PMID- 20860998
OWN - NLM
STAT- MEDLINE
DCOM- 20110131
LR  - 20231103
IS  - 1362-4962 (Electronic)
IS  - 0305-1048 (Print)
IS  - 0305-1048 (Linking)
VI  - 38
IP  - 22
DP  - 2010 Dec
TI  - RNA G-Quadruplexes in the model plant species Arabidopsis thaliana: prevalence 
      and possible functional roles.
PG  - 8149-63
LID - 10.1093/nar/gkq804 [doi]
AB  - Tandem stretches of guanines can associate in hydrogen-bonded arrays to form 
      G-quadruplexes, which are stabilized by K(+) ions. Using computational methods, 
      we searched for G-Quadruplex Sequence (GQS) patterns in the model plant species 
      Arabidopsis thaliana. We found  approximately  1200 GQS with a G(3) repeat sequence motif, most 
      of which are located in the intergenic region. Using a Markov modeled genome, we 
      determined that GQS are significantly underrepresented in the genome. 
      Additionally, we found  approximately  43,000 GQS with a G(2) repeat sequence motif; notably, 
      80% of these were located in genic regions, suggesting that these sequences may 
      fold at the RNA level. Gene Ontology functional analysis revealed that GQS are 
      overrepresented in genes encoding proteins of certain functional categories, 
      including enzyme activity. Conversely, GQS are underrepresented in other 
      categories of genes, notably those for non-coding RNAs such as tRNAs and rRNAs. 
      We also find that genes that are differentially regulated by drought are 
      significantly more likely to contain a GQS. CD-detected K(+) titrations performed 
      on representative RNAs verified formation of quadruplexes at physiological K(+) 
      concentrations. Overall, this study indicates that GQS are present at unique 
      locations in Arabidopsis and that folding of RNA GQS may play important roles in 
      regulating gene expression.
FAU - Mullen, Melissa A
AU  - Mullen MA
AD  - Department of Chemistry, The Pennsylvania State University, University Park, 
      Pennsylvania 16802-5302, USA.
FAU - Olson, Kalee J
AU  - Olson KJ
FAU - Dallaire, Paul
AU  - Dallaire P
FAU - Major, Francois
AU  - Major F
FAU - Assmann, Sarah M
AU  - Assmann SM
FAU - Bevilacqua, Philip C
AU  - Bevilacqua PC
LA  - eng
GR  - R01 GM088813/GM/NIGMS NIH HHS/United States
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20100921
PL  - England
TA  - Nucleic Acids Res
JT  - Nucleic acids research
JID - 0411011
RN  - 0 (DNA, Intergenic)
RN  - 0 (RNA, Plant)
SB  - IM
MH  - Arabidopsis/*genetics
MH  - DNA, Intergenic/chemistry
MH  - *G-Quadruplexes
MH  - Genome, Plant
MH  - Models, Genetic
MH  - RNA, Plant/*chemistry/genetics/physiology
PMC - PMC3001093
EDAT- 2010/09/24 06:00
MHDA- 2011/02/01 06:00
PMCR- 2010/09/21
CRDT- 2010/09/24 06:00
PHST- 2010/09/24 06:00 [entrez]
PHST- 2010/09/24 06:00 [pubmed]
PHST- 2011/02/01 06:00 [medline]
PHST- 2010/09/21 00:00 [pmc-release]
AID - gkq804 [pii]
AID - 10.1093/nar/gkq804 [doi]
PST - ppublish
SO  - Nucleic Acids Res. 2010 Dec;38(22):8149-63. doi: 10.1093/nar/gkq804. Epub 2010 
      Sep 21.