| 12 matches found in 7 documents. Search time: 0.089 seconds. |
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| Title: Specific interactions between Dicer-like proteins and HYL1/DRB-family dsRNA-binding proteins in Arabidopsis thaliana .
| | Author: Hiraguri A Itoh R Kondo N Nomura Y Aizawa D Murai Y Koiwa H Seki M Shinozaki K Fukuhara T | | Journal: Plant Mol . Biol . Citation: V : 57 ( 2 ) P : 173-88 Year: 2005 Type: ARTICLE | | Literature: oryza Field: abstract Doc ID: pub15821876 Accession (PMID): 15821876 | | Abstract: Proteins that specifically bind double-stranded RNA ( dsRNA ) are involved in the regulation of cellular signaling events and gene expression , and are characterized by a conserved dsRNA-binding motif ( dsRBM ) .
Here we report the biochemical properties of nine such gene products , each containing one or two dsRBMs : four Arabidopsis Dicer-like proteins ( DCL1-4 ) , Arabidopsis HYL1 and four of its homologs ( DRB2 , DRB4 , DRB5 and OsDRB1 ) .
DCL1 , DCL3 , HYL1 and the four HYL1 homologs exhibit significant dsRNA-binding activity , indicating that these proteins are involved in RNA metabolism .
The dsRBMs from dsRBM-containing proteins ( dsRBPs ) also function as a protein-protein interaction domain and homo and heterodimerization are essential for biological functioning of these proteins .
We show that DRB4 interacts specifically with DCL4 , and HYL1 most strongly interacts with DCL1 .
These results indicate that each HYL1/DRB family protein interacts with one specific partner among the four Dicer-like proteins .
Localization studies using GFP fusion proteins demonstrate that DCL1 , DCL4 , HYL1 and DRB4 localize in the nucleus , while DRB2 is present in the cytoplasm .
Subcellular localizations of HYL1 , DRB4 , DCL1 and DCL4 further strengthen the notion that HYL1 and DCL1 , and DRB4 and DCL4 , exist as complexes .
The presented data suggest that each member of the HYL1/DRB protein family may individually modulate Dicer function through heterodimerization with a Dicer-like protein in vivo . | Matching Sentences:
[ Sen. 8, subscore: 2.00 ]: Subcellular localizations of HYL1 , DRB4 , DCL1 and DCL4 further strengthen the notion that HYL1 and DCL1 , and DRB4 and DCL4 , exist as complexes .
[ Sen. 2, subscore: 1.00 ]: Here we report the biochemical properties of nine such gene products , each containing one or two dsRBMs : four Arabidopsis Dicer-like proteins ( DCL1-4 ) , Arabidopsis HYL1 and four of its homologs ( DRB2 , DRB4 , DRB5 and OsDRB1 ) .
[ Sen. 3, subscore: 1.00 ]: DCL1 , DCL3 , HYL1 and the four HYL1 homologs exhibit significant dsRNA-binding activity , indicating that these proteins are involved in RNA metabolism .
[ Sen. 5, subscore: 1.00 ]: We show that DRB4 interacts specifically with DCL4 , and HYL1 most strongly interacts with DCL1 .
[ Sen. 7, subscore: 1.00 ]: Localization studies using GFP fusion proteins demonstrate that DCL1 , DCL4 , HYL1 and DRB4 localize in the nucleus , while DRB2 is present in the cytoplasm .
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Score: 2.00 |
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| Title: siRNAs from miRNA sites mediate DNA methylation of target genes .
| | Author: Chellappan P Xia J Zhou X Gao S Zhang X Coutino G Vazquez F Zhang W Jin H | | Journal: Nucleic Acids Res Citation: V : 38 P : 6883-94 Year: 2010 Type: MEDLINE | | Literature: oryza Field: abstract Doc ID: pub20621980 Accession (PMID): 20621980 | | Abstract: Arabidopsis microRNA ( miRNA ) genes ( MIR ) give rise to 20 to 22-nt miRNAs that are generated predominantly by the type III endoribonuclease Dicer-like 1 ( DCL1 ) but do not require any RNA-dependent RNA Polymerases ( RDRs ) or RNA Polymerase IV ( Pol IV ) .
