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Kalbfleisch TS, Hussien AbouEl Ela NA, Li K, Brashear WA, Kochan KJ, Hillhouse AE, Zhu Y, Dhande IS, Kline EJ, Hudson EA, Murphy TD, Thibaud-Nissen F, Smith ML, Doris PA. The Assembled Genome of the Stroke-Prone Spontaneously Hypertensive Rat. Hypertension 2023; 80:138-146. [PMID: 36330812 PMCID: PMC9814308 DOI: 10.1161/hypertensionaha.122.20140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 10/18/2022] [Indexed: 11/06/2022]
Abstract
BACKGROUND We report the creation and evaluation of a de novo assembly of the genome of the spontaneously hypertensive rat, the most widely used model of human cardiovascular disease. METHODS The genome is assembled from long read sequencing (PacBio HiFi and continuous long read data [CLR]) and scaffolded with long-range structural information obtained from Bionano optical maps and proximity ligation sequencing proximity analysis of the genome. The genome assembly was polished with Illumina short reads. Completeness of the assembly was investigated using Benchmarking Universal Single Copy Orthologs analysis. The genome assembly was also evaluated with the rat reference gene set, using NCBI automated protocols. We also generated orthogonal single molecule transcript sequence reads (Iso-Seq) from 8 tissues and used them to validate the coding assembly, to annotate the assembly with RNA transcripts representing unique full length transcript isoforms for each gene and to determine whether divergences between RefSeq sequences and the assembly were attributable to assembly errors or polymorphisms. RESULTS The assembly analysis indicates that this assembly is comparable in contiguity and completeness to the current rat reference assembly, while the use of HiFi sequencing yields an assembly that is more correct at the single base level. Synteny analysis was performed to uncover the extent of synteny and the presence and distribution of chromosomal rearrangements between the reference and this assembly. CONCLUSION The resulting genome assembly is reference quality and captures significant structural variation.
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Affiliation(s)
- Theodore S Kalbfleisch
- Department of Veterinary Science, College of Agriculture, Food, and Environment, University of Kentucky, Lexington, KY (T.S.K., N.A.H., K.L.)
| | - Nahla A Hussien AbouEl Ela
- Department of Veterinary Science, College of Agriculture, Food, and Environment, University of Kentucky, Lexington, KY (T.S.K., N.A.H., K.L.)
| | - Kai Li
- Department of Veterinary Science, College of Agriculture, Food, and Environment, University of Kentucky, Lexington, KY (T.S.K., N.A.H., K.L.)
| | - Wesley A Brashear
- Texas A&M Institute for Genome Sciences and Society, Texas A&M University, College Station, TX (W.A.B., K.J.K., A.E.H.)
| | - Kelli J Kochan
- Texas A&M Institute for Genome Sciences and Society, Texas A&M University, College Station, TX (W.A.B., K.J.K., A.E.H.)
| | - Andrew E Hillhouse
- Texas A&M Institute for Genome Sciences and Society, Texas A&M University, College Station, TX (W.A.B., K.J.K., A.E.H.)
| | - Yaming Zhu
- Center for Human Genetics, Brown Foundation Institute of Molecular Medicine, University of Texas McGovern School of Medicine, Houston, TX (Y.Z., I.S.D., P.A.D.)
| | - Isha S Dhande
- Center for Human Genetics, Brown Foundation Institute of Molecular Medicine, University of Texas McGovern School of Medicine, Houston, TX (Y.Z., I.S.D., P.A.D.)
| | - Eric J Kline
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY (E.J.K., E.A.H, M.L.S.)
| | - Elizabeth A Hudson
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY (E.J.K., E.A.H, M.L.S.)
| | - Terence D Murphy
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD (T.D.M., F.T.-N.)
| | - Françoise Thibaud-Nissen
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD (T.D.M., F.T.-N.)
| | - Melissa L Smith
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY (E.J.K., E.A.H, M.L.S.)
| | - Peter A Doris
- Center for Human Genetics, Brown Foundation Institute of Molecular Medicine, University of Texas McGovern School of Medicine, Houston, TX (Y.Z., I.S.D., P.A.D.)
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Munro D, Wang T, Chitre AS, Polesskaya O, Ehsan N, Gao J, Gusev A, Woods LS, Saba L, Chen H, Palmer A, Mohammadi P. The regulatory landscape of multiple brain regions in outbred heterogeneous stock rats. Nucleic Acids Res 2022; 50:10882-10895. [PMID: 36263809 PMCID: PMC9638908 DOI: 10.1093/nar/gkac912] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 08/17/2022] [Accepted: 10/05/2022] [Indexed: 11/14/2022] Open
Abstract
Heterogeneous Stock (HS) rats are a genetically diverse outbred rat population that is widely used for studying genetics of behavioral and physiological traits. Mapping Quantitative Trait Loci (QTL) associated with transcriptional changes would help to identify mechanisms underlying these traits. We generated genotype and transcriptome data for five brain regions from 88 HS rats. We identified 21 392 cis-QTLs associated with expression and splicing changes across all five brain regions and validated their effects using allele specific expression data. We identified 80 cases where eQTLs were colocalized with genome-wide association study (GWAS) results from nine physiological traits. Comparing our dataset to human data from the Genotype-Tissue Expression (GTEx) project, we found that the HS rat data yields twice as many significant eQTLs as a similarly sized human dataset. We also identified a modest but highly significant correlation between genetic regulatory variation among orthologous genes. Surprisingly, we found less genetic variation in gene regulation in HS rats relative to humans, though we still found eQTLs for the orthologs of many human genes for which eQTLs had not been found. These data are available from the RatGTEx data portal (RatGTEx.org) and will enable new discoveries of the genetic influences of complex traits.
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Affiliation(s)
- Daniel Munro
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA,Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA, USA
| | - Tengfei Wang
- Department of Pharmacology, Addiction Science and Toxicology, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Apurva S Chitre
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Oksana Polesskaya
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Nava Ehsan
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA, USA
| | - Jianjun Gao
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Alexander Gusev
- Division of Population Sciences, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Leah C Solberg Woods
- Section of Molecular Medicine, Department of Internal Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Laura M Saba
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Hao Chen
- Department of Pharmacology, Addiction Science and Toxicology, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Abraham A Palmer
- Correspondence may also be addressed to Abraham A. Palmer. Tel: +1 858 534 2093;
| | - Pejman Mohammadi
- To whom correspondence should be addressed. Tel: +1 858 784 8746;
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Huang YF, Bertrand Y, Guiraud JL, Vialet S, Launay A, Cheynier V, Terrier N, This P. Expression QTL mapping in grapevine--revisiting the genetic determinism of grape skin colour. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2013; 207:18-24. [PMID: 23602095 DOI: 10.1016/j.plantsci.2013.02.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Revised: 02/19/2013] [Accepted: 02/21/2013] [Indexed: 05/20/2023]
Abstract
Expression quantitative locus (eQTL) mapping was proposed as a valuable approach to dissect the genetic basis of transcript variation, one of the prime causes of natural phenotypic variation. Few eQTL studies have been performed on woody species due to the difficulty in sample homogenisation. Based on previous knowledge on berry colour formation, we performed eQTL mapping in field experimentation of grapevine with appropriate sampling criteria. The transcript level of VvUFGT, a key enzyme for anthocyanin synthesis was measured by real-time qRT-PCR in grape berry on a 191-individual pseudo-F1 progeny, derived from a cross between Syrah and Grenache cultivars. Two eQTLs were identified: one, explaining 20%, of genotypic variance and co-locating with VvUFGT itself (cis-eQTL), was principally due to the contrast between Grenache alleles; the other, explaining 35% of genotypic variance, was a trans-eQTL due to Syrah allelic contrast and co-located with VvMYBAs, transcription factors known to activate the expression of VvUFGT. This study assessed and validated the feasibility of eQTL mapping approach in grapevine and offered insights and new hypotheses on grape skin colour formation.
