Cloning of novel trinucleotide-repeat (CAG) containing genes in mouse brain

Critical evaluation of imprinted gene expression by RNA-Seq: a new perspective

In contrast to existing estimates of approximately 200 murine imprinted genes, recent work based on transcriptome sequencing uncovered parent-of-origin allelic effects at more than 1,300 loci in the developing brain and two adult brain regions, including hundreds present in only males or females. Our independent replication of the embryonic brain stage, where the majority of novel imprinted genes were discovered and the majority of previously known imprinted genes confirmed, resulted in only 12.9% concordance among the novel imprinted loci. Further analysis and pyrosequencing-based validation revealed that the vast majority of the novel reported imprinted loci are false-positives explained by technical and biological variation of the experimental approach. We show that allele-specific expression (ASE) measured with RNA–Seq is not accurately modeled with statistical methods that assume random independent sampling and that systematic error must be accounted for to enable accurate identification of imprinted expression. Application of a robust approach that accounts for these effects revealed 50 candidate genes where allelic bias was predicted to be parent-of-origin–dependent. However, 11 independent validation attempts through a range of allelic expression biases confirmed only 6 of these novel cases. The results emphasize the importance of independent validation and suggest that the number of imprinted genes is much closer to the initial estimates.

Typically both copies of mammalian genes are expressed, but in some cases, “imprinting” restricts expression to the maternal or paternal copy. Having two copies of each gene is considered advantageous since in enables compensation when one does not function properly. Why imprinting evolved and its utility to each sex is widely debated, and having a complete catalog of imprinted genes and their functions is essential for fully characterizing this phenomenon. 25 years of screening has revealed about 130 imprinted genes, and the slowing rate of discovery suggests that we are reaching saturation. Two recent studies based on high-throughput sequencing of RNA reported more than 1,300 imprinted genes. To understand the basis of this paradigm shift, we first attempted to reproduce these results. Unable to do so, we performed additional analyses that show that most of these discoveries are due to noise in the experimental approach and assay. We remedy this with new methods that account for this noise and applied them to identify 50 novel putative imprinted genes. These methods will be useful for identifying genuine novel cases of imprinted expression as this type of screening approach becomes broadly utilized.

Analysis of cag-8: A novel poly(Q)-encoding gene in the mouse brain

We identified 13 transcript isoforms of a trinucleotide-repeat-containing gene, cag-8, that is expressed almost exclusively in the mouse brain. The polypeptide deduced from the cDNA consists of 137 AAs, of which 74 are glutamines. The 130-kb gene is composed of 16 exons, from which at least 13 isoforms with variable UTRs are formed by alternative splicing. A strong positive cis-acting element was found in the neuroblastomaxglioma hybrid NG108-15 and human embryonic kidney HEK293 cell lines. The cag-8 protein was localized in the cytosol and in granular bodies within the nucleus. These findings indicate that cag-8 is a novel poly(Q)-encoding gene, the expression of which is confined primarily to the brain.

Human gene mutation in pathology and evolution

Mutations in human gene pathology and evolution represent two sides of the same coin in that the same mechanisms that have frequently been implicated in disease-associated mutagenesis appear also to have been involved in potentiating evolutionary change. Indeed, the mutational spectra of germline mutations responsible for inherited disease, somatic mutations underlying tumorigenesis, polymorphisms (either neutral or functionally significant) and differences between orthologous gene sequences exhibit remarkable similarities, implying that they may have causal mechanisms in common. Since these different categories of mutation share multiple unifying characteristics, they should no longer be viewed as distinct entities but rather as portions of a continuum of genetic change that links population genetics and molecular medicine with molecular evolution.

A Role for Selection in Regulating the Evolutionary Emergence of Disease-Causing and Other Coding CAG Repeats in Humans and Mice

The evolutionary expansion of CAG repeats in human triplet expansion disease genes is intriguing because of their deleterious phenotype. In the past, this expansion has been suggested to reflect a broad genomewide expansion of repeats, which would imply that mutational and evolutionary processes acting on repeats differ between species. Here, we tested this hypothesis by analyzing repeat- and flanking-sequence evolution in 28 repeat-containing genes that had been sequenced in humans and mice and by considering overall lengths and distributions of CAG repeats in the two species. We found no evidence that these repeats were longer in humans than in mice. We also found no evidence for preferential accumulation of CAG repeats in the human genome relative to mice from an analysis of the lengths of repeats identified in sequence databases. We then investigated whether sequence properties, such as base and amino acid composition and base substitution rates, showed any relationship to repeat evolution. We found that repeat-containing genes were enriched in certain amino acids, presumably as the result of selection, but that this did not reflect underlying biases in base composition. We also found that regions near repeats showed higher nonsynonymous substitution rates than the remainder of the gene and lower nonsynonymous rates in genes that contained a repeat in both the human and the mouse. Higher rates of nonsynonymous mutation in the neighborhood of repeats presumably reflect weaker purifying selection acting in these regions of the proteins, while the very low rate of nonsynonymous mutation in proteins containing a CAG repeat in both species presumably reflects a high level of purifying selection. Based on these observations, we propose that the mutational processes giving rise to polyglutamine repeats in human and murine proteins do not differ. Instead, we propose that the evolution of polyglutamine repeats in proteins results from an interplay between mutational processes and selection.

