Pervasive adaptation of gene expression in Drosophila

Pervasive adaptation of gene expression in Drosophila

Armita Nourmohammad, Joachim Rambeau, Torsten Held, Johannes Berg, Michael Lassig
(Submitted on 23 Feb 2015)

Gene expression levels are important molecular quantitative traits that link genotypes to molecular functions and fitness. In Drosophila, population-genetic studies in recent years have revealed substantial adaptive evolution at the genomic level. However, the evolutionary modes of gene expression have remained controversial. Here we present evidence that adaptation dominates the evolution of gene expression levels in flies. We show that 64% of the observed expression divergence across seven Drosophila species are adaptive changes driven by directional selection. Our results are derived from the variation of expression within species and the time-resolved divergence across a family of related species, using a new inference method for selection. We identify functional classes of adaptively regulated genes, as well as sex-specific adaptation occurring predominantly in males. Our analysis opens a new avenue to map system-wide selection on molecular quantitative traits independently of their genetic basis.

Systematic discovery and classification of human cell line essential genes

Systematic discovery and classification of human cell line essential genes
Traver Hart , Megha Chandrashekhar , Michael Aregger , Zachary Steinhart , Kevin R Brown , Stephane Angers , Jason Moffat
doi: http://dx.doi.org/10.1101/015412

The study of gene essentiality in human cells is crucial for elucidating gene function and holds great potential for finding therapeutic targets for diseases such as cancer. Technological advances in genome editing using clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 systems have set the stage for identifying human cell line core and context-dependent essential genes. However, first generation negative selection screens using CRISPR technology demonstrate extreme variability across different cell lines. To advance the development of the catalogue of human core and context-dependent essential genes, we have developed an optimized, ultracomplex, genome-scale gRNA library of 176,500 guide RNAs targeting 17,661 genes and have applied it to negative and positive selection screens in a human cell line. Using an improved Bayesian analytical approach, we find CRISPR-based screens yield double to triple the number of essential genes than were previously observed using systematic RNA interference, including many genes at moderate expression levels that are largely refractory to RNAi methods. We further characterized four essential genes of unknown significance and found that they all likely exist in protein complexes with other essential genes. For example, RBM48 and ARMC7 are both essential nuclear proteins, strongly interact and are commonly amplified across major cancers. Our findings suggest the CRISPR-Cas9 system fundamentally alters the landscape for systematic reverse genetics in human cells for elucidating gene function, identifying disease genes, and uncovering therapeutic targets.

Genetic Variation, Not Cell Type of Origin, Underlies Regulatory Differences in iPSCs

Genetic Variation, Not Cell Type of Origin, Underlies Regulatory Differences in iPSCs
Courtney L Kagan, Nicholas E Banovich, Bryan J Pavlovic, Kristen Patterson, Irene Gallego Romero, Jonathan K Pritchard, Yoav Gilad
doi: http://dx.doi.org/10.1101/013888

The advent of induced pluripotent stem cells (iPSCs) revolutionized Human Genetics by allowing us to generate pluripotent cells from easily accessible somatic tissues. This technology can have immense implications for regenerative medicine, but iPSCs also represent a paradigm shift in the study of complex human phenotypes, including gene regulation and disease. Yet, an unresolved caveat of the iPSC model system is the extent to which reprogrammed iPSCs retain residual phenotypes from their precursor somatic cells. To directly address this issue, we used an effective study design to compare regulatory phenotypes between iPSCs derived from two types of commonly used somatic precursor cells. We show that the cell type of origin only minimally affects gene expression levels and DNA methylation in iPSCs. Instead, genetic variation is the main driver of regulatory differences between iPSCs of different donors.

Digit evolution in gymnophthalmid lizards

Digit evolution in gymnophthalmid lizards
Juliana Roscito, Pedro M. S. Nunes, Miguel T Rodrigues
doi: http://dx.doi.org/10.1101/013953

Background The tetrapod limb is a highly diverse structure, and reduction of the limbs accounts for much of the phenotypes observed within species. Squamate reptiles represent one of the many lineages in which the limbs have been greatly modified from the pentadactyl generalized pattern; within the group, limb-reduced morphologies can vary from minor reductions in size of elements to complete limblessness, with several intermediate forms in between. Even though limb reduction is widespread, it is not clear what are the evolutionary and developmental mechanisms involved in the formation of reduced limb morphologies. Methods In this study, we present an overview of limb morphology within the microteiid lizard group Gymnophthalmidae, focusing on digit number. Results We show that there are two major groups of limb-reduced gymnophthalmids. The first group is formed by lizard-like – and frequently pentadactyl – species, in which minor reductions (such as the loss of 1-2 phalanges mainly in digits I and V) are the rule; these morphologies generally correspond to those seen in other squamates. The second group is formed by species showing more drastic losses, which can include the absence of an externally distinct limb in adults. We also show the expression patterns of Sonic Hedgehog (Shh) in the greatly reduced fore and hindlimb of a serpentiform gymnophthalmid. Conclusions Our discussion focus on identifying shared patterns of limb reduction among tetrapods, and explaining these patterns and the morphological variation within the gymnophthalmids based on the current knowledge of the molecular signaling pathways that coordinate limb development.

