Shapes of Flow Injection Signals: Effect of Refractive Index on Spectrophotometric Signals Obtained for On-Line Formation of Bromine from Bromate, Bromide, and Hydrogen Ion in a Single-Channel Manifold Using Large-Volume Time-Based Injections

The shapes of the spectrophotometric signals obtained with a single-channel manifold for large-volume (4 ml) time-based injections for the six possible combinations of the reagents bromate, bromide and nitric acid in the injectate and carrier stream, by which bromine can be formed on-line, have been determined. The injectate and carrier stream were 5.25 x 10-4 M in bromate, 0.030 M in bromide and 1 M in nitric acid when these reagents were present. The signals consisted of two separate peaks caused by formation of bromine at the front and rear boundaries of the injected bolus. When both injectate and carrier stream were 1 M in nitric acid (i.e., for the reagent combination H+Br03- - H+Br-)the two peaks were of equal height, and the signal was. virtually the same whichever solution was used as the injectate. In reagent combinations where only one solution contained nitric acid the peaks were different in size, the smaller peak being that produced by the boundary in which the acidic solution was flowing behind the other solution. This difference in size between the front and rear peaks was shown to be caused by refractive index effects. When the refractive indices of the two solutions were matched either by increasing the potassium bromide concentration or by making the non-acidic solution 7% in sodium nitrate, the peaks became equal in size. When the potassium bromide concentration was increased there was an appreciable increase in peak size (about 4-fold): the changes in the amount of bromine formed must be due to kinetic or equilibrium effects. This increase in size did not occur when sodium nitrate was used to balance the refractive indices

Chromatin alternates between A and B compartments at kilobase scale for subgenic organization

Nuclear compartments are prominent features of 3D chromatin organization, but sequencing depth limitations have impeded investigation at ultra fine-scale. CTCF loops are generally studied at a finer scale, but the impact of looping on proximal interactions remains enigmatic. Here, we critically examine nuclear compartments and CTCF loop-proximal interactions using a combination of in situ Hi-C at unparalleled depth, algorithm development, and biophysical modeling. Producing a large Hi-C map with 33 billion contacts in conjunction with an algorithm for performing principal component analysis on sparse, super massive matrices (POSSUMM), we resolve compartments to 500 bp. Our results demonstrate that essentially all active promoters and distal enhancers localize in the A compartment, even when flanking sequences do not. Furthermore, we find that the TSS and TTS of paused genes are often segregated into separate compartments. We then identify diffuse interactions that radiate from CTCF loop anchors, which correlate with strong enhancer-promoter interactions and proximal transcription. We also find that these diffuse interactions depend on CTCF's RNA binding domains. In this work, we demonstrate features of fine-scale chromatin organization consistent with a revised model in which compartments are more precise than commonly thought while CTCF loops are more protracted

Human pancreatic islet three-dimensional chromatin architecture provides insights into the genetics of type 2 diabetes

Genetic studies promise to provide insight into the molecular mechanisms underlying type 2 diabetes (T2D). Variants associated with T2D are often located in tissue-specific enhancer clustersor super-enhancers. So far, such domains have been defined through clustering of enhancers in linear genome maps rather than in 3D space. Furthermore, their target genes are often unknown. We have now created promoter capture Hi-C maps in human pancreatic islets. This linked diabetes-associated enhancers with their target genes, often located hundreds of kilobases away. It also revealed >1300 groups of islet enhancers, super-enhancers and active promoters that form 3D hubs, some of which show coordinated glucose-dependent activity. We demonstrate that genetic variation in hubs impacts insulin secret ion heritability, and show that hub annotations can be used for polygenic scores that predict T2D risk driven by islet regulatory variants. Human islet 3D chromatin architecture, therefore, provides a framework for interpretation of T2D GWAS signals

Chromatin alternates between A and B compartments at kilobase scale for subgenic organization

Abstract Nuclear compartments are prominent features of 3D chromatin organization, but sequencing depth limitations have impeded investigation at ultra fine-scale. CTCF loops are generally studied at a finer scale, but the impact of looping on proximal interactions remains enigmatic. Here, we critically examine nuclear compartments and CTCF loop-proximal interactions using a combination of in situ Hi-C at unparalleled depth, algorithm development, and biophysical modeling. Producing a large Hi-C map with 33 billion contacts in conjunction with an algorithm for performing principal component analysis on sparse, super massive matrices (POSSUMM), we resolve compartments to 500 bp. Our results demonstrate that essentially all active promoters and distal enhancers localize in the A compartment, even when flanking sequences do not. Furthermore, we find that the TSS and TTS of paused genes are often segregated into separate compartments. We then identify diffuse interactions that radiate from CTCF loop anchors, which correlate with strong enhancer-promoter interactions and proximal transcription. We also find that these diffuse interactions depend on CTCF’s RNA binding domains. In this work, we demonstrate features of fine-scale chromatin organization consistent with a revised model in which compartments are more precise than commonly thought while CTCF loops are more protracted