Measures relating word frequencies and expectations have been constantly ofinterest in Bioinformatics studies. With sequence data becoming massively available, exhaustiveenumeration of such measures have become concei...Measures relating word frequencies and expectations have been constantly ofinterest in Bioinformatics studies. With sequence data becoming massively available, exhaustiveenumeration of such measures have become conceivable, and yet pose significant computational burdeneven when limited to words of bounded maximum length. In addition, the display of the huge tablespossibly resulting from these counts poses practical problems of visualization and inference.VERBUMCULUS is a suite of software tools for the efficient and fast detection of over- orunder-represented words in nucleotide sequences. The inner core of VERBUMCULUS rests on subtlyinterwoven properties of statistics, pattern matching and combinatorics on words, that enable one tolimit drastically and a priori the set of over-or under-represented candidate words of all lengthsin a given sequence, thereby rendering it more feasible both to detect and visualize such words in afast and practically useful way. This paper is devoted to the description of the facility at theoutset and to report experimental results, ranging from simulations on synthetic data to thediscovery of regulatory elements on the upstream regions of a set of genes of the yeast.展开更多
Bidirectional promoters are relatively abundant in eukaryotic genomes, suggesting that they have an important biological significance. As yet, few of these promoters have been characterized in detail. Here, using a pr...Bidirectional promoters are relatively abundant in eukaryotic genomes, suggesting that they have an important biological significance. As yet, few of these promoters have been characterized in detail. Here, using a promoter：：GUS transgene approach has revealed that the intergenic region of Arabidopsis thaliana divergent genes At1g71850 and At1g71860 is an asymmetric bidirectional promoter, which exhibits an orientation-dependent expression profile. The strength of the forward promoter was greater than that of the reverse promoter, and their tissue specificities were not identical. Deletion analyses revealed that this bidirectional promoter could be divided into three functional regions. The basal level and tissue specificity of the promoter in the reverse orientation were regulated positively by region II and negatively by region III, whereas promoter activity in the forward orientation was regulated negatively by region II and positively by region I. Thus the 52-bp stretch of region II had a dual function, enhancing expression in the reverse orientation and suppressing it in the forward orientation. These results demonstrated that the activity of the At1g71850-At1g71860 bidirectional promoter was modulated by complex interactions between both positive and negative cis-acting elements. These findings will enhance our understanding of the regulatory mechanisms of plant bidirectional promoters.展开更多
基金美国自然科学基金，Purdue Research Foundation，Italian Ministry of University and Research, and the Research Program of the University of Padova 及Purdue Research Foundation，the Italian Ministry of University and Re-search, the Research Program of the University of Padova and Bourns College of Engineering, University of California,Riverside
文摘Measures relating word frequencies and expectations have been constantly ofinterest in Bioinformatics studies. With sequence data becoming massively available, exhaustiveenumeration of such measures have become conceivable, and yet pose significant computational burdeneven when limited to words of bounded maximum length. In addition, the display of the huge tablespossibly resulting from these counts poses practical problems of visualization and inference.VERBUMCULUS is a suite of software tools for the efficient and fast detection of over- orunder-represented words in nucleotide sequences. The inner core of VERBUMCULUS rests on subtlyinterwoven properties of statistics, pattern matching and combinatorics on words, that enable one tolimit drastically and a priori the set of over-or under-represented candidate words of all lengthsin a given sequence, thereby rendering it more feasible both to detect and visualize such words in afast and practically useful way. This paper is devoted to the description of the facility at theoutset and to report experimental results, ranging from simulations on synthetic data to thediscovery of regulatory elements on the upstream regions of a set of genes of the yeast.
基金supported by grants from Shandong Provincial Natural Science Foundation (ZR2011CQ016 to Shijuan Liu)National Natural Science Foundation of China (31200196 to Shijuan Liu and 31170236 to Wei Zhang)
文摘Bidirectional promoters are relatively abundant in eukaryotic genomes, suggesting that they have an important biological significance. As yet, few of these promoters have been characterized in detail. Here, using a promoter：：GUS transgene approach has revealed that the intergenic region of Arabidopsis thaliana divergent genes At1g71850 and At1g71860 is an asymmetric bidirectional promoter, which exhibits an orientation-dependent expression profile. The strength of the forward promoter was greater than that of the reverse promoter, and their tissue specificities were not identical. Deletion analyses revealed that this bidirectional promoter could be divided into three functional regions. The basal level and tissue specificity of the promoter in the reverse orientation were regulated positively by region II and negatively by region III, whereas promoter activity in the forward orientation was regulated negatively by region II and positively by region I. Thus the 52-bp stretch of region II had a dual function, enhancing expression in the reverse orientation and suppressing it in the forward orientation. These results demonstrated that the activity of the At1g71850-At1g71860 bidirectional promoter was modulated by complex interactions between both positive and negative cis-acting elements. These findings will enhance our understanding of the regulatory mechanisms of plant bidirectional promoters.
