NELF-E RRM Undergoes Major Structural Changes in Flexible Protein Regions on Target RNA Binding

Rao, Jampani Nageswara; Schweimer, Kristian; Wenzel, Sabine; Wöhrl, Birgitta M.; Rösch, Paul

doi:10.1021/bi702429m

Cited by 13 publications

(15 citation statements)

References 37 publications

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“…Multiple binding specificities are not uncommon for RNA binding proteins, although different binding sites are sometimes recognized by different binding domains. 43 For a single RNA binding domain, different binding specificities could be obtained through alternate conformations of the domain as observed for U2AF65, 44,45 or structural reorganization upon binding as for NELF-E. 46 In addition, changes in RNA structure have the potential to present a site differently to a binding protein. 47 How the flexibility of Bru binding is achieved is not known, and will likely require structural studies with the protein or domains bound to different substrates for a complete understanding.…”

Section: Methodsmentioning

confidence: 99%

Multiple RNA binding domains of Bruno confer recognition of diverse binding sites for translational repression

Reveal¹,

García²,

Ellington³

et al. 2011

RNA Biology

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Section: Methodsmentioning

confidence: 99%

Multiple RNA binding domains of Bruno confer recognition of diverse binding sites for translational repression

Reveal¹,

García²,

Ellington³

et al. 2011

RNA Biology

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“…Approximately 18 nucleotides of a nascent transcript are buried inside the elongation complex (Gu et al 1996;Andrecka et al 2008), leaving the remainder of the 5′ region exposed for contact with NELF. NELF-E appears to have little if any sequence specificity (Narita et al 2003;Rao et al 2008). In accordance with the lack of sequence specificity, analysis of sequences of 50 promoters with paused Pol II failed to identify a sequence that could be correlated with the location of the paused Pol II .…”

Section: Introductionmentioning

confidence: 94%

“…NELF-E contains an RNA recognition motif (Yamaguchi et al 2002;Rao et al 2008). Mutations that impair the RNA binding activity of this subunit also impair the ability of the NELF complex to inhibit elongation in vitro (Yamaguchi et al 2002).…”

Section: Introductionmentioning

confidence: 99%

Promoter proximal pausing on genes in metazoans

Gilmour

2008

Chromosoma

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The past two decades of research into transcriptional control of protein-encoding genes in eukaryotes have focused on regulatory mechanisms that act by controlling the recruitment of Pol II to a gene's promoter. Recent genome-wide analyses of the distribution of Pol II indicates that Pol II is concentrated in the promoter regions of thousands of genes in human and Drosophila cells. In many cases, Pol II may have initiated transcription but paused in the promoter proximal region. Hence, release of Pol II from the promoter region into the body of a gene is now recognized as a common rate-limiting step in the control of gene expression. Notably, most genes with paused Pol II are expressed indicating that the pause can be transient. What causes Pol II to concentrate in the promoter region and how it is released to transcribe a gene are the focus of this review.

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“…Qualitative binding experiments suggest that NELF-E binds to the lower stem region of TAR RNA [12], [19]. In addition, NMR studies have solved the structure of the RRM domain of NELF-E [24], [25]. This work also used fluorescence equilibrium titrations to test its interaction to single and double stranded RNA fragments of the lower stem of TAR.…”

Section: Introductionmentioning

confidence: 99%

Defining NELF-E RNA Binding in HIV-1 and Promoter-Proximal Pause Regions

et al. 2014

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The four-subunit Negative Elongation Factor (NELF) is a major regulator of RNA Polymerase II (Pol II) pausing. The subunit NELF-E contains a conserved RNA Recognition Motif (RRM) and is proposed to facilitate Poll II pausing through its association with nascent transcribed RNA. However, conflicting ideas have emerged for the function of its RNA binding activity. Here, we use in vitro selection strategies and quantitative biochemistry to identify and characterize the consensus NELF-E binding element (NBE) that is required for sequence specific RNA recognition (NBE: CUGAGGA(U) for Drosophila). An NBE-like element is present within the loop region of the transactivation-response element (TAR) of HIV-1 RNA, a known regulatory target of human NELF-E. The NBE is required for high affinity binding, as opposed to the lower stem of TAR, as previously claimed. We also identify a non-conserved region within the RRM that contributes to the RNA recognition of Drosophila NELF-E. To understand the broader functional relevance of NBEs, we analyzed promoter-proximal regions genome-wide in Drosophila and show that the NBE is enriched +20 to +30 nucleotides downstream of the transcription start site. Consistent with the role of NELF in pausing, we observe a significant increase in NBEs among paused genes compared to non-paused genes. In addition to these observations, SELEX with nuclear run-on RNA enrich for NBE-like sequences. Together, these results describe the RNA binding behavior of NELF-E and supports a biological role for NELF-E in promoter-proximal pausing of both HIV-1 and cellular genes.

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NELF-E RRM Undergoes Major Structural Changes in Flexible Protein Regions on Target RNA Binding

Cited by 13 publications

References 37 publications

Multiple RNA binding domains of Bruno confer recognition of diverse binding sites for translational repression

Multiple RNA binding domains of Bruno confer recognition of diverse binding sites for translational repression

Promoter proximal pausing on genes in metazoans

Defining NELF-E RNA Binding in HIV-1 and Promoter-Proximal Pause Regions

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