FUS-dependent loading of SUV39H1 to OCT4 pseudogene-lncRNA programs a silencing complex with OCT4 promoter specificity

Abstract The resurrection of pseudogenes during evolution produced lncRNAs with new biological function. Here we show that pseudogene-evolution created an Oct4 pseudogene lncRNA that is able to direct epigenetic silencing of the parental Oct4 gene via a 2-step, lncRNA dependent mechanism. The murine Oct4 pseudogene 4 (mOct4P4) lncRNA recruits the RNA binding protein FUS to allow the binding of the SUV39H1 HMTase to a defined mOct4P4 lncRNA sequence element. The mOct4P4-FUS-SUV39H1 silencing complex holds target site specificity for the parental Oct4 promoter and interference with individual components results in loss of Oct4 silencing. SUV39H1 and FUS do not bind parental Oct4 mRNA, confirming the acquisition of a new biological function by the mOct4P4 lncRNA. Importantly, all features of mOct4P4 function are recapitulated by the human hOCT4P3 pseudogene lncRNA, indicating evolutionary conservation. Our data highlight the biological relevance of rapidly evolving lncRNAs that infiltrate into central epigenetic regulatory circuits in vertebrate cells.

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The RNA-binding protein Staufen1 impairs myogenic differentiation via a c-myc–dependent mechanism

Molecular Biology of the Cell ◽

10.1091/mbc.e14-04-0895 ◽

2014 ◽

Vol 25 (23) ◽

pp. 3765-3778 ◽

Cited By ~ 17

Author(s):

Aymeric Ravel-Chapuis ◽

Tara E. Crawford ◽

Marie-Laure Blais-Crépeau ◽

Guy Bélanger ◽

Chase T. Richer ◽

...

Keyword(s):

Skeletal Muscle ◽

Similar Pattern ◽

Rna Binding ◽

Myogenic Differentiation ◽

Rna Binding Protein ◽

C2c12 Cells ◽

Muscle Degeneration ◽

Low Levels ◽

Dependent Mechanism

Recent work has shown that Staufen1 plays key roles in skeletal muscle, yet little is known about its pattern of expression during embryonic and postnatal development. Here we first show that Staufen1 levels are abundant in mouse embryonic muscles and that its expression decreases thereafter, reaching low levels in mature muscles. A similar pattern of expression is seen as cultured myoblasts differentiate into myotubes. Muscle degeneration/regeneration experiments revealed that Staufen1 increases after cardiotoxin injection before returning to the low levels seen in mature muscles. We next prevented the decrease in Staufen1 during differentiation by generating stable C2C12 muscle cell lines overexpressing Staufen1. Cells overexpressing Staufen1 differentiated poorly, as evidenced by reductions in the differentiation and fusion indices and decreases in MyoD, myogenin, MEF2A, and MEF2C, independently of Staufen-mediated mRNA decay. However, levels of c-myc, a factor known to inhibit differentiation, were increased in C2C12 cells overexpressing Staufen1 through enhanced translation. By contrast, the knockdown of Staufen1 decreased c-myc levels in myoblasts. Collectively our results show that Staufen1 is highly expressed during early stages of differentiation/development and that it can impair differentiation by regulating c-myc, thereby highlighting the multifunctional role of Staufen1 in skeletal muscle cells.

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Su1862 RNA Binding Protein Musashi-1 Regulates Tumorigenesis and Angiogenesis via MicroRNA-Dependent Mechanism

Gastroenterology ◽

10.1016/s0016-5085(14)61752-2 ◽

2014 ◽

Vol 146 (5) ◽

pp. S-488

Author(s):

Sripathi M. Sureban ◽

Randal May ◽

Dongfeng Qu ◽

Parthasarathy Chandrakesan ◽

Nathaniel Weygant ◽

...

Keyword(s):

Rna Binding ◽

Binding Protein ◽

Rna Binding Protein ◽

Dependent Mechanism

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Polymerase pausing induced by sequence-specific RNA binding protein drives heterochromatin assembly

10.1101/217968 ◽

2017 ◽

Author(s):

Jahan-Yar Parsa ◽

Selim Boudoukha ◽

Jordan Burke ◽

Christina Homer ◽

Hiten D. Madhani

Keyword(s):

Genome Stability ◽

Rna Binding ◽

De Novo ◽

Binding Protein ◽

Rna Binding Protein ◽

Heterochromatin Formation ◽

Repressor Complex ◽

Polymerase Pausing ◽

Heterochromatin Assembly ◽

Dependent Mechanism

Packaging of pericentromeric DNA into heterochromatin is crucial for genome stability, development and health, yet its endogenous triggers remain poorly understood1. A defining feature of pericentromeric heterochromatin is histone H3 lysine 9 methylation (H3K9me)2–4. In S. pombe, transcripts derived from the pericentromeric dg and dh repeat during S phase5–7 promote heterochromatin formation through two pathways: an RNAi-dependent mechanism involving recruitment of the Clr4 H3K9 methyltransferase complex (CLR-C) via the RITS complex8–13, and RNAi-independent mechanism involving an RNAPII-associated RNA-binding protein Seb1, the repressor complex SHREC, and RNA processing activities14–19. We show here that Seb1 promotes long-lived RNAPII pausing. Pause sites associated with sequence-specific Seb1 RNA binding events are significantly enriched in pericentromeric repeat regions and their presence correlates with the heterochromatin-triggering activities of the corresponding dg and dh DNA fragments. Remarkably, globally increasing RNAPII stalling by other means induces the formation of novel large ectopic heterochromatin domains. Such ectopic heterochromatin occurs even in cells lacking functional RITS, demonstrating that RNAPII pausing can be sufficient to trigger de novo heterochromatin independently of RNAi. These results uncover Seb1-mediated polymerase stalling as a new signal for nucleating heterochromatin assembly in repetitive DNA.

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