey M. Southwick, Devin M. Absher, Richard M. Myers, Thomas E. Reimchen, Bruce E. Deagle, Dolph Schluter, David M. Kingsley. Genes underlying repeated adaptive evolution in natural populations are still largely unknown. Stickleback fish (Gasterosteus aculeatus) have undergone a recent dramatic evolutionary radiat....

Combinatorial Patterning of Chromatin Regulators Uncovered by Genome-wide Location Analysis in Human Cells

Combinatorial Patterning of Chromatin Regulators Uncovered by Genome-wide Location Analysis in Human Cells: Oren Ram, Alon Goren, Ido Amit, Noam Shoresh, Nir Yosef, Jason Ernst, Manolis Kellis, Melissa Gymrek, Robbyn Issner, Michael Coyne, Timothy Durham, Xiaolan Zhang, Julie Donaghey, Charles B. Epstein, Aviv Regev, Bradley E. Bernstein. Hundreds of chromatin regulators (CRs) control chromatin structure and function by catalyzing and binding histone modifications, yet the rules governing these key processes remain obscure. Here, w....

Adaptation to P Element Transposon Invasion in Drosophila melanogaster

Adaptation to P Element Transposon Invasion in Drosophila melanogaster: Jaspreet S. Khurana, Jie Wang, Jia Xu, Birgit S. Koppetsch, Travis C. Thomson, Anetta Nowosielska, Chengjian Li, Phillip D. Zamore, Zhiping Weng, William E. Theurkauf. Transposons evolve rapidly and can mobilize and trigger genetic instability. Piwi-interacting RNAs (piRNAs) silence these genome pathogens, but it is unclear how the piRNA pathway adapts to invasi....

DNA-binding factors shape the mouse methylome at distal regulatory regions

DNA-binding factors shape the mouse methylome at distal regulatory regions:

DNA-binding factors shape the mouse methylome at distal regulatory regions

Nature 480, 7378 (2011). doi:10.1038/nature10716

Authors: Michael B. Stadler, Rabih Murr, Lukas Burger, Robert Ivanek, Florian Lienert, Anne Schöler, Christiane Wirbelauer, Edward J. Oakeley, Dimos Gaidatzis, Vijay K. Tiwari & Dirk Schübeler

Methylation of cytosines is an essential epigenetic modification in mammalian genomes, yet the rules that govern methylation patterns remain largely elusive. To gain insights into this process, we generated base-pair-resolution mouse methylomes in stem cells and neuronal progenitors. Advanced quantitative analysis identified low-methylated regions (LMRs)

Curated collection of yeast transcription factor DNA binding specificity data reveals novel structural and gene regulatory insights

Curated collection of yeast transcription factor DNA binding specificity data reveals novel structural and gene regulatory insights: Background:
Transcription factors (TFs) play a central role in regulating gene expression by interacting with cis-regulatory DNA elements associated with their target genes. Recent surveys have examined the DNA binding specificities of most Saccharomyces cerevisiae TFs, but a comprehensive evaluation of their data has been lacking.
Results:
We analyzed in vitro and in vivo TF-DNA binding data reported in previous large-scale studies to generate a comprehensive, curated resource of DNA binding specificity data for all characterized S. cerevisiae TFs. Our collection comprises DNA binding site motifs and comprehensive in vitro DNA binding specificity data for all possible 8 bp sequences. Investigation of the DNA binding specificities within the basic leucine zipper (bZIP) and VHT1 regulator (VHR) TF families revealed unexpected plasticity in TF-DNA recognition: intriguingly, the VHR TFs, newly characterized by protein binding microarrays in this study, recognize bZIP-like DNA motifs, while the bZIP TF Hac1 recognizes a motif highly similar to the canonical E-box motif of basic helix-loop-helix (bHLH) TFs. We identified several TFs with distinct primary and secondary motifs, which might be associated with different regulatory functions. Finally, integrated analysis of in vivo TF binding data with protein binding microarray data lends further support for indirect DNA binding in vivo by sequence-specific TFs.
Conclusions:
The comprehensive data in this curated collection allow for more accurate analyses of regulatory TF-DNA interactions, in-depth structural studies of TF-DNA specificity determinants, and future experimental investigations of the TFs' predicted target genes and regulatory roles.

