Mutual Repression Enhances the Steepness and Precision of Gene Expression Boundaries

Mutual Repression Enhances the Steepness and Precision of Gene Expression Boundaries:
by Thomas R. Sokolowski, Thorsten Erdmann, Pieter Rein ten Wolde

Embryonic development is driven by spatial patterns of gene expression that determine the fate of each cell in the embryo. While gene expression is often highly erratic, embryonic development is usually exceedingly precise. In particular, gene expression boundaries are robust not only against intra-embryonic fluctuations such as noise in gene expression and protein diffusion, but also against embryo-to-embryo variations in the morphogen gradients, which provide positional information to the differentiating cells. How development is robust against intra- and inter-embryonic variations is not understood. A common motif in the gene regulation networks that control embryonic development is mutual repression between pairs of genes. To assess the role of mutual repression in the robust formation of gene expression patterns, we have performed large-scale stochastic simulations of a minimal model of two mutually repressing gap genes in Drosophila, hunchback (hb) and knirps (kni). Our model includes not only mutual repression between hb and kni, but also the stochastic and cooperative activation of hb by the anterior morphogen Bicoid (Bcd) and of kni by the posterior morphogen Caudal (Cad), as well as the diffusion of Hb and Kni between neighboring nuclei. Our analysis reveals that mutual repression can markedly increase the steepness and precision of the gap gene expression boundaries. In contrast to other mechanisms such as spatial averaging and cooperative gene activation, mutual repression thus allows for gene-expression boundaries that are both steep and precise. Moreover, mutual repression dramatically enhances their robustness against embryo-to-embryo variations in the morphogen levels. Finally, our simulations reveal that diffusion of the gap proteins plays a critical role not only in reducing the width of the gap gene expression boundaries via the mechanism of spatial averaging, but also in repairing patterning errors that could arise because of the bistability induced by mutual repression.

Self-Organized Shuttling: Generating Sharp Dorsoventral Polarity in the Early Drosophila Embryo

Self-Organized Shuttling: Generating Sharp Dorsoventral Polarity in the Early Drosophila Embryo: Michal Haskel-Ittah, Danny Ben-Zvi, Merav Branski-Arieli, Eyal D. Schejter, Ben-Zion Shilo, Naama Barkai.

Morphogen gradients pattern tissues and organs during development. When morphogen production is spatially restricted, diffusion and degradation are sufficient to generate sharp concentration gradi....

Drosophila Brainbow: a recombinase-based fluorescence labeling technique to subdivide neural expression patterns

Drosophila Brainbow: a recombinase-based fluorescence labeling technique to subdivide neural expression patterns:
Drosophila Brainbow: a recombinase-based fluorescence labeling technique to subdivide neural expression patterns

Nature Methods 9, 929 (2012).
doi:10.1038/nmeth1566-929a

Author: Stefanie Hampel, Phuong Chung, Claire E McKellar, Donald Hall, Loren L Looger & Julie H Simpson

Comparative spatiotemporal analysis of Hox gene expression in early stages of intermediate mesoderm formation

Comparative spatiotemporal analysis of Hox gene expression in early stages of intermediate mesoderm formation

Ectopic assembly of heterochromatin in Drosophila [Genetics]

Ectopic assembly of heterochromatin in Drosophila [Genetics]: A persistent question in biology is how cis-acting sequence elements influence trans-acting factors and the local chromatin environment to modulate gene expression. We reported previously that the DNA transposon 1360 can enhance silencing of a reporter in a heterochromatic domain of Drosophila melanogaster. We have now generated a collection of...

Sost-distal enhancer deletion [Genetics]

Sost-distal enhancer deletion [Genetics]: The Wnt antagonist Sost has emerged as a key regulator of bone homeostasis through the modulation of Lrp4/5/6 Wnt coreceptors. In humans, lack of Sclerostin causes sclerosteosis and van Buchem (VB) disease, two generalized skeletal hyperostosis disorders that result from hyperactive Wnt signaling. Unlike sclerosteosis, VB patients lack SOST coding...

