Making sense of Dlx1 antisense RNA

Kraus, Petra; Sivakamasundari, V.; Lim, Siew Lan; Xing, Xing; Lipovich, Leonard; Lufkin, Thomas

doi:10.1016/j.ydbio.2013.01.035

Cited by 41 publications

(40 citation statements)

References 92 publications

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“…5C). 56 This suggests that Dlx1as acts rather as a gene-activating ncRNA than keeping Dlx1 mRNA levels at check. Notably, Dlx1as is associated to both PRC1 and Med12 arguing that transcriptional activation by Mediator-ncRNA complexes is likely inhibited by PRC1.…”

Section: Discussionmentioning

confidence: 99%

“…55 As reported for Hoxd11 mutant mice, 53 ablation of Dlx1as was shown to generate a skeletal phenotype. 56 Therefore, we asked whether Dlx1as had an impact on the transcriptional activation of Hoxd11. To this end we transfected mESCs with either control siRNA or siRNA pools targeting Dlx1as (Fig.…”

Section: Med12 Acts As a Transcriptional Activator Of Key Developmentmentioning

confidence: 99%

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Dual role of Med12 in PRC1-dependent gene repression and ncRNA-mediated transcriptional activation

et al. 2016

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Mediator is considered an enhancer of RNA-Polymerase II dependent transcription but its function and regulation in pluripotent mouse embryonic stem cells (mESCs) remains unresolved. One means of controlling the function of Mediator is provided by the binding of the Cdk8 module (Med12, Cdk8, Ccnc and Med13) to the core Mediator. Here we report that Med12 operates together with PRC1 to silence key developmental genes in pluripotency. At the molecular level, while PRC1 represses genes it is also required to assemble ncRNA containing Med12-Mediator complexes. In the course of cellular differentiation the H2A ubiquitin binding protein Zrf1 abrogates PRC1-Med12 binding and facilitates the association of Cdk8 with Mediator. This remodeling of Mediator-associated protein complexes converts Mediator from a transcriptional repressor to a transcriptional enhancer, which then mediates ncRNA-dependent activation of Polycomb target genes. Altogether, our data reveal how the interplay of PRC1, ncRNA and Mediator complexes controls pluripotency and cellular differentiation.

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Section: Discussionmentioning

confidence: 99%

Section: Med12 Acts As a Transcriptional Activator Of Key Developmentmentioning

confidence: 99%

Dual role of Med12 in PRC1-dependent gene repression and ncRNA-mediated transcriptional activation

et al. 2016

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“…Recently, a number of hallmark reports have revealed the versatile molecular mechanisms of regulation exerted by lncRNA in human or rodent embryonic stem cell (ESC) models, such as interacting with proteins and regulating their function (Hung et al 2011, Ng et al 2013, regulating the action of chromatin-modifying factors by directing interaction (Klattenhoff et al 2013), inactivating X chromosome by direct binding (Ohhata et al 2011), promoting organelle formation (Chen & Carmichael 2009), inhibiting antisense mRNA expression (Santoro et al 2013), promoting antisense mRNA degradation (Kraus et al 2013), regulating mRNA export from nucleus (Chen & Carmichael 2009), acting as competing endogenous RNAs (ceRNAs) to inhibit the function of miRNA (Cheng & Lin 2013), and acting as a decoy which binds DNA-binding proteins and prevents them from approaching target sites in genomic DNA (Kino et al 2010, Redon et al 2010). Given such a wide variety of regulatory roles, the exact molecular regulations conferred by lncRNAs remain to be elucidated.…”

Section: A Novel Regulatory Layer In Cellular Development: Lncrnasmentioning

confidence: 99%

“…First, as a competitor, lncRNA can bind to DNAbinding proteins, such as transcription factors (Hung 2011, Ng 2013, and inhibit their attachment to target DNA. They can also bind complimentarily to some structures in DNA molecules and hinder protein binding to specific antisense mRNA (Kraus et al 2013), or to miRNAs for post-transcriptional regulation (Zhang et al 2010). Secondly, lncRNA can activate epigenetic modifiers or recruit them to specific target sites, thus enhancing DNA methylation (Berghoff et al 2013) and histone modifications (Yap et al 2010, Klattenhoff et al 2013.…”

