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Items: 20

1.

Ribosomes guide pachytene piRNA formation on long intergenic piRNA precursors

(Submitter supplied) PIWI-interacting RNAs (piRNAs) are a class of small non-coding RNAs essential for fertility. In adult mouse testes, most piRNAs are derived from long single-stranded RNAs lacking annotated open reading frames (ORFs). The mechanisms underlying how piRNA sequences are defined during the cleavages of piRNA precursors remain elusive. Here, we show that 80S ribosomes translate the 5′-proximal short ORFs (uORFs) of piRNA precursors. more...
Organism:
Mus musculus; Anolis carolinensis
Type:
Non-coding RNA profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms:
GPL13112 GPL15001
61 Samples
Download data: BED2, TXT
Series
Accession:
GSE65786
ID:
200065786
2.

Coupled protein synthesis and ribosome-guided piRNA processing on mRNAs

(Submitter supplied) piRNAs can derive from transposable elements (TEs), long non-coding RNAs, or the 3'UTR of mRNAs, the last being the least characterized out of the three piRNA classes. In this study, we systematically defined the regulation, biogenesis and function of the 3'UTR piRNAs that are expressed throughout mouse spermatogenesis. These piRNAs are regulated by A-MYB transcription factors, and their precursors are bifunctional mRNAs which are processed into piRNAs after pioneer rounds of translation. more...
Organism:
Mus musculus; Gallus gallus
Type:
Other; Expression profiling by high throughput sequencing
Platforms:
GPL13112 GPL16133
27 Samples
Download data: BIGWIG, TXT
Series
Accession:
GSE155350
ID:
200155350
3.

Mouse MOV10L1 associates with Piwi proteins and is an essential component of the piRNA pathway

(Submitter supplied) Piwi-interacting RNAs (piRNAs) are essential for silencing of transposable elements in the germline but their biogenesis is poorly understood. Here we demonstrate that MOV10L1, a germ cell-specific putative RNA helicase, is associated with Piwi proteins. Genetic disruption of the MOV10L1 RNA helicase domain in mice renders both MILI and MIWI2 devoid of piRNAs. Absence of a functional piRNA pathway in Mov10l1 mutant testes causes loss of DNA methylation and subsequent de-repression of retrotransposons in germ cells. more...
Organism:
Mus musculus
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL9185
3 Samples
Download data
Series
Accession:
GSE21763
ID:
200021763
4.

An Ancient Transcription Factor Initiates the Burst of piRNA Production During Early Meiosis in Mouse Testes (smallRNA-Seq)

(Submitter supplied) Animal germ cells produce PIWI-interacting RNAs (piRNAs), small silencing RNAs that suppress transposons and enable gamete maturation. Mammalian transposon-silencing piRNAs accumulate early in spermatogenesis, whereas pachytene piRNAs are produced later during post-natal spermatogenesis and account for >95% of all piRNAs in the adult mouse testis. Mutants defective for pachytene piRNA pathway proteins fail to produce mature sperm, but neither the piRNA precursor transcripts nor the trigger for pachytene piRNA production is known. more...
Organism:
Gallus gallus; Mus musculus
Type:
Non-coding RNA profiling by high throughput sequencing
4 related Platforms
32 Samples
Download data: BED, CSV
Series
Accession:
GSE45049
ID:
200045049
5.

An Ancient Transcription Factor An Ancient Transcription Factor During Early Meiosis in Mouse Testes (PAS-Seq and CAGE)

(Submitter supplied) Animal germ cells produce PIWI-interacting RNAs (piRNAs), small silencing RNAs that suppress transposons and enable gamete maturation. Mammalian transposon-silencing piRNAs accumulate early in spermatogenesis, whereas pachytene piRNAs are produced later during post-natal spermatogenesis and account for >95% of all piRNAs in the adult mouse testis. Mutants defective for pachytene piRNA pathway proteins fail to produce mature sperm, but neither the piRNA precursor transcripts nor the trigger for pachytene piRNA production is known. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing; Other
Platform:
GPL13112
3 Samples
Download data: BED
Series
Accession:
GSE45048
ID:
200045048
6.

An Ancient Transcription Factor Initiates the Burst of piRNA Production During Early Meiosis in Mouse Testes

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Mus musculus; Gallus gallus
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other; Non-coding RNA profiling by high throughput sequencing
4 related Platforms
56 Samples
Download data: BED
Series
Accession:
GSE44690
ID:
200044690
7.

An Ancient Transcription Factor Initiates the Burst of piRNA Production During Early Meiosis in Mouse Testes (RNA-Seq)

(Submitter supplied) Animal germ cells produce PIWI-interacting RNAs (piRNAs), small silencing RNAs that suppress transposons and enable gamete maturation. Mammalian transposon-silencing piRNAs accumulate early in spermatogenesis, whereas pachytene piRNAs are produced later during post-natal spermatogenesis and account for >95% of all piRNAs in the adult mouse testis. Mutants defective for pachytene piRNA pathway proteins fail to produce mature sperm, but neither the piRNA precursor transcripts nor the trigger for pachytene piRNA production is known. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL13112
14 Samples
Download data: BED, CSV
Series
Accession:
GSE44654
ID:
200044654
8.

