BACKGROUND
the chromosomal band 17q <dig>  contains a common inversion polymorphism linked with neurodegenerative diseases including progressive supranuclear palsy  <cit> , corticobasal degeneration  <cit> , parkinson’s disease  <cit> , and alzheimer’s disease  <cit> .
this inversion of approximately 900 kb is mostly present in populations with european ancestry   <cit> .
this region contains a number of genes, including corticotrophin releasing hormone receptor  <dig>  and microtubule-associated protein tau .
two divergent mapt haplotypes, h <dig> and h <dig> are described with distinct linkage disequilibrium patterns across the region reflecting the inversion status at this locus.
the h <dig> haplotype is inverted and is relatively common in europeans , however, almost absent in african and asian populations.
this configuration is associated with fecundity and appears to be under positive selection in european populations  <cit> .
specific h <dig> haplotypes are associated with the neurodegenerative disorders, whereas the h <dig> haplotype is linked to recurrent deletion events resulting in the 17q <dig>  microdeletion syndrome, characterized by developmental delay and learning disability  <cit> .
the h <dig> haplotype is linked with an increased expression of mapt, resulting in overproduction and aggregation of hyperphosphorylated protein tau in neuronal cell bodies, which is linked to disease pathology of a number of neurodegenerative disorders  <cit> .
however, little is known about the regulation of expression levels of other genes in the region.
in this study we used single nucleotide polymorphism  genotype data to reconstruct inversion haplotypes in the chromosome 17q <dig>  region and studied the effect of the inversion status on gene expression of all known genes in the region in whole blood and different regions of the human brain.
RESULTS
regulation of expression in whole blood
a principal component analysis  was applied to  <dig> snps in the  <dig> ,001- <dig> , <dig> region on chromosome  <dig>  the first principal component  represents the 17q <dig>  inversion genotypes homozygous h <dig>  heterozygous h1/h <dig> and homozygous h2/h <dig>  of the  <dig> individuals,  <dig> were excluded because of ambiguity in master genotype call .
this resulted in three distinct clusters of individuals, representing h1/h <dig> , h1/h <dig>  and h2/h <dig>  genotypes , depicted in figure  <dig>  for  <dig> of the  <dig> genes in the region,  <dig> gene expression probes were available in the blood dataset .
a linear regression analysis showed a positive association of lrrc37a <dig>  with the number of h <dig> alleles.
in contrast, mgc <dig> was negatively associated with the h1/h <dig> genotype  results are given in table  <dig>  we did not detect expression of the mapt gene in blood.
the genes found to be associated to the 17q <dig>  inversion haplotypes are listed in the first column with their corresponding probe ids .
the genes have been tested in two datasets and results of linear regression are given, t, b  and p-values.
the b values indicate the actual change in expression associated with each copy of the h <dig> allele .
the corresponding unadjusted p-values are listed when significant.
not all genes were available or detected in each dataset; n/a = not available on array, dt = did not meet detection threshold in tissue, ns = not significant.
all probes for the genes in the 17q <dig>  region are listed in additional file 1: table s <dig>
regulation of expression in human brain
we consulted a publically available human brain expression dataset consisting of frontal cortex, temporal cortex, cerebellum and pons of  <dig> individuals  <cit> .
master genotypes of the chromosome 17q <dig>  inversion were reconstructed using pc <dig> values of  <dig> snps in the  <dig> ,001- <dig> , <dig> interval.
this resulted in three distinct clusters of individuals, representing h1/h <dig> , h1/h <dig>  and h2/h <dig>  genotypes .
for  <dig> of the  <dig> genes in the inversion region,  <dig> expression probes were available in every brain area .
a linear regression analysis of allele dosage was performed for each brain area separately .
in line with literature, we found a higher expression of mapt to be associated with the h1/h <dig> genotype in frontal cortex  and cerebellum .
in addition, the h1/h <dig> genotype was also associated with increased expression of plekhm <dig> in cerebellum .
in contrast, lower expression of crhr <dig> was associated with this genotype in cerebellum , while undetected in the other brain regions.
finally, decreased expression of lrrc37a was found to be associated with the h1/h <dig> genotype in frontal cortex , temporal cortex  and pons .
no polymorphic snps were detected in the probe sequence that could have confounded the hybridization signal.
when aligning the lrrc37a probe sequence  to refseq rna sequences , it was found that this probe aligns significantly with not only lrrc37a , but also lrrc37a <dig> , lrrc37a <dig>  and lrrc37a <dig> .
therefore, the strong association can be the result of non-specific binding to more than one target gene in this gene family.
alignment of all other significant probes sequences, including lrrc37a <dig>  did not suggest non-specific binding.
discussion
the chromosome 17q <dig>  inversion of the mapt  locus represents one of the most structurally complex and evolutionarily dynamic regions of the genome  <cit> .
