Interlocked Feedforward Loops Control Cell-Type-Specific Rhodopsin Expression in the Drosophila Eye

Interlocked Feedforward Loops Control Cell-Type-Specific Rhodopsin Expression in the Drosophila Eye: "Robert J. Johnston, Yoshiaki Otake, Pranidhi Sood, Nina Vogt, Rudy Behnia, Daniel Vasiliauskas, Elizabeth McDonald, Baotong Xie, Sebastian Koenig, Reinhard Wolf, Tiffany Cook, Brian Gebelein, Edo Kussell, Hideki Nakagoshi, Claude Desplan. How complex networks of activators and repressors lead to exquisitely specific cell-type determination during development is poorly understood. In the Drosophila eye, expression patterns of...."

The Relationship Between Relative Solvent Accessibility and Evolutionary Rate in Protein Evolution [Genome and systems biology]

The Relationship Between Relative Solvent Accessibility and Evolutionary Rate in Protein Evolution [Genome and systems biology]: "

Recent work with Saccharomyces cerevisiae shows a linear relationship between the evolutionary rate of sites and the relative solvent accessibility (RSA) of the corresponding residues in the folded protein. Here, we aim to develop a mathematical model that can reproduce this linear relationship. We first demonstrate that two models that both seem reasonable choices (a simple model in which selection strength correlates with RSA and a more complex model based on RSA-dependent amino acid distributions) fail to reproduce the observed relationship. We then develop a model on the basis of observed site-specific amino acid distributions and show that this model behaves appropriately. We conclude that evolutionary rates are directly linked to the distribution of amino acids at individual sites. Because of this link, any future insight into the biophysical mechanisms that determine amino acid distributions will improve our understanding of evolutionary rates.

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Circumventing Heterozygosity: Sequencing the Amplified Genome of a Single Haploid Drosophila melanogaster Embryo [Methods, technology, and resources]

Circumventing Heterozygosity: Sequencing the Amplified Genome of a Single Haploid Drosophila melanogaster Embryo [Methods, technology, and resources]: "

Heterozygosity is a major challenge to efficient, high-quality genomic assembly and to the full genomic survey of polymorphism and divergence. In Drosophila melanogaster lines derived from equatorial populations are particularly resistant to inbreeding, thus imposing a major barrier to the determination and analyses of genomic variation in natural populations of this model organism. Here we present a simple genome sequencing protocol based on the whole-genome amplification of the gynogenetically derived haploid genome of a progeny of females mated to males homozygous for the recessive male sterile mutation, ms(3)K81. A single 'lane' of paired-end sequences (2 x 76 bp) provides a good syntenic assembly with >95% high-quality coverage (more than five reads). The amplification of the genomic DNA moderately inflates the variation in coverage across the euchromatic portion of the genome. It also increases the frequency of chimeric clones. But the low frequency and random genomic distribution of the chimeric clones limits their impact on the final assemblies. This method provides a solid path forward for population genomic sequencing and offers applications to many other systems in which small amounts of genomic DNA have unique experimental relevance.

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Patterns and Mechanisms of Ancestral Histone Protein Inheritance in Budding Yeast

Patterns and Mechanisms of Ancestral Histone Protein Inheritance in<br> Budding Yeast: "
by Marta Radman-Livaja, Kitty F. Verzijlbergen, Assaf Weiner, Tibor van Welsem, Nir Friedman, Oliver J. Rando, Fred van Leeuwen


Replicating chromatin involves disruption of histone-DNA contacts and subsequent
reassembly of maternal histones on the new daughter genomes. In bulk, maternal
histones are randomly segregated to the two daughters, but little is known about
the fine details of this process: do maternal histones re-assemble at preferred
locations or close to their original loci? Here, we use a recently developed
method for swapping epitope tags to measure the disposition of ancestral histone
H3 across the yeast genome over six generations. We find that ancestral H3 is
preferentially retained at the 5′ ends of most genes, with strongest
retention at long, poorly transcribed genes. We recapitulate these observations
with a quantitative model in which the majority of maternal histones are
reincorporated within 400 bp of their pre-replication locus during replication,
with replication-independent replacement and transcription-related retrograde
nucleosome movement shaping the resulting distributions of ancestral histones.
We find a key role for Topoisomerase I in retrograde histone movement during
transcription, and we find that loss of Chromatin Assembly Factor-1 affects
replication-independent turnover. Together, these results show that specific
loci are enriched for histone proteins first synthesized several generations
beforehand, and that maternal histones re-associate close to their original
locations on daughter genomes after replication. Our findings further suggest
that accumulation of ancestral histones could play a role in shaping histone
modification patterns."

The Mismeasure of Science: Stephen Jay Gould versus Samuel George Morton on Skulls and Bias

The Mismeasure of Science: Stephen Jay Gould versus Samuel George Morton on Skulls and Bias: "
by Jason E. Lewis, David DeGusta, Marc R. Meyer, Janet M. Monge, Alan E. Mann, Ralph L. Holloway
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Convergent transcription confers a bistable switch in Enterococcus faecalis conjugation [Systems Biology]

Convergent transcription confers a bistable switch in Enterococcus faecalis conjugation [Systems Biology]: "Convergent gene pairs with head-to-head configurations are widespread in both eukaryotic and prokaryotic genomes and are speculated to be involved in gene regulation. Here we present a unique mechanism of gene regulation due to convergent transcription from the antagonistic prgX/prgQ operon in Enterococcus faecalis controlling conjugative transfer of the antibiotic resistance plasmid pCF10 from donor cells to recipient cells. Using mathematical modeling and experimentation, we demonstrate that convergent transcription in the prgX/prgQ operon endows the system with the properties of a robust genetic switch through premature termination of elongating transcripts due to collisions between RNA polymerases (RNAPs) transcribing from opposite directions and antisense regulation between complementary counter-transcripts. Evidence is provided for the presence of truncated RNAs resulting from convergent transcription from both the promoters that are capable of sense–antisense interactions. A mathematical model predicts that both RNAP collision and antisense regulation are essential for a robust bistable switch behavior in the control of conjugation initiation by prgX/prgQ operons. Moreover, given that convergent transcription is conserved across species, the mechanism of coupling RNAP collision and antisense interaction is likely to have a significant regulatory role in gene expression."

Direct targets of the D. melanogaster DSXF protein and the evolution of sexual development [RESEARCH ARTICLES]

Direct targets of the D. melanogaster DSXF protein and the evolution of sexual development [RESEARCH ARTICLES]: "Shengzhan D. Luo, Guang W. Shi, and Bruce S. Baker

Uncovering the direct regulatory targets of doublesex (dsx) and fruitless (fru) is crucial for an understanding of how they regulate sexual development, morphogenesis, differentiation and adult functions (including behavior) in Drosophila melanogaster. Using a modified DamID approach, we identified 650 DSX-binding regions in the genome from which we then extracted an optimal palindromic 13 bp DSX-binding sequence. This sequence is functional in vivo, and the base identity at each position is important for DSX binding in vitro. In addition, this sequence is enriched in the genomes of D. melanogaster (58 copies versus approximately the three expected from random) and in the 11 other sequenced Drosophila species, as well as in some other Dipterans. Twenty-three genes are associated with both an in vivo peak in DSX binding and an optimal DSX-binding sequence, and thus are almost certainly direct DSX targets. The association of these 23 genes with optimum DSX binding sites was used to examine the evolutionary changes occurring in DSX and its targets in insects.

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