Genetik Ufku

by Javier Aguilar-Fuentes, Mariana Fregoso, Mariana Herrera, Enrique Reynaud, Cathy Braun, Jean Marc Egly, Mario Zurita

TFIIH participates in RNA polymerase II transcription, nucleotide excision repair, and control of the cell cycle. In humans, certain mutations in the XPB and XPD subunits of TFIIH generate the syndromes trichothiodystrophy (TTD), xeroderma pigmentosum (XP), and Cockayne's syndrome (CS). In contrast, mutations in the p8/TTDA subunit have been linked only to TTD. Cells derived from TTD patients with defects in p8/TTDA have reduced levels of TFIIH. Therefore, it has been proposed that the main function of p8/TTDA is to stabilize and maintain steady-state levels of TFIIH. In Drosophila, mutations in Dmp52 and haywire genes generate phenotypes that share similarities with those associated with mutations in their human counterparts, including reduced TFIIH levels. We report that p8/TTDA overexpression suppressed accumulated developmental defects associated with mutations in the Dmp52 and haywire genes. We also provide evidence suggesting that the rescue of these defects is, in part, because of the recovery of normal TFIIH levels in mutant flies. These results indicate that overexpression of p8/TTDA trans-complemented mutations in other TFIIH subunits and suppressed defects accumulated during fly development. The overexpression of p8/TTDA in wild-type flies increased their UV irradiation resistance, apparently because of more efficient nucleotide excision repair.

by Hongchuan Li, Véronique Pascal, Maureen P. Martin, Mary Carrington, Stephen K. Anderson

Natural killer (NK) cells represent a specialized blood cell that plays an important role in the detection of virus-infected or cancer cells. NK cells recognize and kill diseased cells using receptors for self antigens (HLA) that are frequently altered on aberrant cells. The HLA receptors are known as Killer cell Immunoglobulin-like Receptors, or KIR. Humans possess from four to 14 KIR receptor genes in their genome, and individual NK cells express a subset of the available KIR genes, generating specialized NK cells that detect alterations in specific HLA proteins. The mechanism of this unusual selective gene activation was recently shown by our group to be controlled by a probabilistic bi-directional promoter switch that turns on a given gene at a pre-determined frequency in the NK cell population. The current study shows that the properties of the switches in terms of the relative activity of forward (on) versus reverse (off) promoter activity is directly correlated with the frequency at which a given gene is expressed within the NK cell population. These results have important implications for our understanding of the role of NK cells in viral resistance and bone marrow transplants.

by Guillaume Cambray, Didier Mazel

Evolutionary processes largely rely on the production of diversity. Genetic robustness, by allowing the accumulation of neutral diversity within a population, has been associated with increase in evolutionary potential (evolvability). In this work, we propose to use a well-known source of robustness, the redundancy of the genetic code, to alter the evolvability of any protein. The topology of the code allows synonymous codons to sample different mutational neighborhoods. Using this property, we developed an algorithm to design synonymous sequences with maximally divergent evolutionary potentials relative to the input sequences. At the population level, each of these sequences expands the scope of the evolutionary landscape that can be explored by the encoded protein, and ultimately increase the odds of uncovering adaptive mutants. We applied this principle to evolve new antibiotic resistance phenotype variants. Fundamentally, our results provide an example of how neutral diversity may favor evolvability. Moreover, in light of the rapid development in nucleic acid synthesis, the use of rationally designed synonymous genes offers a profitable enhancement to any directed evolution procedure.

by Randell T. Libby, Katharine A. Hagerman, Victor V. Pineda, Rachel Lau, Diane H. Cho, Sandy L. Baccam, Michelle M. Axford, John D. Cleary, James M. Moore, Bryce L. Sopher, Stephen J. Tapscott, Galina N. Filippova, Christopher E. Pearson, Albert R. La Spada

The human genome contains many repetitive sequences. In 1991, we discovered that excessive lengthening of a three-nucleotide (trinucleotide) repeat sequence could cause a human genetic disease. We now know that this unique type of genetic mutation, known as a “repeat expansion,” occurs in at least 25 different diseases, including inherited neurological disorders such as the fragile X syndrome of mental retardation, myotonic muscular dystrophy, and Huntington's disease. An interesting feature of repeat expansion mutations is that they are genetically unstable, meaning that the repeat expansion changes in length when transmitted from parent to offspring. Thus, expanded repeats violate one major tenet of genetics—i.e., that any given sequence has a low likelihood for mutation. For expanded repeats, the likelihood of further mutation approaches 100%. Understanding why expanded repeats are so mutable has been a challenging problem for genetics research. In this study, we implicate the CTCF protein in the repeat expansion process by showing that mutation of a CTCF binding site, next to an expanded repeat sequence, increases genetic instability in mice. CTCF is an important regulatory factor that controls the expression of genes. As binding sites for CTCF are associated with many repeat sequences, CTCF may play a role in regulating genetic instability in various repeat diseases—not just the one we studied.

