scholarly journals ATP-dependent chromatin assembly is functionally distinct from chromatin remodeling

eLife ◽  
2013 ◽  
Vol 2 ◽  
Author(s):  
Sharon E Torigoe ◽  
Ashok Patel ◽  
Mai T Khuong ◽  
Gregory D Bowman ◽  
James T Kadonaga
Keyword(s):  
Chromatin Remodeling ◽  
Motor Proteins ◽  
Chromatin Assembly ◽  
Histone Chaperones ◽  
Nucleosome Assembly ◽  
Periodic Arrays ◽  
Combined Action ◽  
The Relationship ◽  
Nucleosome Arrays

Chromatin assembly involves the combined action of ATP-dependent motor proteins and histone chaperones. Because motor proteins in chromatin assembly also function as chromatin remodeling factors, we investigated the relationship between ATP-driven chromatin assembly and chromatin remodeling in the generation of periodic nucleosome arrays. We found that chromatin remodeling-defective Chd1 motor proteins are able to catalyze ATP-dependent chromatin assembly. The resulting nucleosomes are not, however, spaced in periodic arrays. Wild-type Chd1, but not chromatin remodeling-defective Chd1, can catalyze the conversion of randomly-distributed nucleosomes into periodic arrays. These results reveal a functional distinction between ATP-dependent nucleosome assembly and chromatin remodeling, and suggest a model for chromatin assembly in which randomly-distributed nucleosomes are formed by the nucleosome assembly function of Chd1, and then regularly-spaced nucleosome arrays are generated by the chromatin remodeling activity of Chd1. These findings uncover an unforeseen level of specificity in the role of motor proteins in chromatin assembly.

scholarly journals The role of aTp-dependent chromatin remodeling factors in chromatin assembly in vivo

2019 ◽  
Vol 23 (2) ◽  
pp. 160-167
Author(s):  
Iu. A. Il’ina ◽  
A. Yu. Konev
Keyword(s):  
Dna Repair ◽  
Chromatin Remodeling ◽  
Molecular Motor ◽  
Chromatin Assembly ◽  
Histone Chaperones ◽  
Nucleosome Assembly ◽  
Male Pronucleus ◽  
Histone Exchange

Chromatin assembly is a fundamental process essential for chromosome duplication subsequent to DNA replication. In addition, histone removal and incorporation take place constantly throughout the cell cycle in the course of DNA-utilizing processes, such as transcription, damage repair or recombination. In vitro studies have revealed that nucleosome assembly relies on the combined action of core histone chaperones and ATP-utilizing molecular motor proteins such as ACF or CHD1. Despite extensive biochemical characterization of ATP-dependent chromatin assembly and remodeling factors, it has remained unclear to what extent nucleosome assembly is an ATP-dependent process in vivo. Our original and published data about the functions of ATP-dependent chromatin assembly and remodeling factors clearly demonstrated that these proteins are important for nucleosome assembly and histone exchange in vivo. During male pronucleus reorganization after fertilization CHD1 has a critical role in the genomescale, replication-independent nucleosome assembly involving the histone variant H3.3. Thus, the molecular motor proteins, such as CHD1, function not only in the remodeling of existing nucleosomes but also in de novo nucleosome assembly from DNA and histones in vivo. ATP-dependent chromatin assembly and remodeling factors have been implicated in the process of histone exchange during transcription and DNA repair, in the maintenance of centromeric chromatin and in the loading and remodeling of nucleosomes behind a replication fork. Thus, chromatin remodeling factors are involved in the processes of both replication-dependent and replication-independent chromatin assembly. The role of these proteins is especially prominent in the processes of large-scale chromatin reorganization; for example, during male pronucleus formation or in DNA repair. Together, ATP-dependent chromatin assembly factors, histone chaperones and chromatin modifying enzymes form a “chromatin integrity network” to ensure proper maintenance and propagation of chromatin landscape.

scholarly journals CO2 dynamics and heterogeneity in a cave atmosphere: role of ventilation patterns and airflow pathways

2021 ◽  
Author(s):  
Lovel Kukuljan ◽  
Franci Gabrovšek ◽  
Matthew D. Covington ◽  
Vanessa E. Johnston
Keyword(s):  
Temporal Variations ◽  
Observation Point ◽  
Spatially Distributed ◽  
Combined Action ◽  
Karst Systems ◽  
The Relationship ◽  
Co2 Dynamics ◽  
Global Carbon