The kinase Sgg modulates temporal development of macrochaetes in Drosophila by phosphorylation of Scute and Pannier [RESEARCH ARTICLES]

The kinase Sgg modulates temporal development of macrochaetes in Drosophila by phosphorylation of Scute and Pannier [RESEARCH ARTICLES]: Mingyao Yang, Emma Hatton-Ellis, and Pat Simpson

Evolution of novel structures is often made possible by changes in the timing or spatial expression of genes regulating development. Macrochaetes, large sensory bristles arranged into species-specific stereotypical patterns, are an evolutionary novelty of cyclorraphous flies and are associated with changes in both the temporal and spatial expression of the proneural genes achaete (ac) and scute (sc). Changes in spatial expression are associated with the evolution of cis-regulatory sequences, but it is not known how temporal regulation is achieved. One factor required for ac-sc expression, the expression of which coincides temporally with that of ac-sc in the notum, is Wingless (Wg; also known as Wnt). Wingless downregulates the activity of the serine/threonine kinase Shaggy (Sgg; also known as GSK-3). We demonstrate that Scute is phosphorylated by Sgg on a serine residue and that mutation of this residue results in a form of Sc with heightened proneural activity that can rescue the loss of bristles characteristic of wg mutants. We suggest that the phosphorylated form of Sc has reduced transcriptional activity such that sc is unable to autoregulate, an essential function for the segregation of bristle precursors. Sgg also phosphorylates Pannier, a transcriptional activator of ac-sc, the activity of which is similarly dampened when in the phosphorylated state. Furthermore, we show that Wg signalling does not act directly via a cis-regulatory element of the ac-sc genes. We suggest that temporal control of ac-sc activity in cyclorraphous flies is likely to be regulated by permissive factors and might therefore not be encoded at the level of ac-sc gene sequences.

Cis-regulatory elements: molecular mechanisms and evolutionary processes underlying divergence

Cis-regulatory elements: molecular mechanisms and evolutionary processes underlying divergence:

Cis-regulatory elements: molecular mechanisms and evolutionary processes underlying divergence

Nature Reviews Genetics 13, 59 (2012).
doi:10.1038/nrg3095

Authors: Patricia J. Wittkopp & Gizem Kalay

Cis-regulatory sequences, such as enhancers and promoters, control development and physiology by regulating gene expression. Mutations that affect the function of these sequences contribute to phenotypic diversity within and between species. With many case studies implicating divergent cis-regulatory activity in phenotypic evolution, researchers

A High-Resolution Whole-Genome Map of Key Chromatin Modifications in the Adult Drosophila melanogaster

A High-Resolution Whole-Genome Map of Key Chromatin Modifications in the Adult Drosophila melanogaster:
by Hang Yin, Sarah Sweeney, Debasish Raha, Michael Snyder, Haifan Lin


Epigenetic research has been focused on cell-type-specific regulation; less is known about common features of epigenetic programming shared by diverse cell types within an organism. Here, we report a modified method for chromatin immunoprecipitation and deep sequencing (ChIP–Seq) and its use to construct a high-resolution map of the Drosophila melanogaster key histone marks, heterochromatin protein 1a (HP1a) and RNA polymerase II (polII). These factors are mapped at 50-bp resolution genome-wide and at 5-bp resolution for regulatory sequences of genes, which reveals fundamental features of chromatin modification landscape shared by major adult Drosophila cell types: the enrichment of both heterochromatic and euchromatic marks in transposons and repetitive sequences, the accumulation of HP1a at transcription start sites with stalled polII, the signatures of histone code and polII level/position around the transcriptional start sites that predict both the mRNA level and functionality of genes, and the enrichment of elongating polII within exons at splicing junctions. These features, likely conserved among diverse epigenomes, reveal general strategies for chromatin modifications.

