Experimental Verification and Evolutionary Origin of 5'-UTR Polyadenylation Sites in Arabidopsis thaliana

Frontiers in Plant Science
Yingdong Zhu, Jack C Vaughn

Abstract

Messenger RNA (mRNA) polyadenylation is an indispensable step during post-transcriptional pre-mRNA processing for most genes in eukaryotes. The usage of one poly(A) site over another is known as alternative polyadenylation (APA). APA has been implicated in gene expression regulation through its role of selecting the ends of a transcript. Recent studies of polyadenylation profiles in the Arabidopsis database unexpectedly predicted that a portion of the poly(A) sites are located in the 5'-UTR, which remains to be experimentally verified. We selected 16 genes from a dataset of 744, based on criteria designed to minimize problems in interpretation. Here, we experimentally verify 5'-UTR-APA in Arabidopsis for 10 of the 16 selected genes, and show for the first time existence of independent polyadenylated 5'-UTR transcripts, arising due to alternative polyadenylation. We used 3'-RACE and sequencing to validate poly(A) sites and northern blot to show that the observed short upstream transcripts do not arise from the 3'-end of a previously unrecognized convergent gene. Evidence is reported showing that two of the independent upstream open reading frame (uORF) transcripts studied, one containing a complex dual uORF, very likely arose by...Continue Reading

References

Nov 26, 1999·Proceedings of the National Academy of Sciences of the United States of America·J H GraberT F Smith
Apr 29, 2004·Journal of Molecular Evolution·Shu-Miaw ChawWen-Hsiung Li
Dec 21, 2004·Nucleic Acids Research·Haibo ZhangBin Tian
Apr 16, 2008·Nucleic Acids Research·Yingjia ShenQingshun Quinn Li
Jun 7, 2008·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Alex V Kochetov
Jul 18, 2008·Current Topics in Microbiology and Immunology·A G Hunt
Aug 1, 2008·BMC Genomics·Michael K TranUte Baumann
Jan 2, 2010·Nucleic Acids Research·Stefania Millevoi, Stéphan Vagner
Jun 16, 2010·Journal of Theoretical Biology·Guoli JiQingshun Quinn Li
Jul 13, 2011·Proceedings of the National Academy of Sciences of the United States of America·Xiaohui WuArthur G Hunt
Sep 20, 2011·Molecular Cell·Dafne Campigli Di GiammartinoJames L Manley
Oct 1, 2011·Nature Methods·Thomas Nordahl PetersenHenrik Nielsen
Sep 1, 2012·Frontiers in Plant Science·Richard A Jorgensen, Ana E Dorantes-Acosta
Oct 3, 2012·Genes & Development·Pia K AndersenTorben Heick Jensen
Nov 9, 2012·The Plant Cell·Patrick E ThomasArthur G Hunt
Feb 14, 2013·Nature Reviews. Molecular Cell Biology·Andrea Du Toit
Oct 29, 2013·Nucleic Acids Research·Klaus WethmarAchim Leutz
Nov 13, 2013·Nature Reviews. Genetics·Vicent Pelechano, Lars M Steinmetz
Apr 4, 2014·Briefings in Bioinformatics·Guoli JiXiaohui Wu
Dec 10, 2014·Methods in Molecular Biology·Xiaohui WuQingshun Quinn Li
Mar 13, 2015·International Journal of Molecular Sciences·Mingyang QuanDeqiang Zhang
Jun 16, 2016·Scientific Reports·Cheng GuoChun Liang

❮ Previous
Next ❯

Citations

Jun 24, 2020·Emerging Microbes & Infections·Dulmini Nanayakkara SapugahawatteMargaret Ip

❮ Previous
Next ❯

Datasets Mentioned

BETA
SRS1295578
BAD44460

Methods Mentioned

BETA
PAT-Seq
chip
PCR
electrophoresis

Software Mentioned

Coding Potential Calculator
Protein
SignalP
blast
ImageQuant
primer

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.