GEO DataSets

(Submitter supplied) MicroRNAs of bilaterian animals undergo posttranscriptional modifications such as methylation, tailing and trimming that regulate miRNA stability and function. To gain insight on the evolution of miRNA posttranscriptional modification, we studied regulation of miRNA stability by methylation in the sea anemone Nematostella vectensis, a representative of Cnidaria, the sister group of Bilateria.

Organism:

Nematostella vectensis

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL23029

30 Samples

Download data: TXT

(Submitter supplied) We explored the potential for small RNA biology in organisms that diverged basal to Bilateria, identifying both miRNAs and piRNAs in Nematsotella and Amphimedon

Organism:

Trichoplax adhaerens; Monosiga brevicollis; Amphimedon queenslandica; Nematostella vectensis

Type:

Non-coding RNA profiling by high throughput sequencing

4 related Platforms

17 Samples

Download data: TXT

(Submitter supplied) Knockdown of NveAGO1 and NveAGO2 in Nematostella results in severe developmental defects. NveAGO1 and NveAGO2 immunoprecipitation reveals subfunctionalization for differential miRNA sorting as well as siRNA specialization.

Organism:

Nematostella vectensis

Type:

Non-coding RNA profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platform:

GPL23029

30 Samples

Download data: XLSX

(Submitter supplied) Bilaterian animals differ from other metazoans in their apparent bilateral symmetry and the development of a third germ layer. Both might have facilitated the evolution of the diverse and complex bilaterian body plans. The first cnidarian genome sequence revealed that despite their morphological simplicity, this sister group to all bilaterians shares an immense genomic complexity with vertebrates. This suggested that it might have been the complexity of gene regulation which increased during the evolution of bilaterians. more...

Organism:

Nematostella vectensis

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL17090 GPL9914

29 Samples

Download data: BED

(Submitter supplied) Recent small RNA sequencing data has uncovered extensive modification of the 3’ end of mature microRNAs (miRNAs). This non-templated nucleotide addition can impact miRNA gene regulatory networks through the control of miRNA stability or by interfering with the repression of target mRNAs. The miRNA modifying enzymes responsible for this regulation remain largely uncharacterized. Here we describe the ability for two related terminal uridyl transferases (TUTases), Zcchc6 (TUT7) and Zcchc11 (TUT4), to 3’ mono-uridylate a specific subset of miRNAs involved in cell differentiation and Hox gene control. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL11154

2 Samples

Download data: TXT

(Submitter supplied) Small RNAs were cloned from wt and tailor mutant cells or ovary tissues to study the role of Tailor in miRNA uridylation

Organism:

Drosophila melanogaster

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL13304

4 Samples

Download data: TXT

(Submitter supplied) Background: The Scylla paramamosain is a very important aquaculture crustacean species in the southeast coastal areas of China including Shantou. For the past few years, mud crab cultured in Niutianyang of Shantou suffered from serious diseases, especially the bacterial diseases (such as Vibrio parahaemolyticus). In eukaryotes, small RNAs can regulate gene expression in post-transcription to act on host-pathogen interaction system. more...

Organism:

Scylla paramamosain

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL15893

2 Samples

Download data: TXT

(Submitter supplied) Small silencing RNAs are key regulators of gene expression in both plants and animals. HEN1-mediated 3’ terminal 2’-O-methylation plays a crucial role in small RNA stability control. In the absence of HEN1, small RNAs are frequently uridylated (untemplated uridine addition) and trimmed, a phenomenon that is conserved across species. However, the underlying molecular mechanism is largely unknown. In this study, we have discovered UTP: RNA uridylyltransferase (URT1) acts redundantly with HESO1 in the uridylation of miRNAs, in addition to its role in oligo-adenylated mRNA uridylation. more...

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL13222

12 Samples

Download data: TXT

(Submitter supplied) Clonorchis sinensis is a zoonotic parasite causing clonorchiasis associated with human diseases such as biliary calculi, cholecystitis, liver cirrhosis, and is classified as carcinogenic to humans for cholangiocarcinoma. MicroRNAs (miRNAs) are non-coding, regulating small RNA molecules essential for the complex life cycle of parasites and involved in parasitic infections. To identify and characterize miRNAs expressed in adult C. more...

Organism:

Clonorchis sinensis

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL10530

1 Sample

Download data: TXT

(Submitter supplied) The role of 3ʹ-5ʹ exonuclease, PARN, in the 3ʹ end miRNA transcriptome in human cells

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL16791

3 Samples

Download data: TXT

(Submitter supplied) We have performed small RNA sequencing in the nematodes Caenorhabditis elegans, C. briggsae, C. remanei and Pristionchus pacificus, which have diverged up to 400 million years ago, to establish the repertoire and evolutionary dynamics of miRNAs in these species. In addition to previously known miRNA genes from C. elegans and C. briggsae we demonstrate expression of many of their homologs in C. remanei and P. more...

Organism:

Caenorhabditis briggsae; Caenorhabditis elegans; Caenorhabditis remanei; Pristionchus pacificus

Type:

Non-coding RNA profiling by high throughput sequencing

4 related Platforms

4 Samples

Download data: FA, QUAL

(Submitter supplied) We provide a broad overview of sequence diversity in An. gambiae mature microRNAs, including annotation of novel microRNAs identified in this study.

Organism:

Anopheles gambiae

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL17644 GPL15693

8 Samples

Download data: TXT

(Submitter supplied) We used HSUR1 – a small non-coding RNA from Herpesvirus saimiri that induces degradation of host miR-27 – to validate structural insights into target-directed miRNA degradation (TDMD). While performing systematic mutagenesis of HSUR1 we noticed that HSUR1 mutants exhibiting complementarity to the extreme 3' end of miR-27, lead to generation of extended miR-27 isoforms (isomiRs). These isomiRs likely represent failed products of TDMD and could mean that features of the pairing between the TDMD target and miRNA dictate which enzymes are recruited to modify the miRNA 3′ end. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL16791

15 Samples

Download data: XLSX

(Submitter supplied) Terminal uridylyl transferases (TUTs) function as integral regulators of microRNA (miRNA) biogenesis by modifying the end structure of precursor miRNA (pre-miRNA). Using biochemistry and deep sequencing techniques, we here investigate the mechanism how human TUT7 recognizes and uridylates pre-miRNAs. We show that the overhang of a pre-miRNA is the key structural element that TUT7 and its paralogues, TUT4 and TUT2, recognize. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL15520

2 Samples

Download data: TXT