Identifying Transcriptional Regulatory Modules Among Different Chromatin States in Mouse Neural Stem Cells

Gene expression regulation is a complex process involving the interplay between transcription factors and chromatin states. Significant progress has been made toward understanding the impact of chromatin states on gene expression. Nevertheless, the mechanism of transcription factors binding combinatorially in different chromatin states to enable selective regulation of gene expression remains an interesting research area. We introduce a nonparametric Bayesian clustering method for inhomogeneous Poisson processes to detect heterogeneous binding patterns of multiple proteins including transcription factors to form regulatory modules in different chromatin states. We applied this approach on ChIP-seq data for mouse neural stem cells containing 21 proteins and observed different groups or modules of proteins clustered within different chromatin states. These chromatin-state-specific regulatory modules were found to have significant influence on gene expression. We also observed different motif preferences for certain TFs between different chromatin states. Our results reveal a degree of interdependency between chromatin states and combinatorial binding of proteins in the complex transcriptional regulatory process. The software package is available on Github at - https://github.com/BSharmi/DPM-LGCP

Synthesis and characteristics of chelating fibers containing imidazoline group or thioamide group

Two types of chelating fibers containing an imidazoline or thioamide group were prepared through the functionalization of hydrazine-modified polyacrylonitrile fiber by ethylenediamine and through the amination and sulfurization reaction of the hydrazine-modified polyacrylonitrile fiber under appropriate conditions, respectively. It is shown that the reaction temperature, time, and agent concentration are the dominant factors in the synthesis of fibrous sorbents. The increase of the ethylenediamine concentration from 33 to 45% (v/v) at 95-98 degreesC results in a twofold higher increase of the fibrous sorbent with the imidazoline group, and a doubling of the reaction time from 2 to 4 h leads to a weight increase of the fibrous sorbent from 10 to 25% (w/w). Raising the temperature by about 5 degreesC significantly accelerates the amination reaction of the hydrazine-modified fiber, but the temperature is an insensitive factor in the thioamide-functionalized reaction of the aminated fiber. The introduction of a thioamide or imidazoline group is further verified by IR spectroscopy analysis. X-ray diffraction spectroscopy indicates the absolute disappearance of crystalline peaks for the fibers containing an imidazoline or thioamide group. However, the crosslinking reaction of the polyacrylonitrile fiber by hydrazine may make up for the effect of the crystallinity on the mechanical strength of the fibers, and the surface crackles of fibrous sorbents are not found by SEM photographs. The adsorption experiment results show that the newly prepared sorbents have high sorption capacities for noble metals in a high acidity, and it is also proved that Au(III) loaded on the chelating fibers may be reduced to Au(0). (C) 2002 John Wiley & Sons, Inc. J Appl Polym Sci 83: 1608-1616, 2002