scholarly journals Biogenesis of a young, 22-nt microRNA in Phaseoleae species by precursor-programmed uridylation

2018 ◽  
Author(s):  
Qili Fei ◽  
Yu Yu ◽  
Li Liu ◽  
Yu Zhang ◽  
Patricia Baldrich ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Small Rnas ◽  
Post Processing ◽  
Young Plant ◽  
Precursor Processing ◽  
Mature Form ◽  
Plant Mirna ◽  
Secondary Sirnas ◽  
Precursor Structure ◽  
Mirna Duplex

ABSTRACTPhased, secondary siRNAs (phasiRNAs) represent a class of small RNAs in plants generated via distinct biogenesis pathways, predominantly dependent on the activity of 22 nt miRNAs. Most 22 nt miRNAs are processed by DCL1 from miRNA precursors containing an asymmetric bulge, yielding a 22/21 nt miRNA/miRNA* duplex. Here we show that miR1510, a soybean miRNA capable of triggering phasiRNA production from numerous NB-LRRs, previously described as 21 nt in its mature form, primarily accumulates as a 22 nt isoform via monouridylation. We demonstrate that in Arabidopsis, this uridylation is performed by HESO1. Biochemical experiments showed that the 3’ terminus of miR1510 is only partially 2’-O-methylated, because of the terminal mispairing in the miR1510/miR1510* duplex that inhibits HEN1 activity in soybean. miR1510 emerged in the Phaseoleae ~41 to 42 MYA with a conserved precursor structure yielding a 22 nt monouridylated form, yet a variant in mung bean is processed directly in a 22 nt mature form. This analysis of miR1510 yields two observations: (1) plants can utilize post-processing modification to generate abundant 22 nt miRNA isoforms to more efficiently regulate target mRNA abundances; (2) comparative analysis demonstrates an example of selective optimization of precursor processing of a young plant miRNA.

scholarly journals Biogenesis of a 22-nt microRNA in Phaseoleae species by precursor-programmed uridylation

2018 ◽  
Vol 115 (31) ◽  
pp. 8037-8042 ◽  
Author(s):  
Qili Fei ◽  
Yu Yu ◽  
Li Liu ◽  
Yu Zhang ◽  
Patricia Baldrich ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Small Rnas ◽  
Leucine Rich Repeat ◽  
Young Plant ◽  
Precursor Processing ◽  
Mature Form ◽  
Plant Mirna ◽  
Secondary Sirnas ◽  
Precursor Structure ◽  
Mirna Duplex

Phased, secondary siRNAs (phasiRNAs) represent a class of small RNAs in plants generated via distinct biogenesis pathways, predominantly dependent on the activity of 22-nt miRNAs. Most 22-nt miRNAs are processed by DCL1 from miRNA precursors containing an asymmetric bulge, yielding a 22/21-nt miRNA/miRNA* duplex. Here we show that miR1510, a soybean miRNA capable of triggering phasiRNA production from numerous nucleotide-binding leucine-rich repeat (NB-LRRs), previously described as 21 nt in its mature form, primarily accumulates as a 22-nt isoform via monouridylation. We demonstrate that, in Arabidopsis, this uridylation is performed by HESO1. Biochemical experiments showed that the 3′ terminus of miR1510 is only partially 2′-O-methylated because of the terminal mispairing in the miR1510/miR1510* duplex that inhibits HEN1 activity in soybean. miR1510 emerged in the Phaseoleae ∼41–42 million years ago with a conserved precursor structure yielding a 22-nt monouridylated form, yet a variant in mung bean is processed directly in a 22-nt mature form. This analysis of miR1510 yields two observations: (i) plants can utilize postprocessing modification to generate abundant 22-nt miRNA isoforms to more efficiently regulate target mRNA abundances; and (ii) comparative analysis demonstrates an example of selective optimization of precursor processing of a young plant miRNA.

Comparative analysis of MGEX products for post-processing multi-GNSS PPP

Measurement ◽  
2019 ◽  
Vol 145 ◽  
pp. 361-369 ◽  
Author(s):  
Berkay Bahadur ◽  
Metin Nohutcu
Keyword(s):  
Comparative Analysis ◽  
Post Processing

scholarly journals Comparative analysis of virus-derived small RNAs within cassava (Manihot esculenta Crantz) infected with cassava brown streak viruses

2016 ◽  
Vol 215 ◽  
pp. 1-11 ◽  
Author(s):  
Emmanuel Ogwok ◽  
Muhammad Ilyas ◽  
Titus Alicai ◽  
Marie E.C. Rey ◽  
Nigel J. Taylor
Keyword(s):  
Comparative Analysis ◽  
Manihot Esculenta ◽  
Small Rnas ◽  
Manihot Esculenta Crantz ◽  
Brown Streak

scholarly journals The Streptochaeta Genome and the Evolution of the Grasses

2021 ◽  
Vol 12 ◽  
Author(s):  
Arun S. Seetharam ◽  
Yunqing Yu ◽  
Sébastien Bélanger ◽  
Lynn G. Clark ◽  
Blake C. Meyers ◽  
...  
Keyword(s):  
Small Rnas ◽  
Rice Genome ◽  
Gene Trees ◽  
Floral Structure ◽  
Final Assembly ◽  
Gene Space ◽  
Secondary Sirnas ◽  
Large Families ◽  
The Common ◽  
Post Transcriptional Regulation