Modeling of Gap Gene Expression in Drosophila Kruppel Mutants

Modeling of Gap Gene Expression in Drosophila Kruppel Mutants:
by Konstantin Kozlov, Svetlana Surkova, Ekaterina Myasnikova, John Reinitz, Maria Samsonova

The segmentation gene network in Drosophila embryo solves the fundamental problem of embryonic patterning: how to establish a periodic pattern of gene expression, which determines both the positions and the identities of body segments. The gap gene network constitutes the first zygotic regulatory tier in this process. Here we have applied the systems-level approach to investigate the regulatory effect of gap gene Kruppel (Kr) on segmentation gene expression. We acquired a large dataset on the expression of gap genes in Kr null mutants and demonstrated that the expression levels of these genes are significantly reduced in the second half of cycle 14A. To explain this novel biological result we applied the gene circuit method which extracts regulatory information from spatial gene expression data. Previous attempts to use this formalism to correctly and quantitatively reproduce gap gene expression in mutants for a trunk gap gene failed, therefore here we constructed a revised model and showed that it correctly reproduces the expression patterns of gap genes in Kr null mutants. We found that the remarkable alteration of gap gene expression patterns in Kr mutants can be explained by the dynamic decrease of activating effect of Cad on a target gene and exclusion of Kr gene from the complex network of gap gene interactions, that makes it possible for other interactions, in particular, between hb and gt, to come into effect. The successful modeling of the quantitative aspects of gap gene expression in mutant for the trunk gap gene Kr is a significant achievement of this work. This result also clearly indicates that the oversimplified representation of transcriptional regulation in the previous models is one of the reasons for unsuccessful attempts of mutant simulations.

[Report] Cis-Acting Transcriptional Repression Establishes a Sharp Boundary in Chordate Embryos

[Report] Cis-Acting Transcriptional Repression Establishes a Sharp Boundary in Chordate Embryos: The conserved tandem arrangement of Pinhead and Admp genes is important for their mutually exclusive expression.

Authors: Kaoru S. Imai, Yutaka Daido, Takehiro G. Kusakabe, Yutaka Satou

Rate of de novo mutations and the importance of father’s age to disease risk

Rate of de novo mutations and the importance of father’s age to disease risk:
Rate of de novo mutations and the importance of father’s age to disease risk

Nature 488, 7412 (2012). doi:10.1038/nature11396

Authors: Augustine Kong, Michael L. Frigge, Gisli Masson, Soren Besenbacher, Patrick Sulem, Gisli Magnusson, Sigurjon A. Gudjonsson, Asgeir Sigurdsson, Aslaug Jonasdottir, Adalbjorg Jonasdottir, Wendy S. W. Wong, Gunnar Sigurdsson, G. Bragi Walters, Stacy Steinberg, Hannes Helgason, Gudmar Thorleifsson, Daniel F. Gudbjartsson, Agnar Helgason, Olafur Th. Magnusson, Unnur Thorsteinsdottir & Kari Stefansson
Mutations generate sequence diversity and provide a substrate for selection. The rate of de novo mutations is therefore of major importance to evolution. Here we conduct a study of genome-wide mutation rates by sequencing the entire genomes of 78 Icelandic parent–offspring trios at high

Chromatin organization is a major influence on regional mutation rates in human cancer cells

Chromatin organization is a major influence on regional mutation rates in human cancer cells:
Chromatin organization is a major influence on regional mutation rates in human cancer cells

Nature 488, 7412 (2012). doi:10.1038/nature11273

Authors: Benjamin Schuster-Böckler & Ben Lehner
Cancer genome sequencing provides the first direct information on how mutation rates vary across the human genome in somatic cells. Testing diverse genetic and epigenetic features, here we show that mutation rates in cancer genomes are strikingly related to chromatin organization. Indeed, at the megabase scale, a single feature—levels of the heterochromatin-associated histone modification H3K9me3—can account for more than 40% of mutation-rate variation, and a combination of features can account for more than 55%. The strong association between mutation rates and chromatin organization is upheld in samples from different tissues and for different mutation types. This suggests that the arrangement of the genome into heterochromatin- and euchromatin-like domains is a dominant influence on regional mutation-rate variation in human somatic cells.

