Cytoplasmic Intron Sequence-Retaining Transcripts Can Be Dendritically Targeted via ID Element Retrotransposons

Buckley, Peter T.; Lee, Miler T.; Sul, Jai‐Yoon; Miyashiro, Kevin; Bell, Thomas; Fisher, Stephen; Kim, Junhyong; Eberwine, James

doi:10.1016/j.neuron.2011.02.028

Cited by 134 publications

(152 citation statements)

References 44 publications

Supporting

Mentioning

146

Contrasting

Unclassified

Order By: Relevance

“…What might label specific mRNAs for dendritic targeting? Buckley et al have identified ID element retrotransposons, a retained class of short interspersed repetitive elements (SINEs), within the introns of several dendritically targeted mRNAs (Buckley et al, 2011). These sequences are sufficient for targeting both endogenous and exogenous transcripts to dendrites, and, accordingly, appear to influence protein distribution within the cell.…”

Section: Rna Targeting and Local Protein Translation In Dendritesmentioning

confidence: 99%

Cell-intrinsic drivers of dendrite morphogenesis

Puram

Bonni

2013

Development

View full text Add to dashboard Cite

The proper formation and morphogenesis of dendrites is fundamental to the establishment of neural circuits in the brain. Following cell cycle exit and migration, neurons undergo organized stages of dendrite morphogenesis, which include dendritic arbor growth and elaboration followed by retraction and pruning. Although these developmental stages were characterized over a century ago, molecular regulators of dendrite morphogenesis have only recently been defined. In particular, studies in Drosophila and mammalian neurons have identified numerous cell-intrinsic drivers of dendrite morphogenesis that include transcriptional regulators, cytoskeletal and motor proteins, secretory and endocytic pathways, cell cycle-regulated ubiquitin ligases, and components of other signaling cascades. Here, we review cell-intrinsic drivers of dendrite patterning and discuss how the characterization of such crucial regulators advances our understanding of normal brain development and pathogenesis of diverse cognitive disorders. KEY WORDS: Cell-intrinsic driver, Dendrite development, Dendrite morphogenesis, Dendrite patterning, Transcription factor, Ubiquitin ligases IntroductionWith their tremendous complexity and diversity, dendrites are one of nature's architectural masterpieces. More than a century ago, Ramón y Cajal proposed an important role for dendrites (referred to at that time as protoplasmic processes) as specialized morphological structures that receive neuronal input (Ramón y Cajal, 1995). Further studies using a variety of neuronal cell types (see Glossary, Box 1) have vastly improved our understanding of dendrite development (Scott and Luo, 2001;Grueber and Jan, 2004). The development of new approaches for studying dendrite morphogenesis (see Box 2) has led to the view that axons and dendrites work in concert to define neuronal connectivity. A key concept that has emerged from such functional studies is that the particular shapes of dendrites are intimately tied to the proper wiring of neuronal circuits and their function (Häusser et al., 2000;Parrish et al., 2007b;Branco et al., 2010;Branco and Häusser, 2011;Gidon and Segev, 2012; Lavzin et al., 2012).Prior to the elaboration of dendrites, neurons undergo axodendritic polarization, whereby the morphologically and functionally distinct axonal and dendritic compartments (see Box 3) are specified. In most neurons, including retinal ganglion neurons, forebrain pyramidal neurons and cerebellar granule neurons, the generation of an axon precedes the development and elaboration of dendrites (Ramón y Cajal, 1995). Although individual neuronal cell Anterodorsal and lateral projection neurons (aPNs and lPNs). These neurons of the Drosophila antennal lobe are crucial for olfactory processing. They receive excitatory input from olfactory receptor neurons in glomeruli and transmit signals to the mushroom body and lateral horn. Cerebellar granule neurons. The most numerous neurons of the brain, these offer an ideal system for biochemical, morphological and physiological studi...

show abstract

Section: Rna Targeting and Local Protein Translation In Dendritesmentioning

confidence: 99%

Cell-intrinsic drivers of dendrite morphogenesis

Puram

Bonni

2013

Development

View full text Add to dashboard Cite

show abstract

“…From each transcript, we obtained from RefSeq (rn4) the 3 ′ UTR sequence as well as the sequence of any cytoplasmically retained introns (Buckley et al 2011). To focus our search on smaller structure elements, we used a sliding window approach to split each 3 ′ UTR and intron sequence into several smaller segments.…”

Section: Application Of Nofold To Novel Motif Discoverymentioning

confidence: 99%

“…Previously, Buckley et al (2011) found that a ∼74-nt hairpin structure within the retained introns of several dendritic transcripts was sufficient to confer dendritic localization in rat hippocampal neurons. These structures were instances of the ID element, a type of rodent SINE retrotransposon element that likely arose from the dendritically localized BC1 gene (Kim et al 1994).…”

Section: Application Of Nofold To Novel Motif Discoverymentioning

confidence: 99%

NoFold: RNA structure clustering without folding or alignment

Middleton

Kim

2014

RNA

Self Cite

View full text Add to dashboard Cite

Structures that recur across multiple different transcripts, called structure motifs, often perform a similar function-for example, recruiting a specific RNA-binding protein that then regulates translation, splicing, or subcellular localization. Identifying common motifs between coregulated transcripts may therefore yield significant insight into their binding partners and mechanism of regulation. However, as most methods for clustering structures are based on folding individual sequences or doing many pairwise alignments, this results in a tradeoff between speed and accuracy that can be problematic for large-scale data sets. Here we describe a novel method for comparing and characterizing RNA secondary structures that does not require folding or pairwise alignment of the input sequences. Our method uses the idea of constructing a distance function between two objects by their respective distances to a collection of empirical examples or models, which in our case consists of 1973 Rfam family covariance models. Using this as a basis for measuring structural similarity, we developed a clustering pipeline called NoFold to automatically identify and annotate structure motifs within large sequence data sets. We demonstrate that NoFold can simultaneously identify multiple structure motifs with an average sensitivity of 0.80 and precision of 0.98 and generally exceeds the performance of existing methods. We also perform a cross-validation analysis of the entire set of Rfam families, achieving an average sensitivity of 0.57. We apply NoFold to identify motifs enriched in dendritically localized transcripts and report 213 enriched motifs, including both known and novel structures.

show abstract

“…By cutting branches, or dendrites, off neurons, Eberwine and his colleagues have discovered that RNA in dendrites can retain nucleotide sequences that target the RNA to that location 4 . They could not have found such information by analysing the RNA of an entire neuron.…”

Section: Profiling Heterogeneitymentioning

confidence: 99%

The deepest differences

Schubert¹

2011

Nature

View full text Add to dashboard Cite

Cytoplasmic Intron Sequence-Retaining Transcripts Can Be Dendritically Targeted via ID Element Retrotransposons

Cited by 134 publications

References 44 publications

Cell-intrinsic drivers of dendrite morphogenesis

Cell-intrinsic drivers of dendrite morphogenesis

NoFold: RNA structure clustering without folding or alignment

The deepest differences

Contact Info

Product

Resources

About