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Cold Spring Harbor Perspectives in... Jun 2022Our understanding of how genomic DNA is tightly packed inside the nucleus, yet is still accessible for vital cellular processes, has grown dramatically over recent years... (Review)
Review
Our understanding of how genomic DNA is tightly packed inside the nucleus, yet is still accessible for vital cellular processes, has grown dramatically over recent years with advances in microscopy and genomics technologies. Computational methods have played a pivotal role in the structural interpretation of experimental data, which helped unravel some organizational principles of genome folding. Here, we give an overview of current computational efforts in mechanistic and data-driven 3D chromatin structure modeling. We discuss strengths and limitations of different methods and evaluate the added value and benefits of computational approaches to infer the 3D structural and dynamic properties of the genome and its underlying mechanisms at different scales and resolution, ranging from the dynamic formation of chromatin loops and topological associated domains to nuclear compartmentalization of chromatin and nuclear bodies.
Topics: Cell Nucleus; Chromatin; Chromatin Assembly and Disassembly; Chromosomes; Genome
PubMed: 34400556
DOI: 10.1101/cshperspect.a039693 -
Cellular and Molecular Life Sciences :... Nov 2003Bacteriophage T4 is one of the most complex viruses. More than 40 different proteins form the mature virion, which consists of a protein shell encapsidating a 172-kbp... (Review)
Review
Bacteriophage T4 is one of the most complex viruses. More than 40 different proteins form the mature virion, which consists of a protein shell encapsidating a 172-kbp double-stranded genomic DNA, a 'tail,' and fibers, attached to the distal end of the tail. The fibers and the tail carry the host cell recognition sensors and are required for attachment of the phage to the cell surface. The tail also serves as a channel for delivery of the phage DNA from the head into the host cell cytoplasm. The tail is attached to the unique 'portal' vertex of the head through which the phage DNA is packaged during head assembly. Similar to other phages, and also herpes viruses, the unique vertex is occupied by a dodecameric portal protein, which is involved in DNA packaging.
Topics: Amino Acid Sequence; Bacteriophage T4; DNA Packaging; DNA, Viral; Molecular Sequence Data; Morphogenesis; Protein Structure, Secondary; Viral Tail Proteins
PubMed: 14625682
DOI: 10.1007/s00018-003-3072-1 -
Proceedings of the National Academy of... Jun 2014Many viruses use molecular motors that generate large forces to package DNA to near-crystalline densities inside preformed viral proheads. Besides being a key step in...
Many viruses use molecular motors that generate large forces to package DNA to near-crystalline densities inside preformed viral proheads. Besides being a key step in viral assembly, this process is of interest as a model for understanding the physics of charged polymers under tight 3D confinement. A large number of theoretical studies have modeled DNA packaging, and the nature of the molecular dynamics and the forces resisting the tight confinement is a subject of wide debate. Here, we directly measure the packaging of single DNA molecules in bacteriophage phi29 with optical tweezers. Using a new technique in which we stall the motor and restart it after increasing waiting periods, we show that the DNA undergoes nonequilibrium conformational dynamics during packaging. We show that the relaxation time of the confined DNA is >10 min, which is longer than the time to package the viral genome and 60,000 times longer than that of the unconfined DNA in solution. Thus, the confined DNA molecule becomes kinetically constrained on the timescale of packaging, exhibiting glassy dynamics, which slows the motor, causes significant heterogeneity in packaging rates of individual viruses, and explains the frequent pausing observed in DNA translocation. These results support several recent hypotheses proposed based on polymer dynamics simulations and show that packaging cannot be fully understood by quasistatic thermodynamic models.
Topics: Adenosine Triphosphate; Bacillus Phages; Bacillus subtilis; DNA Packaging; DNA, Viral; Genome, Viral; Kinetics; Models, Genetic; Models, Molecular; Molecular Dynamics Simulation; Nucleic Acid Conformation; Optical Tweezers; Protein Binding; Time Factors; Viral Proteins; Virus Assembly
PubMed: 24912187
DOI: 10.1073/pnas.1405109111 -
International Journal of Molecular... May 2021The highly complex life cycle of the human malaria parasite, , is based on an orchestrated and tightly regulated gene expression program. In general, eukaryotic... (Review)
Review
The highly complex life cycle of the human malaria parasite, , is based on an orchestrated and tightly regulated gene expression program. In general, eukaryotic transcription regulation is determined by a combination of sequence-specific transcription factors binding to regulatory DNA elements and the packaging of DNA into chromatin as an additional layer. The accessibility of regulatory DNA elements is controlled by the nucleosome occupancy and changes of their positions by an active process called nucleosome remodeling. These epigenetic mechanisms are poorly explored in The parasite genome is characterized by an extraordinarily high AT-content and the distinct architecture of functional elements, and chromatin-related proteins also exhibit high sequence divergence compared to other eukaryotes. Together with the distinct biochemical properties of nucleosomes, these features suggest substantial differences in chromatin-dependent regulation. Here, we highlight the peculiarities of epigenetic mechanisms in , addressing chromatin structure and dynamics with respect to their impact on transcriptional control. We focus on the specialized chromatin remodeling enzymes and discuss their essential function in gene regulation.