i-cisTarget: an integrative genomics method for the prediction of regulatory features and cis-regulatory modules

i-cisTarget: an integrative genomics method for the prediction of regulatory features and cis-regulatory modules:
The field of regulatory genomics today is characterized by the generation of high-throughput data sets that capture genome-wide transcription factor (TF) binding, histone modifications, or DNAseI hypersensitive regions across many cell types and conditions. In this context, a critical question is how to make optimal use of these publicly available datasets when studying transcriptional regulation. Here, we address this question in Drosophila melanogaster for which a large number of high-throughput regulatory datasets are available. We developed i-cisTarget (where the ‘i’ stands for integrative), for the first time enabling the discovery of different types of enriched ‘regulatory features’ in a set of co-regulated sequences in one analysis, being either TF motifs or ‘in vivo’ chromatin features, or combinations thereof. We have validated our approach on 15 co-expressed gene sets, 21 ChIP data sets, 628 curated gene sets and multiple individual case studies, and show that meaningful regulatory features can be confidently discovered; that bona fide enhancers can be identified, both by in vivo events and by TF motifs; and that combinations of in vivo events and TF motifs further increase the performance of enhancer prediction.

Inducible genetic system for the axolotl [Developmental Biology]

Inducible genetic system for the axolotl [Developmental Biology]: Transgenesis promises a powerful means for assessing gene function during amphibian limb regeneration. This approach is complicated, however, by the need for embryonic appendage development to proceed unimpeded despite the genetic alterations one wishes to test later in the context of regeneration. Achieving conditional gene regulation in this amphibian has...

Dissecting sources of quantitative gene expression pattern divergence between Drosophila species

Zeba Wunderlich¹, Meghan D Bragdon¹, Kelly B Eckenrode¹, Tara Lydiard-Martin¹, Sivanne Pearl-Waserman¹ & Angela H DePace¹

The function of a transcriptional circuit is compared in three closely related species of Drosophila. Using quantitative imaging of gene expression, targeted transgenic reporter fly lines, and a computational framework, the sources of their differing expression outputs are identified.

• The logic of the transcriptional circuit controlling expression of the embryonic hunchback posterior stripe is highly conserved between three Drosophila species (D. melanogaster, D. yakuba, and D. pseudoobscura), despite observed differences in the hunchback posterior stripe expression pattern.
• Quantitative expression differences in the hunchback posterior stripe are largely, but not entirely, due to changes in the expression patterns of upstream regulators.
• The set of orthologous cis-regulatory elements (CREs) underlying this circuit direct similar expression patterns in concordance with previous qualitative studies; however, the expression patterns they direct are quantitatively distinct.
• These results indicate that small-scale sequence changes in CREs can impact their function and has broad implications for understanding the importance of transcription factor binding site architecture in CRE function.

Transcription factors: from enhancer binding to developmental control

Transcription factors: from enhancer binding to developmental control:
Transcription factors: from enhancer binding to developmental control

Nature Reviews Genetics 13, 613 (2012).
doi:10.1038/nrg3207

Authors: François Spitz & Eileen E. M. Furlong
Developmental progression is driven by specific spatiotemporal domains of gene expression, which give rise to stereotypically patterned embryos even in the presence of environmental and genetic variation. Views of how transcription factors regulate gene expression are changing owing to recent genome-wide studies of transcription factor

Splicing: Waiting to be spliced

Splicing: Waiting to be spliced:
Splicing: Waiting to be spliced

Nature Reviews Genetics 13, 599 (2012).
doi:10.1038/nrg3310

Author: Hannah Stower
The relevance of co-transcriptional versus post-transcriptional splicing of transcripts is debated. In a recent RNA sequencing (RNA-seq) study of the human inflammatory response, the authors found evidence for the widespread association of incompletely spliced transcripts with chromatin. Thus, this study supports post-transcriptional rather than co-transcriptional

A Genome-Scale Resource for In Vivo Tag-Based Protein Function Exploration in C. elegans

