Abstract:The ribonuclease Dicer is a multidomain enzyme that plays a fundamental role in the biogenesis of small regulatory RNAs (srRNAs), which control gene expression by targeting complementary transcripts and inducing their cleavage or repressing their translation. Recent studies of Dicer’s domains have permitted to propose their roles in srRNA biogenesis. For all of Dicer’s domains except one, called DUF283 (domain of unknown function), their involvement in RNA substrate recognition, binding or cleavage has been po… Show more
“…Very recently, we showed that the DUF283 domain of hDicer can bind 12-nt ssRNA in vitro, though the observed binding was very weak (Kurzynska-Kokorniak et al, 2016). Here, we demonstrated that the full length hDicer does not bind such short ssRNAs (Fig.…”
Section: Binding Between Hdicer and Single-stranded Rnas Of Differentmentioning
confidence: 50%
“…Finally, DUF283 has been found to be responsible for interactions with Dicer protein partners (Ota et al, 2013). Moreover, it has been demonstrated that the separate DUF283 domain of Dicer selectively binds single-stranded RNAs (ssRNAs) in vitro, and accelerates annealing of complementary nucleic acids (Kurzynska-Kokorniak et al, 2016).…”
Ribonuclease Dicer plays a pivotal role in RNA interference pathways by processing long double-stranded RNAs and single-stranded hairpin RNA precursors into small interfering RNAs (siRNAs) and microRNAs (miRNAs), respectively. While details of Dicer regulation by a variety of proteins are being elucidated, less is known about non-protein factors, e.g. RNA molecules, that may influence this enzyme's activity. Therefore, we decided to investigate the question of whether the RNA molecules can function not only as Dicer substrates but also as its regulators. Our previous in vitro studies indicated that the activity of human Dicer can be influenced by short RNA molecules that either bind to Dicer or interact with its substrates, or both. Those studies were carried out with commercial Dicer preparations. Nevertheless, such preparations are usually not homogeneous enough to carry out more detailed RNA-binding studies. Therefore, we have established our own system for the production of human Dicer in insect cells. In this manuscript, we characterize the RNA-binding and RNA-cleavage properties of the obtained preparation. We demonstrate that Dicer can efficiently bind single-stranded RNAs that are longer than ~20-nucleotides. Consequently, we revisit possible scenarios of Dicer regulation by single-stranded RNA species ranging from ~10- to ~60-nucleotides, in the context of their binding to this enzyme. Finally, we show that siRNA/miRNA-sized RNAs may affect miRNA production either by binding to Dicer or by participating in regulatory feedback-loops. Altogether, our studies suggest a broad regulatory role of short RNAs in Dicer functioning.
“…Very recently, we showed that the DUF283 domain of hDicer can bind 12-nt ssRNA in vitro, though the observed binding was very weak (Kurzynska-Kokorniak et al, 2016). Here, we demonstrated that the full length hDicer does not bind such short ssRNAs (Fig.…”
Section: Binding Between Hdicer and Single-stranded Rnas Of Differentmentioning
confidence: 50%
“…Finally, DUF283 has been found to be responsible for interactions with Dicer protein partners (Ota et al, 2013). Moreover, it has been demonstrated that the separate DUF283 domain of Dicer selectively binds single-stranded RNAs (ssRNAs) in vitro, and accelerates annealing of complementary nucleic acids (Kurzynska-Kokorniak et al, 2016).…”
Ribonuclease Dicer plays a pivotal role in RNA interference pathways by processing long double-stranded RNAs and single-stranded hairpin RNA precursors into small interfering RNAs (siRNAs) and microRNAs (miRNAs), respectively. While details of Dicer regulation by a variety of proteins are being elucidated, less is known about non-protein factors, e.g. RNA molecules, that may influence this enzyme's activity. Therefore, we decided to investigate the question of whether the RNA molecules can function not only as Dicer substrates but also as its regulators. Our previous in vitro studies indicated that the activity of human Dicer can be influenced by short RNA molecules that either bind to Dicer or interact with its substrates, or both. Those studies were carried out with commercial Dicer preparations. Nevertheless, such preparations are usually not homogeneous enough to carry out more detailed RNA-binding studies. Therefore, we have established our own system for the production of human Dicer in insect cells. In this manuscript, we characterize the RNA-binding and RNA-cleavage properties of the obtained preparation. We demonstrate that Dicer can efficiently bind single-stranded RNAs that are longer than ~20-nucleotides. Consequently, we revisit possible scenarios of Dicer regulation by single-stranded RNA species ranging from ~10- to ~60-nucleotides, in the context of their binding to this enzyme. Finally, we show that siRNA/miRNA-sized RNAs may affect miRNA production either by binding to Dicer or by participating in regulatory feedback-loops. Altogether, our studies suggest a broad regulatory role of short RNAs in Dicer functioning.
“…The DExD/H domain is located in the base of the L and forms a clamp near the RNase III domain active site [1,10]. A recent study showed that the DUF283 domain of Dicer is capable of binding single-stranded nucleic acid [11]. Figure 1.Dicer structure and functions.( A ) The structure of Dicer.…”
The enzyme Dicer is best known for its role as a riboendonuclease in the small RNA pathway. In this canonical role, Dicer is a critical regulator of the biogenesis of microRNA and small interfering RNA, as well as a growing number of additional small RNAs derived from various sources. Emerging evidence demonstrates that Dicer's endonuclease role extends beyond the generation of small RNAs; it is also involved in processing additional endogenous and exogenous substrates, and is becoming increasingly implicated in regulating a variety of other cellular processes, outside of its endonuclease function. This review will describe the canonical and newly identified functions of Dicer.
“…Some paired 19-mers with a dTdT overhang at the 3' end bind Dicer with high affinity; these sequences are not cleaved by Dicer, are fully transferred to Ago and trigger high-efficiency gene silencing activity [10,11]. Dicer also binds single RNAs at a specific site with high affinity, the function of which is to accelerate hybridization with a partner from the "soup" of RNA metabolism [14]. The newly in situ-formed dsRNA, which is asymmetric, slides into the endonuclease site for cleavage, and the processed RNAi product is transferred successfully into RISC complex.…”
The role of the RNAi/Dicer/Ago system to degrade RNA viruses has been elusive, which prompt authors to think that interferon (IFN) synthesis is essential, relegating the dsRNAs as accessory function. We investigate SARS-CoV-2 genome responsible of the new deadly COVID-19 pandemic for the theoretical possibilities to engage intra pairing within the viral RNA and also hybrid pairing with human transcriptome. Segmental pieces of RNAs that originate from SARS-CoV-2 were computationally searched as a potential source of one strand, the complementary strand being from the host transcriptome. We therefore considered perfect complementarity of host RNA with any piece of SARS-CoV-2 RNA as a collection of theoretical siRNAs potentially Dicer substrates. Few human genes seems targeted by SARS-CoV-2 RNA, among them mitochondrial deubiquitinase USP30 and a subunit of ubiquitin protein ligase complex FBXO21 could explain premature death of infected cell by the collapse of mitochondria.
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