Topological Organization of Multi-chromosomal Regions by Firre

By Ezgi Hacisuleyman, L. Goff, Cole Trapnell, Adam Williams, Jorge Henao-Mejia, Lei Sun, P. McClanahan, David G Hendrickson, Martin Sauvageau, David R. Kelley and 8 more. Nature Structural &Molecular Biology, 2014

596 citations recorded by the source corpus.

RNA, including long noncoding RNA (lncRNA), is known to be an abundant and important structural component of the nuclear matrix. However, the molecular identities, functional roles and localization dynamics of lncRNAs that influence nuclear architecture remain poorly understood. Here, we describe one lncRNA, Firre, that interacts with the nuclear-matrix factor hnRNPU through a 156-bp repeating sequence and localizes across an ~5-Mb domain on the X chromosome. We further observed Firre localization across five distinct trans-chromosomal loci, which reside in spatial proximity to the Firre genomic locus on the X chromosome. Both genetic deletion of the Firre locus and knockdown of hnRNPU resulted in loss of colocalization of these trans-chromosomal interacting loci. Thus, our data suggest a model in which lncRNAs such as Firre can interface with and modulate nuclear architecture across chromosomes.

Subfields: Cancer Research, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/d8ddb84ed354ca7e75edc24fe3cb42e92a6f8ec8

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Citations in the corpus

Mechanisms of long noncoding RNA function in development and disease (2016, background): “FIRRE LincRNA RNA5SP514 Nucleus 3D genome organization 3D genome structure [103]”
Localization and abundance analysis of human lncRNAs at single-cell and single-molecule resolution (2015, background): “More recently, researchers have developed and applied single molecule RNA FISH techniques based on hybridization of multiple short, fluorescently labeled, oligonucleotide probes [23,24] to estimate the absolute level and subcellular localization of even low abundance lncRNAs [8,25-31].”
Genomic positional conservation identifies topological anchor point (tap)RNAs linked to developmental loci (2016, background): “…domains and chromosome conformation, for example by modulating the binding of transcription factors, Mediator and CTCF complexes (Deng et al., 2016; Hacisuleyman et al., 2014; Kung et al., 2015; Lai et al., 2013; Minajigi et al., 2015; Sun et al., 2014; Wang et al., 2014a; Wang et al., 2011; Xiang…”
Linking Long Noncoding RNA Localization and Function. (2016, background): “The matrix protein hnRNP U is required for the accumulation of lncRNA X-inactive specific transcript on the inactive X chromosome [57] and for the in cis accumulation of FIRRE [19], which is essential for their functions.”
Ki-67: more than a proliferation marker (2018, background): “Furthermore, RNAs are important for several higher order chromosome interactions (Hacisuleyman et al. 2014; Yang et al. 2015), including examples at nucleoli (Mohammad et al. 2008; Fedoriw et al. 2012), and these have not been investigated in this regard.”
The multidimensional mechanisms of long noncoding RNA function (2017, background): “a The lncRNA Firre is transcribed from the X chromosome (chrX) and, by binding hnRNP-U, acts as a platform for trans-chromosomal interactions [107].”
MEG3 long noncoding RNA regulates the TGF-β pathway genes through formation of RNA–DNA triplex structures (2015, unknown): “[0-15] MEG3”
Non-coding RNAs in Development and Disease: Background, Mechanisms, and Therapeutic Approaches. (2016, background): “This can be done by adding biotinylated lncRNA to a cell lysate like shown for Braveheart (138), Firre (99), or HOTAIR (181, 228).”