Physiological genomics in PG and beyond: October to December 2005

Mingyu Liang1 and Beverly Ventura2

1 Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin
2 Managing Editor, Physiological Genomics


    INTRODUCTION
 TOP
 INTRODUCTION
 DNA MICROARRAY: BEYOND A...
 HYPERTENSION AND DIABETES
 NEW TOOLS AND APPROACHES...
 REFERENCES
 
PHYSIOLOGICAL GENOMICS (PG) publishes, on a quarterly basis, brief editorial perspectives entitled "Physiological genomics in PG and beyond." These editorial perspectives provide brief, accessible highlights of the studies published in PG in the most recent quarter, and relate those studies to aspects of physiological genomics that are being emphasized in PG and other leading journals.


    DNA MICROARRAY: BEYOND A LIST OF GENES
 TOP
 INTRODUCTION
 DNA MICROARRAY: BEYOND A...
 HYPERTENSION AND DIABETES
 NEW TOOLS AND APPROACHES...
 REFERENCES
 
PG recognizes the value of comprehensive profiles of gene expression and has been at the forefront of publishing studies utilizing DNA microarrays and other high-throughput molecular profiling techniques. A typical expression profiling study compares two or more conditions using DNA microarrays and generates a list of genes considered "differentially expressed" between different conditions according to some criteria. As the fields of expression profiling and physiological genomics evolve, many investigators are exploring new ways to utilize these powerful techniques to generate valuable information beyond a list of differentially expressed genes.

Several examples can be seen this quarter in PG. These studies use gene expression profiling to

  1. identify subpopulations of cells (29a);
  2. generate integrative models (30);
  3. identify potential pharmacological agents with desired effects (11);
  4. annotate new genes and reveal cross-species conservation (26); and
  5. nominate candidate genes within a specific genomic region (20).

In studies previously published in PG, microarray technology and expression profiles have also been used to integrate transcriptomes with other levels of biological control (15, 18, 49, 59), to identify molecular signatures of disease (8, 17), to analyze specific subsets of mRNA (63), to study carbohydrates (55), and to assess the reliability of popular research tools (33, 40). Recent studies published by other leading journals have demonstrated the usefulness of these microarray techniques for determining expression profiles of microRNA (1, 57), positioning patterns of nucleosome (65), DNA methylation (56), RNA alternative splicing (51), potential new exons (16), histone H3.3 variant replacement (35), histone acetylation and methylation (39), protein fingerprinting (42), genomic binding patterns of estrogen receptor (5), and carbohydrate specificity (3) as well as disease molecular signature (2).

The conventional use of DNA microarrays to identify differentially expressed genes will continue to provide new biological insights. Meanwhile, it is evident from the studies published in PG and other leading journals that the power of high-throughput molecular profiling, exemplified by DNA microarray, is multifaceted.


    HYPERTENSION AND DIABETES
 TOP
 INTRODUCTION
 DNA MICROARRAY: BEYOND A...
 HYPERTENSION AND DIABETES
 NEW TOOLS AND APPROACHES...
 REFERENCES
 
PG has recently published a number of studies investigating hypertension, diabetes, and related disorders (7, 10, 1214, 19, 21, 2325, 29, 31, 35, 36, 45, 5254, 58, 60, 62, 64). Studies in this quarter of PG reported

  1. gene expression profiling in diabetic rats with erectile dysfunction (47);
  2. metabolic and blood pressure phenotypes during aging in transgenic rats with altered brain renin-angiotensin systems (22);
  3. autoimmune process and bone in diabetes (23a); and
  4. gene expression profile associated with a blood pressure quantitative trait locus in Dahl salt-sensitive rats (20).

A quantitative assessment of the impact of erectile dysfunction on diabetic patients' quality of life (9) and a possible causal role of specific glycosylation of endothelial nitric oxide synthase in this disorder were recently reported (37).


    NEW TOOLS AND APPROACHES OF PHYSIOLOGICAL GENOMICS
 TOP
 INTRODUCTION
 DNA MICROARRAY: BEYOND A...
 HYPERTENSION AND DIABETES
 NEW TOOLS AND APPROACHES...
 REFERENCES
 
In this quarter, PG published a number of articles describing new tools or new approaches for performing physiological genomic studies, including

  1. the Rat Genome Database (50);
  2. combining sequence analysis and chromatin immunoprecipitation to screen for gene regulatory elements (41); and
  3. noninvasive ultrasound screening of cardiovascular phenotypes of fetal mice with ethylnitrosourea (ENU) mutations (44).

These studies have extended the collection of new tools for physiological genomics published in PG over the past six years, which range from whole animal and molecular techniques, genomic resources, to new software tools (4, 6, 27, 28, 32, 38, 43, 46, 48, 61, 66).


    FOOTNOTES
 
Article published online before print. See web site for date of publication (http://physiolgenomics.physiology.org).

Address for reprint requests and other correspondence: M. Liang, Dept. of Physiology, Medical College of Wisconsin, 8701 Watertown Plank Rd., Milwaukee, WI 53226 (e-mail: mliang{at}mcw.edu).

10.1152/physiolgenomics.00278.2005.


