The Small RNA Profile during Drosophila melanogaster Development
Developmental CellPublished 1 August 2003Open access
Alexei A. Aravin, Mariana Lagos‐Quintana, Abdullah Yalçın, Mihaela Zavolan, Debora S. Marks, Ben Snyder
Citations955
SJR quartileQ1
SJR score5.18
SNIP2.05
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TL;DR
The small RNA profile of Drosophila melanogaster is described as a function of development and 178 repeat-associated small interfering RNAs (rasiRNAs) are isolated, suggesting that small RNAs participate in defining chromatin structure.
Abstract
Small RNAs ranging in size between 20 and 30 nucleotides are involved in different types of regulation of gene expression including mRNA degradation, translational repression, and chromatin modification. Here we describe the small RNA profile of Drosophila melanogaster as a function of development. We have cloned and sequenced over 4000 small RNAs, 560 of which have the characteristics of RNase III cleavage products. A nonredundant set of 62 miRNAs was identified. We also isolated 178 repeat-associated small interfering RNAs (rasiRNAs), which are cognate to transposable elements, satellite and microsatellite DNA, and Suppressor of Stellate repeats, suggesting that small RNAs participate in defining chromatin structure. rasiRNAs are most abundant in testes and early embryos, where regulation of transposon activity is critical and dramatic changes in heterochromatin structure occur.
Keywords
Biochemistry, Genetics and Molecular Biology
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PLANT PHYSIOLOGY<i>Short Integuments1/suspensor1/carpel Factory</i>, a Dicer Homolog, Is a Maternal Effect Gene Required for Embryo Development in Arabidopsis
180 Citations2002Teresa Golden, Stephen E. Schauer +6 more
The cloning of SIN1 is reported, and its identity to the CAF (CARPEL FACTORY) gene important for normal flower morphogenesis and to the SUS1 (SUSPENSOR1) gene essential for embryogenesis is demonstrated, suggesting that maternal Sin1/SUS1/CAF functions early in Arabidopsis development, presumably through posttranscriptional regulation of specific mRNA molecules.
PubMedRNA interference in Trypanosoma brucei: cloning of small interfering RNAs provides evidence for retroposon-derived 24-26-nucleotide RNAs.
173 Citations2001Appolinaire Djikeng, Huafang Shi +2 more
It is shown that activation of RNAi in Trypanosoma bruceiby expression or electroporation of actin dsRNA results in production ofActin siRNAs and that 10% of these RNAs sediment as high-molecular-weight complexes at 100,000 x g.
GeneticsDetailed structure of the Drosophila melanogaster stellate genes and their transcripts.
160 Citations1990Kenneth J. Livak
Analysis using segmental Y deficiencies shows that the Su(Ste) region suppresses both the high levels and efficient splicing of Stellate RNA.
FEBS LettersDiverse molecular interactions of the hnRNP K protein
160 Citations1997Karol Bomsztyk, Isabelle Van Seuningen +3 more
It is suggested that the use of nanofiltration membranes for the recovery of phosphorous with a second type of technology is to be considered as a viable process for recovery of nitrogen in the short term.
Proceedings of the National Academy of SciencesDNA-binding and trans-activation properties of Drosophila E2F and DP proteins.
157 Citations1994Brian David Dynlacht, A.H. Brook +3 more
It is demonstrated that dDP and dE2F interact and cooperate to give sequence-specific DNA binding and optimal trans-activation, which suggest that endogenous Drosophila E2F, like human E1F, may be composed of heterodimers and may be regulated by RB-like proteins.
GeneticsGenetic and Molecular Characterization of sting, a Gene Involved in Crystal Formation and Meiotic Drive in the Male Germ Line of Drosophila melanogaster
153 Citations1999Armin Schmidt, Gioacchino Palumbo +4 more
The sting mutation, caused by a P element inserted into polytene region 32D, was isolated by a screen for male sterile insertions in Drosophila melanogaster and was cloned and shown to code for a putative protein that is 866 amino acids long.
Current Opinion in Plant BiologyRNA silencing: small RNAs as ubiquitous regulators of gene expression
150 Citations2002Olivier Voinnet
Initially identified as an immune system that is targeted against transposons and viruses, RNA silencing is emerging as a fundamental regulatory process that is likely to affect many layers of endogenous gene expression in most, if not all, eukaryotes.