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Affiliation(s)
- Yung-Fen Huang
- INRA, UMR AGAP Amélioration Génétique et Adaptation des Plantes, 2 Place Viala, F-34060 Montpellier, France.
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Zhuang Y, Gala A, Yen Y. Identification of functional genic components of major fusarium head blight resistance quantitative trait loci in wheat cultivar Sumai 3. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2013; 26:442-50. [PMID: 23234406 DOI: 10.1094/mpmi-10-12-0235-r] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Fusarium head blight (FHB) is a devastating disease worldwide, affecting wheat and other small grains. To identify key wheat genes involved in FHB pathogenesis, 406 FHB-related wheat expressed sequence tags functionally identified in Sumai 3 were investigated for their association with FHB-resistance quantitative trait loci (QTL) Fhb1 and Fhb_6BL in 2010 and 2011. A total of 47 candidate genes were identified by bulk analysis, near-isogenic screening and expression QTL mapping, and were finally mapped to their carrier chromosomes with Chinese Spring nulli-tetra deficiency lines. One gene, designated WFhb1_c1 (wheat Fhb1 candidate gene 1), was both functionally associated with and physically located within Fhb1 and was found to be weakly similar (E = 5e+0) to an Arabidopsis gene encoding pectin methyl esterase inhibitor. Two other genes, designated WFI_6BL1 and WFI_6BL2 (wheat-Fusarium interaction genes 6BL1 and 6BL2), were functionally associated with Fhb_6BL but physically mapped on chromosomes 7D and 5A, respectively. WFI_6BL1 was annotated as a 13- lipoxygenase gene and WFI_6BL2 might encode a PR-4-like protein. Our data suggested that i) Fhb1 seems to contribute to FHB resistance by reducing susceptibility in the first 60 h, ii) Fhb_6BL makes its contribution via the jasmonate-mediated pathways, and iii) wheat seems to activate its defense mechanism in the biotrophic phase of FHB pathogenesis.
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Affiliation(s)
- Yongbin Zhuang
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, USA
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Kompass KS, Hoffmann TJ, Witte JS. Parallel biocomputing. SOURCE CODE FOR BIOLOGY AND MEDICINE 2011; 6:4. [PMID: 21418580 PMCID: PMC3068083 DOI: 10.1186/1751-0473-6-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/23/2010] [Accepted: 03/18/2011] [Indexed: 11/10/2022]
Abstract
Background With the advent of high throughput genomics and high-resolution imaging techniques, there is a growing necessity in biology and medicine for parallel computing, and with the low cost of computing, it is now cost-effective for even small labs or individuals to build their own personal computation cluster. Methods Here we briefly describe how to use commodity hardware to build a low-cost, high-performance compute cluster, and provide an in-depth example and sample code for parallel execution of R jobs using MOSIX, a mature extension of the Linux kernel for parallel computing. A similar process can be used with other cluster platform software. Results As a statistical genetics example, we use our cluster to run a simulated eQTL experiment. Because eQTL is computationally intensive, and is conceptually easy to parallelize, like many statistics/genetics applications, parallel execution with MOSIX gives a linear speedup in analysis time with little additional effort. Conclusions We have used MOSIX to run a wide variety of software programs in parallel with good results. The limitations and benefits of using MOSIX are discussed and compared to other platforms.
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Good JM, Vanderpool D, Smith KL, Nachman MW. Extraordinary sequence divergence at Tsga8, an X-linked gene involved in mouse spermiogenesis. Mol Biol Evol 2010; 28:1675-86. [PMID: 21186189 DOI: 10.1093/molbev/msq348] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The X chromosome plays an important role in both adaptive evolution and speciation. We used a molecular evolutionary screen of X-linked genes potentially involved in reproductive isolation in mice to identify putative targets of recurrent positive selection. We then sequenced five very rapidly evolving genes within and between several closely related species of mice in the genus Mus. All five genes were involved in male reproduction and four of the genes showed evidence of recurrent positive selection. The most remarkable evolutionary patterns were found at Testis-specific gene a8 (Tsga8), a spermatogenesis-specific gene expressed during postmeiotic chromatin condensation and nuclear transformation. Tsga8 was characterized by extremely high levels of insertion-deletion variation of an alanine-rich repetitive motif in natural populations of Mus domesticus and M. musculus, differing in length from the reference mouse genome by up to 89 amino acids (27% of the total protein length). This population-level variation was coupled with striking divergence in protein sequence and length between closely related mouse species. Although no clear orthologs had previously been described for Tsga8 in other mammalian species, we have identified a highly divergent hypothetical gene on the rat X chromosome that shares clear orthology with the 5' and 3' ends of Tsga8. Further inspection of this ortholog verified that it is expressed in rat testis and shares remarkable similarity with mouse Tsga8 across several general features of the protein sequence despite no conservation of nucleotide sequence across over 60% of the rat-coding domain. Overall, Tsga8 appears to be one of the most rapidly evolving genes to have been described in rodents. We discuss the potential evolutionary causes and functional implications of this extraordinary divergence and the possible contribution of Tsga8 and the other four genes we examined to reproductive isolation in mice.
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Affiliation(s)
- Jeffrey M Good
- Department of Ecology and Evolutionary Biology, University of Arizona, AZ, USA.