An Ancient Transcription Factor Initiates the Burst of piRNA Production During Early Meiosis in Mouse Testes (ChIP-Seq)

(Submitter supplied) Animal germ cells produce PIWI-interacting RNAs (piRNAs), small silencing RNAs that suppress transposons and enable gamete maturation. Mammalian transposon-silencing piRNAs accumulate early in spermatogenesis, whereas pachytene piRNAs are produced later during post-natal spermatogenesis and account for >95% of all piRNAs in the adult mouse testis. Mutants defective for pachytene piRNA pathway proteins fail to produce mature sperm, but neither the piRNA precursor transcripts nor the trigger for pachytene piRNA production is known. more...
Organism:
Gallus gallus; Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL13112 GPL16133
7 Samples
Download data: BED
Series
Accession:
GSE44588
ID:
200044588
9.

RNA helicase D1PAS1 resolves R-loops and forms a complex for mouse pachytene piRNA biogenesis required for male fertility

(Submitter supplied) To investigate the function of RNA helicase D1PAS1 in mouse spermatogenesis, we established D1Pas1 knockout (KO) and D1Pas1-FLAG knockin (KI) lines in which the D1Pas1 gene has been knocked out by deleting the transcription start site and the 3XFLAG sequences added at the end of C-term by CRISPR/Cas9. We then performed gene expression profiling analysis using data obtained from RNA-seq of 3 different biological replicates at three different developmental stages. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing; Other; Non-coding RNA profiling by high throughput sequencing
Platforms:
GPL17021 GPL34328 GPL24247
36 Samples
Download data: BW, CSV, TXT
Series
Accession:
GSE231983
ID:
200231983
10.

Zucchini-dependent piRNA processing is triggered by recruitment to the cytoplasmic processing machinery

(Submitter supplied) We show that heterologous RNA that lacks complementary piRNAs is processed into piRNAs upon recruitment of several piRNA pathway factors. Our approach utilizes tethering of components of the piRNA pathway to the transcript of a reporter and then small RNA cloning from total RNA from Drosophila ovaries. Our approach allows discrimination of proteins involved in transcription and export of piRNA precursors from components required for the cytoplasmic processing steps. more...
Organism:
Drosophila melanogaster
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL17275
70 Samples
Download data: BEDGRAPH, FA
Series
Accession:
GSE102961
ID:
200102961
11.

Recruitment of Armitage and Yb to a transcript triggers its phased processing into primary piRNAs in Drosophila ovaries

(Submitter supplied) Small RNAs called PIWI -interacting RNAs (piRNAs) are essential for transposon control and fertility in animals. Primary processing is the small RNA biogenesis pathway that uses long single-stranded RNA precursors to generate millions of individual piRNAs, but the molecular mechanisms that identify a transcript as a precursor are poorly understood. Here we demonstrate that artificial tethering of the piRNA biogenesis factor, Armi, to a transcript is sufficient to direct it into primary processing in Drosophila ovaries and in an ovarian cell culture model. more...
Organism:
Drosophila melanogaster
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL13304
108 Samples
Download data: TXT
Series
Accession:
GSE102013
ID:
200102013
12.

MAEL-dependent selective processing of pachytene piRNA precursors and translation of spermiogenic mRNAs

(Submitter supplied) Piwi-interacting small RNAs (piRNAs) of fetal prospermatogonia of mice have been strongly implicated in transposon control. In contrast, little is known about biogenesis and function of abundant piRNAs from adult testes expressed in late spermatocytes and round spermatids. These so-called "pachytene" piRNAs are processed from long non-coding piRNA precursors and have no defined RNA targets in the transcriptome even though their binding partner Piwi, MIWI, is essential for spermiogenesis and fertility. more...
Organism:
Mus musculus
Type:
Non-coding RNA profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform:
GPL13112
17 Samples
Download data: BW, TXT
Series
Accession:
GSE50983
ID:
200050983
13.

Daedalus and Gasz recruit Armitage to mitochondria, bringing piRNA precursors to the biogenesis machinery

(Submitter supplied) The piRNA pathway is a small RNA-based immune system that silences mobile genetic elements in animal germlines. piRNA biogenesis requires a specialised machinery that converts long single-stranded precursors into small RNAs of ~25-nucleotides in length. This process involves factors that operate in two different subcellular compartments: the nuage/Yb-body and mitochondria. How these two sites communicate to achieve accurate substrate selection and efficient processing remains unclear. more...
Organism:
Drosophila melanogaster
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL21306
18 Samples
Download data: BW
Series
Accession:
GSE129321
ID:
200129321
14.