Section: A Novel Regulatory Layer In Cellular Development: Lncrnasmentioning

confidence: 99%

Long noncoding RNAs in spermatogenesis: insights from recent high-throughput transcriptome studies

Luk¹,

Chan²,

Rennert³

et al. 2014

Reproduction

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Spermatogenesis is a complex developmental process in which undifferentiated spermatogonia are differentiated into spermatocytes and spermatids through two rounds of meiotic division and finally giving rise to mature spermatozoa (sperm). These processes involve many testis-or male germ cell-specific gene products that undergo strict developmental regulations. As a result, identifying critical, regulatory genes controlling spermatogenesis provide the clues not only to the regulatory mechanism of spermatogenesis at the molecular level, but also to the identification of candidate genes for infertility or contraceptives development. Despite the biological importance in male germ cell development, the underlying mechanisms of stage-specific gene regulation and cellular transition during spermatogenesis remain largely elusive. Previous genomic studies on transcriptome profiling were largely limited to protein-coding genes. Importantly, protein-coding genes only account for a small percentage of transcriptome; the majority are noncoding transcripts that do not translate into proteins. Although small noncoding RNAs (ncRNAs) such as microRNAs, siRNAs, and Piwi-interacting RNAs are extensively investigated in male germ cell development, the role of long ncRNAs (lncRNAs), commonly defined as ncRNAs longer than 200 bp, is relatively unexplored. Herein, we summarize recent transcriptome studies on spermatogenesis and show examples that a subset of noncoding transcript population, known as lncRNAs, constitutes a novel regulatory target in spermatogenesis.

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“…Indeed, it is emerging that lncRNAs are involved in the pathology of neurological diseases related to imprinting, for instance, Prader-Willi syndrome (PWS) and Angelman syndrome (AS) (Koerner et al, 2009). Additionally, lncRNAs that are Morphologically normal together with mild skull and neurological defects by gene inactivation (Kraus et al, 2013) …”

Section: Lncrnas In Diseases Of the Cns And Brainmentioning

confidence: 99%

Long Non-coding RNAs: key players in brain and central nervous system development

Lv¹,

Liu²,

Liu³

et al. 2014

cmb

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CanadaComputational Molecular Biology (Online, ISSN 1927-5587) ), indexed by international database ProQuest, is an open access, peer reviewed journal publishing original research papers of general interest involving in the computational biology at the molecular level.The Journal is publishing all the latest and outstanding research articles, letters, methods, and reviews in all areas of Computational Molecular Biology, covering new discoveries in molecular biology, from genes to genomes, using statistical, mathematical, and computational methods as well as new development of computational methods and databases in molecular and genome biology.The papers published in the journal are expected to be of interests to computational scientists, biologists, and teachers/students/researchers engaged in biology, as well as are appropriate for R & D personnel and general readers interested in computational technology and biology.Computational Molecular Biology is published independently by BioPublisher. It is committed to publishing and disseminating significant original achievements in the related research fields of molecular biology. Vol.4, No.5, 1-13 (doi: 10.5376/cmb.2014.04.0005) Abstract Regulatory long non-coding RNAs have been emerged as a major contribution of cognitive evolution in mammalian central nervous system and brain tissues. Though proteins have relatively conserved during evolution, the lncRNAs have evolved rapidly to cope with essential and widespread cellular regulation, partly by directing generic protein function. Long non-coding RNAs, highly yet specifically expressed in mammalian brain, provide tissue-and neuronal activity-specific epigenetic and transcriptional regulation. lncRNAs have been documented to be essential for brain development and be involved in brain related diseases. We suggest that lncRNAs are important to modulate diverse central nervous system processes and are the major factor that is important to the brain development, which may be employed to develop novel diagnostic and therapeutic strategies to treat brain related diseases. Moreover, animal models with altered lncRNA expressions and high-throughput approaches would help to understand the mechanisms of lncRNAs in brain development and the etiology of lncRNA-driven human neurological diseases.

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Making sense of Dlx1 antisense RNA

Cited by 41 publications

References 92 publications

Dual role of Med12 in PRC1-dependent gene repression and ncRNA-mediated transcriptional activation

Dual role of Med12 in PRC1-dependent gene repression and ncRNA-mediated transcriptional activation

Long noncoding RNAs in spermatogenesis: insights from recent high-throughput transcriptome studies

Long Non-coding RNAs: key players in brain and central nervous system development

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