Chromatin in the Cell Nucleus: Higher-order Organisation

ABSTRACT Human immunodeficiency virus type 1 (HIV-1) capsid binds host proteins during infection, including cleavage and polyadenylation specificity factor 6 (CPSF6) and cyclophilin A (CypA). We observe that HIV-1 infection induces higher-order CPSF6 formation, and capsid-CPSF6 complexes cotraffic on microtubules. CPSF6-capsid complex trafficking is impacted by capsid alterations that reduce CPSF6 binding or by excess cytoplasmic CPSF6 expression, both of which are associated with decreased HIV-1 infection. Higher-order CPSF6 complexes bind and disrupt HIV-1 capsid assemblies in vitro. Disruption of HIV-1 capsid binding to CypA leads to increased CPSF6 binding and altered capsid trafficking, resulting in reduced infectivity. Our data reveal an interplay between CPSF6 and CypA that is important for cytoplasmic capsid trafficking and HIV-1 infection. We propose that CypA prevents HIV-1 capsid from prematurely engaging cytoplasmic CPSF6 and that differences in CypA cellular localization and innate immunity may explain variations in HIV-1 capsid trafficking and uncoating in CD4+ T cells and macrophages. IMPORTANCE HIV is the causative agent of AIDS, which has no cure. The protein shell that encases the viral genome, the capsid, is critical for HIV replication in cells at multiple steps. HIV capsid has been shown to interact with multiple cell proteins during movement to the cell nucleus in a poorly understood process that may differ during infection of different cell types. In this study, we show that premature or too much binding of one human protein, cleavage and polyadenylation specificity factor 6 (CPSF6), disrupts the ability of the capsid to deliver the viral genome to the cell nucleus. Another human protein, cyclophilin A (CypA), can shield HIV capsid from premature binding to CPSF6, which can differ in CD4+ T cells and macrophages. Better understanding of how HIV infects cells will allow better drugs to prevent or inhibit infection and pathogenesis.

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On the regulation of DNA methylation by higher-order structure in the cell nucleus

Medical Hypotheses ◽

10.1016/0306-9877(91)90071-6 ◽

1991 ◽

Vol 34 (1) ◽

pp. 81-87 ◽

Cited By ~ 2

Author(s):

A. Aranda-Anzaldo

Keyword(s):

Dna Methylation ◽

Cell Nucleus ◽

Higher Order ◽

Order Structure

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Dual systems for all: Higher-order, role-based relational reasoning as a uniquely derived feature of human cognition

Behavioral and Brain Sciences ◽

10.1017/s0140525x19000451 ◽

2019 ◽

Vol 42 ◽

Author(s):

Daniel J. Povinelli ◽

Gabrielle C. Glorioso ◽

Shannon L. Kuznar ◽

Mateja Pavlic

Keyword(s):

Temporal Reasoning ◽

Higher Order ◽

Important Case ◽

Human Cognition ◽

Relational Reasoning ◽

Dual Systems ◽

First Order ◽

Reasoning System ◽

Role Based

Abstract Hoerl and McCormack demonstrate that although animals possess a sophisticated temporal updating system, there is no evidence that they also possess a temporal reasoning system. This important case study is directly related to the broader claim that although animals are manifestly capable of first-order (perceptually-based) relational reasoning, they lack the capacity for higher-order, role-based relational reasoning. We argue this distinction applies to all domains of cognition.

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Organization of transcription and pre-mRNA splicing within the mammalian cell nucleus

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s042482010014021x ◽

1995 ◽

Vol 53 ◽

pp. 768-769

Author(s):

D.L. Spector ◽

S. Huang ◽

S. Kaurin

Keyword(s):

Rna Polymerase Ii ◽

Cell Nucleus ◽

Functional Organization ◽

Mrna Splicing ◽

Splicing Factors ◽

Interchromatin Granule Clusters ◽

Interchromatin Granule ◽

Nuclear Regions ◽

Relationship Of ◽

Perichromatin Fibrils

We have been interested in the organization of RNA polymerase II transcription and pre-mRNA splicing within the cell nucleus. Several models have been proposed for the functional organization of RNA within the eukaryotic nucleus and for the relationship of this organization to the distribution of pre-mRNA splicing factors. One model suggests that RNAs which must be spliced are capable of recruiting splicing factors to the sites of transcription from storage and/or reassembly sites. When one examines the organization of splicing factors in the nucleus in comparison to the sites of chromatin it is clear that splicing factors are not localized in coincidence with heterochromatin (Fig. 1). Instead, they are distributed in a speckled pattern which is composed of both perichromatin fibrils and interchromatin granule clusters. The perichromatin fibrils are distributed on the periphery of heterochromatin and on the periphery of interchromatin granule clusters as well as being diffusely distributed throughout the nucleoplasm. These nuclear regions have been previously shown to represent initial sites of incorporation of 3H-uridine.

