scholarly journals Systematic Characterization of MicroRNA Processing Modes in Plants With Parallel Amplification of RNA Ends

2021 ◽  
Vol 12 ◽  
Author(s):  
Ning Li ◽  
Guodong Ren
Keyword(s):  
Mirna Family ◽  
Mature Mirnas ◽  
Rnase Iii ◽  
Mirna Processing ◽  
Short Loop ◽  
Cloning Method ◽  
Processing Modes ◽  
Microrna Processing ◽  
Contamination Levels

In plants, the RNase III-type enzyme Dicer-like 1 (DCL1) processes most microRNAs (miRNAs) from their primary transcripts called pri-miRNAs. Four distinct processing modes (i.e., short base to loop, sequential base to loop, short loop to base, and sequential loop to base) have been characterized in Arabidopsis, mainly by the Specific Parallel Amplification of RNA Ends (SPARE) approach. However, SPARE is a targeted cloning method which requires optimization of cloning efficiency and specificity for each target. PARE (Parallel Amplification of RNA Ends) is an untargeted method per se and is widely used to identify miRNA mediated target slicing events. A major concern with PARE in characterizing miRNA processing modes is the potential contamination of mature miRNAs. Here, we provide a method to estimate miRNA contamination levels and showed that most publicly available PARE libraries have negligible miRNA contamination. Both the numbers and processing modes detected by PARE were similar to those identified by SPARE in Arabidopsis. PARE also determined the processing modes of 36 Arabidopsis miRNAs that were unexplored by SPARE, suggesting that it can complement the SPARE approach. Using publicly available PARE datasets, we identified the processing modes of 36, 91, 90, and 54 miRNAs in maize, rice, soybean, and tomato, respectively, and demonstrated that the processing mode was conserved overall within each miRNA family. Through its power of tracking miRNA processing remnants, PARE also facilitated miRNA characterization and annotation.

scholarly journals The roles of rice microRNAs in rice-Magnaporthe oryzae interaction

2019 ◽  
Vol 1 (1) ◽  
Author(s):  
Yan Li ◽  
John Martin Jerome Jeyakumar ◽  
Qin Feng ◽  
Zhi-Xue Zhao ◽  
Jing Fan ◽  
...  
Keyword(s):  
Gene Silencing ◽  
Magnaporthe Oryzae ◽  
Functional Characterization ◽  
Mature Mirnas ◽  
Transcriptional Gene Silencing ◽  
Rnase Iii ◽  
Stem Loop ◽  
Mirna Genes ◽  
Stem Loop Structure

AbstractMicroRNAs (miRNAs) are a class of small (20–24 nucleotides (nt) long) non-coding RNAs. One mature miRNA can be transcribed from one or more gene loci known as miRNA genes (MIRs). The transcript of a MIR forms a stem-loop structure that is processed into a 20–24-nt miRNA-5p/−3p duplex by RNase III family endoribonucleases such as Dicer-like1 (DCL1). In turn, the overhang ends of the duplex are methylated by HUA ENHANCER 1 (HEN1), generating stabilized mature miRNAs. The mature miRNAs are loaded onto ARGONAUTE (AGO) proteins, forming a miRNA-induced gene silencing complex (miRISC). Then, the miRISC binds to target sites with sequences complementary to the miRNAs, leading to either cleavage or translational inhibition of the target mRNAs, or methylation of the target sequences, resulting in post-transcriptional and transcriptional gene silencing, respectively. In the past decade, more than 700 miRNAs have been identified in rice, a subset of which have been found to be responsive to the rice blast fungus, Magnaporthe oryzae, or its elicitors. Moreover, members of 10 miRNA families have been found to positively or negatively regulate rice defense against M. oryzae, namely miR160, miR164, miR166, miR167, miR169, miR319, miR396, miR398, miR444 and miR7695. This review summarizes the identification and functional characterization of the miRNAs, which respond to M. oryzae or its elicitors and describes the current understanding of the complicated but well-organized network in the context of rice-M. oryzae interaction.

Molecular Characterization of Arcobacter Isolates Collected in a Poultry Slaughterhouse

2003 ◽  
Vol 66 (3) ◽  
pp. 364-369 ◽  
Author(s):  
KURT HOUF ◽  
LIEVEN DE ZUTTER ◽  
BIEKE VERBEKE ◽  
JAN VAN HOOF ◽  
PETER VANDAMME
Keyword(s):  
Random Amplified Polymorphic Dna ◽  
Processing Plant ◽  
Poultry Products ◽  
Before And After ◽  
Arcobacter Butzleri ◽  
Processing Water ◽  
Contamination Levels ◽  
Almost All ◽  
Skin Samples

In a poultry slaughterhouse, Arcobacter contamination was examined over a period of 1 week to establish possible routes of contamination. Samples were collected from the slaughter equipment and from processing water before the onset of slaughter and from the first broiler flock slaughtered on each sampling day. Characterization of 1,079 isolates by enterobacterial repetitive intergenic consensus–polymerase chain reaction and a random amplified polymorphic DNA assay resulted in the delineation of 159 Arcobacter butzleri and 139 Arcobacter cryaerophilus types. From almost all 140 neck skin samples collected before and after evisceration, A. butzleri and A. cryaerophilus were isolated simultaneously at contamination levels ranging from 101 to 104 CFU/g. Only six A. butzleri types present in the slaughterhouse environment were also present on the broiler carcasses. None of the A. cryaerophilus genotypes were detected in both the neck skin and the environmental samples. All A. butzleri types isolated from the feather samples were also isolated from broiler neck skin samples. The slaughter equipment was contaminated with arcobacters before the onset of slaughter, but it appeared unlikely that contamination through the slaughter equipment alone explained the high contamination levels on poultry products. Arcobacters were also present in processing water, but types present in water and poultry products were different. Characterization of the Arcobacter isolates did not clarify the routes of transmission, probably because of the extreme heterogeneity among Arcobacter isolates. However, the results obtained in this study brought to light insufficient decontamination at the processing plant involved in the study and confirmed the survival capacity of certain A. butzleri strains.