AbstractUnderstanding the dynamics and distribution of CO2 in the subsurface atmosphere of carbonate karst massifs provides important insights into dissolution and precipitation processes, the role of karst systems in the global carbon cycle, and the use of speleothems for paleoclimate reconstructions. We discuss long-term microclimatic observations in a passage of Postojna Cave, Slovenia, focusing on high spatial and temporal variations of pCO2. We show (1) that the airflow through the massif is determined by the combined action of the chimney effect and external winds and (2) that the relationship between the direction of the airflow, the geometry of the airflow pathways, and the position of the observation point explains the observed variations of pCO2. Namely, in the terminal chamber of the passage, the pCO2 is low and uniform during updraft, when outside air flows to the site through a system of large open galleries. When the airflow reverses direction to downdraft, the chamber is fed by inlets with diverse flow rates and pCO2, which enter via small conduits and fractures embedded in a CO2-rich vadose zone. If the spatial distribution of inlets and outlets produces minimal mixing between low and high pCO2 inflows, high and persistent gradients in pCO2 are formed. Such is the case in the chamber, where vertical gradients of up to 1000 ppm/m are observed during downdraft. The results presented in this work provide new insights into the dynamics and composition of the subsurface atmosphere and demonstrate the importance of long-term and spatially distributed observations.

scholarly journals Histone transfer among chaperones

2012 ◽  
Vol 40 (2) ◽  
pp. 357-363 ◽  
Author(s):  
Wallace H. Liu ◽  
Mair E.A. Churchill
Keyword(s):  
Histone H3 ◽  
Histone Chaperone ◽  
Chromatin Assembly ◽  
Histone Chaperones ◽  
Nucleosome Assembly ◽  
Post Translational Modifications ◽  
Chromatin Dynamics ◽  
Nucleosomal Dna ◽  
Chaperone Interactions ◽  
Dependent Processes

The eukaryotic processes of nucleosome assembly and disassembly govern chromatin dynamics, in which histones exchange in a highly regulated manner to promote genome accessibility for all DNA-dependent processes. This regulation is partly carried out by histone chaperones, which serve multifaceted roles in co-ordinating the interactions of histone proteins with modification enzymes, nucleosome remodellers, other histone chaperones and nucleosomal DNA. The molecular details of the processes by which histone chaperones promote delivery of histones among their many functional partners are still largely undefined, but promise to offer insights into epigenome maintenance. In the present paper, we review recent findings on the histone chaperone interactions that guide the assembly of histones H3 and H4 into chromatin. This evidence supports the concepts of histone post-translational modifications and specific histone chaperone interactions as guiding principles for histone H3/H4 transactions during chromatin assembly.

scholarly journals Essential Role of Chromatin Assembly Factor-1–mediated Rapid Nucleosome Assembly for DNA Replication and Cell Division in Vertebrate Cells

2007 ◽  
Vol 18 (1) ◽  
pp. 129-141 ◽  
Author(s):  
Yasunari Takami ◽  
Tatsuya Ono ◽  
Tatsuo Fukagawa ◽  
Kei-ichi Shibahara ◽  
Tatsuo Nakayama
Keyword(s):  
Dna Replication ◽  
Essential Role ◽  
Chromatin Assembly ◽  
Nuclear Antigen ◽  
Nucleosome Assembly ◽  
Chromatin Assembly Factor ◽  
Assembly Factor

Chromatin assembly factor-1 (CAF-1), a complex consisting of p150, p60, and p48 subunits, is highly conserved from yeast to humans and facilitates nucleosome assembly of newly replicated DNA in vitro. To investigate roles of CAF-1 in vertebrates, we generated two conditional DT40 mutants, respectively, devoid of CAF-1p150 and p60. Depletion of each of these CAF-1 subunits led to delayed S-phase progression concomitant with slow DNA synthesis, followed by accumulation in late S/G2 phase and aberrant mitosis associated with extra centrosomes, and then the final consequence was cell death. We demonstrated that CAF-1 is necessary for rapid nucleosome formation during DNA replication in vivo as well as in vitro. Loss of CAF-1 was not associated with the apparent induction of phosphorylations of S-checkpoint kinases Chk1 and Chk2. To elucidate the precise role of domain(s) in CAF-1p150, functional dissection analyses including rescue assays were preformed. Results showed that the binding abilities of CAF-1p150 with CAF-1p60 and DNA polymerase sliding clamp proliferating cell nuclear antigen (PCNA) but not with heterochromatin protein HP1-γ are required for cell viability. These observations highlighted the essential role of CAF-1–dependent nucleosome assembly in DNA replication and cell proliferation through its interaction with PCNA.

