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1-20 of 136759
Journal Article
How bacterial xenogeneic silencer rok distinguishes foreign from self DNA in its resident genome
Nucleic Acids Research, gky836, https://doi.org/10.1093/nar/gky836
Published: 25 September 2018
Journal Article
Monitored eCLIP: high accuracy mapping of RNA-protein interactions
Nucleic Acids Research, gky858, https://doi.org/10.1093/nar/gky858
Published: 25 September 2018
Journal Article
iProX: an integrated proteome resource
Nucleic Acids Research, gky869, https://doi.org/10.1093/nar/gky869
Published: 25 September 2018
Image
Workflow of the proteomics data submission and curation process in iProX. T...
Published: 25 September 2018
Figure 1. Workflow of the proteomics data submission and curation process in iProX. The upper layer (blue rectangles) illustrates the data submission process for users, whereas the bottom layer (orange rectangles) represents the data curation process for iProX curators.
Image
Summary of the datasets released in iProX. Distribution figures of the spec...
Published: 25 September 2018
Figure 2. Summary of the datasets released in iProX. Distribution figures of the species, MS instrument and data size of datasets public available in iProX (by the end of July 2018).
Image
System architecture and infrastructure of iProX. Based on a hyper-converged...
Published: 25 September 2018
Figure 3. System architecture and infrastructure of iProX. Based on a hyper-converged architecture, the application, virtualization and infrastructure layer are implemented for the iProX repository. The infrastructure layer includes hardware resources of computing, storage and network, while the v
Image
Comparison of CLIP, iCLIP, and eCLIP procedures. Scheme of the CLIP protoco...
Published: 25 September 2018
Figure 1. Comparison of CLIP, iCLIP, and eCLIP procedures. Scheme of the CLIP protocol. Immunoprecipitated RNA fragments are coupled to a peptide (blue square) at the crosslinking site (red cross). Reverse-transcription (RT) either stops or reads through the crosslinking site. ( A ) For CLIP, adap
Image
CRISPR/Cas9 editing of eIF4A3. ( A ) Schematic representation of the edited...
Published: 25 September 2018
Figure 2. CRISPR/Cas9 editing of eIF4A3. ( A ) Schematic representation of the edited eIF4A3 gene. C-terminal insertion harbors a TEV proteolytic cleavage site and a 3xHA affinity tag, fused to a Internal Ribosomal Entry Site (IRES2)-controlled puromycin (PuroR) selection cassette encompassed by L
Image
Detailed comparison of the eCLIP and meCLIP protocols. Presentation of the ...
Published: 25 September 2018
Figure 3. Detailed comparison of the eCLIP and meCLIP protocols. Presentation of the different steps involved in eCLIP and meCLIP procedures. Following UV crosslinking, RNase treatment, and RBP purification, an RNA adaptor (green) is ligated at the 3′ end. For meCLIP, a biotinylated RNA linker (bl
Image
Read-through reads percentage for meCLIP depends on experimental conditions...
Published: 25 September 2018
Figure 4. Read-through reads percentage for meCLIP depends on experimental conditions. Libraries generated using ( A ) different cross-linked proteins and ( B ) different reverse transcriptases (RTase) and HA-tagged eIF4A3.
Image
CITS detection is biased by read-through reads. ( A–C ) meCLIP reads mapped...
Published: 25 September 2018
Figure 5. CITS detection is biased by read-through reads. ( A–C ) meCLIP reads mapped on three examples of exons. Each black underline corresponds to a CITS detected with CTK. Read coverage is in Reads Per Million (RPM). ( D ) Venn diagram representing the intersection of peaks detected in the unf
Image
Increased accuracy of cross-linking site positioning. Positioning of 5′ end...