scholarly journals SERRATE interacts with the nuclear exosome targeting (NEXT) complex to degrade primary miRNA precursors in Arabidopsis

2020 ◽  
Vol 48 (12) ◽  
pp. 6839-6854 ◽  
Author(s):  
Mateusz Bajczyk ◽  
Heike Lange ◽  
Dawid Bielewicz ◽  
Lukasz Szewc ◽  
Susheel S Bhat ◽  
...  
Keyword(s):  
Rna Binding ◽  
Mature Mirnas ◽  
Mirna Biogenesis ◽  
Processing Efficiency ◽  
Developmental Defects ◽  
Rna Surveillance ◽  
Mirna Processing ◽  
Rna Targets ◽  
Nuclear Exosome ◽  
Mirna Degradation

Abstract SERRATE/ARS2 is a conserved RNA effector protein involved in transcription, processing and export of different types of RNAs. In Arabidopsis, the best-studied function of SERRATE (SE) is to promote miRNA processing. Here, we report that SE interacts with the nuclear exosome targeting (NEXT) complex, comprising the RNA helicase HEN2, the RNA binding protein RBM7 and one of the two zinc-knuckle proteins ZCCHC8A/ZCCHC8B. The identification of common targets of SE and HEN2 by RNA-seq supports the idea that SE cooperates with NEXT for RNA surveillance by the nuclear exosome. Among the RNA targets accumulating in absence of SE or NEXT are miRNA precursors. Loss of NEXT components results in the accumulation of pri-miRNAs without affecting levels of miRNAs, indicating that NEXT is, unlike SE, not required for miRNA processing. As compared to se-2, se-2 hen2-2 double mutants showed increased accumulation of pri-miRNAs, but partially restored levels of mature miRNAs and attenuated developmental defects. We propose that the slow degradation of pri-miRNAs caused by loss of HEN2 compensates for the poor miRNA processing efficiency in se-2 mutants, and that SE regulates miRNA biogenesis through its double contribution in promoting miRNA processing but also pri-miRNA degradation through the recruitment of the NEXT complex.

scholarly journals The RNase III enzyme Dicer is essential for germinal center B-cell formation

Blood ◽  
2012 ◽  
Vol 119 (3) ◽  
pp. 767-776 ◽  
Author(s):  
Shengli Xu ◽  
Ke Guo ◽  
Qi Zeng ◽  
Jianxin Huo ◽  
Kong-Peng Lam
Keyword(s):  
B Cells ◽  
B Cell ◽  
Germinal Center ◽  
Plasma Cells ◽  
Cytidine Deaminase ◽  
Cell Formation ◽  
Terminal Differentiation ◽  
Mature Mirnas ◽  
Rnase Iii ◽  
Proapoptotic Protein

Abstract MicroRNAs (miRNAs) are short noncoding RNAs that regulate gene expression and are important for pre-B and follicular B lymphopoiesis as demonstrated, respectively, by mb-1-Cre– and cd19-Cre–mediated deletion of Dicer, the RNase III enzyme critical for generating mature miRNAs. To explore the role of miRNAs in B-cell terminal differentiation, we use Aicda-Cre to specifically delete Dicer in activated B cells where activation-induced cytidine deaminase is highly expressed. We demonstrate that mutant mice fail to produce high-affinity class-switched antibodies and generate memory B and long-lived plasma cells on immunization with a T cell–dependent antigen. More importantly, germinal center (GC) B-cell formation is drastically compromised in the absence of Dicer, as a result of defects in cell proliferation and survival. Dicer-deficient GC B cells express higher levels of cell cycle inhibitor genes and proapoptotic protein Bim. Ablation of Bim could partially rescue the defect in GC B-cell formation in Dicer-deficient mice. Taken together, our data suggest that Dicer and probably miRNAs are critical for GC B-cell formation during B-cell terminal differentiation.

Characterization of Ti/TiN Films and SiO2/Ti Interfaces by Use of X-Ray Photoelectron Spectroscopy

1993 ◽  
Vol 318 ◽  
Author(s):  
Joffre Bernard ◽  
Ercan Adem ◽  
Seshadri Ramaswami
Keyword(s):  
Integrated Circuits ◽  
Photoelectron Spectroscopy ◽  
Ambient Air ◽  
Tin Films ◽  
X Ray ◽  
Surface And Interface ◽  
Surface Analysis Techniques ◽  
Contamination Levels ◽  
Reflective Coatings

ABSTRACTThe deposition and processing of thin films, such as barrier metals and anti-reflective coatings, can be enhanced using the information provided by various surface analysis techniques. We will show the application of x-ray photoelectron spectroscopy(XPS) to the production of Ti and TiN films suitable for use in ULSI CMOS integrated circuits. XPS can separate Ti and N photoelectron peaks and detect low (1.0-5.0 atomic%) contamination levels while providing surface and interface chemical state information. In this paper we will show that a) the effect of TiN deposition on subsequent Ti film quality from the same Ti target was determined to be minimal, b) the relation of anneal temperature to the extent of SiO2 reduction by Ti metal was characterized on SiO2/Ti/TiN structures for temperatures from 600°C to 800°C, and c) the absorption of O into TiN films from ambient air was detected and confirmed.

Sign in / Sign up

Export Citation Format

Share Document