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Global profiling of alternative splicing landscape responsive to drought,heat and their combination in wheat (Triticum aestivum L.)
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Zhenshan Liu Jinxia Qin Xuejun Tian Shengbao Xu Yu Wang Hongxia Li Xiaoming Wang Huiru Peng Yingyin Yao Zhaorong Hu Zhongfu Ni Mingming Xin Qixin Sun 《Plant biotechnology journal》2018,16(3):714-726
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Promoter usage and alternative splicing 总被引:1,自引:0,他引:1
Kornblihtt AR 《Current opinion in cell biology》2005,17(3):262-268
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Functional coordination of alternative splicing in the mammalian central nervous system 总被引:2,自引:0,他引:2
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Fagnani M Barash Y Ip JY Misquitta C Pan Q Saltzman AL Shai O Lee L Rozenhek A Mohammad N Willaime-Morawek S Babak T Zhang W Hughes TR van der Kooy D Frey BJ Blencowe BJ 《Genome biology》2007,8(6):R108-17
Background
Alternative splicing (AS) functions to expand proteomic complexity and plays numerous important roles in gene regulation. However, the extent to which AS coordinates functions in a cell and tissue type specific manner is not known. Moreover, the sequence code that underlies cell and tissue type specific regulation of AS is poorly understood.Results
Using quantitative AS microarray profiling, we have identified a large number of widely expressed mouse genes that contain single or coordinated pairs of alternative exons that are spliced in a tissue regulated fashion. The majority of these AS events display differential regulation in central nervous system (CNS) tissues. Approximately half of the corresponding genes have neural specific functions and operate in common processes and interconnected pathways. Differential regulation of AS in the CNS tissues correlates strongly with a set of mostly new motifs that are predominantly located in the intron and constitutive exon sequences neighboring CNS-regulated alternative exons. Different subsets of these motifs are correlated with either increased inclusion or increased exclusion of alternative exons in CNS tissues, relative to the other profiled tissues.Conclusion
Our findings provide new evidence that specific cellular processes in the mammalian CNS are coordinated at the level of AS, and that a complex splicing code underlies CNS specific AS regulation. This code appears to comprise many new motifs, some of which are located in the constitutive exons neighboring regulated alternative exons. These data provide a basis for understanding the molecular mechanisms by which the tissue specific functions of widely expressed genes are coordinated at the level of AS. 相似文献14.
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Galina I. Kravatskaya Vladimir R. Chechetkin Yury V. Kravatsky Vladimir G. Tumanyan 《Genomics》2013,101(1):1-11
The level of supercoiling in the chromosome can affect gene expression. To clarify the basis of supercoiling sensitivity, we analyzed the structural features of nucleotide sequences in the vicinity of promoters for the genes with expression enhanced and decreased in response to loss of chromosomal supercoiling in Escherichia coli. Fourier analysis of promoter sequences for supercoiling-sensitive genes reveals the tendency in selection of sequences with helical periodicities close to 10 nt for relaxation-induced genes and to 11 nt for relaxation-repressed genes. The helical periodicities in the subsets of promoters recognized by RNA polymerase with different sigma factors were also studied. A special procedure was developed for the study of correlations between the intensities of periodicities in promoter sequences and the expression levels of corresponding genes. Significant correlations of expression with the AT content and with AT periodicities about 10, 11, and 50 nt indicate their role in regulation of supercoiling-sensitive genes. 相似文献
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