Published: 25 September 2018
Figure 6. Increased accuracy of cross-linking site positioning. Positioning of 5′ ends of meCLIP reads relative to the exon junction. ( A ) Distribution of eIF4A3-HA meCLIP replicates: truncated reads (red) and read-through reads (blue). ( B ) Distribution of eIF4A3-HA meCLIP replicates: short tru
Image
DNA binding preferences of Rok from protein binding microarray analysis. E...
in How bacterial xenogeneic silencer rok distinguishes foreign from self DNA in its resident genome
> Nucleic Acids Research
Published: 25 September 2018
Figure 1. DNA binding preferences of Rok from protein binding microarray analysis. E -score reflects the relative affinity for a particular 8-mer sequence. Box plots show the E -score distributions of 8-mers with certain characteristics. Bands at the bottom, top, and inside of the box represent
Image
Comparisons of the effect of G/C insertions on AT-rich DNA binding preferen...
in How bacterial xenogeneic silencer rok distinguishes foreign from self DNA in its resident genome
> Nucleic Acids Research
Published: 25 September 2018
Figure 2. Comparisons of the effect of G/C insertions on AT-rich DNA binding preferences of Rok with other xenogeneic silencers H-NS, Lsr2 and MvaT. The PBM data for H-NS, Lsr2 and MvaT were published previously ( 13 , 14 ). ( A and B ) The influence of G/C insertions on DNA binding for Rok, H-N
Image
Solution structure of Rok-C 97–191 . PDB code: 5ZUZ. ( A ) Superposition of...
in How bacterial xenogeneic silencer rok distinguishes foreign from self DNA in its resident genome
> Nucleic Acids Research
Published: 25 September 2018
Figure 3. Solution structure of Rok-C 97–191 . PDB code: 5ZUZ. ( A ) Superposition of backbone traces of the ensemble of 20 conformers of Rok-C 97–191 . ( B ) Ribbon representation of the representative structure of Rok- C 97-191 . ( C ) The topology of the structure of Rok-C 97–191 , which belong
Image
Solution structure of the Rok-C 102-185 /DNA complex. PDB code: 5ZUX. ( A )...
in How bacterial xenogeneic silencer rok distinguishes foreign from self DNA in its resident genome
> Nucleic Acids Research
Published: 25 September 2018
Figure 4. Solution structure of the Rok-C 102-185 /DNA complex. PDB code: 5ZUX. ( A ) Superposition of the protein backbone and DNA for the ensemble of 20 conformers of Rok-C 102–185 in complex with Seq1 DNA. ( B ) Electrostatic potential surface of Rok-C 102–185 protein in the complex. ( C ) Th
Image
Conformational changes of Seq1 DNA upon binding with Rok-C 102–185 . ( A ) ...
in How bacterial xenogeneic silencer rok distinguishes foreign from self DNA in its resident genome
> Nucleic Acids Research
Published: 25 September 2018
Figure 5. Conformational changes of Seq1 DNA upon binding with Rok-C 102–185 . ( A ) Superimpositions of mean structures of Seq1 DNA in Rok-C 102–185 bound (black) and free (gray) forms. ( B and C ) Changes of the axis bending angles and minor groove width of Seq1 DNA upon Rok binding (calculat
Image
DNA binding preferences of Rok towards different 5-bp sequences. The distri...
in How bacterial xenogeneic silencer rok distinguishes foreign from self DNA in its resident genome
> Nucleic Acids Research
Published: 25 September 2018
Figure 6. DNA binding preferences of Rok towards different 5-bp sequences. The distribution of E -scores of all 8-mers containing a specific 5-bp sequence or its complementary sequence is presented using box plot. ( A ) DNA binding preference of Rok toward 5-bp sequences containing only one GC ba
Image
Comparison of the DNA recognition mechanisms of four types of xenogeneic si...
in How bacterial xenogeneic silencer rok distinguishes foreign from self DNA in its resident genome
> Nucleic Acids Research
Published: 25 September 2018
Figure 7. Comparison of the DNA recognition mechanisms of four types of xenogeneic silencers. ( A ) Structure model of the H-NS DNA-binding domain in complex with 3AT DNA ( 13 ). The ‘AT-hook-like’ structure ‘QGR’ are colored blue. ( B ) Structure model of Lsr2 DNA-binding domain in complex with a
Image
Comparison of the DNA binding mode of Rok with other winged helix proteins....
in How bacterial xenogeneic silencer rok distinguishes foreign from self DNA in its resident genome
> Nucleic Acids Research
Published: 25 September 2018
Figure 8. Comparison of the DNA binding mode of Rok with other winged helix proteins. The α3 helix are colored red and the wings are colored magenta. ( A ) The winged helix domain of Rok binds the minor groove of DNA with its wing W1 and α3 helix. ( B ) HNF-3γ binds the major groove of DNA with it