Reprogramming LCLs to iPSCs Results in Recovery of Donor-Specific Gene Expression Signature

Reprogramming LCLs to iPSCs Results in Recovery of Donor-Specific Gene Expression Signature

Samantha M Thomas, Courtney Kagan, Bryan J Pavlovic, Jonathan Burnett, Kristen Patterson, Jonathan K Pritchard, Yoav Gilad
doi: http://dx.doi.org/10.1101/013631

Renewable in vitro cell cultures, such as lymphoblastoid cell lines (LCLs), have facilitated studies that contributed to our understanding of genetic influence on human traits. However, the degree to which cell lines faithfully maintain differences in donor-specific phenotypes is still debated. We have previously reported that standard cell line maintenance practice results in a loss of donor-specific gene expression signatures in LCLs. An alternative to the LCL model is the induced pluripotent stem cell (iPSC) system, which carries the potential to model tissue-specific physiology through the use of differentiation protocols. Still, existing LCL banks represent an important source of starting material for iPSC generation, and it is possible that the disruptions in gene regulation associated with long-term LCL maintenance could persist through the reprogramming process. To address this concern, we studied the effect of reprogramming mature LCLs to iPSCs on the ensuing gene expression patterns within and between six unrelated donor individuals. We show that the reprogramming process results in a recovery of donor-specific gene regulatory signatures. Since environmental contributions are unlikely to be a source of individual variation in our system of highly passaged cultured cell lines, our observations suggest that the effect of genotype on gene regulation is more pronounced in the iPSCs than in the LCL precursors. Our findings indicate that iPSCs can be a powerful model system for studies of phenotypic variation across individuals in general, and the genetic association with variation in gene regulation in particular. We further conclude that LCLs are an appropriate starting material for iPSC generation.

A pooling-based approach to mapping genetic variants associated with DNA methylation

A pooling-based approach to mapping genetic variants associated with DNA methylation

Irene Miriam Kaplow, Julia L MacIsaac, Sarah M Mah, Lisa M McEwen, Michael S Kobor, Hunter B Fraser
doi: http://dx.doi.org/10.1101/013649

DNA methylation is an epigenetic modification that plays a key role in gene regulation. Previous studies have investigated its genetic basis by mapping genetic variants that are associated with DNA methylation at specific sites, but these have been limited to microarrays that cover less than 2% of the genome and cannot account for allele-specific methylation (ASM). Other studies have performed whole-genome bisulfite sequencing on a few individuals, but these lack statistical power to identify variants associated with DNA methylation. We present a novel approach in which bisulfite-treated DNA from many individuals is sequenced together in a single pool, resulting in a truly genome-wide map of DNA methylation. Compared to methods that do not account for ASM, our approach increases statistical power to detect associations while sharply reducing cost, effort, and experimental variability. As a proof of concept, we generated deep sequencing data from a pool of 60 human cell lines; we evaluated almost twice as many CpGs as the largest microarray studies and identified over 2,000 genetic variants associated with DNA methylation. We found that these variants are highly enriched for associations with chromatin accessibility and CTCF binding but are less likely to be associated with traits indirectly linked to DNA, such as gene expression and disease phenotypes. In summary, our approach allows genome-wide mapping of genetic variants associated with DNA methylation in any tissue of any species, without the need for individual-level genotype or methylation data.

DNA-guided establishment of canonical nucleosome patterns in a eukaryotic genome

DNA-guided establishment of canonical nucleosome patterns in a eukaryotic genome

Leslie Y Beh, Noam Kaplan, Manuel M Muller, Tom W Muir, Laura F Landweber
doi: http://dx.doi.org/10.1101/013250

A conserved hallmark of eukaryotic chromatin architecture is the distinctive array of well-positioned nucleosomes downstream of transcription start sites (TSS). Recent studies indicate that trans-acting factors establish this stereotypical array. Here, we present the first genome-wide in vitro and in vivo nucleosome maps for the ciliate Tetrahymena thermophila. In contrast with previous studies in yeast, we find that the stereotypical nucleosome array is preserved in the in vitro reconstituted map, which is governed only by the DNA sequence preferences of nucleosomes. Remarkably, this average in vitro pattern arises from the presence of subsets of nucleosomes, rather than the whole array, in individual Tetrahymena genes. Variation in GC content contributes to the positioning of these sequence-directed nucleosomes, and affects codon usage and amino acid composition in genes. We propose that these ‘seed’ nucleosomes may aid the AT-rich Tetrahymena genome – which is intrinsically unfavorable for nucleosome formation – in establishing nucleosome arrays in vivo in concert with trans-acting factors, while minimizing changes to the coding sequences they are embedded within.