(The FASEB Journal. 1999;13:S157-S166.)
© 1999 FASEB
Implications for interrelationships between nuclear architecture and control of gene expression under microgravity conditions
GARY S. STEIN1,
ANDRÉ J. VAN WIJNEN,
JANET L. STEIN,
JANE B. LIAN,
SHIRWIN H. POCKWINSE and
SANDRA MCNEIL
Department of Cell Biology and Cancer Center, University of Massachusetts Medical Center, Worcester, Massachusetts. E-mail: Gary.Stein@banyan.ummed.edu
1Correspondence: Department of Cell Biology and Cancer Center, University of Massachusetts Medical Center, 55 Lake Ave. North, Worcester, Massachusetts. E-mail: Gary.Stein{at}banyan.ummed.edu
 |
ABSTRACT
|
|---|
Components of nuclear architecture are functionally interrelated
with control of gene expression. There is growing appreciation that
multiple levels of nuclear organization integrate the regulatory cues
that support activation and suppression of genes as well as the
processing of gene transcripts. The linear representation of genes and
promoter elements provide the potential for responsiveness to
physiological regulatory signals. Parameters of chromatin structure and
nucleosome organization support synergism between activities at
independent regulatory sequences and render promoter elements
accessible or refractory to transcription factors. Association of
genes, transcription factors, and the machinery for transcript
processing with the nuclear matrix facilitates fidelity of gene
expression within the three-dimensional context of nuclear
architecture. Mechanisms must be defined that couple nuclear morphology
with enzymatic parameters of gene expression. The recent
characterization of factors that mediate chromatin remodeling and
identification of intranuclear targeting signals that direct
transcription factors to subnuclear domains where gene expression
occurs link genetic and structural components of transcriptional
control. Nuclear reorganization and aberrant intranuclear trafficking
of transcription factors for developmental and tissue-specific control
occurs in tumor cells and in neurological disorders. Compromises in
nuclear structure-function interrelationships can occur as a
consequence of microgravity-mediated perturbations in cellular
architecture.—Stein, G. S., van Wijnen, A. J., Stein,
J. L., Lian, J. B., Pockwinse, S. H., McNeil, S.
Implications for interrelationships between nuclear architecture and
control of gene expression under microgravity conditions.
Key Words: transcription • chromatin • nucleosomes • nuclear matrix
|
INTRODUCTION
|
|---|
MICROGRAVITY CONDITIONS MODIFY cell structure and may
perturb interrelationships of nuclear architecture, cytoarchitecture,
and the extracellular matrix with control of gene expression. Candidate
compromises include aberrations in the signaling pathways responsible
for integration of cellular regulatory cues that mediate activation and
suppression of transcription and posttranscriptional processing of gene
transcripts. In this article, we will focus on recent advances in
understanding the involvement of functional nuclear compartments in the
organization of genes and regulatory factors within the nucleus as well
as the mechanisms that direct components of transcriptional control to
subnuclear sites that support expression. Because of linkages between
nuclear morphology and parameters of gene regulation, the consequences
of microgravity conditions for physiologically responsive gene readout
merits consideration.
|
GENE REGULATION WITHIN THE THREE-DIMENSIONAL CONTEXT OF NUCLEAR
ARCHITECTURE
|
|---|
Transcriptional and posttranscriptional control are governed by
complex and interdependent regulatory events. The biochemical
components of transcription, processing of gene transcripts and the
bidirectional exchange of regulatory macromolecules between the nucleus
and cytoplasm must be stringently modulated to ensure the fidelity of
cell growth and phenotype-restricted gene expression. However, there is
growing appreciation that the representation of factors involved with
each component of gene expression are necessary but insufficient to
facilitate the integration of regulatory signals required for transient
and long-term commitments to physiologically responsive transcriptional
control. How, with a limited representation of gene-specific or
phenotype-restricted promoter regulatory elements and cognate factors
can a threshold concentration for initiation of expression be attained
in intact cells? How are genes and regulatory proteins directed to
sites within the nucleus that support replication and expression? How
are genes and transcripts compositely assembled into complexes and
biochemically modified to support activation and suppression of genes?
These fundamental questions provide a basis for experimentally
addressing the functional implications of nucleic acid
compartmentalization within the nucleus as well as the requirements for
fidelity of interrelationships between nuclear architecture and
parameters of gene expression to sustain biological control.
