Metabolic tagging and purification of nascent RNA: implications for transcriptomics.

Gene expression profiling to analyze cellular responses against different stimuli or conditions is generally performed at the total cellular RNA level. This results in poor resolution of the temporal kinetics of the cellular response and a bias towards detecting up-regulation of short-lived transcripts. Furthermore, changes in transcription rate and RNA stability cannot be distinguished. These problems can be addressed by analyzing nascent RNA instead of total cellular RNA. Throughout the last few years methods have been developed for metabolic tagging and purification of nascent RNA. In this article, we review these experimental procedures and discuss their implications for large-scale gene expression profiling.

[1]  Chris Q. Doe,et al.  TU-tagging: cell type specific RNA isolation from intact complex tissues , 2009, Nature Methods.

[2]  Alexei A. Sharov,et al.  Database for mRNA Half-Life of 19 977 Genes Obtained by DNA Microarray Analysis of Pluripotent and Differentiating Mouse Embryonic Stem Cells , 2008, DNA research : an international journal for rapid publication of reports on genes and genomes.

[3]  F. Staal,et al.  DNA microarray studies of hematopoietic subpopulations. , 2009, Methods in molecular biology.

[4]  Leighton J. Core,et al.  Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters , 2008, Science.

[5]  R. Zimmer,et al.  High-resolution gene expression profiling for simultaneous kinetic parameter analysis of RNA synthesis and decay. , 2008, RNA.

[6]  Marcel H. Schulz,et al.  A Global View of Gene Activity and Alternative Splicing by Deep Sequencing of the Human Transcriptome , 2008, Science.

[7]  Y. Murakami,et al.  Novel DNA Microarray System for Analysis of Nascent mRNAs , 2008, DNA research : an international journal for rapid publication of reports on genes and genomes.

[8]  M. Gerstein,et al.  The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing , 2008, Science.

[9]  K. Kurimoto,et al.  Single-cell cDNA high-density oligonucleotide microarray analysis: detection of individual cell types and properties in complex biological processes. , 2008, Reproductive biomedicine online.

[10]  J. Boothroyd,et al.  RNA analysis by biosynthetic tagging using 4-thiouracil and uracil phosphoribosyltransferase. , 2008, Methods in molecular biology.

[11]  A. Millar,et al.  Genome-Wide Analysis of mRNA Decay Rates and Their Determinants in Arabidopsis thaliana[W] , 2007, The Plant Cell Online.

[12]  R. Young,et al.  A Chromatin Landmark and Transcription Initiation at Most Promoters in Human Cells , 2007, Cell.

[13]  Allen D. Delaney,et al.  Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing , 2007, Nature Methods.

[14]  W. Schmid,et al.  Microarray analysis of newly synthesized RNA in cells and animals , 2007, Proceedings of the National Academy of Sciences.

[15]  K. Schütze,et al.  Noncontact laser microdissection and catapulting for pure sample capture. , 2007, Methods in cell biology.

[16]  Anders F. Andersson,et al.  Global analysis of mRNA stability in the archaeon Sulfolobus , 2006, Genome Biology.

[17]  W. Filipowicz,et al.  Relief of microRNA-Mediated Translational Repression in Human Cells Subjected to Stress , 2006, Cell.

[18]  J. Boothroyd,et al.  Biosynthetic labeling of RNA with uracil phosphoribosyltransferase allows cell-specific microarray analysis of mRNA synthesis and decay , 2005, Nature Biotechnology.

[19]  J. Pérez-Ortín,et al.  Genomic run-on evaluates transcription rates for all yeast genes and identifies gene regulatory mechanisms. , 2004, Molecular cell.

[20]  M. Magnasco,et al.  Decay rates of human mRNAs: correlation with functional characteristics and sequence attributes. , 2003, Genome research.

[21]  J. Gregg,et al.  Allele-specific Holliday junction formation: a new mechanism of allelic discrimination for SNP scoring. , 2003, Genome research.

[22]  G. Church,et al.  Global RNA half-life analysis in Escherichia coli reveals positional patterns of transcript degradation. , 2003, Genome research.

[23]  C. Reilly,et al.  Genome-wide analysis of mRNA decay in resting and activated primary human T lymphocytes. , 2002, Nucleic acids research.

[24]  J. Cherry,et al.  Identification of unstable transcripts in Arabidopsis by cDNA microarray analysis: Rapid decay is associated with a group of touch- and specific clock-controlled genes , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[25]  M. Gorospe,et al.  Global analysis of stress-regulated mRNA turnover by using cDNA arrays , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[26]  Arkady B. Khodursky,et al.  Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[27]  John D. Storey,et al.  Precision and functional specificity in mRNA decay , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[28]  T. Takagi,et al.  Alterations of gene expression during colorectal carcinogenesis revealed by cDNA microarrays after laser-capture microdissection of tumor tissues and normal epithelia. , 2001, Cancer research.

[29]  J. A. Steitz,et al.  HuR and mRNA stability , 2001, Cellular and Molecular Life Sciences CMLS.

[30]  U. Weidle,et al.  The transcriptional program of a human B cell line in response to Myc. , 2001, Nucleic acids research.

[31]  P. Herrlich,et al.  UV-Induced Stabilization of c-fos and Other Short-Lived mRNAs , 2000, Molecular and Cellular Biology.

[32]  J. Lis,et al.  Nuclear run-on assays: assessing transcription by measuring density of engaged RNA polymerases. , 1999, Methods in enzymology.

[33]  M. Gorospe,et al.  p53-Dependent Elevation of p21Waf1Expression by UV Light Is Mediated through mRNA Stabilization and Involves a Vanadate-Sensitive Regulatory System , 1998, Molecular and Cellular Biology.

[34]  P. Nair,et al.  Newly synthesised mRNA as a probe for identification of wound responsive genes from potatoes. , 1995, Indian journal of biochemistry & biophysics.

[35]  C. Beadling,et al.  Isolation of interleukin 2-induced immediate-early genes. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[36]  R. Schlegel,et al.  Selective isolation of newly synthesized mammalian mRNA after in vivo labeling with 4-thiouridine or 6-thioguanosine. , 1988, Analytical biochemistry.

[37]  W. Melvin,et al.  Incorporation of 6-thioguanosine and 4-thiouridine into RNA. Application to isolation of newly synthesised RNA by affinity chromatography. , 1978, European journal of biochemistry.