Here , we identify a novel class of non-conserved MIR genes that give rise to two small RNA species , a 20 to 22-nt species and a 23 to 27-nt species , at the same site .
Genetic analysis using small RNA pathway mutants reveals that the 20 to 22-nt small RNAs are typical miRNAs generated by DCL1 and are associated with Argonaute 1 ( AGO1 ) .
In contrast , the accumulation of the 23 to 27-nt small RNAs from the miRNA-generating sites is dependent on DCL3 , RDR2 and Pol IV , components of the typical heterochromatic small interfering RNA ( hc-siRNA ) pathway .
We further demonstrate that these MIR-derived siRNAs associate with AGO4 and direct DNA methylation at some of their target loci in trans .
In addition , we find that at the miRNA-generating sites , some conserved canonical MIR genes also produce siRNAs , which also induce DNA methylation at some of their target sites .
Our systematic examination of published small RNA deep sequencing datasets of rice and moss suggests that this type of dual functional MIRs exist broadly in plants .
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[ Sen. 1, subscore: 1.00 ]: Arabidopsis microRNA ( miRNA ) genes ( MIR ) give rise to 20 to 22-nt miRNAs that are generated predominantly by the type III endoribonuclease Dicer-like 1 ( DCL1 ) but do not require any RNA-dependent RNA Polymerases ( RDRs ) or RNA Polymerase IV ( Pol IV ) .
[ Sen. 3, subscore: 1.00 ]: Genetic analysis using small RNA pathway mutants reveals that the 20 to 22-nt small RNAs are typical miRNAs generated by DCL1 and are associated with Argonaute 1 ( AGO1 ) .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 1.00 |
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| Title: Genome-wide analysis for discovery of rice microRNAs reveals natural antisense microRNAs ( nat-miRNAs ) .
| | Author: Lu C Jeong DH Kulkarni K Pillay M Nobuta K German R Thatcher SR Maher C Zhang L Ware D Liu B Cao X Meyers BC Green PJ | | Journal: Proc Natl Acad Sci U S A Citation: V : 105 P : 4951-6 Year: 2008 Type: MEDLINE | | Literature: oryza Field: abstract Doc ID: pub18353984 Accession (PMID): 18353984 | | Abstract: Small RNAs ( 21-24 nt ) are involved in gene regulation through translation inhibition , mRNA cleavage , or directing chromatin modifications .
In rice , currently approximately 240 microRNAs ( miRNAs ) have been annotated .
We sequenced more than four million small RNAs from rice and identified another 24 miRNA genes .
Among these , we found a unique class of miRNAs that derive from natural cis-antisense transcript pairs .
This configuration generates miRNAs that can perfectly match their targets .
We provide evidence that the miRNAs function by inducing mRNA cleavage in the middle of their complementary site .
Their production requires Dicer-like 1 ( DCL1 ) activity , which is essential for canonical miRNA biogenesis .
All of the natural antisense miRNAs ( nat-miRNAs ) identified in this study have large introns in their precursors that appear critical for nat-miRNA evolution and for the formation of functional miRNA loci .
These findings suggest that other natural cis-antisense loci with similar exon-intron arrangements could be another source of miRNA genes .
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[ Sen. 7, subscore: 1.00 ]: Their production requires Dicer-like 1 ( DCL1 ) activity , which is essential for canonical miRNA biogenesis .
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Score: 1.00 |
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| Title: Identification of precursor transcripts for 6 novel miRNAs expands the diversity on the genomic organisation and expression of miRNA genes in rice .
| | Author: Lacombe S Nagasaki H Santi C Duval D Piegu B Bangratz M Breitler JC Guiderdoni E Brugidou C Hirsch J Cao X Brice C Panaud O Karlowski WM Sato Y Echeverria M | | Journal: BMC Plant Biol Citation: V : 8 P : 123 Year: 2008 Type: In-Process | | Literature: oryza Field: abstract Doc ID: pub19055717 Accession (PMID): 19055717 | | Abstract: BACKGROUND : The plant miRNAs represent an important class of endogenous small RNAs that guide cleavage of an mRNA target or repress its translation to control development and adaptation to stresses .
MiRNAs are nuclear-encoded genes transcribed by RNA polymerase II , producing a primary precursor that is subsequently processed by DCL1 an RNase III Dicer-like protein .