A historical perspective of nuclear structure-gene expression
interrelationships
During the past several years, there has been an accrual of
insight into the complexities of transcriptional control in eukaryotic
cells. Our concept of a promoter has evolved from the initial
expectation of a single regulatory sequence that determines
transcriptional competency and level of expression. We now appreciate
that transcriptional control is mediated by an interdependent series of
regulatory sequences that reside 5', 3', and within transcribed regions
of genes. Rather than focusing on the minimal sequences required for
transcriptional control to support biological activity, efforts are
being directed toward defining functional limits. Contributions of
distal flanking sequences to regulation of transcription and long-range
chromosomal contexts are being experimentally addressed. This is a
necessity for understanding mechanisms by which multiple promoter
elements are responsive to a broad spectrum of regulatory signals and
how the activities of these regulatory sequences are functionally
integrated. Cross-talk between a series of regulatory domains must be
understood under diverse biological circumstances where expression of
genes supports cell and tissue functions. The overlapping binding sites
for transcription factors within promoter regulatory elements and
protein-protein interactions that influence transcription factor
activity provide further components of the requisite diversity to
accommodate regulatory options for physiologically responsive gene
expression.
Levels of nuclear organization mediating gene expression
There is growing appreciation that nuclear architecture provides a
basis for support of stringently regulated modulation of cell growth
and tissue-specific transcription that is required for differentiation.
Here, evidence points to contributions by multiple levels of nuclear
organization to in vivo transcriptional control where
structural parameters are functionally coupled to regulatory events.
Promoter organization
The primary level of gene organization establishes a linear
ordering of promoter regulatory elements. The representation of
regulatory sequences reflects competency for responsiveness to
physiological regulatory signals. However, interspersion of sequences
between promoter elements that exhibit coordinate and synergistic
activities indicates a requirement for a structural basis for
integration of activities at independent regulatory domains.
Chromatin structure and nuclear organization
Parameters of chromatin structure and nucleosome organization are
a second level of genome architecture that reduces the distance between
promoter elements thereby supporting interactions between the modular
components of transcriptional control (reviewed in refs.
1-3
). Each nucleosome (approximately 140 nucleotide base
pairs wound around a core complex of two each of H3, H4, H2A, and H2B
histone proteins) contracts linear spacing by sevenfold. Higher order
chromatin structure further reduces nucleotide distances between
regulatory sequences. Folding of nucleosome arrays into solenoid-type
structures provides a potential for interactions that support synergism
between promoter elements and responsiveness to multiple signaling
pathways. Chromatin organization renders promoter elements accessible
or refractory to interactions with transcription factors under a broad
spectrum of biological circumstances and mediators of chromatin
remodeling are being defined (1
, 4
,
5
). Modifications in chromatin architecture have been
documented during development, in response to steroid hormones and
within the context of cell cycle and growth control as well as
differentiation (reviewed in refs. 2
and 3
).
Understanding of gene organization in a three-dimensional context has
been significantly facilitated by a transition from the descriptive to
the mechanistic pursuit of chromatin structure and nucleosome
organization. For many years, studies of chromatin were dominated by
high-resolution ultrastructural and biophysical analyses with the
objective of precisely defining structural features of the histone-DNA
complexes under in vivo and in vitro conditions.
But recently pursuit of regulatory mechanisms that interrelate nuclear
structure and function have been successful (reviewed in
1
). Genetic and biochemical approaches have defined
factors and sequences that mediate "heterochromatinization,"
accessibility of nucleosomal DNA to transcription factors, and
integration of activities at multiple promoter elements (reviewed in
4
and 5
).
The nuclear matrix
A third level of nuclear architecture that contributes to
transcriptional control is provided by the nuclear matrix. The
anastomosing network of fibers and filaments that constitute the
nuclear matrix supports the structural properties of the nucleus as a
cellular organelle and accommodates structural modifications associated
with proliferation, differentiation, and changes necessary to sustain
phenotypic requirements of specialized cells (6-11)
.
Regulatory functions of the nuclear matrix include but are by no means
restricted to: DNA replication (12
, 13
), gene
localization (14
, 15
), imposition of physical
constraints on chromatin structure which support formation of loop
domains, concentration and targeting of transcription factors
(16-21)
, RNA processing and transport of gene transcripts
(15
, 22-28
), posttranslational modifications
of chromosomal proteins, as well as imprinting and modification of
chromatin structure (29)
. Similarly, there have been
significant increments in our understanding of contributions by the
nuclear matrix to control of gene expression at the transcriptional and
posttranscriptional levels. Initial studies indicated that the
representation of nuclear matrix proteins reflect cell and tissue
phenotypic properties as well as modifications in gene expression that
occur during differentiation and in tumors (6-11
,
30
). The nuclear matrix has been shown to be involved with
DNA replication (12
, 13
), transcription
(16-21)
, and RNA processing (15
,
22-28
). The recent identification of specific regions of
transcription factors that are responsible for intranuclear trafficking
of regulatory proteins to the nuclear matrix-associated sites (within
the nucleus) that support transcription reinforces the linkage of
nuclear structure to regulation of genes (14)
.
