<i>Evf2 lncRNA</i>/BRG1/DLX1 interactions reveal RNA-dependent chromatin remodeling inhibition

Cajigas, Ivelisse; Leib, David E.; Cochrane, Jesse C.; Luo, Hao; Swyter, Kelsey R.; Chen, Sean; Clark, Brian S.; Thompson, James; Yates, John R.; Kingston, Robert E.; Kohtz, Jhumku D.

doi:10.1242/dev.126318

Cited by 92 publications

(74 citation statements)

References 73 publications

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“…Several cases of co-expression of genic lncRNA-mRNA pairs in an antisense orientation have been reported, and the modes of action of such lncRNAs on the regulation of mRNA loci are multiple and complex [11, 51–54]. Strikingly, we found that the significant correlations between lncRNA and mRNA levels are positive.…”

Section: Resultsmentioning

confidence: 52%

Long noncoding RNA repertoire in chicken liver and adipose tissue

et al. 2017

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BackgroundImproving functional annotation of the chicken genome is a key challenge in bridging the gap between genotype and phenotype. Among all transcribed regions, long noncoding RNAs (lncRNAs) are a major component of the transcriptome and its regulation, and whole-transcriptome sequencing (RNA-Seq) has greatly improved their identification and characterization. We performed an extensive profiling of the lncRNA transcriptome in the chicken liver and adipose tissue by RNA-Seq. We focused on these two tissues because of their importance in various economical traits for which energy storage and mobilization play key roles and also because of their high cell homogeneity. To predict lncRNAs, we used a recently developed tool called FEELnc, which also classifies them with respect to their distance and strand orientation to the closest protein-coding genes. Moreover, to confidently identify the genes/transcripts expressed in each tissue (a complex task for weakly expressed molecules such as lncRNAs), we probed a particularly large number of biological replicates (16 per tissue) compared to common multi-tissue studies with a larger set of tissues but less sampling.ResultsWe predicted 2193 lncRNA genes, among which 1670 were robustly expressed across replicates in the liver and/or adipose tissue and which were classified into 1493 intergenic and 177 intragenic lncRNAs located between and within protein-coding genes, respectively. We observed similar structural features between chickens and mammals, with strong synteny conservation but without sequence conservation. As previously reported, we confirm that lncRNAs have a lower and more tissue-specific expression than mRNAs. Finally, we showed that adjacent lncRNA-mRNA genes in divergent orientation have a higher co-expression level when separated by less than 1 kb compared to more distant divergent pairs. Among these, we highlighted for the first time a novel lncRNA candidate involved in lipid metabolism, lnc_DHCR24, which is highly correlated with the DHCR24 gene that encodes a key enzyme of cholesterol biosynthesis.ConclusionsWe provide a comprehensive lncRNA repertoire in the chicken liver and adipose tissue, which shows interesting patterns of co-expression between mRNAs and lncRNAs. It contributes to improving the structural and functional annotation of the chicken genome and provides a basis for further studies on energy storage and mobilization traits in the chicken.Electronic supplementary materialThe online version of this article (doi:10.1186/s12711-016-0275-0) contains supplementary material, which is available to authorized users.

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Section: Resultsmentioning

confidence: 52%

Long noncoding RNA repertoire in chicken liver and adipose tissue

et al. 2017

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“…Further studies revealed that Evf-2 exists in a complex with DLX1 and the BRG1 chromatin-remodeling factor. Evf-2 inhibits BRG1 activity, thereby providing a mechanism through which a lncRNA can exert a repressive effect while forming a complex with transcriptional activators [72]. These data demonstrate that the lncRNA Evf-2 can recruit both activators and repressors to the Dlx5/6 locus, and highlights the importance of using genetic knockout strategies to complement in vitro knockdown experiments in cell culture.…”

Section: Lncrnas Associated With Homeobox Transcription Factorsmentioning

confidence: 96%

Uncovering the roles of long noncoding RNAs in neural development and glioma progression

Ramos

Attenello

Lim

2016

Neuroscience Letters

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In the past decade, thousands of long noncoding RNAs (lncRNAs) have been identified, and emerging data indicate that lncRNAs can have important biological functions and roles in human diseases including cancer. Many lncRNAs appear to be expressed specifically in the brain, and the roles of lncRNAs in neural stem cells (NSCs) and brain development are now beginning to be discovered. Here we review recent advances in understanding the diversity of lncRNA structure and functions in NSCs and brain development. NSCs in the adult mouse ventricular-subventricular zone (V-SVZ) generate new neurons throughout life, and we discuss how key elements of this adult neurogenic system have facilitated the discovery and functional characterization of known and novel lncRNAs. A review of lncRNAs described in other NSC systems reveals a variety of molecular mechanisms, including binding and recruitment of transcription factors, epigenetic modifiers, and RNA-splicing factors. Finally, we review emerging evidence indicating that specific lncRNAs can be key players driving glial malignancies, and discuss next steps towards an in vivo understanding of lncRNA function in development and disease.

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“…One of the more thoroughly analyzed lncRNAs that regulates brain development is Evf2 ( Dlx6as1 ) [87, 151–153]. Evf2 is expressed in the Shh-responsive cells of the ventral telencephalon during embryonic development and is transcribed from a region that partially overlaps ei, one of the two ultra-conserved enhancers (ei + eii) for the neighboring genes Dlx5 and Dlx6 [87].…”

Section: 3 Lncrna Function In Nervous System Developmentmentioning

confidence: 99%

Understanding the Role of lncRNAs in Nervous System Development

Clark

Blackshaw

2017

Advances in Experimental Medicine and Biology

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The diversity of lncRNAs has expanded within mammals in tandem with the evolution of increased brain complexity, suggesting that lncRNAs play an integral role in this process. In this chapter, we will highlight the identification and characterization of lncRNAs in nervous system development. We discuss the potential role of lncRNAs in nervous system and brain evolution, along with efforts to create comprehensive catalogues that analyze spatial and temporal changes in lncRNA expression during nervous system development. Additionally, we focus on recent endeavors that attempt to assign function to lncRNAs during nervous system development. We highlight discrepancies that have been observed between in vitro and in vivo studies of lncRNA function and the challenges facing researchers in conducting mechanistic analyses of lncRNAs in the developing nervous system. Altogether, this chapter highlights the emerging role of lncRNAs in the developing brain and sheds light on novel, RNA-mediated mechanisms by which nervous system development is controlled.

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Evf2 lncRNA/BRG1/DLX1 interactions reveal RNA-dependent chromatin remodeling inhibition

Cited by 92 publications

References 73 publications

Long noncoding RNA repertoire in chicken liver and adipose tissue

Long noncoding RNA repertoire in chicken liver and adipose tissue

Uncovering the roles of long noncoding RNAs in neural development and glioma progression

Understanding the Role of lncRNAs in Nervous System Development

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