A Genome-Scale Resource for In Vivo Tag-Based Protein Function Exploration in C. elegans: Mihail Sarov, John I. Murray, Kristin Schanze, Andrei Pozniakovski, Wei Niu, Karolin Angermann, Susanne Hasse, Michaela Rupprecht, Elisabeth Vinis, Matthew Tinney, Elicia Preston, Andrea Zinke, Susanne Enst, Tina Teichgraber, Judith Janette, Kadri Reis, Stephan Janosch, Siegfried Schloissnig, Radoslaw K. Ejsmont, Cindie Slightam, Xiao Xu, Stuart K. Kim, Valerie Reinke, A. Francis Stewart, Michael Snyder, Robert H. Waterston, Anthony A. Hyman. Understanding the in vivo dynamics of protein localization and their physical interactions is important for many problems in biology. To enable systematic protein function interrogation in a multi....

Tissue-Specific Mitotic Bookmarking by Hematopoietic Transcription Factor GATA1

Tissue-Specific Mitotic Bookmarking by Hematopoietic Transcription Factor GATA1: Stephan Kadauke, Maheshi I. Udugama, Jan M. Pawlicki, Jordan C. Achtman, Deepti P. Jain, Yong Cheng, Ross C. Hardison, Gerd A. Blobel. Tissue-specific transcription patterns are preserved throughout cell divisions to maintain lineage fidelity. We investigated whether transcription factor GATA1 plays a role in transmitting hematop....

Identification of a DNA methylation-independent imprinting control region at the Arabidopsis MEDEA locus [Research Papers]

Identification of a DNA methylation-independent imprinting control region at the Arabidopsis MEDEA locus [Research Papers]:
Genomic imprinting is exclusive to mammals and seed plants and refers to parent-of-origin-dependent, differential transcription. As previously shown in mammals, studies in Arabidopsis have implicated DNA methylation as an important hallmark of imprinting. The current model suggests that maternally expressed imprinted genes, such as MEDEA (MEA), are activated by the DNA glycosylase DEMETER (DME), which removes DNA methylation established by the DNA methyltransferase MET1. We report the systematic functional dissection of the MEA cis-regulatory region, resulting in the identification of a 200-bp fragment that is necessary and sufficient to mediate MEA activation and imprinted expression, thus containing the imprinting control region (ICR). Notably, imprinted MEA expression mediated by this ICR is independent of DME and MET1, consistent with the lack of any significant DNA methylation in this region. This is the first example of an ICR without differential DNA methylation, suggesting that factors other than DME and MET1 are required for imprinting at the MEA locus.

Genome-wide and Caste-Specific DNA Methylomes of the Ants Camponotus floridanus and Harpegnathos saltator

Genome-wide and Caste-Specific DNA Methylomes of the Ants Camponotus floridanus and Harpegnathos saltator: Roberto Bonasio, Qiye Li, Jinmin Lian, Navdeep S. Mutti, Lijun Jin, Hongmei Zhao, Pei Zhang, Ping Wen, Hui Xiang, Yun Ding, Zonghui Jin, Steven S. Shen, Zongji Wang, Wen Wang, Jun Wang, Shelley L. Berger, Jürgen Liebig, Guojie Zhang, Danny Reinberg. BackgroundAnt societies comprise individuals belonging to different castes characterized by specialized morphologies and behaviors. Because ant embryos can follow different developmental trajector....

A Carboniferous Non-Onychophoran Lobopodian Reveals Long-Term Survival of a Cambrian Morphotype

A Carboniferous Non-Onychophoran Lobopodian Reveals Long-Term Survival of a Cambrian Morphotype: Joachim T. Haug, Georg Mayer, Carolin Haug, Derek E.G. Briggs. Lobopodians, a nonmonophyletic assemblage of worm-shaped soft-bodied animals most closely related to arthropods, show two major morphotypes: long-legged and short-legged forms. The morphotype with....

[Report] Drosophila Dosage Compensation Involves Enhanced Pol II Recruitment to Male X-Linked Promoters

[Report] Drosophila Dosage Compensation Involves Enhanced Pol II Recruitment to Male X-Linked Promoters: Boosting gene expression from the entire X chromosome in males happens mainly at the level of transcription initiation.

