Specific expression of long noncoding RNAs in the mouse brain

By Tim R. Mercer, Marcel E. Dinger, Susan Sunkin, M. Mehler, John S. Mattick. Proceedings of the National Academy of Sciences of the United States of America, 2008

1,142 citations recorded by the source corpus.

Subfields: Cancer Research, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/b5086eb615ef6e116116f67d98afed97b35316c3

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Citations in the corpus

lncRNAdb: a reference database for long noncoding RNAs (2010, background): “…expression levels of both the lncRNAs and their contextually related transcripts in various public microarray experiments, such as NCode data and the GNF atlas (31), as well as the Allen Brain Atlas (32), which includes mouse brain in situ expression data for over 800 expressed lncRNAs (33).”
The functional role of long non-coding RNA in human carcinomas (2011, background): “One such player, the newly discovered long non-coding RNA (lncRNA) genes, demonstrate developmental and tissue specific expression patterns, and aberrant regulation in a variety of diseases, including cancer [18-27].”
lincRNAs: Genomics, Evolution, and Mechanisms (2013, positive): “…human, mouse, and zebrafish suggested that large gene deserts flanking transcription-factor (TF) genes, particularly those with roles in embryonic development, preferentially harbor lincRNAs (Mercer et al., 2008; Guttman et al., 2009; Ulitsky et al., 2011; Pauli et al., 2012; Wamstad et al., 2012).”
Genome-wide computational identification and manual annotation of human long noncoding RNA genes. (2010, background): “The spatiotempo-rally restricted expression patterns of hundreds of other lncRNAs suggest that many other functional roles remain to be discovered (Pollard et al. 2006; Mercer et al. 2008).”
Long noncoding RNAs and the genetics of cancer (2013, background): “…of noncoding RNAs (Carninci et al, 2005), which exhibit exquisite cell-specific and developmental dynamic expression patterns (Dinger et al, 2008; Mercer et al, 2008, 2010; Pang et al, 2009; Cabili et al, 2011; Khaitan et al, 2011), capable of transacting a wide repertoire of regulatory…”
Non‐coding RNAs: regulators of disease (2010, background): “Indeed, a large fraction of lncRNAs is expressed in very precise patterns in the brain [106].”
The Nuclear-Retained Noncoding RNA MALAT1 Regulates Alternative Splicing by Modulating SR Splicing Factor Phosphorylation (2010, background): “…have identified additional novel nrRNAs inmammalian cells, and the characterization of these is expected to reveal important gene-regulatory functions and roles associated with the complexity observed in multicellular organisms (Mercer et al., 2008; Sone et al., 2007; van Bakel et al., 2010).”
MEN epsilon/beta nuclear-retained non-coding RNAs are up-regulated upon muscle differentiation and are essential components of paraspeckles. (2009, positive): “Interestingly, large-scale studies of ncRNAs have shown that many are dynamically regulated during differentiation and exhibit cell- and tissue-specific expression patterns (Ravasi et al. 2006; Dinger et al. 2008; Mercer et al. 2008).”
Genomic positional conservation identifies topological anchor point (tap)RNAs linked to developmental loci (2016, result): “…after treatment with differentiating agents, consistent with previous observations by us and others that show co-regulation of lncRNAs and neighboring genes in different species (e.g. (Cabili et al., 2011; Dinger et al., 2008; Goff et al., 2015; Hezroni et al., 2015; Mercer et al., 2008)).”
3’ end processing of a long nuclear-retained non-coding RNA yields a tRNA-like cytoplasmic RNA (2008, neutral): “Few long ncRNAs have been assigned a function; however, a significant number of these transcripts are unlikely to represent transcriptional “noise” as they have been shown to exhibit cell-type specific expression, localization to specific subcellular compartments, and association with human diseases”
Long noncoding RNAs: functional surprises from the RNA world. (2009, background): “2008), exhibit cell typespecific expression (Ravasi et al. 2006; Mercer et al. 2008), localize to specific subcellular compartments (Hutchinson et al.”
Long Non-coding RNAs in the Cytoplasm (2016, background): “Interestingly, expression of lncRNA is more tissuespecific than that of mRNA [9].”
lncRNAdb v2.0: expanding the reference database for functional long noncoding RNAs (2014, methodology): “Text preprocessing was conducted by an in-house script (available at http://lncrnadb. org/help) and the word cloud was created with R package ‘tm’ (v.0.6) and ‘wordcloud’ (v.2.5). protein-coding genes (30,38–40).”
Large-scale prediction of long non-coding RNA functions in a coding–non-coding gene co-expression network (2011, background): “However, a number of studies have suggested that independently transcribed lncRNAs may still be co-expressed and functionally related to neighboring coding genes (11,21,40,41).”
The Genetic Signatures of Noncoding RNAs (2009, background): “Indeed, a recent study of over 1,300 mouse ncRNAs showed that almost half of them exhibit precise expression patterns in different parts of the brain, including different subregions of the hippocampus, olfactory bulb, neocortex, and cerebellum [52].”