A Genome-wide Study of "Non-3UTR" Polyadenylation Sites in Arabidopsis thaliana.
Alternative polyadenylation has been recognized as a key contributor of gene expression regulation by generating different transcript isoforms with altered 3' ends. Although polyadenylation is well known for marking the end of a 3' UTR, an increasing number of studies have reported previously less-addressed polyadenylation events located in other parts of genes in many eukaryotic organisms. These other locations include 5' UTRs, introns and coding sequences (termed herein as non-3UTR), as well as antisense and intergenic polyadenlation. Focusing on the non-3UTR polyadenylation sites (n3PASs), we detected and characterized more than 11000 n3PAS clusters in the Arabidopsis genome using poly(A)-tag sequencing data (PAT-Seq). Further analyses suggested that the occurrence of these n3PASs were positively correlated with certain characteristics of their respective host genes, including the presence of spliced, diminutive or diverse beginning of 5' UTRs, number of introns and whether introns have extreme lengths. The interaction of the host genes with surrounding genetic elements, like a convergently overlapped gene and associated transposable element, may contribute to the generation of a n3PAS as well. Collectively, these results provide a better understanding of n3PASs, and offer some new insights of the underlying mechanisms for non-3UTR polyadenylation and its regulation in plants.
Department of Biology, Miami University, Oxford, OH 45056, USA.
Cheng
C
Guo
Department of Biology, Miami University, Oxford, OH 45056, USA.
Matthew
M
Spinelli
Department of Biology, Miami University, Oxford, OH 45056, USA.
Man
M
Liu
Key Laboratory of the Ministry of Education for Costal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China.|Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona, CA 91766, USA.
Qingshun Q
QQ
Li
Department of Biology, Miami University, Oxford, OH 45056, USA.
Chun
C
Liang
D020413:3' Untranslated Regions; D020121:5' Untranslated Regions; D017360:Arabidopsis / Q000235:genetics*; D004251:DNA Transposable Elements; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant; D055106:Genome-Wide Association Study; D007438:Introns; D026723:Polyadenylation
D020413:3' Untranslated Regions; D020121:5' Untranslated Regions; D004251:DNA Transposable Elements