BindN: a web-based tool for efficient prediction of DNA and RNA binding sites in amino acid sequences

Wang, Liangjiang; Brown, Susan J.

doi:10.1093/nar/gkl298

Cited by 375 publications

(408 citation statements)

References 15 publications

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“…S4D). In agreement with these results, analysis of the N-terminal domains of mouse YY1 and YY2 proteins by BindN, an RNA-binding prediction server (39), identified two distinct RNA-binding motifs for YY1 that are not conserved in YY2 (Fig. S4E).…”

Section: Yy2 Binds To the Regulatory Regions Of Key Genes For Esc Plusupporting

confidence: 76%

Control of embryonic stem cell self-renewal and differentiation via coordinated alternative splicing and translation of YY2

Tahmasebi

Jafarnejad

Tam

et al. 2016

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

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Translational control of gene expression plays a key role during the early phases of embryonic development. Here we describe a transcriptional regulator of mouse embryonic stem cells (mESCs), Yin-yang 2 (YY2), that is controlled by the translation inhibitors, Eukaryotic initiation factor 4E-binding proteins (4E-BPs). YY2 plays a critical role in regulating mESC functions through control of key pluripotency factors, including Octamer-binding protein 4 (Oct4) and Estrogen-related receptor-β (Esrrb). Importantly, overexpression of YY2 directs the differentiation of mESCs into cardiovascular lineages. We show that the splicing regulator Polypyrimidine tractbinding protein 1 (PTBP1) promotes the retention of an intron in the 5′-UTR of Yy2 mRNA that confers sensitivity to 4E-BP-mediated translational suppression. Thus, we conclude that YY2 is a major regulator of mESC self-renewal and lineage commitment and document a multilayer regulatory mechanism that controls its expression.mRNA translation | 4E-BPs | PTBP | embryonic stem cell | YY2

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Section: Yy2 Binds To the Regulatory Regions Of Key Genes For Esc Plusupporting

confidence: 76%

Control of embryonic stem cell self-renewal and differentiation via coordinated alternative splicing and translation of YY2

Tahmasebi

Jafarnejad

Tam

et al. 2016

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

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“…As the LBD does not have an obvious nucleic acid binding domain, we used two prediction tools, RNABindR and BindN (28,29), to identify putative RNA binding motifs in the RAR␣ LBD. These tools predicted an RNA-binding region in the C terminus of RAR␣ (i.e., the F-domain) that is immediately downstream of helix 12 (H12; Fig.…”

Section: Rar␣ Regulates the Translation Of A Reporter Construct Contamentioning

confidence: 99%

Retinoic acid-gated sequence-specific translational control by RARα

Poon¹,

Chen

2008

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

118

172

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Retinoic acid (RA) plays important roles in development by modulating gene transcription through nuclear receptor activation. Increasing evidence supports a role for RA and RA receptors (RARs) in synaptic plasticity in the brain. We have recently reported that RA mediates a type of homeostatic synaptic plasticity through activation of dendritic protein synthesis, a process that requires dendritically localized RARα and is independent of transcriptional regulation. The molecular basis of this translational regulation by RA/RARα signaling, however, is unknown. Here we show that RARα is actively exported from the nucleus. Cytoplasmic RARα acts as an RNA-binding protein that associates with a subset of mRNAs, including dendritically localized glutamate receptor 1 (GluR1) mRNA. This binding is mediated by the RARα carboxyl terminal F-domain and specific sequence motifs in the 5′UTR of the GluR1 mRNA. Moreover, RARα association with the GluR1 mRNA directly underlies the translational control of GluR1 by RA: RARα represses GluR1 translation, while RA binding to RARα reduces its association with the GluR1 mRNA and relieves translational repression. Taken together, our results demonstrate a ligand-gated translational regulation mechanism mediated by a non-genomic function of RA/RARα signaling.