Small RNA and gene expression profile in the adult testes of the common marmoset

(Submitter supplied) Small RNAs mediate gene silencing by binding Argonaute/Piwi proteins to regulate target RNAs. Here we describe small RNA profiling of the adult testes of Callithrix jacchus, the common marmoset. The most abundant class of small RNAs in the adult testis was piRNAs, while 353 novel miRNAs but few endo-siRNAs were also identified. MARWI, a marmoset homolog of mouse MIWI and a very abundant PIWI in adult testes, associates with piRNAs that show characteristics of mouse pachytene piRNAs. more...
Organism:
Callithrix jacchus
Type:
Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platforms:
GPL18020 GPL17712
3 Samples
Download data: TXT
Series
Accession:
GSE52927
ID:
200052927
15.

Long first exons and epigenetic marks distinguish conserved pachytene piRNA clusters from other mammalian genes

(Submitter supplied) In the male germ cells of eutherian animals, 26–30-nt-long PIWI-interacting RNAs (piRNAs) emerge when spermatocytes enter the pachytene phase of meiosis. These pachytene piRNAs derive from ~100 discrete autosomal loci resemble canonical protein-coding genes and long non-coding RNA-producing genes—they are transcribed by RNA polymerase II, bearing 5´ caps and 3´ poly(A) tails, and their transcripts often contain introns that are removed before nuclear export and processing into piRNAs. more...
Organism:
Mus musculus; Macaca mulatta
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL19057 GPL21120
19 Samples
Download data: BW
Series
Accession:
GSE147724
ID:
200147724
16.

piRNA-guided slicing specifies transcripts for Zucchini dependent, phased piRNA biogenesis

(Submitter supplied) PIWI-clade Argonaute proteins repress transposable elements in animal gonads. Their sequence specificity is conferred via bound ~23-30nt long piRNAs, which are processed from single stranded precursor RNAs. How transcripts are specified as precursors and processed into stereotypical piRNA populations are central unresolved questions. Here we show that piRNA-guided RNA cleavage in Drosophila results not only in generation of a ping-pong partner piRNA but further triggers efficient 3′ directed and phased primary piRNA biogenesis. more...
Organism:
Drosophila melanogaster
Type:
Non-coding RNA profiling by high throughput sequencing; Other
Platform:
GPL13304
26 Samples
Download data: TXT
Series
Accession:
GSE64802
ID:
200064802
17.

Analysis of small RNAs in piRNA pathway mutant mouse testes

(Submitter supplied) Piwi-interacting RNAs are 25-32 nt small RNAs bound to Piwi proteins. To know the steps where factors involved in the piRNA biogenesis (MILI, MIWI2, ZUC (MitoPLD), MVH) work, we sequenced small RNAs from mutant mouse testes and analyzed piRNAs.
Organism:
Mus musculus
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL9250
6 Samples
Download data: TXT
Series
Accession:
GSE20327
ID:
200020327
18.

BTBD18 licenses piRNA-generating loci to support mouse germ cell development

(Submitter supplied) PIWI-interacting RNAs (piRNAs) are small non-coding RNAs essential for animal germ cell development. Despite intense investigation of post-transcriptional processing, piRNA biogenesis at the chromatin level remains enigmatic. Here we document that BTBD18 is a pachytene nuclear protein in mouse testes that occupies intergenic pachytene piRNA-producing loci with remarkable genome-wide specificity. Deficiency of Btbd18 in mice results in disrupted piRNA biogenesis and male sterility. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other; Non-coding RNA profiling by high throughput sequencing
Platform:
GPL17021
86 Samples
Download data: BIGWIG, TXT
Series
Accession:
GSE81470
ID:
200081470
19.

Pachytene piRNA Genes Are Rapidly Diverging Among Modern Humans

(Submitter supplied) In the fetal mouse testis, PIWI Interacting RNAs (piRNAs) guide PIWI proteins to silence transposons, but after birth, most post-pubertal pachytene piRNAs map to genome uniquely and are thought to regulate genes required for male fertility. In human males, the developmental classes, precise genomic origins, and transcriptional regulation of post-natal piRNAs remain undefined. Here, we demarcate the genes and transcripts that produce post-natal piRNAs in human juvenile and adult testes. more...
Organism:
Macaca mulatta; Homo sapiens; Mus musculus
Type:
Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL21120 GPL18573 GPL19057
72 Samples
Download data: BW, NARROWPEAK, TXT
Series
Accession:
GSE135791
ID:
200135791
20.

Small RNA Profiling of Murine Adult Stomach

(Submitter supplied) Murine Adult Stomach Small RNA
Organism:
Mus musculus
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL16331
2 Samples
Download data: TXT
Series
Accession:
GSE53780
ID:
200053780

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