the distinct clades of haplotypes  represent the direct and inverted orientation of the inversion, each with different functional impacts.
specific h <dig> haplotypes are associated with neurodegenerative disorders such as progressive supranuclear palsy  <cit>  and parkinson’s disease  <cit> , whereas the h <dig> haplotype is associated with recurrent microdeletions resulting in the 17q <dig>  microdeletion syndrome  <cit> .
neurodegenerative diseases associated with the h <dig> haplotype exhibit aggregation of hyperphosphorylated protein tau in neuronal cell bodies  <cit> .
gene expression differences have been described for mapt, but there has been no systematic approach to study the effect of inversion status on expression of the other genes at this locus.
we used principal component analysis to identify inversion haplotypes at chromosome 17q <dig> , and observed that the effect of inversion status is not limited to mapt expression levels, but also affects several other genes in the 17q <dig>  region.
in line with literature, we found increased expression of mapt to be associated with the number of h <dig> alleles in brain.
however, we only observed this in frontal cortex and cerebellum, suggesting that regulation of this gene may differ between brain regions.
a previous study identified a specific sequence variant in mapt  in the 17q <dig>  region on the h <dig> haplotype regulating the expression of mapt in neuronal and non-neuronal cell lines  <cit> .
in this study we focused on the effect of the entire inversion on gene expression with use of a robust principal component analysis strategy.
genotype data of this particular snp was available in the brain dataset but was not significantly associated with gene expression values.
importantly, we observed that genes other than mapt are functionally regulated by the inversion haplotypes as well and may therefore be of importance in diseases associated with the inversion region.
the expression of crhr <dig>  is significantly decreased in the h1/h <dig> haplotype and that of plekhm <dig>  member 1) increased.
these associations were found in cerebellum only.
the plekhm <dig> gene is involved in osteopertrosis by affecting vesicular transport and therefore osteoclast-osteoblast cross-talk  <cit> .
currently there is no functional data available on mgc <dig>  that was found to be differentially expressed due to inversion status in whole blood.
mgc <dig> consists of  <dig> exons of which  <dig> are shared with the long isoform of crhr <dig> .
it is therefore possible that these are different splice forms of a single gene, which would suggest that the concurrent association findings with inversion status represent a single event.
the fact that directionality of mgc <dig> expression in blood and crhr <dig> expression in cerebellum is the same in this study supports this view.
the crhr gene is a critical part of the hypothalamic-pituitary-adrenal  axis that mediates stress response and has been implicated in the pathophysiology of stress-related psychiatric disorders.
of the two receptors in this system , overactivity of crhr <dig> in anxiety and depression has been a consistent finding in animal studies  <cit> .
in human, there is evidence for an interaction of crhr <dig> function and stressful life events on vulnerability to depression and alcoholism through regulation of hpa-axis and possibly additional interaction with serotonin transporter loci  <cit> .
in addition, multiple sclerosis  has been associated to hpa-axis activity, specifically genetic variants in crhr <dig> <cit> .
we find increased expression of crhr <dig> associated with h <dig> configuration, suggesting that crhr <dig> activity and/or stress response might also be altered in or contributing to the h <dig> related phenotypes such as developmental delay and learning disability.
there is no functional data available for leucine rich repeat containing  <dig>  member a <dig>  expressed in whole blood and lrrc37a  expressed in brain.
for both genes we observed a significant association with inversion status, however, with opposite effects.
it is important to note that the lrrc <dig> gene family is located at either inversion breakpoints and is therefore likely to be affected by copy number variation that are associated with 17q <dig>  inversion status  <cit>  .
of the lrrc <dig> family, member a <dig>  in particular has been shown to be most variable in copy number  <cit> .
for these reasons, the association between inversion status and gene expression levels of these genes could be entirely due to differences in copy number linked to h <dig> and h <dig> haplotypes.
a recent study finds a strong association between germline hypomethylation and genomic instability, describing that dna methylation deserts are highly enriched for structural rearrangements  <cit> .
the authors report that rare cnvs that are associated with several neuropsychiatric disorders are significantly linked with local hypomethylation.
in fact, germline hypomethylation seems to play a more important role in chromosomal rearrangement than the presence of segmental duplications.
future studies should address whether inversion status of the 17q <dig>  region can be linked to  changes in epigenetic tags.
CONCLUSIONS
in conclusion, our results indicate that the chromosome 17q <dig>  inversion polymorphism associated with several neurodegenerative disorders affects the expression of multiple genes besides mapt in a tissue-specific manner.
it is therefore likely that these other genes may also play a role in pathophysiology of these neurodegenerative disorders.