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“…Braunagel et al reported the association of FP25K with several ODV proteins and, using microsomal membranes, presented evidence suggesting that this may be occurring at the ER membrane (26). Protein domain searches indicated that AcMNPV FP25K is composed of a conserved N-terminal coiled coil, a putative actin binding helix, and a nucleic acid binding motif (43,44). We hypothesized that because of its role in protein-protein interactions, the N-terminal coiled-coil domain of FP25K plays a role in its predominant cytoplasmic localization by associating with ODV proteins.…”

Section: Resultsmentioning

confidence: 99%

Baculovirus FP25K Localization: Role of the Coiled-Coil Domain

Garretson

McCoy

Cheng

2016

J Virol

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Two types of viruses are produced during the baculovirus life cycle: budded virus (BV) and occlusion-derived virus (ODV). A particular baculovirus protein, FP25K, is involved in the switch from BV to ODV production. Previously, FP25K from the model alphabaculovirus Autographa californica multiple nucleopolyhedrovirus (AcMNPV) was shown to traffic ODV envelope proteins. However, FP25K localization and the domains involved are inconclusive. Here we used a quantitative approach to study FP25K subcellular localization during infection using an AcMNPV bacmid virus that produces a functional AcMNPV FP25K-green fluorescent protein (GFP) fusion protein. During cell infection, FP25K-GFP localized primarily to the cytoplasm, particularly amorphous structures, with a small fraction being localized in the nucleus. To investigate the sequences involved in FP25K localization, an alignment of baculovirus FP25K sequences revealed that the N-terminal putative coiled-coil domain is present in all alphabaculoviruses but absent in betabaculoviruses. Structural prediction indicated a strong relatedness of AcMNPV FP25K to long interspersed element 1 (LINE-1) open reading frame 1 protein (ORF1p), which contains an N-terminal coiled-coil domain responsible for cytoplasmic retention. Point mutations and deletions of this domain lead to a change in AcMNPV FP25K localization from cytoplasmic to nuclear. The coiled-coil and C-terminal deletion viruses increased BV production. Furthermore, a betabaculovirus FP25K protein lacking this N-terminal coiled-coil domain localized predominantly to the nucleus and exhibited increased BV production. These data suggest that the acquisition of this N-terminal coiled-coil domain in FP25K is important for the evolution of alphabaculoviruses. Moreover, with the divergence of preocclusion nuclear membrane breakdown in betabaculoviruses and membrane integrity in alphabaculoviruses, this domain represents an alphabaculovirus adaptation for nuclear trafficking of occlusion-associated proteins. IMPORTANCEBaculovirus infection produces two forms of viruses: BV and ODV. Manufacturing of ODV involves trafficking of envelope proteins to the inner nuclear membrane, mediated partly through the FP25K protein. Since FP25K is present in alpha-, beta-, and gammabaculoviruses, it is uncertain if this trafficking function is conserved. In this study, we looked at alpha-and betabaculovirus FP25K trafficking by its localization. Alphabaculovirus FP25K localized primarily to the cytoplasm, whereas betabaculovirus FP25K localized to the nucleus. We found that an N-terminal coiled-coil domain present in all alphabaculovirus FP25K proteins, but absent in betabaculovirus FP25K, was critical for alphabaculovirus FP25K cytoplasmic localization. We believe that this represents an evolutionary process that partly led to the gain of function of this N-terminal coiled-coil domain in alphabaculovirus FP25K to aid in nuclear trafficking of occlusion-associated proteins. Due to betabaculovirus breakdown of the nuclear membrane be...

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BindN: a web-based tool for efficient prediction of DNA and RNA binding sites in amino acid sequences

Cited by 375 publications

References 15 publications

Control of embryonic stem cell self-renewal and differentiation via coordinated alternative splicing and translation of YY2

Control of embryonic stem cell self-renewal and differentiation via coordinated alternative splicing and translation of YY2

Retinoic acid-gated sequence-specific translational control by RARα

Baculovirus FP25K Localization: Role of the Coiled-Coil Domain

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