Topics: Animals; Chromatin Assembly and Disassembly; Epigenesis, Genetic; Gene Expression Regulation; Humans; Life Cycle Stages; Malaria, Falciparum; Plasmodium falciparum; Transcription, Genetic
PubMed: 34068393
DOI: 10.3390/ijms22105168 -
Cellular and Molecular Life Sciences :... Apr 2013The merging of the maternal and paternal genomes into a single pronucleus after fertilization is accompanied by a remarkable reconfiguration of chromatin in the newly... (Review)
Review
The merging of the maternal and paternal genomes into a single pronucleus after fertilization is accompanied by a remarkable reconfiguration of chromatin in the newly formed zygote. The first stages of embryonic chromatin remodeling take place in the absence of ongoing transcription, during a species-specific developmental time-frame. Once post-fertilization chromatin states are organized, zygotic genome activation (ZGA) is initiated, and embryonic transcripts gradually take control of development. We review here transitions in chromatin modifications associated with the onset of ZGA, and the role of transcription factors and DNA motifs in the regulation of ZGA. We propose a model of sequential chromatin remodeling events preceding ZGA, leading to the onset of embryonic transcription.
Topics: Animals; Chromatin; DNA Packaging; Gene Expression Regulation, Developmental; Genome; Humans; Models, Molecular; Nucleotide Motifs; Transcription Factors; Transcriptional Activation; Zygote
PubMed: 22965566
DOI: 10.1007/s00018-012-1143-x -
Epigenetics May 2014Several hierarchical levels of DNA packaging are believed to exist in chromatin, starting from a 10-nm chromatin fiber that is further packed into a 30-nm fiber.... (Review)
Review
Several hierarchical levels of DNA packaging are believed to exist in chromatin, starting from a 10-nm chromatin fiber that is further packed into a 30-nm fiber. Transitions between the 30-nm and 10-nm fibers are thought to be essential for the control of chromatin transcriptional status. However, recent studies demonstrate that in the nuclei, DNA is packed in tightly associated 10-nm fibers that are not compacted into 30-nm fibers. Additionally, the accessibility of DNA in chromatin depends on the local mobility of nucleosomes rather than on decompaction of chromosome regions. These findings argue for reconsidering the hierarchical model of chromatin packaging and some of the basic definitions of chromatin. In particular, chromatin domains should be considered as three-dimensional objects, which may include genomic regions that do not necessarily constitute a continuous domain on the DNA chain.
Topics: Chromatin; Chromatin Assembly and Disassembly; DNA; Histone Code; Humans; Transcription, Genetic
PubMed: 24561903
DOI: 10.4161/epi.28297 -
Biochimica Et Biophysica Acta Jul 2012In contrast to organized hierarchical structure of eukaryotic chromosome, bacterial chromosomes are believed not to have such structures. The genomes of bacteria are... (Review)
Review
In contrast to organized hierarchical structure of eukaryotic chromosome, bacterial chromosomes are believed not to have such structures. The genomes of bacteria are condensed into a compact structure called the nucleoid. Among many architectural, histone-like proteins which associate with the chromosomal DNA is HU which is implicated in folding DNA into a compact structure by bending and wrapping DNA. Unlike the majority of other histone-like proteins, HU is highly conserved in eubacteria and unique in its ability to bind RNA. Furthermore, an HU mutation profoundly alters the cellular transcription profile and consequently has global effects on physiology and the lifestyle of E. coli. Here we provide a short overview of the mechanisms by which the nucleoid is organized into different topological domains. We propose that HU is a major player in creating domain-specific superhelicities and thus influences the transcription profile from the constituent promoters. This article is part of a Special Issue entitled: Chromatin in time and space.
Topics: Chromosomes, Bacterial; DNA Packaging; DNA, Bacterial; DNA, Superhelical; DNA-Binding Proteins; Escherichia coli; Escherichia coli Proteins; Insulator Elements; Nucleic Acid Conformation; RNA, Bacterial
PubMed: 22387214
DOI: 10.1016/j.bbagrm.2012.02.012 -
MBio Jun 2020Archaeal chromatin proteins Cren7 and Sul7d from are DNA benders. To better understand their architectural roles in chromosomal DNA organization, we analyzed DNA...
