Long noncoding RNA genes: conservation of sequence and brain expression among diverse amniotes

Chodroff, Rebecca A.; Goodstadt, Leo; Sirey, Tamara; Oliver, Peter L.; Davies, Kay E.; Green, Eric D.; Molnár, Zoltán; Ponting, Chris P.

doi:10.1186/gb-2010-11-7-r72

Cited by 227 publications

(201 citation statements)

References 67 publications

(97 reference statements)

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“…Twenty-nine (;5%) of the 550 zebra fish lincRNAs and 4.1 to 5.5% of the 3122 mouse lincRNAs were evolutionally conserved as measured by alignment of primary sequences, suggesting a rapid sequence evolution of lincRNAs (Ponjavic et al, 2007;Marques and Ponting, 2009;Ulitsky et al, 2011). Other studies, which used more comprehensive evolutionary analytical methods, reported a higher conservation rate (;11%) of lincRNAs in mouse (Guttman et al, 2009;Chodroff et al, 2010). The low level of evolutionary conservation of Arabidopsis lincRNA in primary sequence is consistent with that previously reported in mammals.…”

Section: Design Of An Identifier System Of Arabidopsis Lincrnasmentioning

confidence: 91%

Genome-Wide Analysis Uncovers Regulation of Long Intergenic Noncoding RNAs in Arabidopsis

et al. 2012

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Long intergenic noncoding RNAs (lincRNAs) transcribed from intergenic regions of yeast and animal genomes play important roles in key biological processes. Yet, plant lincRNAs remain poorly characterized and how lincRNA biogenesis is regulated is unclear. Using a reproducibility-based bioinformatics strategy to analyze 200 Arabidopsis thaliana transcriptome data sets, we identified 13,230 intergenic transcripts of which 6480 can be classified as lincRNAs. Expression of 2708 lincRNAs was detected by RNA sequencing experiments. Transcriptome profiling by custom microarrays revealed that the majority of these lincRNAs are expressed at a level between those of mRNAs and precursors of miRNAs. A subset of lincRNA genes shows organ-specific expression, whereas others are responsive to biotic and/or abiotic stresses. Further analysis of transcriptome data in 11 mutants uncovered SERRATE, CAP BINDING PROTEIN20 (CBP20), and CBP80 as regulators of lincRNA expression and biogenesis. RT-PCR experiments confirmed these three proteins are also needed for splicing of a small group of introncontaining lincRNAs.

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Section: Design Of An Identifier System Of Arabidopsis Lincrnasmentioning

confidence: 91%

Genome-Wide Analysis Uncovers Regulation of Long Intergenic Noncoding RNAs in Arabidopsis

et al. 2012

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“…A recent study has also identified expressed orthologs of a few highly conserved and brain-expressed mouse lncRNAs in species as distant as opossums and chickens (Chodroff et al 2010). However, the number of human lincRNAs that have an orthologous, actively expressed, transcript in other species remains unknown.…”

Section: Expressed Syntenic Orthologs Of Human Lincrnas In Mammals Anmentioning

confidence: 99%

Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses

Cabili¹,

Trapnell²,

Goff³

et al. 2011

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Large intergenic noncoding RNAs (lincRNAs) are emerging as key regulators of diverse cellular processes. Determining the function of individual lincRNAs remains a challenge. Recent advances in RNA sequencing (RNA-seq) and computational methods allow for an unprecedented analysis of such transcripts. Here, we present an integrative approach to define a reference catalog of >8000 human lincRNAs. Our catalog unifies previously existing annotation sources with transcripts we assembled from RNA-seq data collected from~4 billion RNA-seq reads across 24 tissues and cell types. We characterize each lincRNA by a panorama of >30 properties, including sequence, structural, transcriptional, and orthology features. We found that lincRNA expression is strikingly tissue-specific compared with coding genes, and that lincRNAs are typically coexpressed with their neighboring genes, albeit to an extent similar to that of pairs of neighboring protein-coding genes. We distinguish an additional subset of transcripts that have high evolutionary conservation but may include short ORFs and may serve as either lincRNAs or small peptides. Our integrated, comprehensive, yet conservative reference catalog of human lincRNAs reveals the global properties of lincRNAs and will facilitate experimental studies and further functional classification of these genes.