Authors: Thomas Conrad, Florence M. G. Cavalli, Juan M. Vaquerizas, Nicholas M. Luscombe, Asifa Akhtar

Anterior-posterior differences in HoxD chromatin topology in limb development [RESEARCH ARTICLES]

Anterior-posterior differences in HoxD chromatin topology in limb development [RESEARCH ARTICLES]: Iain Williamson, Ragnhild Eskeland, Laura A. Lettice, Alison E. Hill, Shelagh Boyle, Graeme R. Grimes, Robert E. Hill, and Wendy A. Bickmore


A late phase of HoxD activation is crucial for the patterning and growth of distal structures across the anterior-posterior (A-P) limb axis of mammals. Polycomb complexes and chromatin compaction have been shown to regulate Hox loci along the main body axis in embryonic development, but the extent to which they have a role in limb-specific HoxD expression, an evolutionary adaptation defined by the activity of distal enhancer elements that drive expression of 5' Hoxd genes, has yet to be fully elucidated. We reveal two levels of chromatin topology that differentiate distal limb A-P HoxD activity. Using both immortalised cell lines derived from posterior and anterior regions of distal E10.5 mouse limb buds, and analysis in E10.5 dissected limb buds themselves, we show that there is a loss of polycomb-catalysed H3K27me3 histone modification and a chromatin decompaction over HoxD in the distal posterior limb compared with anterior. Moreover, we show that the global control region (GCR) long-range enhancer spatially colocalises with the 5' HoxD genomic region specifically in the distal posterior limb. This is consistent with the formation of a chromatin loop between 5' HoxD and the GCR regulatory module at the time and place of distal limb bud development when the GCR participates in initiating Hoxd gene quantitative collinearity and Hoxd13 expression. This is the first example of A-P differences in chromatin compaction and chromatin looping in the development of the mammalian secondary body axis (limb).

Coordinating genome expression with cell size

Coordinating genome expression with cell size: Samuel Marguerat, Jürg Bähler. Cell size is highly variable; cells from various tissues differ in volume over orders of magnitudes, from tiny lymphocytes to giant neurons, and cells of a given type change size during the cell c....

Human Developmental Enhancers Conserved between Deuterostomes and Protostomes

Human Developmental Enhancers Conserved between Deuterostomes and Protostomes:

by Shoa L. Clarke, Julia E. VanderMeer, Aaron M. Wenger, Bruce T. Schaar, Nadav Ahituv, Gill Bejerano

The identification of homologies, whether morphological, molecular, or genetic, is fundamental to our understanding of common biological principles. Homologies bridging the great divide between deuterostomes and protostomes have served as the basis for current models of animal evolution and development. It is now appreciated that these two clades share a common developmental toolkit consisting of conserved transcription factors and signaling pathways. These patterning genes sometimes show common expression patterns and genetic interactions, suggesting the existence of similar or even conserved regulatory apparatus. However, previous studies have found no regulatory sequence conserved between deuterostomes and protostomes. Here we describe the first such enhancers, which we call bilaterian conserved regulatory elements (Bicores). Bicores show conservation of sequence and gene synteny. Sequence conservation of Bicores reflects conserved patterns of transcription factor binding sites. We predict that Bicores act as response elements to signaling pathways, and we show that Bicores are developmental enhancers that drive expression of transcriptional repressors in the vertebrate central nervous system. Although the small number of identified Bicores suggests extensive rewiring of cis-regulation between the protostome and deuterostome clades, additional Bicores may be revealed as our understanding of cis-regulatory logic and sample of bilaterian genomes continue to grow.

