Leaf development involves many complex genetic interactions,signals between adjacent cells or between more distant tissues and consequent changes in cell fate.This review describes three stages in leaf development whe...Leaf development involves many complex genetic interactions,signals between adjacent cells or between more distant tissues and consequent changes in cell fate.This review describes three stages in leaf development where regulation by small RNAs have been used to modulate gene expression patterns.展开更多
Trans-acting small interfering RNAs （ta-siRNAs） and natural cis-antisense siRNAs （cisnat-siRNAs） are recently discovered small RNAs （sRNAs） involved in post-transcriptional gene silencing, ta-siRNAs are transcri...Trans-acting small interfering RNAs （ta-siRNAs） and natural cis-antisense siRNAs （cisnat-siRNAs） are recently discovered small RNAs （sRNAs） involved in post-transcriptional gene silencing, ta-siRNAs are transcribed from genomic loci and require processing by microRNAs （miRNAs）. cis-nat-siRNAs are derived from antisense RNAs produced by the simultaneous tran- scription of overlapping antisense genes. Their roles in many plant processes, including pathogen response, are mostly unknown. In this work, we employed a bioinformatic approach to identify ta-siRNAs and cis-nat-siRNAs in cassava from two sRNA libraries, one constructed from healthy cassava plants and one from plants inoculated with the bacterium Xanthomonas axonopodis pv. manihotis （Xam）. A total of 54 possible ta-siRNA loci were identified in cassava, including a homo- log of TAS3, the best studied plant ta-siRNA. Fifteen of these loci were induced, while 39 were repressed in response to Xam infection. In addition, 15 possible c/s-natural antisense transcript （cis-NAT） loci producing siRNAs were identified from overlapping antisense regions in the genome, and were found to be differentially expressed upon Xam infection. Roles of sRNAs were predicted by sequence complementarity and our results showed that many sRNAs identified in this work might be directed against various transcription factors. This work represents a significant step toward understanding the roles of sRNAs in the immune response of cassava.展开更多
Trans-acting small interfering RNAs （ta-siRNAs） are plant-specific siRNAs released from TAS precursor tran- scripts after microRNA-dependent cleavage, conversion into double-stranded RNA, and Dicer-dependent phased ...Trans-acting small interfering RNAs （ta-siRNAs） are plant-specific siRNAs released from TAS precursor tran- scripts after microRNA-dependent cleavage, conversion into double-stranded RNA, and Dicer-dependent phased process- ing. Like microRNAs （miRNAs）, ta-siRNAs direct site-specific cleavage of target RNAs at sites of extensive complementarity. Here, we show that the DICER-LIKE 4 protein of Physcomitrella patens （PpDCL4） is essential for the biogenesis of 21 nucleotide （nt） ta-siRNAs. In APpDCL4 mutants, off-sized 23 and 24-nt ta-siRNAs accumulated as the result of PpDCL3 activity. APpDCL4 mutants display severe abnormalities throughout Physcomitrella development, including sterility, that were fully reversed in APpDCL3/APpDCL4 double-mutant plants. Therefore, PpDCL3 activity, not loss of PpDCL4 function per se, is the cause of the APpDCL4 phenotypes. Additionally, we describe several new Physcomitrella trans-acting siRNA loci, three of which belong to a new family, TA56. TAS6 loci are typified by sliced miR156 and miR529 target sites and are in close proximity to PpTAS3 loci.展开更多
MicroRNAs(miRNAs)and small interfering RNAs(siRNAs)regulate gene expression in eukaryotes.Plant miRNAs modulate their targets mainly via messenger RNA(mRNA)cleavage.Small RNA(sRNA)targets have been extensively investi...MicroRNAs(miRNAs)and small interfering RNAs(siRNAs)regulate gene expression in eukaryotes.Plant miRNAs modulate their targets mainly via messenger RNA(mRNA)cleavage.Small RNA(sRNA)targets have been extensively investigated in Arabidopsis using computational prediction,experimental validation,and degradome sequencing.However,small RNA targets are largely unknown in rice(Oryza sativa).Here,we report global identification of small RNA targets using high throughput degradome sequencing in the rice indica cultivar 93-11(Oryza sativa L.ssp.indica).One hundred and seventy-seven transcripts targeted by a total of 87 unique miRNAs were identified.Of targets for the conserved miRNAs between Arabidopsis and rice,transcription factors comprise around 70%(58 in 82),indicating that these miRNAs act as masters of gene regulatory nodes in rice.In contrast,non-conserved miRNAs targeted diverse genes which provide more complex regulatory networks.In addition,5 AUXIN RESPONSE FACTORs(ARFs)cleaved by the TAS3 derived ta-siRNAs were also detected.A total of 40 sRNA targets were further validated via RNA ligasemediated 5′rapid amplification of cDNA ends(RLM 5′-RACE).Our degradome results present a detailed sRNAtarget interaction atlas,which provides a guide for the study of the roles of sRNAs and their targets in rice.展开更多
基金supported by BBRSC (Biotechnology and Biological Sciences Research Council,UK),RERAD (Rural and Environment Research and Analysis Directorate,Scotland) and the McIntyre Begonia Research Trust,UK
文摘Leaf development involves many complex genetic interactions,signals between adjacent cells or between more distant tissues and consequent changes in cell fate.This review describes three stages in leaf development where regulation by small RNAs have been used to modulate gene expression patterns.