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Systems genetics, bioinformatics and eQTL mapping. Genetica 2010; 138:915-24. [DOI: 10.1007/s10709-010-9480-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2010] [Accepted: 07/30/2010] [Indexed: 12/15/2022]
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8
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Colak D, Chishti MA, Al-Bakheet AB, Al-Qahtani A, Shoukri MM, Goyns MH, Ozand PT, Quackenbush J, Park BH, Kaya N. Integrative and comparative genomics analysis of early hepatocellular carcinoma differentiated from liver regeneration in young and old. Mol Cancer 2010; 9:146. [PMID: 20540791 PMCID: PMC2898705 DOI: 10.1186/1476-4598-9-146] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2009] [Accepted: 06/12/2010] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is the third-leading cause of cancer-related deaths worldwide. It is often diagnosed at an advanced stage, and hence typically has a poor prognosis. To identify distinct molecular mechanisms for early HCC we developed a rat model of liver regeneration post-hepatectomy, as well as liver cells undergoing malignant transformation and compared them to normal liver using a microarray approach. Subsequently, we performed cross-species comparative analysis coupled with copy number alterations (CNA) of independent early human HCC microarray studies to facilitate the identification of critical regulatory modules conserved across species. RESULTS We identified 35 signature genes conserved across species, and shared among different types of early human HCCs. Over 70% of signature genes were cancer-related, and more than 50% of the conserved genes were mapped to human genomic CNA regions. Functional annotation revealed genes already implicated in HCC, as well as novel genes which were not previously reported in liver tumors. A subset of differentially expressed genes was validated using quantitative RT-PCR. Concordance was also confirmed for a significant number of genes and pathways in five independent validation microarray datasets. Our results indicated alterations in a number of cancer related pathways, including p53, p38 MAPK, ERK/MAPK, PI3K/AKT, and TGF-beta signaling pathways, and potential critical regulatory role of MYC, ERBB2, HNF4A, and SMAD3 for early HCC transformation. CONCLUSIONS The integrative analysis of transcriptional deregulation, genomic CNA and comparative cross species analysis brings new insights into the molecular profile of early hepatoma formation. This approach may lead to robust biomarkers for the detection of early human HCC.
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Affiliation(s)
- Dilek Colak
- Department of Biostatistics, Epidemiology and Scientific Computing, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia.
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Dietary fat-dependent transcriptional architecture and copy number alterations associated with modifiers of mammary cancer metastasis. Clin Exp Metastasis 2010; 27:279-93. [PMID: 20354763 DOI: 10.1007/s10585-010-9326-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2010] [Accepted: 03/17/2010] [Indexed: 01/01/2023]
Abstract
Breast cancer is a complex disease resulting from a combination of genetic and environmental factors. Among environmental factors, body composition and intake of specific dietary components like total fat are associated with increased incidence of breast cancer and metastasis. We previously showed that mice fed a high-fat diet have shorter mammary cancer latency, increased tumor growth and more pulmonary metastases than mice fed a standard diet. Subsequent genetic analysis identified several modifiers of metastatic mammary cancer along with widespread interactions between cancer modifiers and dietary fat. To elucidate diet-dependent genetic modifiers of mammary cancer and metastasis risk, global gene expression profiles and copy number alterations from mammary cancers were measured and expression quantitative trait loci (eQTL) identified. Functional candidate genes that colocalized with previously detected metastasis modifiers were identified. Additional analyses, such as eQTL by dietary fat interaction analysis, causality and database evaluations, helped to further refine the candidate loci to produce an enriched list of genes potentially involved in the pathogenesis of metastatic mammary cancer.
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Druka A, Potokina E, Luo Z, Jiang N, Chen X, Kearsey M, Waugh R. Expression quantitative trait loci analysis in plants. PLANT BIOTECHNOLOGY JOURNAL 2010; 8:10-27. [PMID: 20055957 DOI: 10.1111/j.1467-7652.2009.00460.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
An expression Quantitative Trait Locus or eQTL is a chromosomal region that accounts for a proportion of the variation in abundance of a mRNA transcript observed between individuals in a genetic mapping population. A single gene can have one or multiple eQTLs. Large scale mRNA profiling technologies advanced genome-wide eQTL mapping in a diverse range of organisms allowing thousands of eQTLs to be detected in a single experiment. When combined with classical or trait QTLs, correlation analyses can directly suggest candidates for genes underlying these traits. Furthermore, eQTL mapping data enables genetic regulatory networks to be modelled and potentially provide a better understanding of the underlying phenotypic variation. The mRNA profiling data sets can also be used to infer the chromosomal positions of thousands of genes, an outcome that is particularly valuable for species with unsequenced genomes where the chromosomal location of the majority of genes remains unknown. In this review we focus on eQTL studies in plants, addressing conceptual and technical aspects that include experimental design, genetic polymorphism prediction and candidate gene identification.
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Affiliation(s)
- Arnis Druka
- Genetics, Scottish Crop Research Institute, Invergowrie, Dundee, UK
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Serikawa T, Mashimo T, Takizawa A, Okajima R, Maedomari N, Kumafuji K, Tagami F, Neoda Y, Otsuki M, Nakanishi S, Yamasaki KI, Voigt B, Kuramoto T. National BioResource Project-Rat and related activities. Exp Anim 2009; 58:333-41. [PMID: 19654430 DOI: 10.1538/expanim.58.333] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
In order to establish a system to facilitate the systematic collection, preservation, and provision of laboratory rats (Rattus norvegicus) and their derivates, the National BioResource Project-Rat (NBRP-Rat) was launched in July 2002. By the end of 2008, more than 500 rat strains had been collected and preserved as live animals, embryos, or sperm. These rat resources are supplied to biomedical scientists in Japan as well as in other countries. This review article introduces NBRP-Rat and highlights the phenome project, recombinant inbred strains, BAC clone libraries, and the ENU-mutant archive, named the Kyoto University Rat Mutant Archive (KURMA). The future direction of rat resources are also discussed.
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Affiliation(s)
- Tadao Serikawa
- Institute of Laboratory Animals, Graduate School of Medicine, Kyoto University
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12
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Le Mignon G, Désert C, Pitel F, Leroux S, Demeure O, Guernec G, Abasht B, Douaire M, Le Roy P, Lagarrigue S. Using transcriptome profiling to characterize QTL regions on chicken chromosome 5. BMC Genomics 2009; 10:575. [PMID: 19954542 PMCID: PMC2792231 DOI: 10.1186/1471-2164-10-575] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2009] [Accepted: 12/02/2009] [Indexed: 11/18/2022] Open
Abstract
Background Although many QTL for various traits have been mapped in livestock, location confidence intervals remain wide that makes difficult the identification of causative mutations. The aim of this study was to test the contribution of microarray data to QTL detection in livestock species. Three different but complementary approaches are proposed to improve characterization of a chicken QTL region for abdominal fatness (AF) previously detected on chromosome 5 (GGA5). Results Hepatic transcriptome profiles for 45 offspring of a sire known to be heterozygous for the distal GGA5 AF QTL were obtained using a 20 K chicken oligochip. mRNA levels of 660 genes were correlated with the AF trait. The first approach was to dissect the AF phenotype by identifying animal subgroups according to their 660 transcript profiles. Linkage analysis using some of these subgroups revealed another QTL in the middle of GGA5 and increased the significance of the distal GGA5 AF QTL, thereby refining its localization. The second approach targeted the genes correlated with the AF trait and regulated by the GGA5 AF QTL region. Five of the 660 genes were considered as being controlled either by the AF QTL mutation itself or by a mutation close to it; one having a function related to lipid metabolism (HMGCS1). In addition, a QTL analysis with a multiple trait model combining this 5 gene-set and AF allowed us to refine the QTL region. The third approach was to use these 5 transcriptome profiles to predict the paternal Q versus q AF QTL mutation for each recombinant offspring and then refine the localization of the QTL from 31 cM (100 genes) at a most probable location confidence interval of 7 cM (12 genes) after determining the recombination breakpoints, an interval consistent with the reductions obtained by the two other approaches. Conclusion The results showed the feasibility and efficacy of the three strategies used, the first revealing a QTL undetected using the whole population, the second providing functional information about a QTL region through genes related to the trait and controlled by this region (HMGCS1), the third could drastically refine a QTL region.
