Identification of novel micrornas in <i>Xenopus laevis</i> metaphase ii arrested eggs

Ambady, Sakthikumar; Wu, Zheyang; Dominko, Tanja

doi:10.1002/dvg.22010

Cited by 35 publications

(26 citation statements)

References 112 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…To start addressing this, we designed and validated a miRNA prediction pipeline that processes unannotated small RNA reads into experimentally detectable, novel miRNAs. Interestingly, while we were writing this paper the sequence of miR-F appeared in a list of putative miRNAs from X. laevis, further validating our prediction pipeline (Ambady et al 2012).…”

Section: Discussionsupporting

confidence: 56%

Small RNA profiling of Xenopus embryos reveals novel miRNAs and a new class of small RNAs derived from intronic transposable elements

Harding¹,

Horswell

Heliot³

et al. 2013

Genome Res.

View full text Add to dashboard Cite

Small RNA control of gene expression is critical for developmental processes in vertebrate embryos. To determine the dynamics of small RNA expression and to uncover novel small RNAs in the early vertebrate embryo, we performed high-throughput sequencing of all small RNAs in Xenopus tropicalis embryos at three developmental time points and in dissected halves of gastrula embryos. This analysis allowed us to identify novel microRNAs and we show that microRNA expression is highly dynamic and spatially localized in early embryos. In addition, we have developed a microRNA prediction pipeline and demonstrate that it has the power to predict new miRNAs that are experimentally detectable in frogs, mice, and humans. By combining the small RNA sequencing with mRNA profiling at the different developmental stages, we identify a new class of small noncoding RNAs that we name siteRNAs, which align in clusters to introns of protein-coding genes. We show that siteRNAs are derived from remnants of transposable elements present in the introns. We find that genes containing clusters of siteRNAs are transcriptionally repressed as compared with all genes. Furthermore, we show that this is true for individual genes containing siteRNA clusters, and that these genes are enriched in specific repressive histone modifications. Our data thus suggest a new mechanism of siteRNA-mediated gene silencing in vertebrates, and provide an example of how mobile elements can affect gene regulation.

show abstract

Section: Discussionsupporting

confidence: 56%

Small RNA profiling of Xenopus embryos reveals novel miRNAs and a new class of small RNAs derived from intronic transposable elements

Harding¹,

Horswell

Heliot³

et al. 2013

Genome Res.

View full text Add to dashboard Cite

show abstract

“…Flanking sequences of mapped reads were subjected to secondary structure analysis to predict pre-miRNA sequences using Mfold software. The criteria used for miRNA annotation and hairpin structure determination are presented in Table 1 [19, 20]. …”

Section: Methodsmentioning

confidence: 99%

Study of MicroRNAs Related to the Liver Regeneration of the Whitespotted Bamboo Shark,Chiloscyllium plagiosum

Zhang

Nie

et al. 2013

BioMed Research International

View full text Add to dashboard Cite

To understand the mechanisms of liver regeneration better to promote research examining liver diseases and marine biology, normal and regenerative liver tissues of Chiloscyllium plagiosum were harvested 0 h and 24 h after partial hepatectomy (PH) and used to isolate small RNAs for miRNA sequencing. In total, 91 known miRNAs and 166 putative candidate (PC) miRNAs were identified for the first time in Chiloscyllium plagiosum. Through target prediction and GO analysis, 46 of 91 known miRNAs were screened specially for cellular proliferation and growth. Differential expression levels of three miRNAs (xtr-miR-125b, fru-miR-204, and hsa-miR-142-3p_R-1) related to cellular proliferation and apoptosis were measured in normal and regenerating liver tissues at 0 h, 6 h, 12 h, and 24 h using real-time PCR. The expression of these miRNAs showed a rising trend in regenerative liver tissues at 6 h and 12 h but exhibited a downward trend compared to normal levels at 24 h. Differentially expressed genes were screened in normal and regenerating liver tissues at 24 h by DDRT-PCR, and ten sequences were identified. This study provided information regarding the function of genes related to liver regeneration, deepened the understanding of mechanisms of liver regeneration, and resulted in the addition of a significant number of novel miRNAs sequences to GenBank.

show abstract

“…However, the reason why some additional mappable sequences (such as groups 2b and 3) may not be selected as candidate radish miRNAs was that they were mapped to the selected miRNAs/pre-miRNAs in miRbase, but could not be mapped to the radish reference sequences. When complete radish genome sequence data becomes available, more radish miRNAs will be obtained (Ambady et al 2012). Many miRNAs have been identified in response to HMs (e.g., Cd, Hg, As, and Al) in rice (Ding et al 2013), M. truncatula (Zhou et al 2012), B. juncea (Srivastava et al 2013) and soybean , which provided a means of exploring the molecular basis for metal adaptive responses in plants (Gielen et al 2012;Gupta et al 2014;Khraiwesh et al 2012;Yang and Chen 2013).…”

Section: Identification Of Pb-responsive Mirnas By Solexa Sequencing mentioning

confidence: 99%

Identification of Radish (Raphanus sativus L.) miRNAs and Their Target Genes to Explore miRNA-Mediated Regulatory Networks in Lead (Pb) Stress Responses by High-Throughput Sequencing and Degradome Analysis

et al. 2014

View full text Add to dashboard Cite

Increasing evidence has revealed that microRNA (miRNA)-mediated gene regulation plays a significant role in response to heavy metal stresses. However, there is little information available about the expression patterns or roles of miRNAs under lead toxicity stress in plants. The radish is an important root vegetable crop with a fleshy taproot as the edible part. It was of vital importance to investigate the response mechanisms and explore the regulatory network at the molecular level under the heavy metal stresses in radish. In the present study, using high-throughput sequencing and degradome analysis, a genome-wide identification of radish miRNA and their targets under the exposure of Pb stress was conducted. A total of 74 known and 173 potential novel miRNAs were successfully identified from two radish root libraries of one untreated control (CK) and one Pb-stressed (Pb500). Of these, 25 known and nine novel miRNAs were significantly differentially expressed and identified as Pbresponsive miRNAs. Degradome analysis revealed that 1,979 miRNA-mRNA target transcripts could potentially be cleaved. Gene Ontology (GO) analysis revealed that these target transcripts were predominately involved in the regulation of transcription, defense responses, and binding related terms. The identified target genes for Pb-responsive miRNAs were mainly involved in stress-related signal sensing and transduction, specific metal uptake and homeostasis mechanisms. Additionally, the expression patterns of 20 Pbresponsive miRNAs and six target genes were validated by quantitative real-time PCR (qRT-PCR). These results provide fundamental insights into the miRNA-mediated regulatory networks and molecular mechanisms underlying plant responsiveness to Pb stresses.

show abstract

Identification of novel micrornas in Xenopus laevis metaphase ii arrested eggs

Cited by 35 publications

References 112 publications

Small RNA profiling of Xenopus embryos reveals novel miRNAs and a new class of small RNAs derived from intronic transposable elements

Small RNA profiling of Xenopus embryos reveals novel miRNAs and a new class of small RNAs derived from intronic transposable elements

Study of MicroRNAs Related to the Liver Regeneration of the Whitespotted Bamboo Shark,Chiloscyllium plagiosum

Identification of Radish (Raphanus sativus L.) miRNAs and Their Target Genes to Explore miRNA-Mediated Regulatory Networks in Lead (Pb) Stress Responses by High-Throughput Sequencing and Degradome Analysis

Contact Info

Product

Resources

About