dnase  (Worthington Biochemical)

Journal: Viral Applications of Green Fluorescent Protein

Article Title: Identification of Viral Peptide Fragments for Vaccine Development

doi: 10.1007/978-1-59745-559-6_18

Figure Lengend Snippet: Fragment library construction for SARS-CoV spike. a Fragmentation of target gene digested by DNase I. b Reassembled gene fragments..

Article Snippet: In the random digestion step, the use of DNase I in the presence of MnCl2 is critical as this protocol will generate DNA fragments of relatively uniform sizes, which facilitates the reassembly step ( 17 , also see Note ).

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Journal:

Article Title: Characterization of the survival motor neuron (SMN) promoter provides evidence for complex combinatorial regulation in undifferentiated and differentiated P19 cells

doi: 10.1042/BJ20041024

Figure Lengend Snippet: Summary of in vivo DMS, UVC and DNase I footprints of the mouse Smn proximal promoter

Article Snippet: Specifically, we used DMS, UVC irradiation and DNase I as DNA-modifying agents to map single-strand DNA breaks, comparing in vitro (naked DNA) and in vivo (living cells) footprints.

Techniques: In Vivo

Journal: bioRxiv

Article Title: Transcriptional regulatory logic of the diurnal cycle in the mouse liver

doi: 10.1101/077818

Figure Lengend Snippet: Characteristics of DHSs. A. Distribution of distances between DHSs and nearest active TSSs. We observe a bimodal distribution, with a first mode corresponding to DHSs in promoter regions (centered on 100 bp from the TSS) and a second mode centered on 10 kb from TSSs. B. Repartition of DHSs within three classes depending on their distance from the nearest TSS: 47% are more than 10 kb from a TSS and are classified as distal, 28% are between 1 kb and 10 kb away and are classified as proximal, and DHSs located 1 kb or less from a TSS represent 24% of all sites. C.-D. Pol II, DHS and H3K27ac signals around TSSs and distal DHSs (averages over all sites). Profiles were normalized so that the maximum around the TSS is 100%. E. DNase I signals (all time points are merged in the ZT All track) near the Albumin gene. Footprint detected using the Wellington algorithm are shown below the detected DHS sites. The promoter region is enlarged at the bottom, showing that the wide footprint detected in our data corresponds to previously established transcription factor binding sites (the colored boxed indicate protein complexes previously identified in [ 47 ]). Many sensitive regions locate din the gene body do not display footprints, probably due to high transcription of Alb in the liver.

Article Snippet: Movie S2: Dynamics of DNase I, Pol II and H3K27ac at the Npas2 locus.

Techniques: Binding Assay

Journal: bioRxiv

Article Title: Transcriptional regulatory logic of the diurnal cycle in the mouse liver

doi: 10.1101/077818

Figure Lengend Snippet: Genomic profiles of DNase I cuts around double E-boxes with a spacer of 6 bp (E1-E2 sp6) at all time points. The analysis is identical to that in Figure 6A. The analysis for ZT6 in Bmal1 -/- mice is also shown.

Article Snippet: Movie S2: Dynamics of DNase I, Pol II and H3K27ac at the Npas2 locus.

Techniques: Mouse Assay

Journal: bioRxiv

Article Title: Transcriptional regulatory logic of the diurnal cycle in the mouse liver

doi: 10.1101/077818

Figure Lengend Snippet: Genome-wide rhythms in DNase I signals are synchronous with Pol II transcription and histone acetylation. A. Number of DHSs with statistically significant cycling DNase I signals (left), H3K27ac signals (middle), or Pol II signals (right) at three different thresholds (p

Article Snippet: Movie S2: Dynamics of DNase I, Pol II and H3K27ac at the Npas2 locus.

Techniques: Genome Wide

Journal: bioRxiv

Article Title: Transcriptional regulatory logic of the diurnal cycle in the mouse liver

doi: 10.1101/077818

Figure Lengend Snippet: Location-dependent footprint characteristics of DHSs A. Visualization of DNase I signal (red) around the Rev-erb α promoter with the footprints (detected by Wellington) annotated in black, on top. This region contains BMAL1 binding sites (blue) with E-box motifs, annotated on the bottom line, which is marked by a characteristic footprint. The DNase I cleavage pattern is lower at the binding site, reflecting protection of the DNA from digestion, whereas high signals are observed on the edges of the binding site. B. Number of footprints within DHSs (+/- 300 bp around the peak center). TSS regions contain more footprints on average. More than half of distal regions contain a footprint. C. Number of footprints detected in DHSs in function of (relative) H3K36me3 signal.

Article Snippet: Movie S2: Dynamics of DNase I, Pol II and H3K27ac at the Npas2 locus.

Techniques: Binding Assay

Journal: bioRxiv

Article Title: Transcriptional regulatory logic of the diurnal cycle in the mouse liver

doi: 10.1101/077818

Figure Lengend Snippet: Measured DNase I-seq signals near the Dbp gene, compared with previously reporter DHSs in a reference study [ 30 ] (marked site_1 to site_7). [ 30 ] found seven hypersensitive sites while we detected six DHSs using our peak calling at compatible locations (black marks). Moreover, [ 30 ] reported high (sites 2, 4, 6, and 7, in green), or lower (sites 1, 3 and 5 in blue), amplitudes in rhythmic DNase I digestion efficiency, consistent with the DNase I-seq signals (visual inspection). Sites 2, 4, and 7 contain E-boxes that are binding sites for CLOCK and BMAL1. Locations of BMAL1 ChIP-seq signals (bottom track) [ 17 ] clearly overlaps strongest DNase I peaks.