基金funded by Dirección de Investigaciones Sede Bogotá(Grant No.201010011438)Colciencias(Contract No. 221-2008)
文摘Trans-acting small interfering RNAs （ta-siRNAs） and natural cis-antisense siRNAs （cisnat-siRNAs） are recently discovered small RNAs （sRNAs） involved in post-transcriptional gene silencing, ta-siRNAs are transcribed from genomic loci and require processing by microRNAs （miRNAs）. cis-nat-siRNAs are derived from antisense RNAs produced by the simultaneous tran- scription of overlapping antisense genes. Their roles in many plant processes, including pathogen response, are mostly unknown. In this work, we employed a bioinformatic approach to identify ta-siRNAs and cis-nat-siRNAs in cassava from two sRNA libraries, one constructed from healthy cassava plants and one from plants inoculated with the bacterium Xanthomonas axonopodis pv. manihotis （Xam）. A total of 54 possible ta-siRNA loci were identified in cassava, including a homo- log of TAS3, the best studied plant ta-siRNA. Fifteen of these loci were induced, while 39 were repressed in response to Xam infection. In addition, 15 possible c/s-natural antisense transcript （cis-NAT） loci producing siRNAs were identified from overlapping antisense regions in the genome, and were found to be differentially expressed upon Xam infection. Roles of sRNAs were predicted by sequence complementarity and our results showed that many sRNAs identified in this work might be directed against various transcription factors. This work represents a significant step toward understanding the roles of sRNAs in the immune response of cassava.
文摘Trans-acting small interfering RNAs （ta-siRNAs） are plant-specific siRNAs released from TAS precursor tran- scripts after microRNA-dependent cleavage, conversion into double-stranded RNA, and Dicer-dependent phased process- ing. Like microRNAs （miRNAs）, ta-siRNAs direct site-specific cleavage of target RNAs at sites of extensive complementarity. Here, we show that the DICER-LIKE 4 protein of Physcomitrella patens （PpDCL4） is essential for the biogenesis of 21 nucleotide （nt） ta-siRNAs. In APpDCL4 mutants, off-sized 23 and 24-nt ta-siRNAs accumulated as the result of PpDCL3 activity. APpDCL4 mutants display severe abnormalities throughout Physcomitrella development, including sterility, that were fully reversed in APpDCL3/APpDCL4 double-mutant plants. Therefore, PpDCL3 activity, not loss of PpDCL4 function per se, is the cause of the APpDCL4 phenotypes. Additionally, we describe several new Physcomitrella trans-acting siRNA loci, three of which belong to a new family, TA56. TAS6 loci are typified by sliced miR156 and miR529 target sites and are in close proximity to PpTAS3 loci.
基金This work was supported by National Basic Research Program of China(Nos.2009CB941500 and 2005CB522400 to X.C.)by National Natural Science Foundation of China(Grant Nos.30870534 and 30621001 to X.C.).
文摘MicroRNAs(miRNAs)and small interfering RNAs(siRNAs)regulate gene expression in eukaryotes.Plant miRNAs modulate their targets mainly via messenger RNA(mRNA)cleavage.Small RNA(sRNA)targets have been extensively investigated in Arabidopsis using computational prediction,experimental validation,and degradome sequencing.However,small RNA targets are largely unknown in rice(Oryza sativa).Here,we report global identification of small RNA targets using high throughput degradome sequencing in the rice indica cultivar 93-11(Oryza sativa L.ssp.indica).One hundred and seventy-seven transcripts targeted by a total of 87 unique miRNAs were identified.Of targets for the conserved miRNAs between Arabidopsis and rice,transcription factors comprise around 70%(58 in 82),indicating that these miRNAs act as masters of gene regulatory nodes in rice.In contrast,non-conserved miRNAs targeted diverse genes which provide more complex regulatory networks.In addition,5 AUXIN RESPONSE FACTORs(ARFs)cleaved by the TAS3 derived ta-siRNAs were also detected.A total of 40 sRNA targets were further validated via RNA ligasemediated 5′rapid amplification of cDNA ends(RLM 5′-RACE).Our degradome results present a detailed sRNAtarget interaction atlas,which provides a guide for the study of the roles of sRNAs and their targets in rice.