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“…In contrast, other lncRNAs are evolutionarily conserved. Some orthologous lncRNAs exhibit similar expression patterns in the embryonic and postnatal brains of birds, marsupials, and eutherian mammals, implying that they have fundamental roles in brain development [13]. Furthermore, a large proportion of lncRNAs expressed in the developing brain are associated, because of their genomic context, with protein-coding genes known to play roles in neural Regulate other long and short non-coding RNAs at the epigenetic, transcriptional, and post-transcriptional level Serve as hosts for the biogenesis of certain short non-coding RNAs Act as microRNA sinks/sponges that bind to miRNAs, sequestering them away from their target mRNAs Bind to microRNA binding sites in mRNAs, masking these sites and preventing miRNA-mediated regulatory events Have dual roles as long non-coding RNA transcripts and as substrates for translation Nuclear architecture Act as scaffolds for the formation of subnuclear domains and their dynamic reorganization gene regulation and brain development.…”

Section: Brain Developmentmentioning

confidence: 99%

“…Data from animal models, as well as human tissues, reveals patterns that are regional; cell type-, subcellular compartment-, and developmental stagespecific; activity-dependent; and even sexually dimorphic [7,[10][11][12][13][14][15][18][19][20]]. An increasing number of studies are focused on interrogating the corresponding neurobiological roles played by these lncRNAs.…”

Section: Understanding the Biology Of Lncrnasmentioning

confidence: 99%

“…Other lncRNA genes have evolved quite rapidly in a lineage-specific manner, suggesting that they served as substrates for evolutionary innovations, including the emergence of human brain structure and higher-order cognitive and behavioral functions [10]. Conspicuously, a large proportion of lncRNAs are preferentially expressed in the brains of humans and other species in specific temporal and spatial profiles [7,[11][12][13][14]. ncRNAs, as a whole, and lncRNAs, in particular, are extremely relevant within the nervous system, where they are implicated in mediating many aspects of brain evolution, development, homeostasis, and plasticity [10,15].…”

Section: Introductionmentioning

confidence: 99%

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Long Non-coding RNAs: Novel Targets for Nervous System Disease Diagnosis and Therapy

2013

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The human genome encodes tens of thousands of long non-coding RNAs (lncRNAs), a novel and important class of genes. Our knowledge of lncRNAs has grown exponentially since their discovery within the last decade. lncRNAs are expressed in a highly cell-and tissue-specific manner, and are particularly abundant within the nervous system. lncRNAs are subject to post-transcriptional processing and inter-and intra-cellular transport. lncRNAs act via a spectrum of molecular mechanisms leveraging their ability to engage in both sequence-specific and conformational interactions with diverse partners (DNA, RNA, and proteins). Because of their size, lncRNAs act in a modular fashion, bringing different macromolecules together within the three-dimensional context of the cell. lncRNAs thus coordinate the execution of transcriptional, post-transcriptional, and epigenetic processes and critical biological programs (growth and development, establishment of cell identity, and deployment of stress responses). Emerging data reveal that lncRNAs play vital roles in mediating the developmental complexity, cellular diversity, and activitydependent plasticity that are hallmarks of brain. Corresponding studies implicate these factors in brain aging and the pathophysiology of brain disorders, through evolving paradigms including the following: (i) genetic variation in lncRNA genes causes disease and influences susceptibility; (ii) epigenetic deregulation of lncRNAs genes is associated with disease; (iii) genomic context links lncRNA genes to disease genes and pathways; and (iv) lncRNAs are otherwise interconnected with known pathogenic mechanisms. Hence, Electronic supplementary material The online version of this article

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Long noncoding RNA genes: conservation of sequence and brain expression among diverse amniotes

Cited by 227 publications

References 67 publications

Genome-Wide Analysis Uncovers Regulation of Long Intergenic Noncoding RNAs in Arabidopsis

Genome-Wide Analysis Uncovers Regulation of Long Intergenic Noncoding RNAs in Arabidopsis

Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses

Long Non-coding RNAs: Novel Targets for Nervous System Disease Diagnosis and Therapy

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