@article{fdi:010044233,
  title = {{I}dentification of precursor transcripts for 6 novel mi{RNA}s expands the diversity on the genomic organisation and expression of mi{RNA} genes in rice},
  author = {{L}acombe, {S}{\'e}verine and {N}agasaki, {H}. and {S}anti, {C}. and {D}uval, {D}. and {P}iegu, {B}. and {B}angratz, {M}artine and {B}reitler, {J}.{C}. and {G}uiderdoni, {E}. and {B}rugidou, {C}hristophe and {H}irsch, {J}. and {C}ao, {X}. and {B}rice, {C}. and {P}anaud, {O}. and {K}arlowski, {W}.{M}. and {S}ato, {Y}. and {E}cheverria, {M}anuel},
  editor = {},
  language = {{ENG}},
  abstract = {{B}ackground: {T}he plant mi{RNA}s represent an important class of endogenous small {RNA}s that guide cleavage of an m{RNA} target or repress its translation to control development and adaptation to stresses. {M}i{RNA}s are nuclear-encoded genes transcribed by {RNA} polymerase {II}, producing a primary precursor that is subsequently processed by {DCL}1 an {RN}ase {III} {D}icer-like protein. {I}n rice hundreds of mi{RNA}s have been described or predicted, but little is known on their genes and precursors which are important criteria to distinguish them from si{RNA}s. {H}ere we develop a combination of experimental approaches to detect novel mi{RNA}s in rice, identify their precursor transcripts and genes and predict or validate their m{RNA} targets. {R}esults: {W}e produced four c{DNA} libraries from small {RNA} fractions extracted from distinct rice tissues. {B}y in silico analysis we selected 6 potential novel mi{RNA}s, and confirmed that their expression requires {O}s{DCL}1. {W}e predicted their targets and used 5'{RACE} to validate cleavage for three of them, targeting a {PPR}, an {SPX} domain protein and a {GT}-like transcription factor respectively. {I}n addition, we identified precursor transcripts for the 6 mi{RNA}s expressed in rice, showing that these precursors can be efficiently processed using a transient expression assay in transfected {N}icotiana benthamiana leaves. {M}ost interestingly, we describe two precursors producing tandem mi{RNA}s, but in distinct arrays. {W}e focus on one of them encoding osa-mi{R}159a.2, a novel mi{RNA} produced from the same stem-loop structure encoding the conserved osa-mi{R}159a.1. {W}e show that this dual osa-mi{R}159a.2-osa-mi{R}159a.1 structure is conserved in distant rice species and maize. {F}inally we show that the predicted m{RNA} target of osa-mi{R}159a.2 encoding a {GT}-like transcription factor is cleaved in vivo at the expected site. {C}onclusion: {T}he combination of approaches developed here identified six novel mi{RNA}s expressed in rice which can be clearly distinguished from si{RNA}s. {I}mportantly, we show that two mi{RNA}s can be produced from a single precursor, either from tandem stem-loops or tandemly arrayed in a single stem-loop. {T}his suggests that processing of these precursors could be an important regulatory step to produce one or more functional mi{RNA}s in plants and perhaps coordinate cleavage of distinct targets in the same plant tissue.},
  keywords = {},
  booktitle = {},
  journal = {{B}mc {P}lant {B}iology},
  volume = {8},
  numero = {},
  pages = {123},
  ISSN = {1471-2229},
  year = {2008},
  DOI = {10.1186/1471-2229-8-123},
  URL = {https://www.documentation.ird.fr/hor/fdi:010044233},
}