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Quantitative EPMA of nitrogen : A tricky element in the electron-probe microanalyzer

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100132741 ◽

1992 ◽

Vol 50 (2) ◽

pp. 1622-1623

Author(s):

G.F. Bastin ◽

H.J.M. Heijligers

Keyword(s):

Background Subtraction ◽

Electron Probe ◽

Detection System ◽

Higher Order ◽

Light Elements ◽

Strong Suppression ◽

Electron Probe Microanalyzer ◽

Quantitative Epma ◽

Peak Count ◽

Lead Stearate

Among the ultra-light elements B, C, N, and O nitrogen is the most difficult element to deal with in the electron probe microanalyzer. This is mainly caused by the severe absorption that N-Kα radiation suffers in carbon which is abundantly present in the detection system (lead-stearate crystal, carbonaceous counter window). As a result the peak-to-background ratios for N-Kα measured with a conventional lead-stearate crystal can attain values well below unity in many binary nitrides . An additional complication can be caused by the presence of interfering higher-order reflections from the metal partner in the nitride specimen; notorious examples are elements such as Zr and Nb. In nitrides containing these elements is is virtually impossible to carry out an accurate background subtraction which becomes increasingly important with lower and lower peak-to-background ratios. The use of a synthetic multilayer crystal such as W/Si (2d-spacing 59.8 Å) can bring significant improvements in terms of both higher peak count rates as well as a strong suppression of higher-order reflections.

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Immunolocalization of nuclear antigens in cryofixed cells which have been prepared by molecular distillation drying or freeze-substitution

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100162053 ◽

1990 ◽

Vol 48 (3) ◽

pp. 898-899

Author(s):

David L. Spector ◽

Robert J. Derby

Keyword(s):

Cell Nucleus ◽

Molecular Distillation ◽

Functional Organization ◽

Freeze Substitution ◽

3 Dimensional ◽

Small Nuclear Ribonucleoprotein ◽

Nuclear Antigens ◽

Dimensional Reconstruction ◽

Nuclear Regions ◽

Immunoperoxidase Labeling

Studies in our laboratory are involved in evaluating the structural and functional organization of the mammalian cell nucleus. Since several major classes (U1, U2, U4/U6, U5) of small nuclear ribonucleoprotein particles (snRNPs) play a crucial role in the processing of pre-mRNA molecules, we have been interested in the localization of these particles within the cell nucleus. Using pre-embedding immunoperoxidase labeling combined with 3-dimensional reconstruction, we have recently shown that nuclear regions enriched in snRNPs form a reticular network within the nucleoplasm which extends between the nucleolar surface and the nuclear envelope. In the present study we were inte rested in extending these nuclear localizations using cell preparation techniques which avoid slow penetration of fixatives, chemical crosslinking of potential antigens and solvent extraction. CHOC 400 cells were cryofixed using a CF 100 ultra rapid cooling device (LifeCell Corp.). After cryofixation cells were molecular distillation dried, vapor osmicated, in filtra ted in 100% Spurr resin in vacuo and polymerized in molds a t 60°C. Using this procedure we were able to evaluate the distribution of snRNPs in resin embedded cells which had not been chemically fixed, incubated in cryoprotectants or extracted with solvents.

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Effects of Higher-Order Laue Zone reflections on structure images

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100148083 ◽

1993 ◽

Vol 51 ◽

pp. 450-451

Author(s):

H. S. Kim ◽

S. S. Sheinin

Keyword(s):

Wave Vector ◽

Theoretical Calculations ◽

Reciprocal Lattice ◽

Image Plane ◽

Bloch Wave ◽

Dynamical Theory ◽

Higher Order ◽

Lattice Image ◽

Lattice Vector ◽

Image Position

The importance of image simulation in interpreting experimental lattice images is well established. Normally, in carrying out the required theoretical calculations, only zero order Laue zone reflections are taken into account. In this paper we assess the conditions for which this procedure is valid and indicate circumstances in which higher order Laue zone reflections may be important. Our work is based on an analysis of the requirements for obtaining structure images i.e. images directly related to the projected potential. In the considerations to follow, the Bloch wave formulation of the dynamical theory has been used.The intensity in a lattice image can be obtained from the total wave function at the image plane is given by: where ϕg(z) is the diffracted beam amplitide given by In these equations,the z direction is perpendicular to the entrance surface, g is a reciprocal lattice vector, the Cg(i) are Fourier coefficients in the expression for a Bloch wave, b(i), X(i) is the Bloch wave excitation coefficient, ϒ(i)=k(i)-K, k(i) is a Bloch wave vector, K is the electron wave vector after correction for the mean inner potential of the crystal, T(q) and D(q) are the transfer function and damping function respectively, q is a scattering vector and the summation is over i=l,N where N is the number of beams taken into account.

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