Dynamic histone marks in the hippocampus and cortex facilitate memory consolidation

Dynamic histone marks in the hippocampus and cortex facilitate memory consolidation:
Dynamic histone marks in the hippocampus and cortex facilitate memory consolidation

Nature Communications 3, 991 (2012). doi:10.1038/ncomms1997

Authors: Johannes Gräff, Bisrat T. Woldemichael, Dominik Berchtold, Grégoire Dewarrat & Isabelle M. Mansuy

A map of the cis-regulatory sequences in the mouse genome

A map of the cis-regulatory sequences in the mouse genome:

A map of the cis-regulatory sequences in the mouse genome

Nature 488, 7409 (2012). doi:10.1038/nature11243

Authors: Yin Shen, Feng Yue, David F. McCleary, Zhen Ye, Lee Edsall, Samantha Kuan, Ulrich Wagner, Jesse Dixon, Leonard Lee, Victor V. Lobanenkov & Bing Ren

The laboratory mouse is the most widely used mammalian model organism in biomedical research. The 2.6 × 109 bases of the mouse genome possess a high degree of conservation with the human genome, so a thorough annotation of the mouse genome will be of significant value to understanding the function of the human genome. So far, most of the functional sequences in the mouse genome have yet to be found, and the cis-regulatory sequences in particular are still poorly annotated. Comparative genomics has been a powerful tool for the discovery of these sequences, but on its own it cannot resolve their temporal and spatial functions. Recently, ChIP-Seq has been developed to identify cis-regulatory elements in the genomes of several organisms including humans, Drosophila melanogaster and Caenorhabditis elegans. Here we apply the same experimental approach to a diverse set of 19 tissues and cell types in the mouse to produce a map of nearly 300,000 murine cis-regulatory sequences. The annotated sequences add up to 11% of the mouse genome, and include more than 70% of conserved non-coding sequences. We define tissue-specific enhancers and identify potential transcription factors regulating gene expression in each tissue or cell type. Finally, we show that much of the mouse genome is organized into domains of coordinately regulated enhancers and promoters. Our results provide a resource for the annotation of functional elements in the mammalian genome and for the study of mechanisms regulating tissue-specific gene expression.

A complete insect from the Late Devonian period

A complete insect from the Late Devonian period:
A complete insect from the Late Devonian period

Nature 488, 7409 (2012). doi:10.1038/nature11281

Authors: Romain Garrouste, Gaël Clément, Patricia Nel, Michael S. Engel, Philippe Grandcolas, Cyrille D’Haese, Linda Lagebro, Julien Denayer, Pierre Gueriau, Patrick Lafaite, Sébastien Olive, Cyrille Prestianni & André Nel
After terrestrialization, the diversification of arthropods and vertebrates is thought to have occurred in two distinct phases, the first between the Silurian and the Frasnian stages (Late Devonian period) (425–385 million years (Myr) ago), and the second characterized by the emergence of numerous new major taxa, during the Late Carboniferous period (after 345 Myr ago). These two diversification periods bracket the depauperate vertebrate Romer’s gap (360–345 Myr ago) and arthropod gap (385–325 Myr ago), which could be due to preservational artefact. Although a recent molecular dating has given an age of 390 Myr for the Holometabola, the record of hexapods during the Early–Middle Devonian (411.5–391 Myr ago, Pragian to Givetian stages) is exceptionally sparse and based on fragmentary remains, which hinders the timing of this diversification. Indeed, although Devonian Archaeognatha are problematic, the Pragian of Scotland has given some Collembola and the incomplete insect Rhyniognatha, with its diagnostic dicondylic, metapterygotan mandibles. The oldest, definitively winged insects are from the Serpukhovian stage (latest Early Carboniferous period). Here we report the first complete Late Devonian insect, which was probably a terrestrial species. Its ‘orthopteroid’ mandibles are of an omnivorous type, clearly not modified for a solely carnivorous diet. This discovery narrows the 45-Myr gap in the fossil record of Hexapoda, and demonstrates further a first Devonian phase of diversification for the Hexapoda, as in vertebrates, and suggests that the Pterygota diversified before and during Romer’s gap.

A Synthetic Biology Framework for Programming Eukaryotic Transcription Functions

A Synthetic Biology Framework for Programming Eukaryotic Transcription Functions: Ahmad S. Khalil, Timothy K. Lu, Caleb J. Bashor, Cherie L. Ramirez, Nora C. Pyenson, J. Keith Joung, James J. Collins.