Archaeal chromatin proteins Cren7 and Sul7d from are DNA benders. To better understand their architectural roles in chromosomal DNA organization, we analyzed DNA compaction by Cren7 and Sis7d, a Sul7d family member, from at the single-molecule (SM) level by total single-molecule internal reflection fluorescence microscopy (SM-TIRFM) and atomic force microscopy (AFM). We show that both Cren7 and Sis7d were able to compact singly tethered λ DNA into a highly condensed structure in a three-step process and that Cren7 was over an order of magnitude more efficient than Sis7d in DNA compaction. The two proteins were similar in DNA bending kinetics but different in DNA condensation patterns. At saturating concentrations, Sis7d formed randomly distributed clusters whereas Cren7 generated a single and highly condensed core on plasmid DNA. This observation is consistent with the greater ability of Cren7 than of Sis7d to bridge DNA. Our results offer significant insights into the mechanism and kinetics of chromosomal DNA organization in Crenarchaea. A long-standing question is how chromosomal DNA is packaged in Crenarchaeota, a major group of archaea, which synthesize large amounts of unique small DNA-binding proteins but in general contain no archaeal histones. In the present work, we tested our hypothesis that the two well-studied crenarchaeal chromatin proteins Cren7 and Sul7d compact DNA by both DNA bending and bridging. We show that the two proteins are capable of compacting DNA, albeit with different efficiencies and in different manners, at the single molecule level. We demonstrate for the first time that the two proteins, which have long been regarded as DNA binders and benders, are able to mediate DNA bridging, and this previously unknown property of the proteins allows DNA to be packaged into highly condensed structures. Therefore, our results provide significant insights into the mechanism and kinetics of chromosomal DNA organization in Crenarchaeota.
Topics: Archaea; Chromosomal Proteins, Non-Histone; DNA Packaging; DNA, Archaeal; DNA-Binding Proteins; Kinetics; Microscopy, Atomic Force; Models, Molecular; Sulfolobus
PubMed: 32518188
DOI: 10.1128/mBio.00804-20 -
Cell Reports Mar 2016Ring NTPases are a class of ubiquitous molecular motors involved in basic biological partitioning processes. dsDNA viruses encode ring ATPases that translocate their...
Ring NTPases are a class of ubiquitous molecular motors involved in basic biological partitioning processes. dsDNA viruses encode ring ATPases that translocate their genomes to near-crystalline densities within pre-assembled viral capsids. Here, X-ray crystallography, cryoEM, and biochemical analyses of the dsDNA packaging motor in bacteriophage phi29 show how individual subunits are arranged in a pentameric ATPase ring and suggest how their activities are coordinated to translocate dsDNA. The resulting pseudo-atomic structure of the motor and accompanying functional analyses show how ATP is bound in the ATPase active site; identify two DNA contacts, including a potential DNA translocating loop; demonstrate that a trans-acting arginine finger is involved in coordinating hydrolysis around the ring; and suggest a functional coupling between the arginine finger and the DNA translocating loop. The ability to visualize the motor in action illuminates how the different motor components interact with each other and with their DNA substrate.
Topics: Adenosine Triphosphatases; Adenosine Triphosphate; Arginine; Bacillus Phages; Bacillus subtilis; Capsid; Cryoelectron Microscopy; Crystallography, X-Ray; DNA; DNA Packaging; DNA, Viral; Gene Expression; Hydrolysis; Models, Molecular; Protein Domains; Protein Structure, Secondary; Protein Subunits; Viral Proteins; Virus Assembly
PubMed: 26904950
DOI: 10.1016/j.celrep.2016.01.058 -
Cell Stress & Chaperones Jan 2020Studies on chromatin structure and function have gained a revived popularity. Histone chaperones are significant players in chromatin organization. They play a... (Review)
Review
Studies on chromatin structure and function have gained a revived popularity. Histone chaperones are significant players in chromatin organization. They play a significant role in vital nuclear functions like transcription, DNA replication, DNA repair, DNA recombination, and epigenetic regulation, primarily by aiding processes such as histone shuttling and nucleosome assembly/disassembly. Like the other eukaryotes, plants also have a highly orchestrated and dynamic chromatin organization. Plants seem to have more isoforms within the same family of histone chaperones, as compared with other organisms. As some of these are specific to plants, they must have evolved to perform functions unique to plants. However, it appears that only little effort has gone into understanding the structural features of plant histone chaperones and their structure-function relationships. Studies on plant histone chaperones are essential for understanding their role in plant chromatin organization and how plants respond during stress conditions. This review is on the structural and functional aspects of plant histone chaperone families, specifically those which bind to H2A-H2B, viz nucleosome assembly protein (NAP), nucleoplasmin (NPM), and facilitates chromatin transcription (FACT). Here, we also present comparative analyses of these plant histone chaperones with available histone chaperone structures. The review hopes to incite interest among researchers to pursue further research in the area of plant chromatin and the associated histone chaperones.
Topics: Chromatin; Chromatin Assembly and Disassembly; Epigenesis, Genetic; Histone Chaperones; Humans; Molecular Chaperones; Structure-Activity Relationship
PubMed: 31707537
DOI: 10.1007/s12192-019-01050-7