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Manderson EN, Birch AH, Shen Z, Mes-Masson AM, Provencher D, Tonin PN. Molecular Genetic Analysis of a Cell Adhesion Molecule With Homology to L1CAM, Contactin 6, and Contactin 4 Candidate Chromosome 3p26pter Tumor Suppressor Genes in Ovarian Cancer. Int J Gynecol Cancer 2009; 19:513-25. [DOI: 10.1111/igc.0b013e3181a3cd38] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
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Potokina E, Druka A, Kearsey MJ. Transcript profiling and expression level mapping. Methods Mol Biol 2009; 513:81-92. [PMID: 19347647 DOI: 10.1007/978-1-59745-427-8_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Transcript abundance data from cRNA hybridizations to Affymetrix microarrays can potentially be used to identify genetic markers to facilitate high-throughput genotyping. We have shown that it is easily possible to use the information from Affymetrix expression arrays to accurately identify over 4,000 robust polymorphic transcript-derived markers (TDMs). We developed the method to identity TDM polymorphisms from experiments involving two tissues in two commercial varieties of barley and their doubled-haploid progeny. These TDMs represent ~18% of the total barley genes on the chip and can be used to predict the genotypes in an F(1)-derived, doubled-haploid population. According to our estimates, 35% of the TDMs reveal nucleotide polymorphism of the particular gene (single feature polymorphisms, SFPs) while 65% mark polymorphism resulting in extreme variation of gene expression (genetic expression markers, GEMs). These latter are probably mainly cis-acting regulators while a small proportion, approximately 5%, are loosely or un-linked transregulators.
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Affiliation(s)
- Elena Potokina
- School of Biosciences, University of Birmingham, Birmingham, UK
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Fujita A, Gomes LR, Sato JR, Yamaguchi R, Thomaz CE, Sogayar MC, Miyano S. Multivariate gene expression analysis reveals functional connectivity changes between normal/tumoral prostates. BMC SYSTEMS BIOLOGY 2008; 2:106. [PMID: 19055846 PMCID: PMC2628381 DOI: 10.1186/1752-0509-2-106] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2008] [Accepted: 12/05/2008] [Indexed: 11/10/2022]
Abstract
BACKGROUND Prostate cancer is a leading cause of death in the male population, therefore, a comprehensive study about the genes and the molecular networks involved in the tumoral prostate process becomes necessary. In order to understand the biological process behind potential biomarkers, we have analyzed a set of 57 cDNA microarrays containing approximately 25,000 genes. RESULTS Principal Component Analysis (PCA) combined with the Maximum-entropy Linear Discriminant Analysis (MLDA) were applied in order to identify genes with the most discriminative information between normal and tumoral prostatic tissues. Data analysis was carried out using three different approaches, namely: (i) differences in gene expression levels between normal and tumoral conditions from an univariate point of view; (ii) in a multivariate fashion using MLDA; and (iii) with a dependence network approach. Our results show that malignant transformation in the prostatic tissue is more related to functional connectivity changes in their dependence networks than to differential gene expression. The MYLK, KLK2, KLK3, HAN11, LTF, CSRP1 and TGM4 genes presented significant changes in their functional connectivity between normal and tumoral conditions and were also classified as the top seven most informative genes for the prostate cancer genesis process by our discriminant analysis. Moreover, among the identified genes we found classically known biomarkers and genes which are closely related to tumoral prostate, such as KLK3 and KLK2 and several other potential ones. CONCLUSION We have demonstrated that changes in functional connectivity may be implicit in the biological process which renders some genes more informative to discriminate between normal and tumoral conditions. Using the proposed method, namely, MLDA, in order to analyze the multivariate characteristic of genes, it was possible to capture the changes in dependence networks which are related to cell transformation.
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Affiliation(s)
- André Fujita
- Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Luciana Rodrigues Gomes
- Chemistry Institute, University of São Paulo, Av. Lineu Prestes, 748, São Paulo-SP, 05508-900, Brazil
| | - João Ricardo Sato
- Mathematics, Computation and Cognition Center, Universidade Federal do ABC, Rua Santa Adélia, 166 – Santo André, 09210-170, Brazil
| | - Rui Yamaguchi
- Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Carlos Eduardo Thomaz
- Department of Electrical Engineering, Centro Universitário da FEI, Av. Humberto de Alencar Castelo Branco, 3972 – São Bernardo do Campo, 09850-901, Brazil
| | - Mari Cleide Sogayar
- Chemistry Institute, University of São Paulo, Av. Lineu Prestes, 748, São Paulo-SP, 05508-900, Brazil
| | - Satoru Miyano
- Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
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16
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Potokina E, Druka A, Luo Z, Moscou M, Wise R, Waugh R, Kearsey M. Tissue-dependent limited pleiotropy affects gene expression in barley. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2008; 56:287-296. [PMID: 18643973 DOI: 10.1111/j.1365-313x.2008.03601.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Non-synonymous coding mutations in a gene change the resulting protein, no matter where it is expressed, but the effects of cis-regulatory mutations could be spatially or temporally limited - a phenomenon termed limited pleiotropy. Here, we report the genome-wide occurrence of limited pleiotropy of cis-regulatory mutations in barley (Hordeum vulgare L.) using Affymetrix analysis of 22,840 genes in a population of 139 doubled haploid lines derived from a cross between the cultivars Steptoe (St) and Morex (Mx). We identified robust cis-acting expression regulators that segregate as major genes in two successive ontogenetic stages: germinating embryo tissues and seedling leaves from the embryonic axis. We show that these polymorphisms may be consistent in both tissues or may cause a dramatic change in transcript abundance in one tissue but not in another. We also show that the parental allele that increases expression can vary with the tissue, suggesting nucleotide polymorphism in enhancer sequences. Because of the limited pleiotropy of cis-regulating mutations, the number of cis expression quantitative trait loci (cis-eQTLs) discovered by 'genetical genomics' is strongly affected by the particular tissue or developmental stage studied. Given that limited pleiotropy is a common feature of cis-regulatory mutations in barley, we predict that the phenomenon would be relevant to developmental and/or tissue-specific interactions across wide taxonomic boundaries in both plants and animals.
