The
            <i>Air</i>
            Noncoding RNA Epigenetically Silences Transcription by Targeting G9a to Chromatin

Nagano, Takashi; Mitchell, Jennifer A.; Sanz, Lionel A.; Pauler, Florian M.; Ferguson-Smith, Anne C.; Feil, Robert; Fraser, Peter

doi:10.1126/science.1163802

Cited by 849 publications

(661 citation statements)

References 19 publications

Supporting

Mentioning

642

Contrasting

Unclassified

Order By: Relevance

“…To understand the roles of lncRNAs in the pathogenesis of PCOS, subsequent loss-offunction experiments using RNAi-mediated knockdown in cell lines or animal models will validate associations between lncRNAs and corresponding functional pathways and physiological outcomes. Moreover, the subcellular localization of lncRNAs which could be detected by RNA fluorescence in situ hybridization will provide clues to their biological functions [52]. Ultimately, the differential expression of lncRNAs maybe facilitate the classification of PCOS disease into distinct subtypes and the development of lncRNA-based therapies.…”

Section: Discussionmentioning

confidence: 99%

Aberrant expression of long noncoding RNAs in cumulus cells isolated from PCOS patients

Huang

Hao

Bao

et al. 2015

J Assist Reprod Genet

View full text Add to dashboard Cite

Purpose To describe the long noncoding RNA (lncRNA) profiles in cumulus cells isolated from polycystic ovary syndrome (PCOS) patients by employing a microarray and in-depth bioinformatics analysis. This information will help us understand the occurrence and development of PCOS. Methods In this study, we used a microarray to describe lncRNA profiles in cumulus cells isolated from ten patients (five PCOS and five normal women). Several differentially expressed lncRNAs were chosen to validate the microarray results by quantitative RT-PCR (qRT-PCR). Then, the differentially expressed lncRNAs were classified into three subgroups (HOX loci lncRNA, enhancer-like lncRNA, and lincRNA) to deduce their potential features. Furthermore, a lncRNA/mRNA co-expression network was constructed by using the Cytoscape software (V2.8.3, http://www.cytoscape.org/). Results We observed that 623 lncRNAs and 260 messenger RNAs (mRNAs) were significantly up-or down-regulated (≥2-fold change), and these differences could be used to discriminate cumulus cells of PCOS from those of normal pat i e n t s . F i v e d i f f e r e n t i a l l y e x p r e s s e d l n c R N A s (XLOC_011402, ENST00000454271, ENST00000433673, ENST00000450294, and ENST00000432431) were selected to validate the microarray results using quantitative RT-PCR (qRT-PCR). The qRT-PCR results were consistent with the microarray data. Further analysis indicated that many differentially expressed lncRNAs were transcribed from chromosome 2 and may act as enhancers to regulate their neighboring protein-coding genes. Forty-three lncRNAs and 29 mRNAs were used to construct the coding-non-coding gene coexpression network. Most pairs positively correlated, and one mRNA correlated with one or more lncRNAs. Conclusions Our study is the first to determine genome-wide lncRNA expression patterns in cumulus cells isolated from PCOS patients by microarray. The results show that clusters of lncRNAs were aberrantly expressed in cumulus cells of PCOS patients compared with those of normal women, which revealed that lncRNAs differentially expressed in PCOS and normal women may contribute to the occurrence of PCOS and affect oocyte development.

show abstract

Section: Discussionmentioning

confidence: 99%

Aberrant expression of long noncoding RNAs in cumulus cells isolated from PCOS patients

Huang

Hao

Bao

et al. 2015

J Assist Reprod Genet

View full text Add to dashboard Cite

show abstract

“…In mammals, there are hundreds of imprinted long noncoding RNAs, such as Air, H19, and Kcnq1ot1 (13,34,35). Most of these RNAs play important regulatory roles within their imprinted clusters (29).…”

Section: Discussionmentioning

confidence: 99%

“…Meanwhile, a number of imprinted noncoding RNAs, such as kcnq1ot1 antisense noncoding RNA and Air noncoding RNA (12,13), were reported to participate in the developmental regulation of imprinted expression of protein-coding genes and to act on transcriptional silencing. Recent studies in Arabidopsis and rice suggest that there exist a large number of imprinted genes in plants as well (14)(15)(16)(17).…”

mentioning

confidence: 99%

Extensive, clustered parental imprinting of protein-coding and noncoding RNAs in developing maize endosperm

Zhang

Zhao

Xie

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

165

226

View full text Add to dashboard Cite

Although genetic imprinting was discovered in maize 40 years ago, its exact extent in the triploid endosperm remains unknown. Here, we have analyzed global patterns of allelic gene expression in developing maize endosperms from reciprocal crosses between inbreds B73 and Mo17. We have defined an imprinted gene as one in which the relative expression of the maternal and paternal alleles differ at least fivefold in both hybrids of the reciprocal crosses. We found that at least 179 genes (1.6% of protein-coding genes) expressed in the endosperm are imprinted, with 68 of them showing maternal preferential expression and 111 paternal preferential expression. Additionally, 38 long noncoding RNAs were imprinted. The latter are transcribed in either sense or antisense orientation from intronic regions of normal protein-coding genes or from intergenic regions. Imprinted genes show a clear pattern of clustering around the genome, with a number of imprinted genes being adjacent to each other. Analysis of allele-specific methylation patterns of imprinted loci in the hybrid endosperm identified 21 differentially methylated regions (DMRs) of several hundred base pairs in length, corresponding to both imprinted genes and noncoding transcripts. All DMRs identified are uniformly hypomethylated in maternal alleles and hypermethylated in paternal alleles, regardless of the imprinting direction of their corresponding loci. Our study indicates highly extensive and complex regulation of genetic imprinting in maize endosperm, a mechanism that can potentially function in the balancing of the gene dosage of this triploid tissue.

show abstract

“…This result is reminiscent of Air (Airn), which also functions in mechanistically distinct cis and trans roles to regulate gene expression. 54,55 Dbp2 is a co-transcriptional RNA chaperone and bona fide RNA helicase whose activity is necessary for assembly of RNAbinding proteins, Yra1, Mex67, and Nab2 onto poly(A) C RNAs. 56,57 During transcription, both messenger and long non-coding RNAs are co-transcriptionally bound with a set of RNA-binding proteins to form a ribonucleoprotein complex (RNP), which then undergoes a variety of processing steps, including capping, splicing, termination, and polyadenylation.…”

mentioning

confidence: 99%

LncRNAs: Bridging environmental sensing and gene expression

2016

View full text Add to dashboard Cite

The survival of all organisms is dependent on complex, coordinated responses to environmental cues. Non-coding RNAs have been identified as major players in regulation of gene expression, with recent evidence supporting roles for long non-coding (lnc)RNAs in both transcriptional and post-transcriptional control. Evidence from our laboratory shows that lncRNAs have the ability to form hybridized structures called R-loops with specific DNA target sequences in S. cerevisiae, thereby modulating gene expression. In this Point of View, we provide an overview of the nature of lncRNA-mediated control of gene expression in the context of our studies using the GAL gene cluster as a model for controlling the timing of transcription.

show abstract

The Air Noncoding RNA Epigenetically Silences Transcription by Targeting G9a to Chromatin

Cited by 849 publications

References 19 publications

Aberrant expression of long noncoding RNAs in cumulus cells isolated from PCOS patients

Aberrant expression of long noncoding RNAs in cumulus cells isolated from PCOS patients

Extensive, clustered parental imprinting of protein-coding and noncoding RNAs in developing maize endosperm

LncRNAs: Bridging environmental sensing and gene expression

Contact Info

Product

Resources

About