Recommended References. Suggestion: – Look up the reference on-line. Get the News and Views article too (See end of this ref.)




НазваниеRecommended References. Suggestion: – Look up the reference on-line. Get the News and Views article too (See end of this ref.)
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Genomics and Proteomics Methodologies



Freeman,W.M., Robertson,D.J., and Vrana,K.E. (2000). Fundamentals of DNA hybridization arrays for gene expression analysis. Biotechniques 29, 1042-1055.
Abstract: DNA hybridization arrays [also known as macroarrays, microarrays and/or high-density oligonucleotide arrays (Gene Chips)] bring gene expression analysis to a genomic scale by permitting investigators to simultaneously examine changes in the expression of literally thousands of genes. For hybridization arrays, the general approach is to immobilize gene-specific sequences (probes) on a solid state matrix (nylon membranes, glass microscope slides, silicon/ceramic chips). These sequences are then queried with labeled copies of nucleic acids from biological samples (targets). The underlying theory is that the greater the expression of a gene, the greater the amount of labeled target, and hence, the greater output signal. In spite of the simplicity of the experimental design, there are at least four different platforms and several different approaches to processing and labeling the biological samples. Moreover, investigators must also determine whether they will utilize commercially available arrays or generate their own. This review will cover the status of the hybridization array field with an eye toward underlying principles and available technologies. Future developments and technological trends will also be evaluated

Benes,V. and Muckenthaler,M. (2003). Standardization of protocols in cDNA microarray analysis. Trends Biochem Sci. 28, 244-249.
Abstract: Systematic variations can occur at various steps of a cDNA microarray experiment and affect the measurement of gene expression levels. Accepted standards integrated into every cDNA microarray analysis can assess these variabilities and aid the interpretation of cDNA microarray experiments from different sources. A universally applicable approach to evaluate parameters such as input and output ratios, signal linearity, hybridization specificity and consistency across an array, as well as normalization strategies, is the utilization of exogenous control genes as spike-in and negative controls. We suggest that the use of such control sets, together with a sufficient number of experimental repeats, in-depth statistical analysis and thorough data validation should be made mandatory for the publication of cDNA microarray data
Notes: http://www.sciencedirect.com/science?_ob=MImg&_imagekey=B6TCV-48FCFSM-1-6&_cdi=5180&_user=1543922&_orig=search&_coverDate=05%2F31%2F2003&_qd=1&_sk=999719994&view=c&wchp=dGLbVlb-zSkWW&md5=b462d6d2083be3a63b25b9f37e0f67fe&ie=/sdarticle.pdf

Bader,G.D., Heilbut,A., Andrews,B., Tyers,M., Hughes,T., and Boone,C. (2003). Functional genomics and proteomics: charting a multidimensional map of the yeast cell. Trends Cell Biol 13, 344-356.
Abstract: The challenge of large-scale functional genomics projects is to build a comprehensive map of the cell including genome sequence and gene expression data, information on protein localization, structure, function and expression, post-translational modifications, molecular and genetic interactions and phenotypic descriptions. Some of this broad set of functional genomics data has been already assembled for the budding yeast. Even though molecular cartography of the yeast cell is still far from comprehensive, functional genomics has begun to forge connections between disparate cellular events and to foster numerous hypotheses. Here we review several different genomics and proteomics technologies and describe bioinformatics methods for exploring these data to make new discoveries
Notes: http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TCX-48R7C4Y-1&_coverDate=07%2F31%2F2003&_alid=241319003&_rdoc=1&_fmt=&_orig=search&_qd=1&_cdi=5182&_sort=d&view=c&_acct=C000053639&_version=1&_urlVersion=0&_userid=1543922&md5=0f821473c0eabb3c76cb31637d1f77b8

Mann,M., Hendrickson,R.C., and Pandey,A. (2001). Analysis of proteins and proteomes by mass spectrometry. Annu. Rev Biochem 70, 437-473.
Abstract: A decade after the discovery of electrospray and matrix-assisted laser desorption ionization (MALDI), methods that finally allowed gentle ionization of large biomolecules, mass spectrometry has become a powerful tool in protein analysis and the key technology in the emerging field of proteomics. The success of mass spectrometry is driven both by innovative instrumentation designs, especially those operating on the time-of-flight or ion-trapping principles, and by large-scale biochemical strategies, which use mass spectrometry to detect the isolated proteins. Any human protein can now be identified directly from genome databases on the basis of minimal data derived by mass spectrometry. As has already happened in genomics, increased automation of sample handling, analysis, and the interpretation of results will generate an avalanche of qualitative and quantitative proteomic data. Protein-protein interactions can be analyzed directly by precipitation of a tagged bait followed by mass spectrometric identification of its binding partners. By these and similar strategies, entire protein complexes, signaling pathways, and whole organelles are being characterized. Posttranslational modifications remain difficult to analyze but are starting to yield to generic strategies