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Affiliation(s)
- Elena Potokina
- School of Biosciences, The University of Birmingham, Birmingham B15 2TT, UK,Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, UK,Laboratory of Population & Quantitative Genetics, School of Life Sciences, Institute of Biomedical Sciences, Fudan University, Shanghai 200433, China,Bioinformatics and Computational Biology Graduate Program & Department of Plant Pathology, Iowa State University, Ames, IA 50011-1020, USA, andCorn Insects and Crop Genetics Research, USDA-ARS, Iowa State University, Ames, IA 50011-1020, USA
| | - Arnis Druka
- School of Biosciences, The University of Birmingham, Birmingham B15 2TT, UK,Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, UK,Laboratory of Population & Quantitative Genetics, School of Life Sciences, Institute of Biomedical Sciences, Fudan University, Shanghai 200433, China,Bioinformatics and Computational Biology Graduate Program & Department of Plant Pathology, Iowa State University, Ames, IA 50011-1020, USA, andCorn Insects and Crop Genetics Research, USDA-ARS, Iowa State University, Ames, IA 50011-1020, USA
| | - Zewei Luo
- School of Biosciences, The University of Birmingham, Birmingham B15 2TT, UK,Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, UK,Laboratory of Population & Quantitative Genetics, School of Life Sciences, Institute of Biomedical Sciences, Fudan University, Shanghai 200433, China,Bioinformatics and Computational Biology Graduate Program & Department of Plant Pathology, Iowa State University, Ames, IA 50011-1020, USA, andCorn Insects and Crop Genetics Research, USDA-ARS, Iowa State University, Ames, IA 50011-1020, USA
| | - Matthew Moscou
- School of Biosciences, The University of Birmingham, Birmingham B15 2TT, UK,Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, UK,Laboratory of Population & Quantitative Genetics, School of Life Sciences, Institute of Biomedical Sciences, Fudan University, Shanghai 200433, China,Bioinformatics and Computational Biology Graduate Program & Department of Plant Pathology, Iowa State University, Ames, IA 50011-1020, USA, andCorn Insects and Crop Genetics Research, USDA-ARS, Iowa State University, Ames, IA 50011-1020, USA
| | - Roger Wise
- School of Biosciences, The University of Birmingham, Birmingham B15 2TT, UK,Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, UK,Laboratory of Population & Quantitative Genetics, School of Life Sciences, Institute of Biomedical Sciences, Fudan University, Shanghai 200433, China,Bioinformatics and Computational Biology Graduate Program & Department of Plant Pathology, Iowa State University, Ames, IA 50011-1020, USA, andCorn Insects and Crop Genetics Research, USDA-ARS, Iowa State University, Ames, IA 50011-1020, USA
| | - Robbie Waugh
- School of Biosciences, The University of Birmingham, Birmingham B15 2TT, UK,Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, UK,Laboratory of Population & Quantitative Genetics, School of Life Sciences, Institute of Biomedical Sciences, Fudan University, Shanghai 200433, China,Bioinformatics and Computational Biology Graduate Program & Department of Plant Pathology, Iowa State University, Ames, IA 50011-1020, USA, andCorn Insects and Crop Genetics Research, USDA-ARS, Iowa State University, Ames, IA 50011-1020, USA
| | - Mike Kearsey
- School of Biosciences, The University of Birmingham, Birmingham B15 2TT, UK,Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, UK,Laboratory of Population & Quantitative Genetics, School of Life Sciences, Institute of Biomedical Sciences, Fudan University, Shanghai 200433, China,Bioinformatics and Computational Biology Graduate Program & Department of Plant Pathology, Iowa State University, Ames, IA 50011-1020, USA, andCorn Insects and Crop Genetics Research, USDA-ARS, Iowa State University, Ames, IA 50011-1020, USA
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17
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Liu G, Peng HR, Ni ZF, Qin DD, Song FW, Song GS, Sun QX. [Integrating genetic and gene expression data: methods and applications of eQTL mapping]. YI CHUAN = HEREDITAS 2008; 30:1228-1236. [PMID: 18779184 DOI: 10.3724/sp.j.1005.2008.01228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The availability of high-throughput genotyping technologies and microarray assays has allowed researchers to investigate genetic variations that influence levels of gene expression. Expression Quantitative Trait Locus (eQTL) mapping methods have been used to identify the genetic basis of gene expression. Similar to traditional QTL studies, the main goal of eQTL is to identify the genomic locations to which the expression traits are linked. Although microarrays provide the expression data of thousands of transcripts, standard QTL mapping methods, which are able to handle at most tens of traits, cannot be applied directly. As a result, it is necessary to consider the statistical principles involved in the design and analysis of these experiments. In this paper, we reviewed individual selection, experimental design of microarray, normalization of gene expression data, mapping methods, and explaining of results and proposed potential methodological problems for such analyses. Finally, we discussed the applications of this integrative genomic approach to estimate heritability of transcripts, identify candidate genes, construct gene networks, and understand interactions between genes, genes and environments.
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Affiliation(s)
- Gang Liu
- Department of Plant Genetics & Breeding and State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing 100193, China
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18
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Ponsuksili S, Jonas E, Murani E, Phatsara C, Srikanchai T, Walz C, Schwerin M, Schellander K, Wimmers K. Trait correlated expression combined with expression QTL analysis reveals biological pathways and candidate genes affecting water holding capacity of muscle. BMC Genomics 2008; 9:367. [PMID: 18671879 PMCID: PMC2529315 DOI: 10.1186/1471-2164-9-367] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2008] [Accepted: 07/31/2008] [Indexed: 11/30/2022] Open
Abstract
Background Leakage of water and ions and soluble proteins from muscle cells occurs during prolonged exercise due to ischemia causing muscle damage. Also post mortem anoxia during conversion of muscle to meat is marked by loss of water and soluble components from the muscle cell. There is considerable variation in the water holding capacity of meat affecting economy of meat production. Water holding capacity depends on numerous genetic and environmental factors relevant to structural and biochemical muscle fibre properties a well as ante and post slaughter metabolic processes. Results Expression microarray analysis of M. longissimus dorsi RNAs of 74 F2 animals of a resource population showed 1,279 transcripts with trait correlated expression to water holding capacity. Negatively correlated transcripts were enriched in functional categories and pathways like extracellular matrix receptor interaction and calcium signalling. Transcripts with positive correlation dominantly represented biochemical processes including oxidative phosphorylation, mitochondrial pathways, as well as transporter activity. A linkage analysis of abundance of trait correlated transcripts revealed 897 expression QTL (eQTL) with 104 eQTL coinciding with QTL regions for water holding capacity; 96 transcripts had trans acting and 8 had cis acting regulation. Conclusion The complex relationships between biological processes taking place in live skeletal muscle and meat quality are driven on the one hand by the energy reserves and their utilisation in the muscle and on the other hand by the muscle structure itself and calcium signalling. Holistic expression profiling was integrated with QTL analysis for the trait of interest and for gene expression levels for creation of a priority list of genes out of the orchestra of genes of biological networks relevant to the liability to develop elevated drip loss.
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Affiliation(s)
- Siriluck Ponsuksili
- Research Institute for the Biology of Farm Animals (FBN), Research Group Functional Genomics, Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany.