scholarly journals Distinct histone H3–H4 binding modes of sNASP reveal the basis for cooperation and competition of histone chaperones

2021 ◽  
Author(s):  
Chao-Pei Liu ◽  
Wenxing Jin ◽  
Jie Hu ◽  
Mingzhu Wang ◽  
Jingjing Chen ◽  
...  
Keyword(s):  
De Novo ◽  
Critical Role ◽  
Histone H3 ◽  
Coiled Coil ◽  
Dynamic Network ◽  
Histone Chaperones ◽  
Binding Modes ◽  
Nucleosome Assembly ◽  
Partially Unfolded

Chromosomal duplication requires de novo assembly of nucleosomes from newly synthesized histones, and the process involves a dynamic network of interactions between histones and histone chaperones. sNASP and ASF1 are two major histone H3–H4 chaperones found in distinct and common complexes, yet how sNASP binds H3–H4 in the presence and absence of ASF1 remains unclear. Here we show that, in the presence of ASF1, sNASP principally recognizes a partially unfolded Nα region of histone H3, and in the absence of ASF1, an additional sNASP binding site becomes available in the core domain of the H3–H4 complex. Our study also implicates a critical role of the C-terminal tail of H4 in the transfer of H3–H4 between sNASP and ASF1 and the coiled-coil domain of sNASP in nucleosome assembly. These findings provide mechanistic insights into coordinated histone binding and transfer by histone chaperones.

scholarly journals Nap1 Links Transcription Elongation, Chromatin Assembly, and Messenger RNP Complex Biogenesis

2008 ◽  
Vol 28 (7) ◽  
pp. 2113-2124 ◽  
Author(s):  
Brian C. Del Rosario ◽  
Lucy F. Pemberton
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Chromatin Remodeling ◽  
Transcription Elongation ◽  
Mrna Export ◽  
Transcript Level ◽  
Chromatin Assembly ◽  
Regulation Of Transcription ◽  
Histone Chaperones ◽  
Coding Region ◽  
Rnp Complex

ABSTRACT Chromatin remodeling is central to the regulation of transcription elongation. We demonstrate that the conserved Saccharomyces cerevisiae histone chaperone Nap1 associates with chromatin. We show that Nap1 regulates transcription of PHO5, and the increase in transcript level and the higher phosphatase activity plateau observed for Δnap1 cells suggest that the net function of Nap1 is to facilitate nucleosome reassembly during transcription elongation. To further our understanding of histone chaperones in transcription elongation, we identified factors that regulate the function of Nap1 in this process. One factor investigated is an essential mRNA export and TREX complex component, Yra1. Nap1 interacts directly with Yra1 and genetically with other TREX complex components and the mRNA export factor Mex67. Additionally, we show that the recruitment of Nap1 to the coding region of actively transcribed genes is Yra1 dependent and that its recruitment to promoters is TREX complex independent. These observations suggest that Nap1 functions provide a new connection between transcription elongation, chromatin assembly, and messenger RNP complex biogenesis.

ATRX in chromatin assembly and genome architecture during development and disease

2011 ◽  
Vol 89 (5) ◽  
pp. 435-444 ◽  
Author(s):  
Nathalie G. Bérubé
Keyword(s):  
Gene Regulation ◽  
Chromatin Remodeling ◽  
Chromatin Structure ◽  
Higher Order ◽  
Chromatin Assembly ◽  
Genome Architecture ◽  
Chromatin Conformation ◽  
Mammalian Development ◽  
Mitosis And Meiosis

The regulation of genome architecture is essential for a variety of fundamental cellular phenomena that underlie the complex orchestration of mammalian development. The ATP-dependent chromatin remodeling protein ATRX is emerging as a key regulatory component of nucleosomal dynamics and higher order chromatin conformation. Here we provide an overview of the role of ATRX at chromatin and during development, and discuss recent studies exposing a repertoire of ATRX functions at heterochromatin, in gene regulation, and during mitosis and meiosis. Exciting new progress on several fronts suggest that ATRX operates in histone variant deposition and in the modulation of higher order chromatin structure. Not surprisingly, dysfunction or absence of ATRX protein has devastating consequences on embryonic development and leads to human disease.

Negotiating the nucleosome: factors that allow RNA polymerase II to elongate through chromatinThis paper is one of a selection of papers published in this Special Issue, entitled 28th International West Coast Chromatin and Chromosome Conference, and has undergone the Journal's usual peer review process.