Chromatin-associated RNA interference components contribute to transcriptional regulation in Drosophila

Chromatin-associated RNA interference components contribute to transcriptional regulation in Drosophila:

Chromatin-associated RNA interference components contribute to transcriptional regulation in Drosophila

Nature 480, 7377 (2011). doi:10.1038/nature10492

Authors: Filippo M. Cernilogar, Maria Cristina Onorati, Greg O. Kothe, A. Maxwell Burroughs, Krishna Mohan Parsi, Achim Breiling, Federica Lo Sardo, Alka Saxena, Keita Miyoshi, Haruhiko Siomi, Mikiko C. Siomi, Piero Carninci, David S. Gilmour, Davide F. V. Corona & Valerio Orlando

RNA interference (RNAi) pathways have evolved as important modulators of gene expression that operate in the cytoplasm by degrading RNA target molecules through the activity of short (21–30 nucleotide) RNAs. RNAi components have been reported to have a role in the nucleus, as they are involved in epigenetic regulation and heterochromatin formation. However, although RNAi-mediated post-transcriptional gene silencing is well documented, the mechanisms of RNAi-mediated transcriptional gene silencing and, in particular, the role of RNAi components in chromatin dynamics, especially in animal multicellular organisms, are elusive. Here we show that the key RNAi components Dicer 2 (DCR2) and Argonaute 2 (AGO2) associate with chromatin (with a strong preference for euchromatic, transcriptionally active, loci) and interact with the core transcription machinery. Notably, loss of function of DCR2 or AGO2 showed that transcriptional defects are accompanied by the perturbation of RNA polymerase II positioning on promoters. Furthermore, after heat shock, both Dcr2 and Ago2 null mutations, as well as missense mutations that compromise the RNAi activity, impaired the global dynamics of RNA polymerase II. Finally, the deep sequencing of the AGO2-associated small RNAs (AGO2 RIP-seq) revealed that AGO2 is strongly enriched in small RNAs that encompass the promoter regions and other regions of heat-shock and other genetic loci on both the sense and antisense DNA strands, but with a strong bias for the antisense strand, particularly after heat shock. Taken together, our results show that DCR2 and AGO2 are globally associated with transcriptionally active loci and may have a pivotal role in shaping the transcriptome by controlling the processivity of RNA polymerase II.

Regulatory evolution through divergence of a phosphoswitch in the transcription factor CEBPB

Regulatory evolution through divergence of a phosphoswitch in the transcription factor CEBPB:

Regulatory evolution through divergence of a phosphoswitch in the transcription factor CEBPB

Nature 480, 7377 (2011). doi:10.1038/nature10595

Authors: Vincent J. Lynch, Gemma May & Günter P. Wagner

There is an emerging consensus that gene regulation evolves through changes in cis-regulatory elements and transcription factors. Although it is clear how nucleotide substitutions in cis-regulatory elements affect gene expression, it is not clear how amino-acid substitutions in transcription factors influence gene regulation. Here we show that amino-acid changes in the transcription factor CCAAT/enhancer binding protein-β (CEBPB, also known as C/EBP-β) in the stem-lineage of placental mammals changed the way it responds to cyclic AMP/protein kinase A (cAMP/PKA) signalling. By functionally analysing resurrected ancestral proteins, we identify three amino-acid substitutions in an internal regulatory domain of CEBPB that are responsible for the novel function. These amino-acid substitutions reorganize the location of key phosphorylation sites, introducing a new site and removing two ancestral sites, reversing the response of CEBPB to GSK-3β-mediated phosphorylation from repression to activation. We conclude that changing the response of transcription factors to signalling pathways can be an important mechanism of gene regulatory evolution.

Role of sequence encoded {kappa}B DNA geometry in gene regulation by Dorsal

Role of sequence encoded {kappa}B DNA geometry in gene regulation by Dorsal:

Many proteins of the Rel family can act as both transcriptional activators and repressors. However, mechanism that discerns the ‘activator/repressor’ functions of Rel-proteins such as Dorsal (Drosophila homologue of mammalian NFB) is not understood. Using genomic, biophysical and biochemical approaches, we demonstrate that the underlying principle of this functional specificity lies in the ‘sequence-encoded structure’ of the B-DNA. We show that Dorsal-binding motifs exist in distinct activator and repressor conformations. Molecular dynamics of DNA-Dorsal complexes revealed that repressor B-motifs typically have A-tract and flexible conformation that facilitates interaction with co-repressors. Deformable structure of repressor motifs, is due to changes in the hydrogen bonding in A:T pair in the ‘A-tract’ core. The sixth nucleotide in the nonameric B-motif, ‘A’ (A₆) in the repressor motifs and ‘T’ (T₆) in the activator motifs, is critical to confer this functional specificity as A₆ -> T₆ mutation transformed flexible repressor conformation into a rigid activator conformation. These results highlight that ‘sequence encoded B DNA-geometry’ regulates gene expression by exerting allosteric effect on binding of Rel proteins which in turn regulates interaction with co-regulators. Further, we identified and characterized putative repressor motifs in Dl-target genes, which can potentially aid in functional annotation of Dorsal gene regulatory network.

Improved accuracy of supervised CRM discovery with interpolated Markov models and cross-species comparison

Improved accuracy of supervised CRM discovery with interpolated Markov models and cross-species comparison:

Despite recent advances in experimental approaches for identifying transcriptional cis-regulatory modules (CRMs, ‘enhancers’), direct empirical discovery of CRMs for all genes in all cell types and environmental conditions is likely to remain an elusive goal. Effective methods for computational CRM discovery are thus a critically needed complement to empirical approaches. However, existing computational methods that search for clusters of putative binding sites are ineffective if the relevant TFs and/or their binding specificities are unknown. Here, we provide a significantly improved method for ‘motif-blind’ CRM discovery that does not depend on knowledge or accurate prediction of TF-binding motifs and is effective when limited knowledge of functional CRMs is available to ‘supervise’ the search. We propose a new statistical method, based on ‘Interpolated Markov Models’, for motif-blind, genome-wide CRM discovery. It captures the statistical profile of variable length words in known CRMs of a regulatory network and finds candidate CRMs that match this profile. The method also uses orthologs of the known CRMs from closely related genomes. We perform in silico evaluation of predicted CRMs by assessing whether their neighboring genes are enriched for the expected expression patterns. This assessment uses a novel statistical test that extends the widely used Hypergeometric test of gene set enrichment to account for variability in intergenic lengths. We find that the new CRM prediction method is superior to existing methods. Finally, we experimentally validate 12 new CRM predictions by examining their regulatory activity in vivo in Drosophila; 10 of the tested CRMs were found to be functional, while 6 of the top 7 predictions showed the expected activity patterns. We make our program available as downloadable source code, and as a plugin for a genome browser installed on our servers.

Polycomb-Repressed Genes Have Permissive Enhancers that Initiate Reprogramming

Polycomb-Repressed Genes Have Permissive Enhancers that Initiate Reprogramming: Phillippa C. Taberlay, Theresa K. Kelly, Chun-Chi Liu, Jueng Soo You, Daniel D. De Carvalho, Tina B. Miranda, Xianghong J. Zhou, Gangning Liang, Peter A. Jones. Key regulatory genes, suppressed by Polycomb and H3K27me3, become active during normal differentiation and induced reprogramming. Using the well-characterized enhancer/promoter pair of MYOD1</i....

Cofactor Binding Evokes Latent Differences in DNA Binding Specificity between Hox Proteins

Cofactor Binding Evokes Latent Differences in DNA Binding Specificity between Hox Proteins: Matthew Slattery, Todd Riley, Peng Liu, Namiko Abe, Pilar Gomez-Alcala, Iris Dror, Tianyin Zhou, Remo Rohs, Barry Honig, Harmen J. Bussemaker, Richard S. Mann. Members of transcription factor families typically have similar DNA binding specificities yet execute unique functions in vivo. Transcription factors often bind DNA as multiprotein complexes, rais....

