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Updated: Feb 7, 2026

Fluorescence Based Primer Extension Technique to Determine Transcriptional Starting Points and Cleavage Sites of RNases In Vivo
Published on: October 31, 2014
Determination and analysis of the pre-mRNA cleavage sites in Arabidopsis
Yongfeng Jin1, Yinghao Chen, Zhaohui Gong
1Institute of Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, PR China. jinyf@zju.edu.cn <jinyf@zju.edu.cn>
Abstract:
Alignment of the Arabidopsis cDNA to genome DNA sequences revealed that approximately half of the mRNAs were found to contain 3' non-templated nucleotide addition prior to the poly(A) sequence. These findings suggest that we can more precisely determine the cleavage sites. Based on the nucleotide downstream of cleavage sites, we are able to derive a hierarchy of cleavage preferences A>>U>C>>G. Interestingly, the completely different hierarchy of preferences was derived to be U>>A>>G>C, based on the nucleotide upstream of cleavage sites. Dinucleotide AU is the most preferred composition for cleavage. The determination of the cleavage sites and systematical analysis can help in the enhancement of 3'-processing site prediction and mechanistic understanding of 3'-end processing in plant.
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