2007 ◽  
Vol 85 (4) ◽  
pp. 426-434 ◽  
Author(s):  
Jennifer A. Armstrong
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Chromatin Remodeling ◽  
Peer Review Process ◽  
Histone Variants ◽  
Transcriptional Elongation ◽  
Histone Chaperones ◽  
Nucleosome Assembly ◽  
Pol Ii ◽  
Assembly Factors

Initiation by RNA polymerase II (Pol II) involves a host of enzymes, and the process of elongation appears similarly complex. Transcriptional elongation through chromatin requires the coordinated efforts of Pol II and its associated transcription factors: C-terminal domain kinases, elongation complexes, chromatin-modifying enzymes, chromatin remodeling factors, histone chaperones (nucleosome assembly factors), and histone variants. This review examines the following: (i) the consequences of the encounter between elongating Pol II and a nucleosome, and (ii) chromatin remodeling factors and nucleosome assembly factors that have recently been identified as important for the elongation stage of transcription.

scholarly journals CO2 Dynamics and Heterogeneity in a Cave Atmosphere: Role of Ventilation Patterns and Airflow Pathways

2021 ◽  
Author(s):  
Lovel Kukuljan ◽  
Franci Gabrovsek ◽  
Matthew D. Covington ◽  
Vanessa E. Johnston
Keyword(s):  
Temporal Variations ◽  
Observation Point ◽  
Spatially Distributed ◽  
Combined Action ◽  
Karst Systems ◽  
The Relationship ◽  
Co2 Dynamics ◽  
Global Carbon

Abstract Understanding the dynamics and distribution of CO2 in the subsurface atmosphere of carbonate karst massifs provides important insights into dissolution and precipitation processes, the role of karst systems in the global carbon cycle, and the use of speleothems for paleoclimate reconstructions. We discuss long-term microclimatic observations in a passage of Postojna Cave, Slovenia, focusing on high spatial and temporal variations of pCO2. We show 1) that the airflow through the massif is determined by the combined action of the chimney effect and external winds and 2) that the relationship between the direction of the airflow, the geometry of the airflow pathways, and the position of the observation point explains the observed variations of pCO2. Namely, in the terminal chamber of the passage, the pCO2 is low and uniform during updraft, when outside air flows to the site through a system of large open galleries. When the airflow reverses direction to downdraft, the chamber is fed by inlets with diverse flow rate and pCO2, which enter via small conduits and fractures embedded in a CO2-rich vadose zone. If the spatial distribution of inlets and outlets produces minimal mixing between low and high pCO2 inflows, high and persistent gradients in pCO2 are formed. Such is the case in the chamber, where vertical gradients of up to 1000 ppm/m is observed during downdraft. The results presented in this work provide new insights into the dynamics and composition of the subsurface atmosphere and demonstrate the importance of long-term and spatially distributed observations.

scholarly journals In Vivo Study of the Nucleosome Assembly Functions of ASF1 Histone Chaperones in Human Cells

2008 ◽  
Vol 28 (11) ◽  
pp. 3672-3685 ◽  
Author(s):  
Angélique Galvani ◽  
Régis Courbeyrette ◽  
Morgane Agez ◽  
Françoise Ochsenbein ◽  
Carl Mann ◽  
...  
Keyword(s):  
Dna Synthesis ◽  
Histone H3 ◽  
Direct Determination ◽  
Human Cells ◽  
Chromatin Assembly ◽  
Histone Chaperones ◽  
Nucleosome Assembly ◽  
Assembly Factor

ABSTRACT Histone chaperones have been implicated in nucleosome assembly and disassembly as well as histone modification. ASF1 is a highly conserved histone H3/H4 chaperone that synergizes in vitro with two other histone chaperones, chromatin assembly factor 1 (CAF-1) and histone repression A factor (HIRA), in DNA synthesis-coupled and DNA synthesis-independent nucleosome assembly. Here, we identify mutants of histones H3.1 and H3.3 that are unable to interact with human ASF1A and ASF1B isoforms but that are still competent to bind CAF-1 and HIRA, respectively. We show that these mutant histones are inefficiently deposited into chromatin in vivo. Furthermore, we found that both ASF1A and ASF1B participate in the DNA synthesis-independent deposition of H3.3 in HeLa cells, thus highlighting an unexpected role for ASF1B in this pathway. This pathway does not require interaction of ASF1 with HIRA. We provide the first direct determination that ASF1A and ASF1B play a role in the efficiency of nucleosome assembly in vivo in human cells.

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