Identification and characterization of novel amphioxus microRNAs by Solexa sequencing

Chen, Xi; Li, Qibin; Wang, Jin; Guo, Xing; Jiang, Xiangrui; Ren, Zhenning; Weng, Chun-Yue; Sun, Guoxiang; Wang, Xiuqiang; Liu, Yaping; Ma, Lijia; Chen, Jun-Yuan; Wang, Jun; Zen, Ke; Zhang, Junfeng; Zhang, Chenyu

doi:10.1186/gb-2009-10-7-r78

Cited by 139 publications

(128 citation statements)

References 35 publications

(87 reference statements)

Supporting

Mentioning

121

Contrasting

Unclassified

Order By: Relevance

“…The sequencing procedure was conducted as previously described [5,52]. Briefly, total RNA was extracted from 100 ml of serum using the Trizol Reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's instructions.…”

Section: Solexa Sequencingmentioning

confidence: 99%

Exogenous plant MIR168a specifically targets mammalian LDLRAP1: evidence of cross-kingdom regulation by microRNA

et al. 2011

Self Cite

View full text Add to dashboard Cite

Our previous studies have demonstrated that stable microRNAs (miRNAs) in mammalian serum and plasma are actively secreted from tissues and cells and can serve as a novel class of biomarkers for diseases, and act as signaling molecules in intercellular communication. Here, we report the surprising finding that exogenous plant miRNAs are present in the sera and tissues of various animals and that these exogenous plant miRNAs are primarily acquired orally, through food intake. MIR168a is abundant in rice and is one of the most highly enriched exogenous plant miRNAs in the sera of Chinese subjects. Functional studies in vitro and in vivo demonstrated that MIR168a could bind to the human/mouse low-density lipoprotein receptor adapter protein 1 (LDLRAP1) mRNA, inhibit LDLRAP1 expression in liver, and consequently decrease LDL removal from mouse plasma. These findings demonstrate that exogenous plant miRNAs in food can regulate the expression of target genes in mammals.

show abstract

Section: Solexa Sequencingmentioning

confidence: 99%

Exogenous plant MIR168a specifically targets mammalian LDLRAP1: evidence of cross-kingdom regulation by microRNA

et al. 2011

Self Cite

View full text Add to dashboard Cite

show abstract

“…As a high-throughput sequencing technology producing highly accurate, reproducible, and quantitative readouts of small RNA expression, Solexa can detect and define all RNA molecules including miRNA with various expression levels, and can unambiguously distinguish miRNAs from other small RNAs by referencing to various established RNA libraries [7,15]. Using this method, we detected a total of 2 487 394 reads for mature milk Muscle-specific [20][21][22] Table S1).…”

Section: Genome-wide Mirna Expression Profiling In Cow Milk At Differmentioning

confidence: 99%

“…The sequencing procedure was conducted as previously described [7,15]. Briefly, 2.5 ml mature milk, colostrum, or serum from each cow was pooled together.…”

Section: Solexa Sequencingmentioning

confidence: 99%

Identification and characterization of microRNAs in raw milk during different periods of lactation, commercial fluid, and powdered milk products

et al. 2010

Self Cite

View full text Add to dashboard Cite

Recent baby formula milk powder contamination incidents have shown that the classic markers or standards in milk quality control are insufficient in identifying "manipulated" poor-quality milk. In the present study, we demonstrated for the first time that cow milk contains large amounts of microRNAs (miRNAs) and that the unique expression profile of milk-specific miRNAs can serve as a novel indicator and possible new standard for the quality control of raw milk and milk-related commercial products, such as fluid milk and powdered formula milk. First, using Solexa sequencing, we systematically screened miRNA expression in raw milk and identified a total of 245 miRNAs in raw milk. Unlike other classic biomarkers whose expression levels are nearly identical at different periods of lactation, individual miRNAs can be significantly altered during lactation process, implicating that miRNAs may be a more accurate indicator to reflect the quality alteration of milk. Second, using TaqMan probe-based miRNA quantitative RT-PCR, we further identified seven miRNAs that have a relatively consistent expression throughout the lactation process, and more importantly, the expression profile of these seven milk-specific miRNAs can serve as an ideal biomarker for discriminating poor-quality or "manipulated" milk from pure raw milk, as well as for the quality control of commercial milk products, such as fluid milk and powdered formula milk. Together, our findings provide a basis for understanding the physiological role of milk miRNAs and a new potential standard for determining the quality of raw milk or milk-related commercial products.

show abstract

“…Remaining unmatched sequences were aligned to the mouse genome build mm9 with a perfect match requirement in Sequery v1.0 (31). Sequences that aligned to the genome were categorized as novel endo-siRNA, miRNA, snoRNA, and pil-RNA based on length, nucleotide composition, and secondary structures using Sequery v1.0, MIREAP 0.2, and snoREPORT 1.0 (32,33). Remaining sequences that aligned to the genome but were not categorized were kept as unidentifiable small RNAs.…”

Section: Methodsmentioning

confidence: 99%

A Novel Class of Somatic Small RNAs Similar to Germ Cell Pachytene PIWI-interacting Small RNAs

Ortogero

Schuster

Oliver

et al. 2014

Journal of Biological Chemistry

View full text Add to dashboard Cite

Background: Germ cells exclusively express PIWI-interacting small RNAs for transposon and gene regulation. Results: Somatic cells express similar RNAs that do not require known small RNA proteins and that partially complement mRNAs. Conclusion: These somatic small RNAs represent a novel small RNA population, which potentially regulates mRNA translation. Significance: Defining novel small RNAs is essential for elucidating the mechanisms that control gene expression.

show abstract

Identification and characterization of novel amphioxus microRNAs by Solexa sequencing

Cited by 139 publications

References 35 publications

Exogenous plant MIR168a specifically targets mammalian LDLRAP1: evidence of cross-kingdom regulation by microRNA

Exogenous plant MIR168a specifically targets mammalian LDLRAP1: evidence of cross-kingdom regulation by microRNA

Identification and characterization of microRNAs in raw milk during different periods of lactation, commercial fluid, and powdered milk products

A Novel Class of Somatic Small RNAs Similar to Germ Cell Pachytene PIWI-interacting Small RNAs

Contact Info

Product

Resources

About