In rice hundreds of miRNAs have been described or predicted , but little is known on their genes and precursors which are important criteria to distinguish them from siRNAs .
Here we develop a combination of experimental approaches to detect novel miRNAs in rice , identify their precursor transcripts and genes and predict or validate their mRNA targets .
RESULTS : We produced four cDNA libraries from small RNA fractions extracted from distinct rice it issues .
By in silico analysis we selected 6 potential novel miRNAs , and confirmed that their expression requires OsDCL1 .
We predicted their targets and used 5RACE to validate cleavage for three of them , targeting a PPR , an SPX domain protein and a GT-like transcription factor respectively .
In addition , we identified precursor transcripts for the 6 miRNAs expressed in rice , showing that these precursors can be efficiently processed using a transient expression assay in transfected Nicotiana benthamiana leaves .
Most interestingly , we describe two precursors producing tandem miRNAs , but in distinct arrays .
We focus on one of them encoding osa-miR159a . 2 , a novel miRNA produced from the same stem-loop structure encoding the conserved osa-miR159a . 1 .
We show that this dual osa-miR159a . 2-osa-miR159a . 1 structure is conserved in distant rice species and maize .
Finally we show that the predicted mRNA target of osa-miR159a . 2 encoding a GT-like transcription factor is cleaved in vivo at the expected site .
CONCLUSION : The combination of approaches developed here identified six novel miRNAs expressed in rice which can be clearly distinguished from siRNAs .
Importantly , we show that two miRNAs can be produced from a single precursor , either from tandem stem-loops or tandemly arrayed in a single stem-loop .
This suggests that processing of these precursors could be an important regulatory step to produce one or more functional miRNAs in plants and perhaps coordinate cleavage of distinct targets in the same plant it issue .
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[ Sen. 2, subscore: 1.00 ]: MiRNAs are nuclear-encoded genes transcribed by RNA polymerase II , producing a primary precursor that is subsequently processed by DCL1 an RNase III Dicer-like protein .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
Score: 1.00 |
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| Title: Plant polycistronic precursors containing non-homologous microRNAs target transcripts encoding functionally related proteins .
| | Author: Merchan F Boualem A Crespi M Frugier F | | Journal: Genome Biol Citation: V : 10 P : R136 Year: 2009 Type: Publisher | | Literature: oryza Field: abstract Doc ID: pub19951405 Accession (PMID): 19951405 | | Abstract: ABSTRACT : BACKGROUND : MicroRNAs ( miRNAs ) are endogenous single-stranded small RNAs that regulate the expression of specific mRNAs involved in diverse biological processes .
In plants , miRNAs are generally encoded as a single species in independent transcriptional units , referred to as MIRNA genes , in contrast to animal miRNAs , which are frequently clustered .
RESULTS : We performed a comparative genomic analysis in three model plants ( rice , poplar and Arabidopsis ) and characterized miRNA clusters containing two to eight miRNA species .
These clusters usually encode miRNAs of the same family and certain share a common evolutionary origin across monocot and dicot lineages .
In addition , we identified miRNA clusters harboring miRNAs with unrelated sequences that are usually not evolutionarily conserved .
Strikingly , non-homologous miRNAs from the same cluster were predicted to target transcripts encoding related proteins .
At least four Arabidopsis non-homologous clusters were expressed as single transcriptional units .
Overexpression of one of these polycistronic precursors , producing Ath-miR859 and Ath-miR774 , led to the DCL1-dependent accumulation of both miRNAs and down-regulation of their different mRNA targets encoding F-box proteins .
CONCLUSIONS : In addition to polycistronic precursors carrying related miRNAs , plants also contain precursors allowing coordinated expression of non-homologous miRNAs to co-regulate functionally related target transcripts .
This mechanism paves the way for using polycistronic MIRNA precursors as a new molecular tool for plant biologists to simultaneously control the expression of different genes .
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[ Sen. 8, subscore: 1.00 ]: Overexpression of one of these polycistronic precursors , producing Ath-miR859 and Ath-miR774 , led to the DCL1-dependent accumulation of both miRNAs and down-regulation of their different mRNA targets encoding F-box proteins .
| | Supplemental links/files: reference in endnote online text related articles pubmed citation | |