Article Snippet: Movie S2: Dynamics of DNase I, Pol II and H3K27ac at the Npas2 locus.

Techniques: Binding Assay, Chromatin Immunoprecipitation

Journal: bioRxiv

Article Title: Transcriptional regulatory logic of the diurnal cycle in the mouse liver

doi: 10.1101/077818

Figure Lengend Snippet: Chromatin accessibility is generally similar in Bmal1 -/- and wild-type mice, but lower at BMAL1 bound sites in the former. A. The Rev-erb α (left) and Gsk3a (right) promoters, where DHSs are indicated with black ticks at the top. DNase I signal (in red) is strongly reduced in Bmal1 -/- mice at sites bound by BMAL1:CLOCK in WT mice (BMAL1 ChIP-seq signal in blue) in the Rev-erb α promoter, but similar in WT and Bmal1 -/- mice at the Gsk3a promoter, not bound by BMAL1. The vertical scale is the same for all four DNase I tracks, as well as for both BMAL1 ChiP-seq tracks. B. Comparison of DNase I signals at ZT6 in Bmal1 -/- versus WT mice. All DHSs overlapping BMAL1 ChIP-seq peaks in [ 17 ] are shown (n=1555). C. Boxplots showing DNase I intensity at the same sites as in B, at peak (ZT6) and trough (ZT18) activities of BMAL1 in the WT, and at ZT6 in Bmal1 -/- mice. D.-E Same as B-C, but using overlap with USF1 ChIP-seq peaks [ 73 ] to select DHSs (n=1705).

Article Snippet: Movie S2: Dynamics of DNase I, Pol II and H3K27ac at the Npas2 locus.

Techniques: Mouse Assay, Chromatin Immunoprecipitation

Journal: bioRxiv

Article Title: Transcriptional regulatory logic of the diurnal cycle in the mouse liver

doi: 10.1101/077818

Figure Lengend Snippet: DNase I hypersensitivity is rhythmic during diurnal cycles in mouse liver. A. DNase I hypersensitivity, Pol II density, and H3K27ac enrichment at the Dbp locus. The DHS track shows the frequency nucleotide-resolved DNase I cuts, while H3K27ac and Pol II ChIP-seq signals are smoothed over 100 bp. All time points are overlaid. The center of each DHS-enriched region is indicated on top and corresponds exactly with previously identified DHSs ( Fig S1 ). B. Zoom-in around the DHS at the TSS of Dbp (position marked with a star also in A) reveals dynamics of DNase I cuts around the clock. Both DNase I and H3K27ac signals are maximal at ZT10 and minimal at ZT22, consistent with BMAL1-mediated activation of Dbp transcription. C. Read counts (in log 2 units) for DNase 1 cuts (in windows of +/- 300 bp) centered on the Dbp TSS. Idem for Pol II and H3K27Ac ChIP-seq reads (in windows of +/- 1000 bp) centered on the same DHS and cosine fits show a common peak time around ZT10. Peak to trough amplitudes are about 16-fold for Pol II, and approximately 4-fold for both DNase I and H3K27ac. D. Phases and amplitudes of all DHS sites located in the neighborhood of the Dbp gene (nearest-TSS association according to annotation). Distances from the center of the plot indicate log 2 -amplitudes, and angles (clockwise from ZT0) indicate peak times. We observed that all regions oscillate around a common phase of ZT10. E.-H. Similar to A-D but for Npas2 , which has an opposite phase to Dbp , i.e. it peaks near ZT22.

Article Snippet: Movie S2: Dynamics of DNase I, Pol II and H3K27ac at the Npas2 locus.

Techniques: Chromatin Immunoprecipitation, Activation Assay

Journal: bioRxiv

Article Title: Transcriptional regulatory logic of the diurnal cycle in the mouse liver

doi: 10.1101/077818

Figure Lengend Snippet: BMAL1 footprints indicate temporally changing protein-DNA complexes, consistent with binding of a hetero-tetramer to DNA. A. Genomic profiles of DNase I cuts around double E-boxes with a spacer of 6 bp (E1-E2 sp6). We selected n=249 E1-E2 sp6 motifs overlapping a BMAL1 ChIP-seq peak, and show the average of profiles for loci classified as bound by the mixture model (posterior probability > 0.5). At ZT6, we observed that nucleotides around both E-boxes are protected. In contrast, at ZT18, the width of the protected region is reduced by approximately half, with the second E-box no longer protected from digestion. The signals are anchored to the motif position. Orientation of sites and signals is according to the best match to the E1-E2 sp6 motif. In Bmal1 -/- , only one E-box appears occupied. B. Width (left-side y-axis, green) of the protected region in WT and in Bmal1 -/- , for E1-E2 sp6 motifs occupied by BMAL1. Fraction of predicted occupied sites is shown in blue (right-side y-axis). C. Two views of the 3D computational model of the CLOCK:BMAL1 hetero-tetramer showing two heterodimers of CLOCK:BMAL1 occupying an E1-E2 sp6 site. The two heterodimers are shown in green and blue, while darker green and darker blue correspond to BMAL1 and lighter colors to CLOCK proteins. Information content along the DNA strands is shown in grey with highly constrained nucleotides of the motif in red.

Article Snippet: Movie S2: Dynamics of DNase I, Pol II and H3K27ac at the Npas2 locus.

Techniques: Binding Assay, Chromatin Immunoprecipitation