Eukaryotic deoxyribonucleic acid(DNA)is wrapped around histone octamers(HOs)to form nucleosome core particles(NCPs),which in turn interact with linker DNA and linker histones to assemble chromatin fibers with more com...Eukaryotic deoxyribonucleic acid(DNA)is wrapped around histone octamers(HOs)to form nucleosome core particles(NCPs),which in turn interact with linker DNA and linker histones to assemble chromatin fibers with more complex,high-order structures.The molecular properties of chromatin are dynamically regulated by several factors,such as post-translational modifications and effector proteins,to maintain genome stability.In the past two decades,high-resolution techniques have led to many breakthroughs in understanding the molecular mechanisms that govern chromatin regulation.Nuclear magnetic resonance(NMR)has emerged as one of the major techniques in this field,providing new insights into the nucleosomes and nucleosome-protein complexes in different states ranging from soluble form to condensed states.Solution-state NMR has proven valuable in elucidating the conformational dynamics and molecular interactions for histone N-terminal tails,histone core regions and DNA with the combination of specific isotopic labeling.Solid-state NMR,which is not constrained by the high molecular weights of complexes like nucleosomes,has been applied to capture the structural and dynamical characteristics of both flexible tails and rigid histone core regions in nucleosomes and their complexes with effector proteins.Furthermore,the combination of the two techniques allows tracking molecular properties of nucleosomes during phase separation processes,which potentially play essential roles in chromatin regulation.This review summarizes recent advances in NMR studies of chromatin structure and dynamics.It highlighted that NMR revealed unique molecular characteristics for nucleosomes that are often invisible experimentally by other techniques like cryogenic electron microscopy(cryo-EM)and X-ray diffraction(XRD).I envision that,with future ef-forts such as the development of NMR methods and optimization of sample production protocols,solution-state NMR and solid-state NMR will provide invaluable information to expand our understanding of chromatin activity and its regulatory processes.展开更多
The genome wide dynamic profiling of chromatin accessibility in early osteogenic differentiation of human mesenchymal stem cells(MSCs)has not been reported.In this study,the sixth generation primary cultured human MSC...The genome wide dynamic profiling of chromatin accessibility in early osteogenic differentiation of human mesenchymal stem cells(MSCs)has not been reported.In this study,the sixth generation primary cultured human MSCs were treated with osteogenic inducer for 0 day,3 days,5 days and 7 days,respectively,and then harvested for assay for transposase accessible chromatin using sequencing(ATAC seq).The numbers of chromatin accessibility,the specific activated DNA motifs in chromatin accessibility regions and the functional enrichment analysis of peak adjacent genes were analyzed by bioinformatics.展开更多
The chromatin folding patterns in air and liquid were studied by atomicforce microscopy (AFM). A gentle water-air interface method was adopted to spreadchromatin from interphase nucleus of chicken erythrocyte. The chr...The chromatin folding patterns in air and liquid were studied by atomicforce microscopy (AFM). A gentle water-air interface method was adopted to spreadchromatin from interphase nucleus of chicken erythrocyte. The chromatin was ah-sorbed on APS-Inica surfaCe and studied with AFM. Beads-on-a-string were observedand many higher-order structures such as superbeads with dimensions 40-60urn indiameter and 4-7 urn in height were found to string together to make chromatin fibers.When sample spreading and absorbing time were shortened, higher-order chromatinfibers with 60-120 urn in width were observed in air as well as under water environment. These chromatin structures may reflect chromatin folding patterns in the livingcells.展开更多
基金supported by funds from the National Natural Science Foundation of China(grant number:32201006)Guangdong Province(grant number:2021QN02Y103,2022ZDZX2061,2022KCXTD034)2023 Stable Support Plan Program of Shenzhen Colleges and Universities Fund.
文摘Eukaryotic deoxyribonucleic acid(DNA)is wrapped around histone octamers(HOs)to form nucleosome core particles(NCPs),which in turn interact with linker DNA and linker histones to assemble chromatin fibers with more complex,high-order structures.The molecular properties of chromatin are dynamically regulated by several factors,such as post-translational modifications and effector proteins,to maintain genome stability.In the past two decades,high-resolution techniques have led to many breakthroughs in understanding the molecular mechanisms that govern chromatin regulation.Nuclear magnetic resonance(NMR)has emerged as one of the major techniques in this field,providing new insights into the nucleosomes and nucleosome-protein complexes in different states ranging from soluble form to condensed states.Solution-state NMR has proven valuable in elucidating the conformational dynamics and molecular interactions for histone N-terminal tails,histone core regions and DNA with the combination of specific isotopic labeling.Solid-state NMR,which is not constrained by the high molecular weights of complexes like nucleosomes,has been applied to capture the structural and dynamical characteristics of both flexible tails and rigid histone core regions in nucleosomes and their complexes with effector proteins.Furthermore,the combination of the two techniques allows tracking molecular properties of nucleosomes during phase separation processes,which potentially play essential roles in chromatin regulation.This review summarizes recent advances in NMR studies of chromatin structure and dynamics.It highlighted that NMR revealed unique molecular characteristics for nucleosomes that are often invisible experimentally by other techniques like cryogenic electron microscopy(cryo-EM)and X-ray diffraction(XRD).I envision that,with future ef-forts such as the development of NMR methods and optimization of sample production protocols,solution-state NMR and solid-state NMR will provide invaluable information to expand our understanding of chromatin activity and its regulatory processes.
文摘The genome wide dynamic profiling of chromatin accessibility in early osteogenic differentiation of human mesenchymal stem cells(MSCs)has not been reported.In this study,the sixth generation primary cultured human MSCs were treated with osteogenic inducer for 0 day,3 days,5 days and 7 days,respectively,and then harvested for assay for transposase accessible chromatin using sequencing(ATAC seq).The numbers of chromatin accessibility,the specific activated DNA motifs in chromatin accessibility regions and the functional enrichment analysis of peak adjacent genes were analyzed by bioinformatics.
文摘The chromatin folding patterns in air and liquid were studied by atomicforce microscopy (AFM). A gentle water-air interface method was adopted to spreadchromatin from interphase nucleus of chicken erythrocyte. The chromatin was ah-sorbed on APS-Inica surfaCe and studied with AFM. Beads-on-a-string were observedand many higher-order structures such as superbeads with dimensions 40-60urn indiameter and 4-7 urn in height were found to string together to make chromatin fibers.When sample spreading and absorbing time were shortened, higher-order chromatinfibers with 60-120 urn in width were observed in air as well as under water environment. These chromatin structures may reflect chromatin folding patterns in the livingcells.
