Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays Export

@article{citeulike:321002, abstract = {10.1073/pnas.112318199 Much of the information available about factors that affect mRNA decay in , and by inference in other bacteria, has been gleaned from study of less than 25 of the \^{a}‰ˆ4,300 predicted messages. To investigate these factors more broadly, we examined the half-lives and steady-state abundance of known and predicted mRNAs at single-gene resolution by using two-color fluorescent DNA microarrays. An rRNA-based strategy for normalization of microarray data was developed to permit quantitation of mRNA decay after transcriptional arrest by rifampicin. We found that globally, mRNA half-lives were similar in nutrient-rich media and defined media in which the generation time was approximately tripled. A wide range of stabilities was observed for individual mRNAs of , although \^{a}‰ˆ80\% of all mRNAs had half-lives between 3 and 8 min. Genes having biologically related metabolic functions were commonly observed to have similar stabilities. Whereas the half-lives of a limited number of mRNAs correlated positively with their abundance, we found that overall, increased mRNA stability is not predictive of increased abundance. Neither the density of putative sites of cleavage by RNase E, which is believed to initiate mRNA decay in , nor the free energy of folding of 5\^{a}€² or 3\^{a}€² untranslated region sequences was predictive of mRNA half-life. Our results identify previously unsuspected features of mRNA decay at a global level and also indicate that generalizations about decay derived from the study of individual gene transcripts may have limited applicability.}, address = {Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.}, author = {Bernstein, Jonathan A. and Khodursky, Arkady B. and Lin, Pei-Hsun and Lin-Chao, Sue and Cohen, Stanley N.}, citeulike-article-id = {321002}, citeulike-linkout-0 = {http://dx.doi.org/10.1073/pnas.112318199}, citeulike-linkout-1 = {http://www.pnas.org/content/99/15/9697.abstract}, citeulike-linkout-2 = {http://www.pnas.org/content/99/15/9697.full.pdf}, citeulike-linkout-3 = {http://www.pnas.org/cgi/content/abstract/99/15/9697}, citeulike-linkout-4 = {http://view.ncbi.nlm.nih.gov/pubmed/12119387}, citeulike-linkout-5 = {http://www.hubmed.org/display.cgi?uids=12119387}, day = {23}, doi = {10.1073/pnas.112318199}, issn = {0027-8424}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, keywords = {ecoli, expression, refs\_jme05}, month = {July}, number = {15}, pages = {9697--9702}, posted-at = {2005-09-15 13:10:27}, priority = {4}, title = {Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays}, url = {http://dx.doi.org/10.1073/pnas.112318199}, volume = {99}, year = {2002} }

TY - JOUR ID - citeulike:321002 L3 - citeulike-article-id:321002 N2 - 10.1073/pnas.112318199 Much of the information available about factors that affect mRNA decay in , and by inference in other bacteria, has been gleaned from study of less than 25 of the ≈4,300 predicted messages. To investigate these factors more broadly, we examined the half-lives and steady-state abundance of known and predicted mRNAs at single-gene resolution by using two-color fluorescent DNA microarrays. An rRNA-based strategy for normalization of microarray data was developed to permit quantitation of mRNA decay after transcriptional arrest by rifampicin. We found that globally, mRNA half-lives were similar in nutrient-rich media and defined media in which the generation time was approximately tripled. A wide range of stabilities was observed for individual mRNAs of , although ≈80% of all mRNAs had half-lives between 3 and 8 min. Genes having biologically related metabolic functions were commonly observed to have similar stabilities. Whereas the half-lives of a limited number of mRNAs correlated positively with their abundance, we found that overall, increased mRNA stability is not predictive of increased abundance. Neither the density of putative sites of cleavage by RNase E, which is believed to initiate mRNA decay in , nor the free energy of folding of 5′ or 3′ untranslated region sequences was predictive of mRNA half-life. Our results identify previously unsuspected features of mRNA decay at a global level and also indicate that generalizations about decay derived from the study of individual gene transcripts may have limited applicability. IS - 15 JF - Proceedings of the National Academy of Sciences of the United States of America SN - 0027-8424 AD - Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA. EP - 9702 TI - Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays VL - 99 SP - 9697 KW - ecoli KW - expression KW - refs_jme05 AU - Bernstein, Jonathan AU - Khodursky, Arkady AU - Lin, Pei-Hsun AU - Lin-Chao, Sue AU - Cohen, Stanley PY - 2002/07/23/ UR - http://dx.doi.org/10.1073/pnas.112318199 ER -