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Updated: Jul 20, 2026
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Detection of miRNA Targets in High-throughput Using the 3'LIFE Assay
Published on: May 25, 2015
In silico detection of control signals: mRNA 3'-end-processing sequences in diverse species
J H Graber1, C R Cantor, S C Mohr
1Center for Advanced Biotechnology, Department of Biomedical Engineering, Boston University, 36 Cummington St., Boston, MA 02215, USA.
Summary
mRNA 3' end processing signals are not universally conserved across species. Signal efficiency depends on multiple elements, not just a single sequence, allowing for compensation between elements.
Area of Science:
- Molecular Biology
- Genomics
- Bioinformatics
Background:
- mRNA 3'-end processing is crucial for gene expression regulation.
- The canonical AAUAAA hexamer is considered a primary polyadenylation signal.
- Previous studies suggested widespread conservation of AAUAAA across eukaryotes.
Purpose of the Study:
- To investigate the conservation and usage of mRNA 3'-end processing signals across six diverse eukaryotic species.
- To analyze the role of the canonical AAUAAA element and its variants in different organisms.
- To develop a broader understanding of polyadenylation signal complexity.
Main Methods:
- Analysis of over 20,000 3'-expressed sequence tags (ESTs).
- Comparative genomics approach across yeast, rice, Arabidopsis, fruit fly, mouse, and human.
- Sequence analysis to identify and quantify polyadenylation signal elements and their variants.
Main Results:
- The canonical AAUAAA signal usage and conservation vary significantly across species, being weak in plants and yeast.
- Even in animals, AAUAAA is less universal than previously thought; single-base variants show correlation with processing efficiency.
- Plant polyadenylation signals share similarities with yeast signals in content and arrangement, differing from animal signals.
- The complete polyadenylation signal is an aggregate of multiple elements, not a single required sequence.
Conclusions:
- A broadened concept of mRNA 3'-end processing signals is proposed, emphasizing combinatorial action of multiple elements.
- Signal efficiency is a function of all elements, where weak elements can be compensated by strong ones.
- Identifying 3'-end processing signals effectively requires moving beyond simple consensus sequence identification.
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