Characterization of trinucleotide- and tandem repeat-containing transcripts obtained from human spinal cord cDNA library by high-density filter hybridization

In order to identify trinucleotide- and tandem repeat-containing transcripts in human spinal cord, hybridization of a high-density spinal cord cDNA library filter was carried out using a radioactively labeled degenerate oligonucleotide designed to detect different trinucleotide repeats including those known to occur in disease-associated expansions, in a single step. The sequence analysis of the trinucleotide repeat-containing transcripts (TNRTs) revealed 23 known mammalian genes with trinucleotide repeat-containing regions (TNRs), some of which were not previously reported to contain TNRs, and 18 cDNA clones with no or insignificant sequence homology to known genes. Amongst the known genes detected was the fragile X gene (FMR-1) containing (CGG)30. Other genes containing extended TNRs of 9 to 21 repeats were calcium-dependent protease, ATBF1-A, ferritin H chain, and the G protein Gsalpha2. Ten sequences containing perfect TNRs and two sequences containing perfect tandem repeats (derived from 11 TNRTs) were further analyzed for allelic variation using primers flanking the TNR, and five were shown to exhibit two to five alleles per TNR. These transcripts were further investigated for their chromosomal localization where unknown or only partially characterized. The transcripts that were polymorphic in the TNR region were ATBF1-A (a homeodomain protein), clone 390013 on chromosome Xp11, a member of the family of the 14.3.3 protein kinase C regulators, a human translation initiation factor (an isolog of the yeast Suilisol gene 1), and a novel sequence (TR21). Only the first two transcripts showed the presence of rare expanded alleles. Characterization of polymorphic TNRs in novel and even known genes expressed in human spinal cord is likely to help in the identification of new candidates for genes involved in neurodegenerative disorders.

Msh2 deficiency prevents in vivo somatic instability of the CAG repeat in Huntington disease transgenic mice

Huntington disease (HD), an autosomal dominant, progressive neurodegenerative disorder, is caused by an expanded CAG repeat sequence leading to an increase in the number of glutamine residues in the encoded protein. The normal CAG repeat range is 5-36, whereas 38 or more repeats are found in the diseased state; the severity of disease is roughly proportional to the number of CAG repeats. HD shows anticipation, in which subsequent generations display earlier disease onsets due to intergenerational repeat expansion. For longer repeat lengths, somatic instability of the repeat size has been observed both in human cases at autopsy and in transgenic mouse models containing either a genomic fragment of human HD exon 1 (ref. 9) or an expanded repeat inserted into the endogenous mouse gene Hdh (ref. 10). With increasing repeat number, the protein changes conformation and becomes increasingly prone to aggregation, suggesting important functional correlations between repeat length and pathology. Because dinucleotide repeat instability is known to increase when the mismatch repair enzyme MSH2 is missing, we examined instability of the HD CAG repeat by crossing transgenic mice carrying exon 1 of human HD (ref. 16) with Msh2-/- mice. Our results show that Msh2 is required for somatic instability of the CAG repeat.

Instability of the CAG repeat in immortalized fibroblast cell cultures from Huntington's disease transgenic mice

Huntington's Disease transgenic mice were used for an exploration into the stability of a trinucleotide repeat. The brain shows heterogeneous somatic instability that increases quantitatively with age. To test somatic CAG-repeat alterations during long-term culture, DNA was extracted from transgenic tissue, primary fibroblasts, and SV40-immortalized fibroblasts at intervals of approximately 100 cell doublings. In fibroblasts derived from an adult mouse, there was an initial short truncation of the repeat, followed by an emerging population of cells showing continuous slow expansion. After 15 months in continuous culture (approximately 600 cell doublings following transformation) the major CAG peak has increased from 155 to approximately 170 triplets. This in vitro system can now be used to assay factors that affect instability.