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19
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Sampson JN, Self SG. Identifying trait clusters by linkage profiles: application in genetical genomics. ACTA ACUST UNITED AC 2008; 24:958-64. [PMID: 18310620 DOI: 10.1093/bioinformatics/btn064] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
MOTIVATION Genes often regulate multiple traits. Identifying clusters of traits influenced by a common group of genes helps elucidate regulatory networks and can improve linkage mapping. METHODS We show that the Pearson correlation coefficient, rho L, between two LOD score profiles can, with high specificity and sensitivity, identify pairs of genes that have their transcription regulated by shared quantitative trait loci (QTL). Furthermore, using theoretical and/or empirical methods, we can approximate the distribution of rho L under the null hypothesis of no common QTL. Therefore, it is possible to calculate P-values and false discovery rates for testing whether two traits share common QTL. We then examine the properties of rho L through simulation and use rho L to cluster genes in a genetical genomics experiment examining Saccharomyces cerevisiae. RESULTS Simulations show that rho L can have more power than the clustering methods currently used in genetical genomics. Combining experimental results with Gene Ontology (GO) annotations show that genes within a purported cluster often share similar function. SOFTWARE R-code included in online Supplementary Material.
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Affiliation(s)
- Joshua N Sampson
- Department of Biostatistics, University of Washington and Statistical Center for HIV/AIDS Research and Prevention, Seattle, WA, USA.
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20
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Kuramoto T, Nakanishi S, Serikawa T. Functional polymorphisms in inbred rat strains and their allele frequencies in commercially available outbred stocks. Physiol Genomics 2008; 33:205-11. [PMID: 18212005 DOI: 10.1152/physiolgenomics.00222.2007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Polymorphisms that have been proven to influence gene functions are called functional polymorphisms. It is significant to know the distribution of functional polymorphisms in the rat, widely used in animal models for human diseases. In this study, we assessed 16 functional polymorphisms consisting of 3 coat color and 13 disease-associated genes in 136 rat strains, as a part of the genetic profiling program of the National Bio Resource Project for the Rat (NBRP-Rat). Polymorphisms of Cdkn1a, Fcgr3, Grp10, Lss, and Fdft1, which were proven to function in prostate tumorigenesis, glomerulonephritis, hyperphagia, and cholesterol biosynthesis, were shared among various inbred strains. These findings indicated that most rat strains harbored the disease-associated alleles and suggested that many unidentified functional polymorphisms might exist in inbred rat strains. The functional polymorphisms shared in inbred strains were also observed within outbred stocks available commercially. Therefore, this implies that experimental plans based on either rat inbred strains or outbred stocks need to be carefully designed with a full understanding of the genetic characteristics of the animals. To select the most suitable strains for experiments, the NBRP-Rat will periodically improve and update the genetic profiles of rat strains.
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Affiliation(s)
- Takashi Kuramoto
- Institute of Laboratory Animals, Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto, Japan.
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21
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Potokina E, Druka A, Luo Z, Wise R, Waugh R, Kearsey M. Gene expression quantitative trait locus analysis of 16 000 barley genes reveals a complex pattern of genome-wide transcriptional regulation. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2008; 53:90-101. [PMID: 17944808 DOI: 10.1111/j.1365-313x.2007.03315.x] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Transcript abundance from cRNA hybridizations to Affymetrix microarrays can be used for simultaneous marker development and genome-wide gene expression quantitative trait locus (eQTL) analysis of crops. We have previously shown that it is easily possible to use Affymetrix expression arrays to profile individuals from a segregating population to accurately identify robust polymorphic molecular genetic markers. We applied the method to identify more than 2000 genetic polymorphisms (transcript derived markers, TDMs) from an experiment involving two commercial varieties of barley (Hordeum vulgare; Steptoe and Morex) and their doubled-haploid progeny. With this set of TDMs, we constructed a genetic map and used it for the genome-wide eQTL analysis of about 16 000 genes in a relatively large population (n = 139). We identified 23 738 significant eQTLs at a genome-wide significance (P </= 0.05), affecting the expression of 12 987 genes. Over a third of these genes with expression variation have only one identified eQTL while the rest have two to six. A large proportion of the quantitatively controlled transcripts appear to be regulated by both cis and trans effects. More than half of the quantitatively controlled transcripts appear to be primarily regulated by cis eQTLs in this population. We show that although there appear to be eQTL hotspots many of these are in chromosomal regions of low recombination, such as genetic centromeres, and so have a high gene density per centimorgan. Some chromosomal regions have a significant excess of eQTL over the number expected from gene density, and many of these are biased towards eQTL for which the allele from one particular parent increases the expression level.
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Affiliation(s)
- Elena Potokina
- School of Biosciences, The University of Birmingham, Birmingham B15 2TT, UK
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22
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Ruden DM, Rasouli P, Lu X. Potential long-term consequences of fad diets on health, cancer, and longevity: lessons learned from model organism studies. Technol Cancer Res Treat 2007; 6:247-54. [PMID: 17535033 DOI: 10.1177/153303460700600312] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
While much of the third world starves, many in the first world are undergoing an obesity epidemic, and the related epidemics of type II diabetes, heart disease, and other diseases associated with obesity. The amount of economic wealth being directly related to a decline in health by obesity is ironic because rich countries contribute billions of dollars to improve the health of their citizens. Nevertheless, nutritional experiments in model organisms such as yeast, C. elegans, Drosophila, and mice confirm that "caloric restriction" (CR), which is defined generally as a 30-40% decrease in caloric intake, a famine-like condition for humans seen only in the poorest of countries, promotes good health and increases longevity in model organisms. Because caloric restriction, and dieting in general, requires a great deal of will power to deal with the feelings of deprivation, many fad diets, such as the Atkins, South Beach, and Protein Power, have been developed which allow people to lose weight purportedly without the severe feelings of deprivation. However, the long-term effects of such fad diets are not known and few experiments have been performed in the laboratory to investigate possible side affects and adverse consequences. In this paper, we review studies with fad-like dietary conditions in humans and model organisms, and we propose a "Dietary Ames Test" to rapidly screen fad diets, dietary supplements, and drugs for potential long-term health consequences in model organisms.
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Affiliation(s)
- Douglas M Ruden
- Institute for Environmental, Health Sciences, 2727 2nd Avenue, Room 4000, Wayne State University, Detroit, MI 48201, USA.