    REFERENCES
 TOP
 INTRODUCTION
 DNA MICROARRAY: BEYOND A...
 HYPERTENSION AND DIABETES
 NEW TOOLS AND APPROACHES...
 REFERENCES
 

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  19. Guo M, Wu MH, Korompai F, and Yuan SY. Upregulation of PKC genes and isozymes in cardiovascular tissues during early stages of experimental diabetes. Physiol Genomics 12: 139–146, 2003.[Abstract/Free Full Text]
  20. Joe B, Letwin NE, Garrett MR, Dhindaw S, Frank B, Sultana R, Verratti K, Rapp JP, and Lee NH. Transcriptional profiling with a blood pressure QTL interval-specific oligonucleotide array. Physiol Genomics 23: 318–326, 2005.[Abstract/Free Full Text]
  21. Kaneko Y, Herrera VL, Didishvili T, and Ruiz-Opazo N. Sex-specific effects of dual ET-1/ANG II receptor (Dear) variants in Dahl salt-sensitive/resistant hypertension rat model. Physiol Genomics 20: 157–164, 2005.[Abstract/Free Full Text]
  22. Kasper SO, Carter CS, Ferrario CM, Ganten D, Ferder LF, Sonntag WE, Gallagher PE, and Diz DI. Growth, metabolism, and blood pressure disturbances during aging in transgenic rats with altered brain renin-angiotensin systems. Physiol Genomics 23: 311–317, 2005.[Abstract/Free Full Text]
  23. Kim JH, Stewart TP, Zhang W, Kim HY, Nishina PM, and Naggert JK. Type 2 diabetes mouse model TallyHo carries an obesity gene on chromosome 6 that exaggerates dietary obesity. Physiol Genomics 22: 171–181, 2005.[Abstract/Free Full Text]
  24. Kloting N, Follak N, and Kloting I. Is there an autoimmune process in bone? Gene expression studies in diabetic and nondiabetic BB rats as well as BB rat-related and -unrelated rat strains. Physiol Genomics 24: 59–64, 2005.
  25. Kloting N, Wilke B, and Kloting I. Phenotypic and genetic analyses of subcongenic BB.SHR rat lines shorten the region on chromosome 4 bearing gene(s) for underlying facets of metabolic syndrome. Physiol Genomics 18: 325–330, 2004.[Abstract/Free Full Text]
  26. Knoll KE, Pietrusz JL, and Liang M. Tissue-specific transcriptome responses in rats with early streptozotocin-induced diabetes. Physiol Genomics 21: 222–229, 2005.[Abstract/Free Full Text]
  27. Kwekel JC, Burgoon LD, Burt JW, Harkema JR, and Zacharewski JR. A cross-species analysis of the rodent uterotrophic program: elucidation of conserved responses and targets of estrogen signaling. Physiol Genomics 23: 327–342, 2005.[Abstract/Free Full Text]
  28. Laffin JJS, Scheetz TE, Bonaldo MF, Reiter RS, Chang S, Eyestone M, Abdulkawy H, Brown B, Roberts C, Tack D, Kucaba T, Lin JJC, Sheffield VC, Casavant TL, and Soares MB. A comprehensive nonredundant expressed sequence tag collection for the developing Rattus norvegicus heart. Physiol Genomics 17: 245–252, 2004.[Abstract/Free Full Text]
  29. Legato J, Knepper MA, Star RA, and Mejia R. Database for renal collecting duct regulatory and transporter proteins. Physiol Genomics 13: 179–181, 2003.[Abstract/Free Full Text]
  30. Liang M, Yuan B, Rute E, Greene AS, Olivier M, and Cowley AW Jr. Insights into Dahl salt-sensitive hypertension revealed by temporal patterns of renal medullary gene expression. Physiol Genomics 12: 229–237, 2003.[Abstract/Free Full Text]
  31. Liang SX, Summer R, Sun X, and Fine A. Gene expression profiling and localization of Hoechst-effluxing CD45– and CD45+ cells in the embryonic mouse lung. Physiol Genomics 23: 172–181, 2005.[Abstract/Free Full Text]
  32. Loor JJ, Dann HM, Everts RE, Oliveira R, Green CA, Janovick-Guretzky NA, Rodriguez-Zas SL, Lewin JA, and Drackley JK. Temporal gene expression profiling of liver from periparturient dairy cows reveals complex adaptive mechanisms in hepatic function. Physiol Genomics 23: 217–226, 2005.[Abstract/Free Full Text]
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  36. Mito Y, Henikoff JG, and Henikoff S. Genome-scale profiling of histone H3.3 replacement patterns. Nat Genet 37: 1090–1097, 2005.[CrossRef][ISI][Medline]
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  38. Morrison J, Knoll K, Hessner MJ, and Liang M. Effect of high glucose on gene expression in mesangial cells: upregulation of the thiol pathway is an adaptational response. Physiol Genomics 17: 271–282, 2004.[Abstract/Free Full Text]
  39. Musicki B, Kramer MF, Becker RE, and Burnett AL. Inactivation of phosphorylated endothelial nitric oxide synthase (Ser-1177) by O-GlcNAc in diabetes-associated erectile dysfunction. Proc Natl Acad Sci USA 102: 11870–11875, 2005.[Abstract/Free Full Text]
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