by Kevin V. Morris, Sharon Santoso, Anne-Marie Turner, Chiara Pastori, Peter G. Hawkins

Non-coding RNAs have been shown to modulate transcriptional expression of genes in human cells. This form of gene regulation has been shown to be the result of RNA directing silent state epigenetic changes to the targeted gene promoter. Shortly after this seminal observation, small RNAs targeted to AT-rich regions of gene promoters were shown to modulate gene activation, termed RNA activation. While much is known regarding non-coding RNA-mediated transcriptional gene silencing, the mechanism of RNA activation has remained elusive. Here, we present evidence that RNA activation is the result of deregulation of endogenous bidirectional transcription. The antisense transcript in the bidirectionally transcribed gene is shown here to be operative in directing silent state epigenetic marks to the sense gene promoter. Suppression of the antisense transcript results in gene activation. Overall, these data support the notion that bidirectional transcription is an endogenous mechanism whereby RNA-directed gene regulation is operative and that RNA activation is the result of a disruption of this endogenous pathway. An understanding of this mode of RNA-based regulation will prove exceptionally useful in understanding gene expression as well as potential therapeutic approaches to controlling gene expression in human cells.

by S. Leah Etheridge, Saugata Ray, Shuangding Li, Natasha S. Hamblet, Nardos Lijam, Michael Tsang, Joy Greer, Natalie Kardos, Jianbo Wang, Daniel J. Sussman, Ping Chen, Anthony Wynshaw-Boris

Multi-gene families, comprising a set of very similar genes with shared nucleotide sequences, are common in mammals. Individual family members may be expressed in different places and perform separate functions. Alternatively, the genes may have redundant functions, but distinct dosage requirements. Mammals share three Dishevelled (Dvl) family members and while the roles of Dvl1 and Dvl2 have been described previously, the functions of Dvl3 have remained elusive. Here, we show that the lack of Dvl3 in mice affects the formation of the heart, neural tube, and inner ear. We further show that the defects in these tissues are much more severe when the mice are deficient in more than one Dvl family member, indicating redundant functions for these genes. Congenital heart disease affects approximately 75 in every 1,000 live human births, and approximately 30% of these diseases are due to disruptions in the outflow tract, the region affected in mice lacking Dvl genes. Neural tube defects, similar to those observed in the Dvl mutants, are also common in humans. The animal models described here provide useful tools to elucidate the genetic mechanisms that underlie these abnormalities and may provide novel ways of treating these disorders in the future.

by Khyobeni Mozhui, Daniel C. Ciobanu, Thomas Schikorski, Xusheng Wang, Lu Lu, Robert W. Williams

A major goal of genetics is to understand how variation in DNA sequence gives rise to differences among individuals that influence traits such as disease risk. This is challenging. Most traits are the result of a complex interplay of genetic and environmental factors. One of the first steps in the path from DNA to these complex traits is the production of mRNA molecules. Understanding how sequence differences modulate expression of different RNAs is fundamental to understanding the molecular origins of complex traits. Here, we combine classic gene mapping methods with microarray technology to characterize and quantify RNA levels in different crosses of mice. We focused on a hotspot on chromosome 1 that controls the expression of a large number of different types of RNAs in the brain. This hotspot also controls many disease traits, including anxiety levels, and vulnerability to seizure in mice and humans. We show that this hotspot is made up of several distinct functional regions, one of which has an unusually strong and selective effect on aminoacyl-tRNA synthetases and other genes involved in protein translation.

by Erik C. Madsen, Jonathan D. Gitlin

Copper is an essential nutrient required for multiple biologic functions. Proper uptake, transport, and excretion of copper are critical for use of this metal while reducing its inherent toxicity. While several key proteins involved in this process have been identified, there are still gaps in our understanding of copper metabolism—particularly during early development. We have used zebrafish, a genetically useful animal model system, to study genetic interactions with copper deficiency during development. We treated mutant embryonic zebrafish with a chelator that reduces the level of available copper and screened for mutants that displayed a copper deficient phenotype only in the presence of the chelator. We identified and characterized two mutants that advance our understanding of copper metabolism during the early periods of development, as well as show an interaction between copper metabolism and another fundamental pathway—that of proton transport. Our results expand our knowledge of copper metabolism and illustrate the power of this type of genetic screen in zebrafish to elucidate mechanisms of nutrient metabolism.

