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Dissecting the Role of Transposon-Insertions for Allelic Underexpression of Eleven Candidate Transposon-Regulated Cellular Genes

English title Dissecting the Role of Transposon-Insertions for Allelic Underexpression of Eleven Candidate Transposon-Regulated Cellular Genes
Applicant Excoffier Laurent
Number 120379
Funding scheme Project funding
Research institution Abteilung für Humangenetik Universitätsklinik für Kinderheilkunde Inselspital
Institution of higher education University of Berne - BE
Main discipline Genetics
Start/End 01.05.2008 - 31.10.2011
Approved amount 275'846.00
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Keywords (7)

transposon; transposon silencing; gene regulation; epigenetics; gene positioning; allelic expression; structural genome variation

Lay Summary (English)

Lead
Lay summary
Aims; our genetic heritage or genome is physically organized in the form of 23 pairs of equivalent chromosomes, tightly coiled microscopic rod-like structures composed of DNA and proteins. The key functional genome units are called genes. Our genome contains ~25’000 such genes 10’000 times smaller than microscopically visible chromosome bands. Surprisingly however, genes comprise only a tiny portion of the whole DNA space, whereas a considerable fraction is occupied by elements once considered genomic parasites, namely transposons. These “jumping genes” usually move from one genome place to another, but almost completely lost mobility in humans, where they behave as near neutral variants. Nonetheless, at least some acquired novel functions and became “regular genes”, as they now help to regulate other genes, or took on roles as structural genome elements. While comparing genes that differ only with respect to presence or absence of one specific transposon, we noticed that transposon-containing genes were less active than transposon-free variants. This suggests that some transposons were recruited to regulate genes. Therefore, the seminal aim of our project is to characterize in depth eleven model genes carrying or not transposons for which this applies. Specifically, we aim at proving the causative role of transposons for reduced gene activity, at understanding how this is brought about, and at identifying the consequences for transposon carriers with respect to certain traits and diseases.Relevance; these observations make biological sense; during evolution we learned to suppress transposons, since their mobility threatened us. Subsequently, it became economic to divert this mastery for novel purposes, namely for (negative) gene regulation. This project will therefore expand our understanding of transposon control, of global negative gene regulators, and of the role of transposons for certain traits and diseases (e.g. athletic performance, cardiovascular disease). Scientific details and methods; we will determine the activity of eleven candidate transposon regulated genes with established methods in humans. The causative role of transposons for reduced gene activity will be addressed by integrating human genes with and without transposons into the genome of mice and by comparing their activity. We will then evaluate structural proteins (histones) associated with genes carrying or not transposons, and their localisation within the nucleus, giving us clues as to their different activity. Finally, we will test whether candidate genes known to repress transposons in another species exert a similar function in humans. Interestingly, these suppressor genes once were themselves transposons, suggesting that evolution used “fire to fight fire”.
Direct link to Lay Summary Last update: 21.02.2013

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Abstract

Transposable elements (TEs or transposons) comprise a large fraction of most eu-karyotic genomes, up to 50% of our own. Since active TEs are highly mutagenic, they were long considered purely parasitic elements that tend to increase in copy number at the expense of the host’s fitness. Most TEs however, do not actively transpose, persist as phenotypically cryptic genetic variation or play an increasingly appreciated role as gene regulatory elements, for example as promoters, enhancers, insulators, and building blocks for epigenetic diversity. Several recent studies, particularly the diploid genome sequence of an indi-vidual human uncovered a high, hitherto largely underestimated rate of TE-insertion polymorphisms; specifically, 2583 TEs occupy ~0.9 Mb variant DNA bases, equaling 1/12 of total DNA-, and 1/3 of SNP-variation. Despite this, the impact of TEs on cel-lular gene regulation and function has not yet been systematically addressed. We found a significant, tissue-restricted reduction of mRNA transcripts for alleles of a cellular gene carrying one TE-type. Consistent with this, others identified TE-associated, tissue-restricted underexpression of alleles of ten additional genes carry-ing other major variant TE-classes. Together, this suggests that a subset of alleles carrying TEs is negatively regulated in a cell-type specific fashion. We postulate that TEs are responsible for allele-specific underexpression and that heterozygotes are maintained in the population via positive selection, because heterozygotes can ex-press the gene at a wider range. In analogy to emerging themes in monoallelic gene expression, we hypothesize that TE-induced allele-specific underexpression is mostly the consequence of coregulated, tissue-restricted TE-transcription generating differential chromatin marks on otherwise homologous alleles, and of physical seg-regation of alleles to separate nuclear domains depending on their TE-carrier status. To address this, we will first corroborate TE-dependent allele-specific under-expression of ten cellular genes reported by others, then quantify tissue-restricted TE-transcription for all eleven cellular genes, compare epigenetic marks across loci with allele-specific chromatin immunoprecipitation, and determine nuclear localiza-tion of alleles according to their TE-carrier status with FISH. When appropriate, al-ternative models for underexpression will be explored, for instance interference with transcription, mRNA-processing and -stability, and negative regulatory factors. For two genes, selected for their biological and medical importance, we will corroborate the TE-dependence of underexpression in cis using BAC-transgenic mice. TE-dependent underexpression phenotypes are anticipated for several among the eleven genes that are dosage sensitive. For instance, FOG2 haploinsufficiency per-turbs gonadal and heart development, and tissue-specific loss of the MAP3K gene TAK1 causes vascular disease, skin- and immune-defects. Finally, a variant TE in the angiotensin I converting enzyme gene ACE accounts for half of the variance of circulating enzyme levels and is associated with various phenotypes (myocardial in-farction, Alzheimer disease, type II diabetes and obesity), pointing to a role for TE-associated underexpression in complex, polygenic traits. For these reasons, this study will give us new insight into the mechanisms of allele-specific expression con-trolled by variant TEs, and provide a basis to relate heritable gene expression to phenotypes, quantitative traits and diseases; these findings will in the future certainly be extended to other variant TEs described by the diploid genome sequence.
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