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23
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Kesavan C, Baylink DJ, Kapoor S, Mohan S. Novel loci regulating bone anabolic response to loading: expression QTL analysis in C57BL/6JXC3H/HeJ mice cross. Bone 2007; 41:223-30. [PMID: 17543594 DOI: 10.1016/j.bone.2007.04.185] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2007] [Revised: 03/30/2007] [Accepted: 04/17/2007] [Indexed: 11/22/2022]
Abstract
Variations in the expression levels of bone marker genes among the inbred strains of mice in response to mechanical loading (ML) are largely determined by genetic factors. To explore this, we performed four-point bending on tibiae of 10-week female F2 mice of B6XC3H cross using 9N at 2 Hz, 36 cycles, once per day for 12 days. We collected tibiae from these mice for RNA extraction. We then measured the expression changes of bone marker genes, bone sialoprotein (BSP), alkaline phosphatase (ALP) and housekeeping genes, beta-actin and peptidylprolyl isomerase A (PPIA), by using real-time PCR in both the loaded and the non-loaded tibiae of F2 mice (n=241). A genome-wide scan was performed using 111 micro satellite markers in DNA sample collected from these mice. Mean increase in gene expression, expressed as fold change, ranges from 2.8 to 3.0 for BSP and 2.7 to 2.8 for ALP. Both showed a skewed distribution with a heritability response of 87 to 91%. Absence of significant correlation between the increased gene expression vs. body weight (BW) and bone size (BS) suggests that bone response to loading is independent of BS or BW. Non-parametric mapping (MapQTL program 5) revealed that BSP and ALP expression in response to bending was regulated by several significant and suggestive QTL: Loci regulating both BSP and ALP were located on Chr 8 (60.1 cM), 16 (45.9 cM), 17 (14.2 cM), 18 (38.0 cM) and Chr 19 (3.3 cM); Loci specific to BSP were found on Chrs 1 (LOD score 10.4 at 91.8 cM), 5 (5.2 at 73.2 cM) and 9 (7.0 at 13.1 cM); Loci regulating only ALP were found on Chrs 1 (7.6 at 46 and 75.4 cM), 3 (8.3 at 47 cM) and 4 (5.6 at 54.6 cM). QTLs on Chrs 1, 3, 8, 9, 17 and 18 correspond to QTLs we previously reported by pQCT measurements, thus validating these findings. In addition, we found that the QTL associated with non-loaded tibiae for BSP and ALP on Chrs 4, 16 and 18 was identical to the QTLs associated with ML. This finding suggests that regions on these chromosomes are responsible for natural variation in expression of BSP and ALP as well as for ML. This is the first expression study to provide evidence for the presence of multiple genetic loci regulating bone anabolic response to loading in the B6XC3H intercross and will lead to a better understanding of how exercise improves the skeletal mass.
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Affiliation(s)
- Chandrasekhar Kesavan
- Musculoskeletal Disease Center, Jerry L. Pettis VA Medical Center, 11201 Benton Street, Loma Linda, CA 92357, USA
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24
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Lee NH. Physiogenomic strategies and resources to associate genes with rat models of heart, lung and blood disorders. Exp Physiol 2007; 92:992-1002. [PMID: 17591683 DOI: 10.1113/expphysiol.2006.036350] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
As is the case for many human disorders, cardiovascular disease is a complex ailment exhibiting a multifactorial mode of transmission. Rat models have been developed to aid in the analysis of this complex genetic and phenotypic disorder. The purpose of this brief review is to describe current gene expression profiling strategies that have been implemented to search for candidate causative genes of disease phenotypes in animal models. Strategies include integrating gene expression information with linkage analysis, expression profiling chromosome-substituted and/or congenic rat strains, correlating gene expression with physiological data across a panel of rodent strains, and linking expression quantitative trait loci to physiological quantitative trait loci. A primary goal of these strategies is to narrow and prioritize the search for causal genes of physiological interest. Also discussed are ways to harness two recent publicly available resources that have been created to investigate the role of genes and environment on cardiovascular physiology and pathophysiology.
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Affiliation(s)
- Norman H Lee
- Department of Pharmacology and Physiology, The George Washington University Medical Center, 2300 Eye Street NW, Washington, DC 20037, USA.
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Wang SS, Schadt EE, Wang H, Wang X, Ingram-Drake L, Shi W, Drake TA, Lusis AJ. Identification of pathways for atherosclerosis in mice: integration of quantitative trait locus analysis and global gene expression data. Circ Res 2007; 101:e11-30. [PMID: 17641228 DOI: 10.1161/circresaha.107.152975] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
We report a combined genetic and genomic analysis of atherosclerosis in a cross between the strains C3H/HeJ and C57BL/6J on a hyperlipidemic apolipoprotein E-null background. We incorporated sex and sex-by-genotype interactions into our model selection procedure to identify 10 quantitative trait loci for lesion size, revealing a level of complexity greater than previously thought. Of the known risk factors for atherosclerosis, plasma triglyceride levels and plasma glucose to insulin ratios were particularly strongly, but negatively, associated with lesion size. We performed expression array analysis for 23,574 transcripts of the livers and adipose tissues of all 334 F2 mice and identified more than 10,000 expression quantitative trait loci that either mapped to the gene encoding the transcript, implying cis regulation, or to a separate locus, implying trans-regulation. The gene expression data allowed us to identify candidate genes that mapped to the atherosclerosis quantitative trait loci and for which the expression was regulated in cis. Genes highly correlated with lesions were enriched in certain known pathways involved in lesion development, including cholesterol metabolism, mitochondrial oxidative phosphorylation, and inflammation. Thus, global gene expression in peripheral tissues can reflect the systemic perturbations that contribute to atherosclerosis.
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Affiliation(s)
- Susanna S Wang
- Department of Human Genetics, University of California at Los Angeles, Los Angeles, CA 90095-1679, USA
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26
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Luo ZW, Potokina E, Druka A, Wise R, Waugh R, Kearsey MJ. SFP genotyping from affymetrix arrays is robust but largely detects cis-acting expression regulators. Genetics 2007; 176:789-800. [PMID: 17409081 PMCID: PMC1894608 DOI: 10.1534/genetics.106.067843] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The recent development of Affymetrix chips designed from assembled EST sequences has spawned considerable interest in identifying single-feature polymorphisms (SFPs) from transcriptome data. SFPs are valuable genetic markers that potentially offer a physical link to the structural genes themselves. However, most current SFP prediction methodologies were developed for sequenced species although SFPs are particularly valuable for species with complex and unsequenced genomes. To establish the sensitivity and specificity of prediction, we explored four methods for identifying SFPs from experiments involving two tissues in two commercial barleys and their doubled-haploid progeny. The methods were compared in terms of numbers of SFPs predicted and their ability to identify known sequence polymorphisms in the features, to confirm existing SNP genotypes and to match existing maps and individual haplotypes. We identified >4000 separate SFPs that accurately predicted the SNP genotype of >98% of the doubled-haploid (DH) lines. They were highly enriched for features containing sequence polymorphisms but all methods uniformly identified a majority of SFPs ( approximately 64%) in features for which there was no sequence polymorphism while 5% mapped to different locations, indicating that "SFPs" mainly represent polymorphism in cis-acting regulators. All methods are efficient and robust at predicting markers for gene mapping.