by Vijayalakshmi V. Subramanian, Sharon E. Bickel

In humans, chromosome segregation errors during meiosis are the leading cause of birth defects and miscarriages. Moreover, as women age, these errors increase dramatically. For accurate segregation during the first meiotic division, homologous chromosomes must remain physically associated until anaphase I. Normally, attachments along the arms of sister chromatids keep the recombinant homologues together. Human oocytes complete meiotic recombination during fetal development and arrest until ovulation. Therefore, accurate segregation of homologous chromosomes during the first meiotic division requires that recombinant chromosomes remain associated for decades. One hypothesis to explain why segregation errors increase as women age is that the connections between sister chromatids deteriorate over time and allow recombinant homologues to dissociate prematurely. Here, we address this hypothesis using Drosophila as a model system. We find that when Drosophila oocytes undergo experimentally induced aging, recombinant homologues missegregate during meiosis I. Furthermore, the meiotic stage at which Drosophila oocytes are most vulnerable to age-induced errors is analogous to the stage at which human oocytes remain arrested for decades. Together, our data argue that aging does cause premature loss of the connections between meiotic chromosomes and that this is a major determinant of segregation errors in both Drosophila and human oocytes.

by Rafael Romero-Calderón, Guido Uhlenbrock, Jolanta Borycz, Anne F. Simon, Anna Grygoruk, Susan K. Yee, Amy Shyer, Larry C. Ackerson, Nigel T. Maidment, Ian A. Meinertzhagen, Bernhard T. Hovemann, David E. Krantz

Neurons, the cells in the brain responsible for carrying information, communicate with each other using a class of chemicals known as neurotransmitters. One family of neurotransmitters, the monoamines, includes dopamine, serotonin, and histamine, all of which play major physiological roles. However, unlike dopamine and serotonin, the regulation of the brain's histamine content is poorly understood. We are using the fruitfly Drosophila melanogaster to study the storage and release of histamine from brain cells. Both mammals and insects use a class of proteins called transporters to store amines, but, to date, amine transporters have been thought to be restricted to neurons. We have found that the support cells, or glia, that facilitate the function of neurons in the fly's visual system contain a new form of monoamine transporter. Despite its circumscribed distribution, this protein is required to maintain normal levels of histamine throughout the visual system. We speculate that other animals may use a similar strategy to regulate the function of this important neurotransmitter.

by Danika Bannasch, Noa Safra, Amy Young, Nili Karmi, R. S. Schaible, G. V. Ling

Animals excrete waste products in their urine. When most mammals metabolize compounds, called purines, they produce allantoin as one waste product in their urine. Humans, great apes, and Dalmatian dogs produce a different breakdown product, uric acid. This leads to high levels of uric acid in the urine and blood. In humans, this can result in diseases such as kidney stones and gout and may cause hypertension. In Dalmatians, high uric acid levels result in bladder stones that often have to be removed surgically. The cause of high uric acid levels in humans and great apes is not the same as in the Dalmatian dog. Here we report the genetic cause of the Dalmatian condition. This change is shared by dogs from unrelated breeds, indicating that it predates the separation of dog breeds. The gene that causes excretion of uric acid in Dalmatians is important for controlling the amount of uric acid in human blood and is therefore important for human diseases. It is not clear why humans and great apes have evolved to excrete uric acid, but it appears that some dogs have developed a different mechanism that leads to the same result: elevations in urine and blood uric acid levels.

by Leonid Teytelman, Michael B. Eisen, Jasper Rine

Many plants, fungi, pathogens, and animals have chromosome regions that are silenced. Special proteins change the chromosome structure in these domains, turning genes off or lowering their expression levels. We found an increased frequency of DNA mutations in these silenced regions of closely related yeasts. This increase is likely due to silencing proteins interfering with DNA repair or replication. Accurate replication of genetic information with minimal mutations is usually critical for the survival and fitness of an organism; however, there are examples where a high mutation rate is beneficial. The silenced regions of chromosomes are often associated with virus-like transposable elements, and with genes that are important in responding to environmental changes. Hence, it is possible that elevated DNA mutations in silenced regions contribute to genome defense against transposable elements or increased genetic diversity to cope with variation in surrounding conditions.

by Yehudit Hasin, Tsviya Olender, Miriam Khen, Claudia Gonzaga-Jauregui, Philip M. Kim, Alexander Eckehart Urban, Michael Snyder, Mark B. Gerstein, Doron Lancet, Jan O. Korbel

