Genomic detection of new yeast pre-mRNA 3'-end-processing signals.

To investigate Saccharomyces cerevisiae 3'-end-processing signals, a set of 1352 unique pre-mRNA 3'-end-processing sites, corresponding to 861 different genes, was identified by alignment of expressed sequence tag sequences with the complete yeast genome. Nucleotide word frequencies in the vicinity of the cleavage sites were analyzed to reveal the signal element features. In addition to previously recognized processing signals, two previously uncharacterized components of the 3'-end-processing signal sequence were discovered, specifically a predominance of U-rich sequences located on either side of the cleavage site. One of these, the downstream U-rich signal, provides a further link between the 3'-end-processing mechanisms of yeast and higher eukaryotes. Analysis of the complete set of 3'-end-processing sites by means of a discrimination function supports a 'contextual' model in which the sum total effectiveness of the signals in all four elements determines whether or not processing occurs.

[1]  Edward N. Trifonov,et al.  Interfering contexts of regulatory sequence elements , 1996, Comput. Appl. Biosci..

[2]  J. Manley,et al.  The End of the Message--Another Link Between Yeast and Mammals , 1996, Science.

[3]  T. D. Schneider,et al.  Sequence logos: a new way to display consensus sequences. , 1990, Nucleic acids research.

[4]  F. Sherman,et al.  Signals that produce 3' termini in CYC1 mRNA of the yeast Saccharomyces cerevisiae , 1993, Molecular and cellular biology.

[5]  Marco M. Kessler,et al.  Cleavage Factor II of Saccharomyces cerevisiaeContains Homologues to Subunits of the Mammalian Cleavage/ Polyadenylation Specificity Factor and Exhibits Sequence-specific, ATP-dependent Interaction with Precursor RNA* , 1997, The Journal of Biological Chemistry.

[6]  H. Domdey,et al.  Dependence of Yeast Pre-mRNA 3′-End Processing on CFT1: A Sequence Homolog of the Mammalian AAUAAA Binding Factor , 1996, Science.

[7]  R. A. Leibler,et al.  On Information and Sufficiency , 1951 .

[8]  P. Brown,et al.  Yeast microarrays for genome wide parallel genetic and gene expression analysis. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[9]  F. Sherman,et al.  3'-end-forming signals of yeast mRNA. , 1996, Trends in biochemical sciences.

[10]  S. Kullback,et al.  Information Theory and Statistics , 1959 .

[11]  S Audic,et al.  Alternate polyadenylation in human mRNAs: a large-scale analysis by EST clustering. , 1998, Genome research.

[12]  L. Minvielle-Sebastia,et al.  A multisubunit 3′ end processing factor from yeast containing poly(A) polymerase and homologues of the subunits of mammalian cleavage and polyadenylation specificity factor , 1997, The EMBO journal.

[13]  L. Minvielle-Sebastia,et al.  A comparison of mammalian and yeast pre-mRNA 3'-end processing. , 1997, Current opinion in cell biology.

[14]  F. Sherman,et al.  Signals sufficient for 3'-end formation of yeast mRNA , 1996, Molecular and cellular biology.

[15]  J. Manley,et al.  Mechanism and regulation of mRNA polyadenylation. , 1997, Genes & development.

[16]  S Audic,et al.  Visualizing the competitive recognition of TATA-boxes in vertebrate promoters. , 1998, Trends in genetics : TIG.

[17]  C. Guthrie,et al.  Essential Yeast Protein with Unexpected Similarity to Subunits of Mammalian Cleavage and Polyadenylation Specificity Factor (CPSF) , 1996, Science.

[18]  A. C. Rencher.  Methods of multivariate analysis , 1995 .

[19]  P. Brown,et al.  Exploring the metabolic and genetic control of gene expression on a genomic scale. , 1997, Science.

[20]  B. Barrell,et al.  Life with 6000 Genes , 1996, Science.