Eukaryotic gene regulation



Garvie,C.W. and Wolberger,C. (2001). Recognition of specific DNA sequences. Mol Cell 8, 937-946.
Abstract: Proteins that recognize specific DNA sequences play a central role in the regulation of transcription. The tremendous increase in structural information on protein-DNA complexes has uncovered a remarkable structural diversity in DNA binding folds, while at the same time revealing common themes in binding to target sites in the genome
Notes: http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WSR-44N9D1G-4&_coverDate=11%2F21%2F2001&_alid=271368136&_rdoc=1&_fmt=&_orig=search&_qd=1&_cdi=7053&_sort=d&view=c&_acct=C000053639&_version=1&_urlVersion=0&_userid=1543922&md5=e1dfc7527f72cee9dafd7637140ac073

Passner,J.M., Ryoo,H.D., Shen,L., Mann,R.S., and Aggarwal,A.K. (1999). Structure of a DNA-bound Ultrabithorax-Extradenticle homeodomain complex. Nature 397, 714-719.
Abstract: During the development of multicellular organisms, gene expression must be tightly regulated, both spatially and temporally. One set of transcription factors that are important in animal development is encoded by the homeotic (Hox) genes, which govern the choice between alternative developmental pathways along the anterior-posterior axis. Hox proteins, such as Drosophila Ultrabithorax, have low DNA-binding specificity by themselves but gain affinity and specificity when they bind together with the homeoprotein Extradenticle (or Pbxl in mammals). To understand the structural basis of Hox-Extradenticle pairing, we determine here the crystal structure of an Ultrabithorax-Extradenticle-DNA complex at 2.4 A resolution, using the minimal polypeptides that form a cooperative heterodimer. The Ultrabithorax and Extradenticle homeodomains bind opposite faces of the DNA, with their DNA-recognition helices almost touching each other. However, most of the cooperative interactions arise from the YPWM amino-acid motif of Ultrabithorax-located amino-terminally to its homeodomain-which forms a reverse turn and inserts into a hydrophobic pocket on the Extradenticle homeodomain surface. Together, these protein-DNA and protein-protein interactions define the general principles by which homeotic proteins interact with Extradenticle (or Pbx1) to affect development along the anterior-posterior axis of animals
Notes: http://www.nature.com/nature/journal/v397/n6721/abs/397714a0_fs.html

Ptashne,M. and Gann,A. (2002). Genes & Signals. Cold Spring Harbor).
Notes: An excellent and concise book QH450 P83

Odom,D.T., Zizlsperger,N., Gordon,D.B., Bell,G.W., Rinaldi,N.J., Murray,H.L., Volkert,T.L., Schreiber,J., Rolfe,P.A., Gifford,D.K., Fraenkel,E., Bell,G.I., and Young,R.A. (2004). Control of pancreas and liver gene expression by HNF transcription factors. Science 303, 1378-1381.
Abstract: The transcriptional regulatory networks that specify and maintain human tissue diversity are largely uncharted. To gain insight into this circuitry, we used chromatin immunoprecipitation combined with promoter microarrays to identify systematically the genes occupied by the transcriptional regulators HNF1alpha, HNF4alpha, and HNF6, together with RNA polymerase II, in human liver and pancreatic islets. We identified tissue-specific regulatory circuits formed by HNF1alpha, HNF4alpha, and HNF6 with other transcription factors, revealing how these factors function as master regulators of hepatocyte and islet transcription. Our results suggest how misregulation of HNF4alpha can contribute to type 2 diabetes

Davidson,E.H., Rast,J.P., Oliveri,P., Ransick,A., Calestani,C., Yuh,C.H., Minokawa,T., Amore,G., Hinman,V., Arenas-Mena,C., Otim,O., Brown,C.T., Livi,C.B., Lee,P.Y., Revilla,R., Rust,A.G., Pan,Z., Schilstra,M.J., Clarke,P.J., Arnone,M.I., Rowen,L., Cameron,R.A., McClay,D.R., Hood,L., and Bolouri,H. (2002). A genomic regulatory network for development. Science 295, 1669-1678.
Abstract: Development of the body plan is controlled by large networks of regulatory genes. A gene regulatory network that controls the specification of endoderm and mesoderm in the sea urchin embryo is summarized here. The network was derived from large-scale perturbation analyses, in combination with computational methodologies, genomic data, cis-regulatory analysis, and molecular embryology. The network contains over 40 genes at present, and each node can be directly verified at the DNA sequence level by cis-regulatory analysis. Its architecture reveals specific and general aspects of development, such as how given cells generate their ordained fates in the embryo and why the process moves inexorably forward in developmental time
Notes: http://www.sciencemag.org/cgi/content/full/295/5560/1669
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