Subnuclear functional compartments
We are just beginning to comprehend the significance of nuclear
domains in the control of gene expression. However, it is apparent that
local nuclear environments that are generated by the multiple aspects
of nuclear structure are intimately tied to developmental expression of
cell growth and tissue-specific genes. Historically, control of gene
expression and characterization of structural features of the nucleus
were conceptually and experimentally pursued as minimally integrated
questions. Nuclear structure and function were independently pursued in
parallel with the appreciation that several components of nuclear
architecture are associated with parameters of gene expression or
control of specific classes of genes. There is longstanding acceptance
that the nucleolus is the site of ribosomal gene expression. The
nuclear pore is recognized as a site for facilitating the import and
retention of gene regulatory factors as well as the export of gene
transcripts (31
and reviewed in 32
).
Biochemical and morphological determinants for nuclear import, export,
and retention have provided valuable insight into the regulated and
regulatory features of this principal interface for informational
exchange between the nucleus and cytoplasm (31)
. SC35
domains have been extensively studied from the standpoints of RNA
splicing and the dynamic recruitment of transcript processing factors
(24
, 27
, 33-36
). PML bodies and
coiled bodies have been associated with control of gene expression and
undergo modifications in structure and, potentially, function in cancer
cells (34
, 37-39
). Because these components
of nuclear architecture have been defined by immunoreactive proteins
and/or ultrastructural imaging as well as by biochemical criteria, a
viable basis has been established for linkage with gene regulatory
mechanisms. Taken together, these components of nuclear architecture
facilitate the biological requirements for physiologically responsive
modifications in gene expression within the contexts of: 1)
homeostatic control involving rapid, short-term, and transient
responsiveness; 2) developmental control that is progressive
and stage-specific; and 3) differentiation-related control
that is associated with long-term phenotypic commitments to gene
expression for support of structural and functional properties of cells
and tissues.
From a broad biological perspective, reflecting diverse regulatory
requirements as well as phenotype-specific and physiologically
responsive representation of nuclear structural proteins, there is a
reciprocally functional relationship between nuclear structure and gene
expression. Nuclear structure is a primary determinant of
transcriptional control and the expressed genes modulate the regulatory
components of nuclear architecture. Thus, the power of addressing gene
expression within the three-dimensional context of nuclear structure
would be difficult to overestimate. Membrane-mediated initiation of
signaling pathways that ultimately influence transcription have been
recognized for some time. Here, the mechanisms that sense, amplify,
dampen, and/or integrate regulatory signals involve structural as well
as functional components of cellular membranes. Extending the
structure-regulation paradigm to nuclear architecture expands the
cellular context in which cell structure-gene expression
interrelationships are operative.
|
INTRANUCLEAR TARGETING OF TRANSCRIPTION FACTORS
|
|---|
An understanding of interrelationships between nuclear structure
and gene expression necessitates knowledge of the composition,
organization, and regulation of sites within the nucleus that are
dedicated to replication, transcription, and processing of gene
transcripts. These highly organized subnuclear compartments that
support the assembly of transcription and replication factors, together
with accessory proteins, into macromolecular complexes have been
designated regulatory "machines" or "factories." During the
past several years there have been developments in reagents and
instrumentation to enhance the resolution of nucleic acid and protein
detection by in situ hybridization and immunofluorescence
analyses. The combined application of isotopic and non-isotopic
methods, together with a new generation of high-resolution techniques
for quantitation and three-dimensional reconstruction of "captured
images," is providing new insights into the intranuclear distribution
of genes and regulatory factors. We are beginning to make the
transition from descriptive in situ mapping of genes,
transcripts, and regulatory factors to visualization of gene expression
from the three-dimensional perspective of nuclear architecture.
Initially, in situ approaches were primarily utilized for
intracellular localization of nucleic acids and proteins that were
shown by biochemical analyses to contribute to control of gene
expression. We are now applying high-resolution in situ
analyses for characterization of gene regulatory mechanisms under
in vivo conditions.