Copy-number variants (CNVs) are deletions and duplications of DNA segments, responsible for most of the genome variation in mammals. To help elucidate the impact of CNVs on evolution and function, we provide a high-resolution CNV map of the largest gene superfamily in humans, i.e., the olfactory receptor (OR) gene superfamily. Our map reveals twice as many olfactory CNVs per person than previously reported, indicating considerable OR dosage variations in humans. In particular, our findings indicate that CNVs are specifically enriched among evolutionary “young” ORs, some of which originated following the human-chimpanzee split, implying that CNVs may play an important role in the gene-birth and gene-loss processes that continuously shape the human OR repertoire. Furthermore, we describe 15 OR gene loci showing frequent human-specific deletion alleles. Additionally, we present evidence for a recent non-allelic homologous recombination event involving a pair of OR genes, forming a novel fusion OR that may harbor novel odorant-binding properties. Such events may potentially relate to individual functional “holes” in the human smell-detection repertoire, and future studies will address the specific chemosensory impact of our genomic variation map.

by Tobias Warnecke, Nizar N. Batada, Laurence D. Hurst

Why do some parts of genes evolve slower than others? How can we account for the amino acid make-up of different parts of a protein? Answers to these questions are usually framed by reference to what the protein does and how it does it. This framework is, however, naïve. We now know that selection can act also on mRNA, for example, to ensure introns are removed properly. Here, we provide the first evidence that the way DNA works also affects gene and protein evolution. In living cells, most DNA wraps around histone protein structures to form nucleosomes, the basic building blocks of chromatin. Protein-coding sequence is no exception. Looking at genes in baker's yeast, we find that sequence between nucleosomes, linker sequence, is slow evolving. Both mutations that change the gene but not the protein and those that change gene and protein are affected. We argue that selection for correct nucleosome positioning, rather than differences in mutational processes, can explain this observation. Linker also exhibits distinct patterns of codon and amino acid usage, which reflect that DNA of linker needs to be rigid to prevent nucleosome formation. These results show that the way DNA works impacts on how genes evolve.

by Agostinho Antunes, Jennifer L. Troyer, Melody E. Roelke, Jill Pecon-Slattery, Craig Packer, Christiaan Winterbach, Hanlie Winterbach, Graham Hemson, Laurence Frank, Philip Stander, Ludwig Siefert, Margaret Driciru, Paul J. Funston, Kathy A. Alexander, Katherine C. Prager, Gus Mills, David Wildt, Mitch Bush, Stephen J. O'Brien, Warren E. Johnson

The lion Panthera leo, a formidable carnivore with a complex cooperative social system, has fascinated humanity since pre-historical times, inspiring hundreds of religious and cultural allusions. Here, we use a comprehensive sample of 357 individuals from most of the major lion populations in Africa and Asia. We assayed appropriately informative autosomal, Y-chromosome, and mitochondrial genetic markers, and assessed the prevalence and genetic variation of the lion-specific feline immunodeficiency virus (FIVPle), a lentivirus analogous to human immunodeficiency virus (HIV) that causes AIDS-like immunodeficiency disease in domestic cats. We compare the large multigenic dataset from lions with patterns of genetic variation of the FIVPle to characterize the population-genomic legacy of lions. We refute the hypothesis that African lions consist of a single panmictic population, highlighting the importance of preserving populations in decline rather than prioritizing larger-scale conservation efforts. Interestingly, lion and FIVPle variation revealed evidence of unsuspected genetic diversity even in the well-studied lion population of the Serengeti Ecosystem, which consists of recently admixed animals derived from three distinct genetic groups.

by Lucas Kempf, Kristin K. Nicodemus, Bhaskar Kolachana, Radhakrishna Vakkalanka, Beth A. Verchinski, Michael F. Egan, Richard E. Straub, Venkata A. Mattay, Joseph H. Callicott, Daniel R. Weinberger, Andreas Meyer-Lindenberg

Schizophrenia is a major mental illness affecting 1% of the population. It is known that genetics plays a role in the disease susceptibility, and it is thought that the illness is a complex disorder involving multiple genes. We show that the schizophrenia susceptibility gene, PRODH, conveys its risk through a variation that increases its enzyme activity. We further show that protection is associated with variations that decrease enzyme activity and these protective variations are enriched in their unaffected siblings. We then used brain imaging of structure and memory function to dissect the risk and protective haplotypes differential effects, and found that the schizophrenia risk haplotype was associated with decreased striatal gray matter volume and increased subcortical to frontal lobe functional connectivity, while the schizophrenia protective haplotype was associated with trend-level increase of frontal lobe volume and decreased subcortical to frontal lobe connectivity. These findings indicate a new target for treating schizophrenia and characterize associated structural and functional deficits.