Eukaryotic DNA is hierarchically packaged into chromatin to fit inside the nucleus.Dynamics of the chromatin structure plays a critical role in transcriptional regulation and other biological processes that involve DN...Eukaryotic DNA is hierarchically packaged into chromatin to fit inside the nucleus.Dynamics of the chromatin structure plays a critical role in transcriptional regulation and other biological processes that involve DNA,such as DNA replication and DNA repair.Many factors,including histone variants,histone modification,DNA methylation and the binding of non-histone architectural proteins regulate the structure of chromatin.Although the structure of nucleosomes,the fundamental repeating unit of chromatin,is clear,there is still much discussion on the higher-order levels of chromatin structure.Identifying the structural details and dynamics of higher-order chromatin fibers is therefore very important for understanding the organization and regulation of gene activities.Here,we review studies on the dynamics of chromatin higherorder structure and its relationship with gene transcription.展开更多
Spatial expression patterns of homeobox （HOX） genes delineate positional identity of primary fibroblasts from different topo- graphic sites. The molecular mechanism underlying the establishing or maintaining of HOX ...Spatial expression patterns of homeobox （HOX） genes delineate positional identity of primary fibroblasts from different topo- graphic sites. The molecular mechanism underlying the establishing or maintaining of HOX gene expression pattern remains an attractive developmental issue to be addressed. Our previous work suggested a critical role of CTCF/cobesin-mediated high- er-order chromatin structure in RA-induced HOXA activation in human teratocarcinoma NT2/D1 cells. This study investigated the recruitment of CTCF and cohesin, and the higher-order chromatin structure of the HOXA locus in fetal lung and adult foreskin fibroblasts, which display complementary HOXA gene expression patterns. Chromatin contacts between the CTCF-binding sites were observed with lower frequency in human foreskin fibroblasts. This observation is consistent with the lower level of cohesin recruitment and 5＇ HOXA gene expression in the same cells. We also showed that CTCF-binding site A56 （CBSA56） related chromatin structures exhibit the most notable changes in between the two types of cell, and hence may stand for one of the key CTCF-binding sites for cell-type specific chromatin structure organization. Together, these results im- ply that CTCF/cohesin coordinates HOXA cluster higher-order chromatin structure and expression during development, and provide insight into the relationship between cell-type specific chromatin organization and the spatial collinearity.展开更多
Linker histones, e.g., H1, are best known for their ability to bind to nucleosomes and stabilize both nucleosome structure and condensed higher-order chromatin structures. However, over the years many investigators ha...Linker histones, e.g., H1, are best known for their ability to bind to nucleosomes and stabilize both nucleosome structure and condensed higher-order chromatin structures. However, over the years many investigators have reported specific interactions between linker histones and proteins involved in important cellular processes. The purpose of this review is to highlight evidence indicating an important alternative mode of action for H1, namely protein-protein interactions. We first review key aspects of the traditional view of linker histone action, including the importance of the H1 C-terminal domain. We then discuss the current state of knowledge of linker histone interactions with other proteins, and, where possible, highlight the mechanism of linker histone-mediated protein-protein interactions. Taken together, the data suggest a combinatorial role for the linker histones, functioning both as primary chromatin architectural proteins and simultaneously as recruitment hubs for proteins involved in accessing and modifying the chromatin fiber.展开更多
It is shown that each lattice equation in the Toda hierarchy can be factored by an integrable symplectic map and a finite dimensional integrable Hamiltonian system via higher order constraint relating the potential ...It is shown that each lattice equation in the Toda hierarchy can be factored by an integrable symplectic map and a finite dimensional integrable Hamiltonian system via higher order constraint relating the potential and square eigenfunctions. The classical Poisson structure and r matrix for the constrained flows are presented. 展开更多
基金supported by the National Natural Science Foundation of China(Grant Nos.31000566 and 31071147)the National Basic Research Program(973 Program)of China(Grant No.2009CB825501).
文摘Eukaryotic DNA is hierarchically packaged into chromatin to fit inside the nucleus.Dynamics of the chromatin structure plays a critical role in transcriptional regulation and other biological processes that involve DNA,such as DNA replication and DNA repair.Many factors,including histone variants,histone modification,DNA methylation and the binding of non-histone architectural proteins regulate the structure of chromatin.Although the structure of nucleosomes,the fundamental repeating unit of chromatin,is clear,there is still much discussion on the higher-order levels of chromatin structure.Identifying the structural details and dynamics of higher-order chromatin fibers is therefore very important for understanding the organization and regulation of gene activities.Here,we review studies on the dynamics of chromatin higherorder structure and its relationship with gene transcription.
基金supported by the National Natural Science Foundation of China(31030026)the National Basic Research Program(2011CB-965203)the PUMC Youth funds(3332013138)
文摘Spatial expression patterns of homeobox （HOX） genes delineate positional identity of primary fibroblasts from different topo- graphic sites. The molecular mechanism underlying the establishing or maintaining of HOX gene expression pattern remains an attractive developmental issue to be addressed. Our previous work suggested a critical role of CTCF/cobesin-mediated high- er-order chromatin structure in RA-induced HOXA activation in human teratocarcinoma NT2/D1 cells. This study investigated the recruitment of CTCF and cohesin, and the higher-order chromatin structure of the HOXA locus in fetal lung and adult foreskin fibroblasts, which display complementary HOXA gene expression patterns. Chromatin contacts between the CTCF-binding sites were observed with lower frequency in human foreskin fibroblasts. This observation is consistent with the lower level of cohesin recruitment and 5＇ HOXA gene expression in the same cells. We also showed that CTCF-binding site A56 （CBSA56） related chromatin structures exhibit the most notable changes in between the two types of cell, and hence may stand for one of the key CTCF-binding sites for cell-type specific chromatin structure organization. Together, these results im- ply that CTCF/cohesin coordinates HOXA cluster higher-order chromatin structure and expression during development, and provide insight into the relationship between cell-type specific chromatin organization and the spatial collinearity.
文摘Linker histones, e.g., H1, are best known for their ability to bind to nucleosomes and stabilize both nucleosome structure and condensed higher-order chromatin structures. However, over the years many investigators have reported specific interactions between linker histones and proteins involved in important cellular processes. The purpose of this review is to highlight evidence indicating an important alternative mode of action for H1, namely protein-protein interactions. We first review key aspects of the traditional view of linker histone action, including the importance of the H1 C-terminal domain. We then discuss the current state of knowledge of linker histone interactions with other proteins, and, where possible, highlight the mechanism of linker histone-mediated protein-protein interactions. Taken together, the data suggest a combinatorial role for the linker histones, functioning both as primary chromatin architectural proteins and simultaneously as recruitment hubs for proteins involved in accessing and modifying the chromatin fiber.
文摘It is shown that each lattice equation in the Toda hierarchy can be factored by an integrable symplectic map and a finite dimensional integrable Hamiltonian system via higher order constraint relating the potential and square eigenfunctions. The classical Poisson structure and r matrix for the constrained flows are presented.