Transcription factor organization provides a blueprint for nuclear
structure-function interrelationships
Identification of an intranuclear trafficking signal
The organization and activities of transcription factors provide a
paradigm for addressing interrelationships of nuclear architecture with
transcriptional control. Association of CBF
/AML transcription
factors with the nuclear matrix has permitted direct examination of
mechanisms for targeting regulatory factors to subnuclear domains that
support transcription. CBF/AML-related factors (core binding factor
/acute myelogenous leukemia factors) are expressed in tissues of the
lymphoid, myeloid, and osteoblast lineages where they are key
components of mechanisms mediating tissue-specific transcription
(40-60)
.
Insight into the regulated and regulatory activities of AML
transcription factors are provided by functional interactions with
nuclear architecture. Both biochemical and immunofluorescence analyses
have shown that AML transcription factors associate with the nuclear
matrix in situ (14
, 42
,
46
). Antibody staining patterns indicate a punctate
nuclear distribution of AML proteins. Taken together, these
observations are consistent with the concept that the nuclear matrix is
functionally involved in gene localization and in the concentration and
subnuclear localization of regulatory factors (3
,
14
, 16
, 17
, 28
,
35
, 61-64
).
The initial indication that nuclear matrix association of AML
factors is required for maximal activity was provided by the
observation that transcriptionally active AML-1B (amino acid 1–480)
associates with the nuclear matrix but inactive AML-1 (amino acids
1–250) does not (14)
. This localization of AML was
established by biochemical fractionation and in situ
immunofluorescence. A similar association of AML-1B, AML-2, and AML-3
with the nuclear matrix occurs, indicating that a common intranuclear
targeting mechanism may be operative for the family of AML
transcription factors (42)
. Variations in the partitioning
of the transcriptionally active AML-1B and the inactive AML-1 between
subnuclear fractions permitted development of a strategy to identify a
region of the AML transcription factors that are directing the
regulatory proteins to the nuclear matrix. A series of deletion and
internal mutations were constructed and assayed for competency to
associate with the nuclear matrix by Western analysis of biochemically
prepared nuclear fractions and by in situ immunostaining
after transfection into intact cells. As schematically illustrated in
Figure 1
and shown by immunofluorescence images (14)
, association
of AML-1B with the nuclear matrix is independent of DNA binding and
requires a nuclear matrix targeting signal, a 31-amino-acid segment
near the carboxy terminus that is distinct from nuclear localization
signals (14)
. Fusion of the AML-1B nuclear matrix
targeting signal to the heterologous GAL4-(1–147) protein
directs GAL4 to the nuclear matrix (14)
. Thus, the nuclear
matrix targeting signal functions autonomously and is necessary as well
as sufficient to target the transcriptionally active AML-1B to the
nuclear matrix.
View larger version (46K):
[in this window]
[in a new window]
|
Figure 1. Delineation of the nuclear matrix targeting signal of CBFA2/AML-1B. A
panel of HA-epitope tagged deletion mutants of AML-1B was assayed by
immunofluorescence analysis for nuclear import (Nucleus) and nuclear
matrix association (Nuclear Matrix). Carboxy-terminal segments of
AML-1B were also fused to the heterologous GAL4 DNA binding domain
(amino acid 1–147) and analyzed similarly. The key finding is that the
NMTS (amino acid 351–381) autonomously mediates nuclear matrix
association of the GAL4 reporter protein (third line from below).
|
|
These results provide insight into mechanisms by which gene regulatory
factors are targeted to the nuclear matrix. The existence of a nuclear
matrix targeting module that functions independently of the AML-1B DNA
binding domain provides evidence for the specificity of these
factors/nuclear matrix interactions. Specific targeting argues against
indiscriminate attachment of such proteins to the nuclear matrix during
subcellular fractionation. These findings are an indication of
mechanisms involved in the selective trafficking of proteins to
specialized domains within the nucleus to become components of
functional complexes. At least two trafficking signals appear to be
required for subnuclear targeting of AML transcription factors; the
first supports nuclear import (nuclear localization signal) and a
second mediates association with the nuclear matrix
(nuclearmatrix targeting signal; Fig. 2
).The multiplicity of determinants for nuclear localization and
alternative splicing of AML mRNA may provide the requisite complexity
to support targeting to specific sites within the nucleus in response
to diverse biological conditions. Furthermore, because gene regulation
by AML-1B involves contributions by other factors such as CBFß
(47
, 65
), ETS-1 (66)
, and C/EBP
(67)
, AML-1B may facilitate recruitment of these factors
to the nuclear matrix.