Eukaryotic transcription factors (TFs) perform complex and combinatorial functions within transcriptional networks. Here, we present a synthetic framework for systematically constructing eukaryoti....

[Brevia] Explosive Backpacks in Old Termite Workers

[Brevia] Explosive Backpacks in Old Termite Workers: As Neocapritermes taracua termites age, they develop a suicidal toxic apparatus that bursts during aggressive encounters.

Authors: J. Šobotník, T. Bourguignon, R. Hanus, Z. Demianová, J. Pytelková, M. Mareš, P. Foltynová, J. Preisler, J. Cvačka, J. Krasulová, Y. Roisin

WntA shapes butterfly wing pattern diversity [Evolution]

WntA shapes butterfly wing pattern diversity [Evolution]: Although animals display a rich variety of shapes and patterns, the genetic changes that explain how complex forms arise are still unclear. Here we take advantage of the extensive diversity of Heliconius butterflies to identify a gene that causes adaptive variation of black wing patterns within and between species. Linkage mapping in two species groups, gene-expression analysis in seven species, and pharmacological treatments all indicate that cis-regulatory evolution of the WntA ligand underpins discrete changes in color pattern features across the Heliconius genus. These results illustrate how the direct modulation of morphogen sources can generate a wide array of unique morphologies, thus providing a link between natural genetic variation, pattern formation, and adaptation.

LSD1/CoREST molecular recognition dynamics [Chemistry]

LSD1/CoREST molecular recognition dynamics [Chemistry]: The complex of lysine-specific demethylase-1 (LSD1/KDM1A) with its corepressor protein CoREST is an exceptionally relevant target for epigenetic drugs. Here, we provide insight into the local and global changes of LSD1/CoREST conformational dynamics that occur upon H3 binding on the basis of a total cumulative time of one microsecond molecular dynamics simulation. The LSD1/CoREST complex functions as an allosteric nanoscale-binding clamp, which is regulated by substrate binding. In the unbound state, LSD1/CoREST reversibly visits clamp states that are more open or significantly more closed compared with the available X-ray crystal structures. The Lys triad of residues Lys355, Lys357, and Lys359 gates the entrance of the H3 pocket. H3 binding shifts the pocket breathing dynamics toward open, higher-volume states while reducing the overall flexibility of the LSD1/CoREST nanoscale clamp. We show that the H3 pocket is an allosteric site for the regulation of the rotation of the amino oxidase domain with respect to the Tower domain. The allosteric mechanism relies on the specific reduction of nanoscale domain rotation upon local H3-tail binding. Instead, clamp opening/closing motions that do not involve domain rotation only reduce in amplitude yet are dominant in the bound state. Overall, our data suggest that the H3 binding pocket is a central target site to (i) switch off LSD1 amino oxidase activity, thus H3-tail demethylation; (ii) block the competitive binding of transcription factors; and (iii) prevent chromatin anchoring to LSD1/CoREST. This study underscores the importance of receptor flexibility for future epigenetic drug discovery.

Topology and Dynamics of the Zebrafish Segmentation Clock Core Circuit

Topology and Dynamics of the Zebrafish Segmentation Clock Core Circuit:
by Christian Schröter, Saúl Ares, Luis G. Morelli, Alina Isakova, Korneel Hens, Daniele Soroldoni, Martin Gajewski, Frank Jülicher, Sebastian J. Maerkl, Bart Deplancke, Andrew C. Oates

During vertebrate embryogenesis, the rhythmic and sequential segmentation of the body axis is regulated by an oscillating genetic network termed the segmentation clock. We describe a new dynamic model for the core pace-making circuit of the zebrafish segmentation clock based on a systematic biochemical investigation of the network's topology and precise measurements of somitogenesis dynamics in novel genetic mutants. We show that the core pace-making circuit consists of two distinct negative feedback loops, one with Her1 homodimers and the other with Her7:Hes6 heterodimers, operating in parallel. To explain the observed single and double mutant phenotypes of her1, her7, and hes6 mutant embryos in our dynamic model, we postulate that the availability and effective stability of the dimers with DNA binding activity is controlled in a “dimer cloud” that contains all possible dimeric combinations between the three factors. This feature of our model predicts that Hes6 protein levels should oscillate despite constant hes6 mRNA production, which we confirm experimentally using novel Hes6 antibodies. The control of the circuit's dynamics by a population of dimers with and without DNA binding activity is a new principle for the segmentation clock and may be relevant to other biological clocks and transcriptional regulatory networks.

