RT Journal
A1 Breakfield, Natalie W.
A1 Corcoran, David L.
A1 Petricka, Jalean J.
A1 Shen, Jeffrey
A1 Sae-Seaw, Juthamas
A1 Rubio-Somoza, Ignacio
A1 Weigel, Detlef
A1 Ohler, Uwe
A1 Benfey, Philip N.
T1 High-resolution experimental and computational profiling of tissue-specific known and novel miRNAs in Arabidopsis
JF Genome Research 
JO Genome Research 
YR 2012 
FD January 01 
VO 22 
IS 1 
SP 163 
OP 176 
DO 10.1101/gr.123547.111 
UL http://genome.cshlp.org/content/22/1/163.abstract 
AB Small non-coding RNAs (ncRNAs) are key regulators of plant development through modulation of the processing, stability, and translation of larger RNAs. We present small RNA data sets comprising more than 200 million aligned Illumina sequence reads covering all major cell types of the root as well as four distinct developmental zones. MicroRNAs (miRNAs) constitute a class of small ncRNAs that are particularly important for development. Of the 243 known miRNAs, 133 were found to be expressed in the root, and most showed tissue- or zone-specific expression patterns. We identified 66 new high-confidence miRNAs using a computational pipeline, PIPmiR, specifically developed for the identification of plant miRNAs. PIPmiR uses a probabilistic model that combines RNA structure and expression information to identify miRNAs with high precision. Knockdown of three of the newly identified miRNAs results in altered root growth phenotypes, confirming that novel miRNAs predicted by PIPmiR have functional relevance.