Predicting mutation outcome from early stochastic variation in genetic interaction partners

Predicting mutation outcome from early stochastic variation in genetic interaction partners:

Predicting mutation outcome from early stochastic variation in genetic interaction partners

Nature 480, 7376 (2011). doi:10.1038/nature10665

Authors: Alejandro Burga, M. Olivia Casanueva & Ben Lehner

Many mutations, including those that cause disease, only have a detrimental effect in a subset of individuals. The reasons for this are usually unknown, but may include additional genetic variation and environmental risk factors. However, phenotypic discordance remains even in the absence of genetic variation, for example between monozygotic twins, and incomplete penetrance of mutations is frequent in isogenic model organisms in homogeneous environments. Here we propose a model for incomplete penetrance based on genetic interaction networks. Using Caenorhabditis elegans as a model system, we identify two compensation mechanisms that vary among individuals and influence mutation outcome. First, feedback induction of an ancestral gene duplicate differs across individuals, with high expression masking the effects of a mutation. This supports the hypothesis that redundancy is maintained in genomes to buffer stochastic developmental failure. Second, during normal embryonic development we find that there is substantial variation in the induction of molecular chaperones such as Hsp90 (DAF-21). Chaperones act as promiscuous buffers of genetic variation, and embryos with stronger induction of Hsp90 are less likely to be affected by an inherited mutation. Simultaneously quantifying the variation in these two independent responses allows the phenotypic outcome of a mutation to be more accurately predicted in individuals. Our model and methodology provide a framework for dissecting the causes of incomplete penetrance. Further, the results establish that inter-individual variation in both specific and more general buffering systems combine to determine the outcome inherited mutations in each individual.

Wing patterning gene redefines the mimetic history of Heliconius butterflies [Evolution]

Wing patterning gene redefines the mimetic history of Heliconius butterflies [Evolution]: The mimetic butterflies Heliconius erato and Heliconius melpomene have undergone parallel radiations to form a near-identical patchwork of over 20 different wing-pattern races across the Neotropics. Previous molecular phylogenetic work on these radiations has suggested that similar but geographically disjunct color patterns arose multiple times independently in each species. The neutral markers used in these studies, however, can move freely across color pattern boundaries, and therefore might not represent the history of the adaptive traits as accurately as markers linked to color pattern genes. To assess the evolutionary histories across different loci, we compared relationships among races within H. erato and within H. melpomene using a series of unlinked genes, genes linked to color pattern loci, and optix, a gene recently shown to control red color-pattern variation. We found that although unlinked genes partition populations by geographic region, optix had a different history, structuring lineages by red color patterns and supporting a single origin of red-rayed patterns within each species. Genes closely linked (80–250 kb) to optix exhibited only weak associations with color pattern. This study empirically demonstrates the necessity of examining phenotype-determining genomic regions to understand the history of adaptive change in rapidly radiating lineages. With these refined relationships, we resolve a long-standing debate about the origins of the races within each species, supporting the hypothesis that the red-rayed Amazonian pattern evolved recently and expanded, causing disjunctions of more ancestral patterns.

Discriminative prediction of mammalian enhancers from DNA sequence [METHOD]

Discriminative prediction of mammalian enhancers from DNA sequence [METHOD]:

Accurately predicting regulatory sequences and enhancers in entire genomes is an important but difficult problem, especially in large vertebrate genomes. With the advent of ChIP-seq technology, experimental detection of genome-wide EP300/CREBBP bound regions provides a powerful platform to develop predictive tools for regulatory sequences and to study their sequence properties. Here, we develop a support vector machine (SVM) framework which can accurately identify EP300-bound enhancers using only genomic sequence and an unbiased set of general sequence features. Moreover, we find that the predictive sequence features identified by the SVM classifier reveal biologically relevant sequence elements enriched in the enhancers, but we also identify other features that are significantly depleted in enhancers. The predictive sequence features are evolutionarily conserved and spatially clustered, providing further support of their functional significance. Although our SVM is trained on experimental data, we also predict novel enhancers and show that these putative enhancers are significantly enriched in both ChIP-seq signal and DNase I hypersensitivity signal in the mouse brain and are located near relevant genes. Finally, we present results of comparisons between other EP300/CREBBP data sets using our SVM and uncover sequence elements enriched and/or depleted in the different classes of enhancers. Many of these sequence features play a role in specifying tissue-specific or developmental-stage-specific enhancer activity, but our results indicate that some features operate in a general or tissue-independent manner. In addition to providing a high confidence list of enhancer targets for subsequent experimental investigation, these results contribute to our understanding of the general sequence structure of vertebrate enhancers.