A Pooled shRNA Screen Identifies Rbm15, Spen, and Wtap as Factors Required for Xist RNA-Mediated Silencing

Moindrot, Benoît; Cerase, Andrea; Coker, Heather; Masui, Osamu; Grijzenhout, Anne; Pintacuda, Greta; Schermelleh, Lothar; Nesterova, Tatyana B.; Brockdorff, Neil

doi:10.1016/j.celrep.2015.06.053

Cited by 243 publications

(309 citation statements)

References 40 publications

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“…Alternatively, although lincRNAs interact with PRC2, this interaction may not be required for Polycomb recruitment, with the lincRNA instead repressing gene expression by another mechanism, which then allows for Polycomb recruitment (Brockdorff 2013). For example, a number of studies recently determined that Xist RNA interacts with the transcriptional repressor SPEN (also known as SHARP) and that this is required for gene silencing (Chu et al 2015;McHugh et al 2015;Minajigi et al 2015;Moindrot et al 2015;Monfort et al 2015).…”

Section: Discussionmentioning

confidence: 99%

The interaction of PRC2 with RNA or chromatin is mutually antagonistic

et al. 2016

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Polycomb repressive complex 2 (PRC2) modifies chromatin to maintain genes in a repressed state during development. PRC2 is primarily associated with CpG islands at repressed genes and also possesses RNA binding activity. However, the RNAs that bind PRC2 in cells, the subunits that mediate these interactions, and the role of RNA in PRC2 recruitment to chromatin all remain unclear. By performing iCLIP for PRC2 in comparison with other RNA binding proteins, we show here that PRC2 binds nascent RNA at essentially all active genes. Although interacting with RNA promiscuously, PRC2 binding is enriched at specific locations within RNAs, primarily exon-intron boundaries and the 3 ′ UTR. Deletion of other PRC2 subunits reveals that SUZ12 is sufficient to establish this RNA binding profile. Contrary to prevailing models, we also demonstrate that the interaction of PRC2 with RNA or chromatin is mutually antagonistic in cells and in vitro. RNA degradation in cells triggers PRC2 recruitment to CpG islands at active genes. Correspondingly, the release of PRC2 from chromatin in cells increases RNA binding. Consistent with this, RNA and nucleosomes compete for PRC2 binding in vitro. We propose that RNA prevents PRC2 recruitment to chromatin at active genes and that mutual antagonism between RNA and chromatin underlies the pattern of PRC2 chromatin association across the genome.

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Section: Discussionmentioning

confidence: 99%

The interaction of PRC2 with RNA or chromatin is mutually antagonistic

et al. 2016

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“…Interestingly, our RNAi screen targeting splicing factors did not identify any new additional sex determination genes, indicating that there are a limited number of genes yet to be identified in this pathway. Finally, intriguingly, three recent studies have identified SPEN and Rbm15 (the mouse and human ortholog of Nito) as factors interacting with Xist, the long noncoding RNA that is essential for dosage compensation in mammals (36)(37)(38). Clearly, future experiments such as RNA-seq will be necessary to elucidate the mechanism and logic of Nito-mediated signaling events.…”

Section: Discussionmentioning

confidence: 99%

spenito is required for sex determination in Drosophila melanogaster

Dong

Perrimon

2015

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

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Sex-lethal (Sxl) encodes the master regulator of the sex determination pathway in Drosophila and acts by controlling sex identity in both soma and germ line. In females Sxl maintains its own expression by controlling the alternative splicing of its own mRNA. Here, we identify a novel sex determination gene, spenito (nito) that encodes a SPEN family protein. Loss of nito activity results in stem cell tumors in the female germ line as well as female-to-male somatic transformations. We show that Nito is a ubiquitous nuclear protein that controls the alternative splicing of the Sxl mRNA by interacting with Sxl protein and pre-mRNA, suggesting that it is directly involved in Sxl auto-regulation. Given that SPEN family proteins are frequently mutated in cancers, our results suggest that these factors might be implicated in tumorigenesis through splicing regulation.germ-line stem cell | sex determination | alternative splicing S ex determination in Drosophila is under the control of the master regulatory gene Sex-lethal (Sxl) (1). Sxl acts downstream of the X-chromosome counting mechanism and encodes a female-specific RNA binding protein. Once activated, Sxl maintains its own expression by regulating the alternative splicing of its pre-mRNA. Sxl controls female fate by controlling somatic and germ-line sex identity as well as dosage compensation (2). In female somatic cells, Sxl controls the alternative splicing of transformer (tra), which together with transformer2 (tra2) controls the alternative splicing of doublesex (dsx) and fruitless (fru). dsx and fru in turn encode sex-specific transcription factors that control male versus female morphology, physiology, and behavior (3, 4). In addition, Sxl represses the male-specific dosage compensation system by regulating male-specific lethal 2 (msl-2) both at the level of alternative splicing and translational control (5

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“…These initial Xist-coated DNA regions (black regions) sample different locations of the nucleus (44,45,23,46,47) and when they come into close proximity of the nuclear lamina, are sequestered at the nuclear lamina through an interaction between Xist and LBR (middle panel). Because DNA that interacts with the nuclear lamina undergoes more constrained mobility (23,24), this recruitment changes the 3-dimensional organization of X-chromosome (15,48,49) and repositions active genes (green regions) closer the Xist transcription locus enabling Xist, and its SHARP/SMRT/HDAC3 silencing complex (11,18,22), to spread to these new sites by 3-dimensional proximity transfer. These sites are then recruited to the nuclear lamina, effectively bringing another set of active genes (yellow regions) into closer contact with the Xist transcription locus (right panel).…”

Section: Fig S6 δRs-lbr and δTm-lbr Localize Properly In The Nucleamentioning

confidence: 99%

Xist recruits the X chromosome to the nuclear lamina to enable chromosome-wide silencing

Chen

Blanco

Jackson

et al. 2016

Science

255

210

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Plunging into a domain of silence Female mammals have two X chromosomes. One must be silenced to “balance” gene dosage with male XY cells. The Xist long noncoding RNA coats the inactive X chromosome in female mammalian cells. Chen et al. show that the Xist RNA helps recruit the X chromosome to the internal rim of the cell nucleus, a region where gene expression is silenced. Xist is recruited to the domain through an interaction with the Lamin B receptor. This recruitment allows the Xist RNA to spread across the future inactive X chromosome, shutting down gene expression. Science , this issue p. 468

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A Pooled shRNA Screen Identifies Rbm15, Spen, and Wtap as Factors Required for Xist RNA-Mediated Silencing

Cited by 243 publications

References 40 publications

The interaction of PRC2 with RNA or chromatin is mutually antagonistic

The interaction of PRC2 with RNA or chromatin is mutually antagonistic

spenito is required for sex determination in Drosophila melanogaster

Xist recruits the X chromosome to the nuclear lamina to enable chromosome-wide silencing

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