Journal of General VirologyThe novel genome organization of the insect picorna-like virus Drosophila C virus suggests this virus belongs to a previously undescribed virus family.
147 Citations1998Karyn N. Johnson, Peter D. Christian
The finding of this novel genome organization for DCV shows that this virus is not a member of the Picornaviridae as previously thought, but belongs to a distinct and hitherto unrecognized virus family.
Current BiologyPosttranscriptional Gene Silencing Is Not Compromised in the Arabidopsis CARPEL FACTORY (DICER-LIKE1) Mutant, a Homolog of Dicer-1 from Drosophila
139 Citations2003E. Jean Finnegan, Rogério Margis +1 more
It is reported that the same caf mutant does not block either PTGS or siRNA production induced by self-complementary hairpin RNA, which suggests either that this mutation only impairs miRNA formation or, more interestingly, that plants have two distinct dicer-like enzymes, one for miRNA and another for siRNAi production.
PLANT PHYSIOLOGYShort RNAs Can Identify New Candidate Transposable Element Families in Arabidopsis
135 Citations2002Michael Florian Mette, J. van der Winden +2 more
It is suggested that mining the Arabidopsis genome for transposable elements by DNA sequence similarity searches and analysis protocols is revealing previously unidentified families of TEs and providing insights into TE structure, mobility, distribution, and diversity.
Developmental BiologyCoordinate regulation of small temporal RNAs at the onset of Drosophila metamorphosis
126 Citations2003Arash Bashirullah, Amy E. Pasquinelli +4 more
It is found that let-7 and miR-125 are coordinately expressed in late larvae and prepupae, in synchrony with the high titer ecdysone pulses that initiate metamorphosis, raising the possibility of a temporal signal that is distinct from the well-characterized ecDysone-EcR pathway.
Current BiologyMicroRNAs: Hidden in the Genome
124 Citations2002Eric G. Moss
Genes for tiny RNAs have been found to be plentiful in the genomes of worms, flies, humans and probably all animals, and some have been conserved through evolution.
Current Protocols in Molecular BiologyCloning of Small <scp>RNA</scp> Molecules
98 Citations2005Sébastien Pfeffer, Mariana Lagos‐Quintana +1 more
Procedures to record the profile of small RNAs expressed in cultured cells or tissues are described and it is recommended to directionally concatamerize the relatively short PCR products before cloning in order to increase the number of RNA sequences obtained per clone.
GeneticsGenetic analysis of Stellate elements of Drosophila melanogaster.
95 Citations1994G. Palumbo, Silvia Bonaccorsi +2 more
It is found that meiosis is disrupted after synapsis and that cry-induced meiotic drive is probably not mediated by Ste, and that the abnormality in chromosome condensation and the frequency of nondisjunction are related to Ste copy number.
Journal of Molecular BiologyIdentification, Molecular Cloning, Expression and Chromosome Mapping of a Family of Transformation Upregulated hnRNP-K Proteins Derived by Alternative Splicing
93 Citations1994Kurt Dejgaard, Henrik Leffers +6 more
The hnRNP-K family has been implicated in pre-mRNA metabolism of transcripts containing cytidine-rich sequences and its results point towards a role during cell cycle progression.
Nucleic Acids ResearchRNomics in Drosophila melanogaster: identification of 66 candidates for novel non-messenger RNAs
86 Citations2013Guozhong Yuan, Christian Klämbt +3 more
By generating a specialised cDNA library from four different developmental stages of Drosophila melanogaster, 66 candidates for small non-messenger RNAs (snmRNAs) are identified and confirmed their expression by northern blot analysis and detection of two RNA species from this group implies that certain snmRNA species are processed from alternatively spliced pre-m RNAs.
Advances in genetics11 RNAi (nematodes: Caenorhabditis elegans)
82 Citations2002Alla Grishok, Carlos Fernando Mello
This chapter describes the history of the discovery of RNAi, its systemic nature, inheritance, and connection to other homology-dependent silencing phenomena like co-suppression and transcriptional gene silencing, and discusses RNAi-deficient mutants in C. elegans.
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