In this work, we sequenced and annotated the genome of Streptochaeta angustifolia, one of two genera in the grass subfamily Anomochlooideae, a lineage sister to all other grasses. The final assembly size is over 99% of the estimated genome size. We find good collinearity with the rice genome and have captured most of the gene space. Streptochaeta is similar to other grasses in the structure of its fruit (a caryopsis or grain) but has peculiar flowers and inflorescences that are distinct from those in the outgroups and in other grasses. To provide tools for investigations of floral structure, we analyzed two large families of transcription factors, AP2-like and R2R3 MYBs, that are known to control floral and spikelet development in rice and maize among other grasses. Many of these are also regulated by small RNAs. Structure of the gene trees showed that the well documented whole genome duplication at the origin of the grasses (ρ) occurred before the divergence of the Anomochlooideae lineage from the lineage leading to the rest of the grasses (the spikelet clade) and thus that the common ancestor of all grasses probably had two copies of the developmental genes. However, Streptochaeta (and by inference other members of Anomochlooideae) has lost one copy of many genes. The peculiar floral morphology of Streptochaeta may thus have derived from an ancestral plant that was morphologically similar to the spikelet-bearing grasses. We further identify 114 loci producing microRNAs and 89 loci generating phased, secondary siRNAs, classes of small RNAs known to be influential in transcriptional and post-transcriptional regulation of several plant functions.

scholarly journals Comparative analysis of small RNAs released by the filarial nematode Litomosoides sigmodontis in vitro and in vivo

2019 ◽  
Vol 13 (11) ◽  
pp. e0007811 ◽  
Author(s):  
Juan F. Quintana ◽  
Sujai Kumar ◽  
Alasdair Ivens ◽  
Franklin W. N. Chow ◽  
Anna M. Hoy ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Small Rnas ◽  
Filarial Nematode ◽  
Litomosoides Sigmodontis

scholarly journals Comparative Analysis of Cotton Small RNAs and Their Target Genes in Response to Salt Stress

Genes ◽  
2017 ◽  
Vol 8 (12) ◽  
pp. 369 ◽  
Author(s):  
Zujun Yin ◽  
Xiulan Han ◽  
Yan Li ◽  
Junjuan Wang ◽  
Delong Wang ◽  
...  
Keyword(s):  
Salt Stress ◽  
Comparative Analysis ◽  
Small Rnas ◽  
Target Genes

Distinct Populations of Primary and Secondary Effectors During RNAi in C. elegans

Science ◽  
2006 ◽  
Vol 315 (5809) ◽  
pp. 241-244 ◽  
Author(s):  
Julia Pak ◽  
Andrew Fire
Keyword(s):  
Rna Interference ◽  
Small Rnas ◽  
De Novo ◽  
Messenger Rnas ◽  
Cellular Regulation ◽  
Rdrp Activity ◽  
Antisense Transcripts ◽  
Double Stranded Rna ◽  
C Elegans ◽  
Secondary Sirnas

RNA interference (RNAi) is a phylogenetically widespread gene-silencing process triggered by double-stranded RNA. In plants and Caenorhabditis elegans, two distinct populations of small RNAs have been proposed to participate in RNAi: “Primary siRNAs” (derived from DICER nuclease-mediated cleavage of the original trigger) and “secondary siRNAs” [additional small RNAs whose synthesis requires an RNA-directed RNA polymerase (RdRP)]. Analyzing small RNAs associated with ongoing RNAi in C. elegans, we found that secondary siRNAs constitute the vast majority. The bulk of secondary siRNAs exhibited structure and sequence indicative of a biosynthetic mode whereby each molecule derives from an independent de novo initiation by RdRP. Analysis of endogenous small RNAs indicated that a fraction derive from a biosynthetic mechanism that is similar to that of secondary siRNAs formed during RNAi, suggesting that small antisense transcripts derived from cellular messenger RNAs by RdRP activity may have key roles in cellular regulation.

scholarly journals Functional specialization of monocot DCL3 and DCL5 proteins through the evolution of the PAZ domain

2021 ◽  
Author(s):  
Shirui Chen ◽  
Wei Liu ◽  
Masahiro Naganuma ◽  
Yukihide Tomari ◽  
Hiro-oki Iwakawa
Keyword(s):  
Small Rnas ◽  
Rna Silencing ◽  
Functional Differentiation ◽  
Small Interfering Rnas ◽  
Double Stranded Rna ◽  
Secondary Sirnas ◽  
Fixed End ◽  
Paz Domain ◽  
Reproductive Processes

Monocot DICER-LIKE3 (DCL3) and DCL5 produce distinct 24-nt heterochromatic small interfering RNAs (hc-siRNAs) and phased secondary siRNAs (phasiRNAs). The former small RNAs are linked to plant heterochromatin, and the latter to reproductive processes. It is assumed that these DCLs evolved from an ancient "eudicot-type" DCL3 ancestor, which may have produced both types of siRNAs. However, how functional differentiation was achieved after gene duplication remains elusive. Here, we find that monocot DCL3 and DCL5 exhibit biochemically distinct preferences for 3′ overhangs and 5′ phosphates, consistent with the structural properties of their in vivo double-stranded RNA substrates. Importantly, these distinct substrate specificities are determined by the PAZ domains of DCL3 and DCL5 which have accumulated mutations during the course of evolution. These data explain the mechanism by which these DCLs cleave their cognate substrates from a fixed end, ensuring the production of functional siRNAs. Our study also indicates how plants have diversified and optimized RNA silencing mechanisms during evolution.

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