Systematic Dissection of Roles for Chromatin Regulators in a Yeast Stress Response

Systematic Dissection of Roles for Chromatin Regulators in a Yeast Stress Response:
by Assaf Weiner, Hsiuyi V. Chen, Chih Long Liu, Ayelet Rahat, Avital Klien, Luis Soares, Mohanram Gudipati, Jenna Pfeffner, Aviv Regev, Stephen Buratowski, Jeffrey A. Pleiss, Nir Friedman, Oliver J. Rando

Packaging of eukaryotic genomes into chromatin has wide-ranging effects on gene transcription. Curiously, it is commonly observed that deletion of a global chromatin regulator affects expression of only a limited subset of genes bound to or modified by the regulator in question. However, in many single-gene studies it has become clear that chromatin regulators often do not affect steady-state transcription, but instead are required for normal transcriptional reprogramming by environmental cues. We therefore have systematically investigated the effects of 83 histone mutants, and 119 gene deletion mutants, on induction/repression dynamics of 170 transcripts in response to diamide stress in yeast. Importantly, we find that chromatin regulators play far more pronounced roles during gene induction/repression than they do in steady-state expression. Furthermore, by jointly analyzing the substrates (histone mutants) and enzymes (chromatin modifier deletions) we identify specific interactions between histone modifications and their regulators. Combining these functional results with genome-wide mapping of several histone marks in the same time course, we systematically investigated the correspondence between histone modification occurrence and function. We followed up on one pathway, finding that Set1-dependent H3K4 methylation primarily acts as a gene repressor during multiple stresses, specifically at genes involved in ribosome biosynthesis. Set1-dependent repression of ribosomal genes occurs via distinct pathways for ribosomal protein genes and ribosomal biogenesis genes, which can be separated based on genetic requirements for repression and based on chromatin changes during gene repression. Together, our dynamic studies provide a rich resource for investigating chromatin regulation, and identify a significant role for the “activating” mark H3K4me3 in gene repression.

Transcription initiation by human RNA polymerase II visualized at single-molecule resolution [Research Papers]

Transcription initiation by human RNA polymerase II visualized at single-molecule resolution [Research Papers]:
Forty years of classical biochemical analysis have identified the molecular players involved in initiation of transcription by eukaryotic RNA polymerase II (Pol II) and largely assigned their functions. However, a dynamic picture of Pol II transcription initiation and an understanding of the mechanisms of its regulation have remained elusive due in part to inherent limitations of conventional ensemble biochemistry. Here we have begun to dissect promoter-specific transcription initiation directed by a reconstituted human Pol II system at single-molecule resolution using fluorescence video-microscopy. We detected several stochastic rounds of human Pol II transcription from individual DNA templates, observed attenuation of transcription by promoter mutations, observed enhancement of transcription by activator Sp1, and correlated the transcription signals with real-time interactions of holo-TFIID molecules at individual DNA templates. This integrated single-molecule methodology should be applicable to studying other complex biological processes.

Evolutionary History and Adaptation from High-Coverage Whole-Genome Sequences of Diverse African Hunter-Gatherers

Evolutionary History and Adaptation from High-Coverage Whole-Genome Sequences of Diverse African Hunter-Gatherers: Joseph Lachance, Benjamin Vernot, Clara C. Elbers, Bart Ferwerda, Alain Froment, Jean-Marie Bodo, Godfrey Lema, Wenqing Fu, Thomas B. Nyambo, Timothy R. Rebbeck, Kun Zhang, Joshua M. Akey, Sarah A. Tishkoff. To reconstruct modern human evolutionary history and identify loci that have shaped hunter-gatherer adaptation, we sequenced the whole genomes of five individuals in each of three different hunter....