Papers by Maite G. Barrón
Nucleic Acids Research, 2014
Transposable elements (TEs) are the most active, diverse and ancient component 42 in a broad rang... more Transposable elements (TEs) are the most active, diverse and ancient component 42 in a broad range of genomes. As such, a complete understanding of genome function 43 and evolution cannot be achieved without a thorough understanding of TE impact and 44 biology. However, in-depth analyses of TEs still represent a challenge due to the 45 repetitive nature of these genomic entities. In this work, we present a broadly applicable 46 and flexible tool: T-lex2. T-lex2 is the only available software that allows routine, 47 automatic, and accurate genotyping of individual TE insertions and estimation of their 48 population frequencies both using individual strain and pooled next-generation 49 sequencing (NGS) data. Furthermore, T-lex2 also assesses the quality of the calls 50 allowing the identification of miss-annotated TEs and providing the necessary 51 information to re-annotate them. Although we tested the fidelity of T-lex2 using the high 52 quality Drosophila melanogaster genome, the flexible and customizable design of T-53 lex2 allows running it in any genome and for any type of TE insertion. Overall, T-lex2 54 represents a significant improvement in our ability to analyze the contribution of TEs to 55 genome function and evolution as well as learning about the biology of TEs. T-lex2 is 56 freely available online at http://petrov.stanford.edu/cgi-bin/Tlex.html. 57 58 on October 20, 2014 http://biorxiv.org/ Downloaded from 59 60
Annual Review of Genetics, 2014
Drosophila melanogaster indicate that consistent forces are affecting TEs independently of their ... more Drosophila melanogaster indicate that consistent forces are affecting TEs independently of their modes of transposition and regulation. New sequencing technologies enable biologists to sample genomes at an unprecedented scale in order to quantify genome-wide polymorphism for annotated and novel TE insertions. In this review, we first present new insights gleaned from high-throughput data for population genomics studies of D. melanogaster. We then consider the latest population genomics models for TE evolution and present examples of functional evidence revealed by genome-wide studies of TE population dynamics in D. melanogaster. Although most of the TE insertions are deleterious or neutral, some TE insertions increase the fitness of the individual that carries them and play a role in the genome adaptation.
Nature, 2012
A major challenge of biology is understanding the relationship between molecular genetic variatio... more A major challenge of biology is understanding the relationship between molecular genetic variation and variation in quantitative traits, including fitness. This relationship determines our ability to predict phenotypes from genotypes and to understand how evolutionary forces shape variation within and between species. Previous efforts to dissect the genotype-phenotype map were based on incomplete genotypic information. Here, we describe the Drosophila melanogaster Genetic Reference Panel (DGRP), a community resource for analysis of population genomics and quantitative traits. The DGRP consists of fully sequenced inbred lines derived from a natural population. Population genomic analyses reveal reduced polymorphism in centromeric autosomal regions and the X chromosome, evidence for positive and negative selection, and rapid evolution of the X chromosome. Many variants in novel genes, most at low frequency, are associated with quantitative traits and explain a large fraction of the phenotypic variance. The DGRP facilitates genotype-phenotype mapping using the power of Drosophila genetics.
Elucidating the fitness effects of natural genetic variants is one of the current major
challeng... more Elucidating the fitness effects of natural genetic variants is one of the current major
challenges in evolutionary biology. Understanding the interplay between genotype,
phenotype and environment is necessary to make accurate predictions of important
biological outcomes such as stress resistance or yield in economically important plants
and animals, and disease in humans. Based on population frequency patterns and footprints
of selection at the DNA level, the transposable element Bari-Jheh, inserted in
the intergenic region of Juvenile Hormone Epoxy Hydrolase (Jheh) genes, was previously
identified as putatively adaptive. However, the adaptive effect of this mutation
remained elusive. In this work, we integrate information on transcription factor binding
sites, available ChIP-Seq data, gene expression analyses and phenotypic assays to
identify the functional and the mechanistic underpinnings of Bari-Jheh. We show that
Bari-Jheh adds extra antioxidant response elements upstream of Jheh1 and Jheh2 genes.
Accordingly, we find that Bari-Jheh is associated with upregulation of Jheh1 and Jheh2
and with resistance to oxidative stress induced by two different compounds relevant
for natural D. melanogaster populations. We further show that TEs other than
Bari-Jheh might be playing a role in the D. melanogaster response to oxidative stress.
Overall our results contribute to the understanding of resistance to oxidative stress in
natural populations and highlight the role of transposable elements in environmental
adaptation. The replicability of fitness effects on different genetic backgrounds also
suggests that epistatic interactions do not seem to dominate the genetic architecture of
oxidative stress resistance.
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Papers by Maite G. Barrón
challenges in evolutionary biology. Understanding the interplay between genotype,
phenotype and environment is necessary to make accurate predictions of important
biological outcomes such as stress resistance or yield in economically important plants
and animals, and disease in humans. Based on population frequency patterns and footprints
of selection at the DNA level, the transposable element Bari-Jheh, inserted in
the intergenic region of Juvenile Hormone Epoxy Hydrolase (Jheh) genes, was previously
identified as putatively adaptive. However, the adaptive effect of this mutation
remained elusive. In this work, we integrate information on transcription factor binding
sites, available ChIP-Seq data, gene expression analyses and phenotypic assays to
identify the functional and the mechanistic underpinnings of Bari-Jheh. We show that
Bari-Jheh adds extra antioxidant response elements upstream of Jheh1 and Jheh2 genes.
Accordingly, we find that Bari-Jheh is associated with upregulation of Jheh1 and Jheh2
and with resistance to oxidative stress induced by two different compounds relevant
for natural D. melanogaster populations. We further show that TEs other than
Bari-Jheh might be playing a role in the D. melanogaster response to oxidative stress.
Overall our results contribute to the understanding of resistance to oxidative stress in
natural populations and highlight the role of transposable elements in environmental
adaptation. The replicability of fitness effects on different genetic backgrounds also
suggests that epistatic interactions do not seem to dominate the genetic architecture of
oxidative stress resistance.
challenges in evolutionary biology. Understanding the interplay between genotype,
phenotype and environment is necessary to make accurate predictions of important
biological outcomes such as stress resistance or yield in economically important plants
and animals, and disease in humans. Based on population frequency patterns and footprints
of selection at the DNA level, the transposable element Bari-Jheh, inserted in
the intergenic region of Juvenile Hormone Epoxy Hydrolase (Jheh) genes, was previously
identified as putatively adaptive. However, the adaptive effect of this mutation
remained elusive. In this work, we integrate information on transcription factor binding
sites, available ChIP-Seq data, gene expression analyses and phenotypic assays to
identify the functional and the mechanistic underpinnings of Bari-Jheh. We show that
Bari-Jheh adds extra antioxidant response elements upstream of Jheh1 and Jheh2 genes.
Accordingly, we find that Bari-Jheh is associated with upregulation of Jheh1 and Jheh2
and with resistance to oxidative stress induced by two different compounds relevant
for natural D. melanogaster populations. We further show that TEs other than
Bari-Jheh might be playing a role in the D. melanogaster response to oxidative stress.
Overall our results contribute to the understanding of resistance to oxidative stress in
natural populations and highlight the role of transposable elements in environmental
adaptation. The replicability of fitness effects on different genetic backgrounds also
suggests that epistatic interactions do not seem to dominate the genetic architecture of
oxidative stress resistance.