 the chromosomal band 17q contains a common inversion polymorphism linked with neurodegenerative diseases including progressive supranuclear palsy, corticobasal degeneration, parkinson’s disease, and alzheimer’s disease. this inversion of approximately 900 kb is mostly present in populations with european ancestry. this region contains a number of genes, including corticotrophin releasing hormone receptor and microtubule-associated protein tau. two divergent mapt haplotypes, h and h are described with distinct linkage disequilibrium patterns across the region reflecting the inversion status at this locus. the h haplotype is inverted and is relatively common in europeans, however, almost absent in african and asian populations. this configuration is associated with fecundity and appears to be under positive selection in european populations. specific h haplotypes are associated with the neurodegenerative disorders, whereas the h haplotype is linked to recurrent deletion events resulting in the 17q microdeletion syndrome, characterized by developmental delay and learning disability. the h haplotype is linked with an increased expression of mapt, resulting in overproduction and aggregation of hyperphosphorylated protein tau in neuronal cell bodies, which is linked to disease pathology of a number of neurodegenerative disorders. however, little is known about the regulation of expression levels of other genes in the region. in this study we used single nucleotide polymorphism genotype data to reconstruct inversion haplotypes in the chromosome 17q region and studied the effect of the inversion status on gene expression of all known genes in the region in whole blood and different regions of the human brain.  regulation of expression in whole blood a principal component analysis was applied to snps in the,001-, region on chromosome the first principal component represents the 17q inversion genotypes homozygous h heterozygous h1/h and homozygous h2/h of the individuals, were excluded because of ambiguity in master genotype call. this resulted in three distinct clusters of individuals, representing h1/h, h1/h and h2/h genotypes, depicted in figure for of the genes in the region, gene expression probes were available in the blood dataset. a linear regression analysis showed a positive association of lrrc37a with the number of h alleles. in contrast, mgc was negatively associated with the h1/h genotype results are given in table we did not detect expression of the mapt gene in blood. the genes found to be associated to the 17q inversion haplotypes are listed in the first column with their corresponding probe ids. the genes have been tested in two datasets and results of linear regression are given, t, b and p-values. the b values indicate the actual change in expression associated with each copy of the h allele. the corresponding unadjusted p-values are listed when significant. not all genes were available or detected in each dataset; n/a = not available on array, dt = did not meet detection threshold in tissue, ns = not significant. all probes for the genes in the 17q region are listed in additional file 1: table s regulation of expression in human brain we consulted a publically available human brain expression dataset consisting of frontal cortex, temporal cortex, cerebellum and pons of individuals. master genotypes of the chromosome 17q inversion were reconstructed using pc values of snps in the,001-, interval. this resulted in three distinct clusters of individuals, representing h1/h, h1/h and h2/h genotypes. for of the genes in the inversion region, expression probes were available in every brain area. a linear regression analysis of allele dosage was performed for each brain area separately. in line with literature, we found a higher expression of mapt to be associated with the h1/h genotype in frontal cortex and cerebellum. in addition, the h1/h genotype was also associated with increased expression of plekhm in cerebellum. in contrast, lower expression of crhr was associated with this genotype in cerebellum, while undetected in the other brain regions. finally, decreased expression of lrrc37a was found to be associated with the h1/h genotype in frontal cortex, temporal cortex and pons. no polymorphic snps were detected in the probe sequence that could have confounded the hybridization signal. when aligning the lrrc37a probe sequence to refseq rna sequences, it was found that this probe aligns significantly with not only lrrc37a, but also lrrc37a, lrrc37a and lrrc37a. therefore, the strong association can be the result of non-specific binding to more than one target gene in this gene family. alignment of all other significant probes sequences, including lrrc37a did not suggest non-specific binding. discussion the chromosome 17q inversion of the mapt locus represents one of the most structurally complex and evolutionarily dynamic regions of the genome. the distinct clades of haplotypes represent the direct and inverted orientation of the inversion, each with different functional impacts. specific h haplotypes are associated with neurodegenerative disorders such as progressive supranuclear palsy and parkinson’s disease, whereas the h haplotype is associated with recurrent microdeletions resulting in the 17q microdeletion syndrome. neurodegenerative diseases associated with the h haplotype exhibit aggregation of hyperphosphorylated protein tau in neuronal cell bodies. gene expression differences have been described for mapt, but there has been no systematic approach to study the effect of inversion status on expression of the other genes at this locus. we used principal component analysis to identify inversion haplotypes at chromosome 17q, and observed that the effect of inversion status is not limited to mapt expression levels, but also affects several other genes in the 17q region. in line with literature, we found increased expression of mapt to be associated with the number of h alleles in brain. however, we only observed this in frontal cortex and cerebellum, suggesting that regulation of this gene may differ between brain regions. a previous study identified a specific sequence variant in mapt in the 17q region on the h haplotype regulating the expression of mapt in neuronal and non-neuronal cell lines. in this study we focused on the effect of the entire inversion on gene