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Affiliation(s)
- Z. W. Luo
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, Scotland, United Kingdom, Laboratory of Population and Quantitative Genetics, Department of Biostatistics, School of Life Sciences, Institute of Biomedical Sciences, Fudan University, Shanghai 200433, China and Corn Insects and Crop Genetics Research, USDA–ARS, Department of Plant Pathology and Center for Plant Responses to Environmental Stresses, Iowa State University, Ames, Iowa 50011-1020
| | - E. Potokina
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, Scotland, United Kingdom, Laboratory of Population and Quantitative Genetics, Department of Biostatistics, School of Life Sciences, Institute of Biomedical Sciences, Fudan University, Shanghai 200433, China and Corn Insects and Crop Genetics Research, USDA–ARS, Department of Plant Pathology and Center for Plant Responses to Environmental Stresses, Iowa State University, Ames, Iowa 50011-1020
| | - A. Druka
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, Scotland, United Kingdom, Laboratory of Population and Quantitative Genetics, Department of Biostatistics, School of Life Sciences, Institute of Biomedical Sciences, Fudan University, Shanghai 200433, China and Corn Insects and Crop Genetics Research, USDA–ARS, Department of Plant Pathology and Center for Plant Responses to Environmental Stresses, Iowa State University, Ames, Iowa 50011-1020
| | - R. Wise
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, Scotland, United Kingdom, Laboratory of Population and Quantitative Genetics, Department of Biostatistics, School of Life Sciences, Institute of Biomedical Sciences, Fudan University, Shanghai 200433, China and Corn Insects and Crop Genetics Research, USDA–ARS, Department of Plant Pathology and Center for Plant Responses to Environmental Stresses, Iowa State University, Ames, Iowa 50011-1020
| | - R. Waugh
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, Scotland, United Kingdom, Laboratory of Population and Quantitative Genetics, Department of Biostatistics, School of Life Sciences, Institute of Biomedical Sciences, Fudan University, Shanghai 200433, China and Corn Insects and Crop Genetics Research, USDA–ARS, Department of Plant Pathology and Center for Plant Responses to Environmental Stresses, Iowa State University, Ames, Iowa 50011-1020
| | - M. J. Kearsey
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, Scotland, United Kingdom, Laboratory of Population and Quantitative Genetics, Department of Biostatistics, School of Life Sciences, Institute of Biomedical Sciences, Fudan University, Shanghai 200433, China and Corn Insects and Crop Genetics Research, USDA–ARS, Department of Plant Pathology and Center for Plant Responses to Environmental Stresses, Iowa State University, Ames, Iowa 50011-1020
- Corresponding author: School of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom. E-mail:
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27
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Passe CMM, Cooper G, Quirk CC. The murine p8 gene promoter is activated by activating transcription factor 4 (ATF4) in the gonadotrope-derived LbetaT2 cell line. Endocrine 2006; 30:81-91. [PMID: 17185796 DOI: 10.1385/endo:30:1:81] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2006] [Revised: 06/09/2006] [Accepted: 06/22/2006] [Indexed: 11/11/2022]
Abstract
The factor p8 is a high mobility group (HMG) A family member that is upregulated during the cellular stress response in numerous tissues. Because expression of this protein encourages cellular transformation, our goal is to characterize the mechanism by which the p8 gene is regulated. Using LbetaT2 cells as a model of a transformed cell in which p8 plays a role in tumor formation, we dissected the p8 promoter into its minimal functional units and found that activating transcription factor 4 (ATF4), a factor also upregulated during cellular stress responses, enhances p8 promoter activity in a dose-dependent manner. In addition, ATF4 binds in the highly conserved major activation domain of the p8 proximal promoter between -130 and -100 bp. Furthermore, we show that six of the nine base pairs that encompass the putative element are essential for ATF4 binding. These findings increase our knowledge of the mechanisms regulating the p8 gene in a genetically defined tumor model.
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Kadarmideen HN, von Rohr P, Janss LLG. From genetical genomics to systems genetics: potential applications in quantitative genomics and animal breeding. Mamm Genome 2006; 17:548-64. [PMID: 16783637 PMCID: PMC3906707 DOI: 10.1007/s00335-005-0169-x] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2005] [Accepted: 02/21/2006] [Indexed: 11/04/2022]
Abstract
This article reviews methods of integration of transcriptomics (and equally proteomics and metabolomics), genetics, and genomics in the form of systems genetics into existing genome analyses and their potential use in animal breeding and quantitative genomic modeling of complex traits. Genetical genomics or the expression quantitative trait loci (eQTL) mapping method and key findings in this research are reviewed. Various procedures and potential uses of eQTL mapping, global linkage clustering, and systems genetics are illustrated using actual analysis on recombinant inbred lines of mice with data on gene expression (for diabetes- and obesity-related genes), pathway, and single nucleotide polymorphism (SNP) linkage maps. Experimental and bioinformatics difficulties and possible solutions are discussed. The main uses of this systems genetics approach in quantitative genomics were shown to be in refinement of the identified QTL, candidate gene and SNP discovery, understanding gene-environment and gene-gene interactions, detection of candidate regulator genes/eQTL, discriminating multiple QTL/eQTL, and detection of pleiotropic QTL/eQTL, in addition to its use in reconstructing regulatory networks. The potential uses in animal breeding are direct selection on heritable gene expression measures, termed “expression assisted selection,” and genetical genomic selection of both QTL and eQTL based on breeding values of the respective genes, termed “expression-assisted evaluation.”
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Affiliation(s)
- Haja N Kadarmideen
- Statistical Animal Genetics Group, Institute of Animal Science, Swiss Federal Institute of Technology, ETH Zentrum (UNS D7), Universitaetstrasse 65, CH 8092 Zürich, Switzerland.
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Petretto E, Mangion J, Pravanec M, Hubner N, Aitman TJ. Integrated gene expression profiling and linkage analysis in the rat. Mamm Genome 2006; 17:480-9. [PMID: 16783629 DOI: 10.1007/s00335-005-0181-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2005] [Accepted: 01/24/2006] [Indexed: 12/01/2022]
Abstract
The combined application of genome-wide expression profiling from microarray experiments with genetic linkage analysis enables the mapping of expression quantitative trait loci (eQTLs) which are primary control points for gene expression across the genome. This approach allows for the dissection of primary and secondary genetic determinants of gene expression. The cis-acting eQTLs in practice are easier to investigate than the trans-regulated eQTLs because they are under simpler genetic control and are likely to be due to sequence variants within the gene itself or its neighboring regulatory elements. These genes are therefore candidates both for variation in gene expression and for contributions to whole-body phenotypes, particularly when these are located within known and relevant physiologic QTLs. Multiple trans-acting eQTLs tend to cluster to the same genetic location, implying shared regulatory control mechanisms that may be amenable to network analysis to identify gene clusters within the same metabolic pathway. Such clusters may ultimately underlie development of individual complex, whole-body phenotypes. The combined expression and linkage approach has been applied successfully in several mammalian species, including the rat which has specific features that demonstrate its value as a model for studying complex traits.
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Affiliation(s)
- Enrico Petretto
- MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College, London W12 0NN, United Kingdom
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