expression with use of a robust principal component analysis strategy. genotype data of this particular snp was available in the brain dataset but was not significantly associated with gene expression values. importantly, we observed that genes other than mapt are functionally regulated by the inversion haplotypes as well and may therefore be of importance in diseases associated with the inversion region. the expression of crhr is significantly decreased in the h1/h haplotype and that of plekhm member 1) increased. these associations were found in cerebellum only. the plekhm gene is involved in osteopertrosis by affecting vesicular transport and therefore osteoclast-osteoblast cross-talk. currently there is no functional data available on mgc that was found to be differentially expressed due to inversion status in whole blood. mgc consists of exons of which are shared with the long isoform of crhr. it is therefore possible that these are different splice forms of a single gene, which would suggest that the concurrent association findings with inversion status represent a single event. the fact that directionality of mgc expression in blood and crhr expression in cerebellum is the same in this study supports this view. the crhr gene is a critical part of the hypothalamic-pituitary-adrenal axis that mediates stress response and has been implicated in the pathophysiology of stress-related psychiatric disorders. of the two receptors in this system, overactivity of crhr in anxiety and depression has been a consistent finding in animal studies. in human, there is evidence for an interaction of crhr function and stressful life events on vulnerability to depression and alcoholism through regulation of hpa-axis and possibly additional interaction with serotonin transporter loci. in addition, multiple sclerosis has been associated to hpa-axis activity, specifically genetic variants in crhr. we find increased expression of crhr associated with h configuration, suggesting that crhr activity and/or stress response might also be altered in or contributing to the h related phenotypes such as developmental delay and learning disability. there is no functional data available for leucine rich repeat containing member a expressed in whole blood and lrrc37a expressed in brain. for both genes we observed a significant association with inversion status, however, with opposite effects. it is important to note that the lrrc gene family is located at either inversion breakpoints and is therefore likely to be affected by copy number variation that are associated with 17q inversion status. of the lrrc family, member a in particular has been shown to be most variable in copy number. for these reasons, the association between inversion status and gene expression levels of these genes could be entirely due to differences in copy number linked to h and h haplotypes. a recent study finds a strong association between germline hypomethylation and genomic instability, describing that dna methylation deserts are highly enriched for structural rearrangements. the authors report that rare cnvs that are associated with several neuropsychiatric disorders are significantly linked with local hypomethylation. in fact, germline hypomethylation seems to play a more important role in chromosomal rearrangement than the presence of segmental duplications. future studies should address whether inversion status of the 17q region can be linked to changes in epigenetic tags.  in conclusion, our results indicate that the chromosome 17q inversion polymorphism associated with several neurodegenerative disorders affects the expression of multiple genes besides mapt in a tissue-specific manner. it is therefore likely that these other genes may also play a role in pathophysiology of these neurodegenerative disorders. 
two divergent mapt haplotypes, h and h are described with distinct linkage disequilibrium patterns across the region reflecting the inversion status at this locus. we find the expression of several genes in and at the borders of the inversion to be affected; specific either to whole blood or different regions of the human brain. given the link between the inversion status and different neurological diseases, these genes may also be involved in disease pathology, possibly in a tissue-specific manner. however, our results show that the inversion status affects expression of other genes in the 17q region as well. studies thus far have focused on the expression of mapt in the inversion region. the mapt h haplotype has been associated with progressive supranuclear palsy, corticobasal degeneration, parkinson’s disease and alzheimer’s disease, while the h is linked to recurrent deletion events associated with the 17q microdeletion syndrome, a disease characterized by developmental delay and learning disability. chromosome 17q contains a common inversion polymorphism of approximately 900 kb in populations with european ancestry.
 chromosome 17q contains a common inversion polymorphism of approximately 900 kb in populations with european ancestry. two divergent mapt haplotypes, h and h are described with distinct linkage disequilibrium patterns across the region reflecting the inversion status at this locus. the mapt h haplotype has been associated with progressive supranuclear palsy, corticobasal degeneration, parkinson’s disease and alzheimer’s disease, while the h is linked to recurrent deletion events associated with the 17q microdeletion syndrome, a disease characterized by developmental delay and learning disability.  in this study, we investigate the effect of the inversion on the expression of genes in the 17q region. we find the expression of several genes in and at the borders of the inversion to be affected; specific either to whole blood or different regions of the human brain. the h haplotype was found to be associated with an increased expression of lrrc37a plekh1m and mapt. in contrast, a decreased expression of mgc lrrc37a and crhr was associated with h  studies thus far have focused on the expression of mapt in the inversion region. however, our results show that the inversion status affects expression of other genes in the 17q region as well. given the link between the inversion status and different neurological diseases, these genes may also be involved in disease pathology, possibly in a tissue-specific manner. 