View larger version (60K):
[in this window]
[in a new window]
|
Figure 2. Intracellular trafficking of the CBFA/AML class of transcription
factors supports gene activation. (A) Differential
intracellular routing of distinct CBFA/AML factors depending on
presence of specific subcellular targeting signals (blue, red) in
protein isoforms encoded by mRNA splice variants. (B) Model
of the molecular sorting mechanisms that occur to support selective
targeting of CBFA/AML factors to transcriptionally active domains. This
involves nuclear localization signal (NLS; blue) -dependent nuclear
import (Step 1), specific association with the nuclear matrix (vertical
and horizontal lines) in response to the presence of a nuclear matrix
targeting signal (NMTS; red; Step 2), and a requirement for a promoter
recognition function of a sequence-specific DNA binding domain (DBD;
yellow; Step 3) to associate with active chromatin (thick wavy line).
These three steps together result in RNA pol II0-mediated
activation of AML-responsive genes.
|
|
Functional consequences for intranuclear targeting of transcription
factors
Association of genes and cognate factors with the nuclear matrix
may support the formation and/or activities of nuclear domains that
facilitate transcriptional control (29
, 35
,
46
, 61
, 68-76
). Recent results
from our laboratory indicate that the association of AML transcription
factors with the nuclear matrix is obligatory for activity
(15)
. Active transcription is required for colocalization
of AML-1B and RNA polymerase II at the nuclear matrix (15)
(Figure 3
).The promoter recognition function of the runt homology
domain of AML-1B, and thus the consequential interactions with AML
responsive genes is essential for formation of transcriptionally active
foci containing AML and RNA polymerase II in the nuclear matrix
(15)
. In addition, the nuclear matrix targeting signal
supports transactivation when associated with an appropriate promoter
and transcriptional activity of the nuclear matrix targeting signal
depends on association with the nuclear matrix (15)
. Taken
together, targeting of AML transcription factors to the nuclear matrix
is important for their function and transcription. However, components
of the nuclear matrix that function as acceptor sites remain to be
established. Characterization of such nuclear matrix components will
add an additional dimension to characterizing molecular mechanisms
associated with gene expression, the targeting of regulatory proteins
to specific spatial domains within the nucleus.
View larger version (27K):
[in this window]
[in a new window]
|
Figure 3. CBFA2/AML-1B is directed to transcriptionally active nuclear foci that
contain the hyperphosphorylated form of RNA polymerase II (pol
II0). Panels A and B show
co-localization of a subset of AML-1B with RNA pol II0 in
the nuclear matrix of human SAOS-2 osteosarcoma cells. The images were
obtained by immunofluorescence microscopy using antibodies against
AML-1B (green) and RNA pol II0 (red), whereas
co-localization is reflected by yellow signals. Immunofluorescence
signals were recorded using standard 35 mm slide photography
(A) or a CCD camera interfaced with a digital microscope
system (B).
|
|
Implications for modified nuclear structure in tumor cells
Transformed and tumor cells exhibit striking alterations in nuclear
morphology as well as in the representation and intranuclear
distribution of nucleic acids and regulatory factors
In both leukemias and solid tumor cells there are modifications in
components of nuclear architecture that are involved in control of gene
expression. Examples include mutations of the AML, ALL, and PML loci in
leukemias that accompany changes in gene expression and the subnuclear
organization of encoded transcription factors. In colon tumor cells,
modifications in the subnuclear distribution of the APC (adenomatous
polyposis coli) factor are observed. These factors are associated with
nuclear architecture and the alterations in relationships with nuclear
architecture appear to be related to changes in gene control.
Implications of aberrant intranuclear transcription factor
targeting for control of transcription in tumor cells
Reflecting alterations in nuclear organization that are the
hallmarks of cancer cells, the gene locus encoding the CBF2/AML-1
transcription factor is frequently the target of chromosomal
translocations in human leukemia. Mapping of the nuclear matrix
targeting signal to exon 8 reveals that this domain is not present in
the t(8;21) fusion protein (AML-1/ETO), but is replaced by sequences
from the MTG8 gene (77
, 78
). Thus,
intranuclear targeting of the AML-1B transcription factor may be
abrogated because of gene rearrangements in leukemic cells. Fidelity of
transcriptional control may involve localization of gene regulatory
proteins to the correct subnuclear region. For example, PML bodies are
nuclear structures that are associated with the nuclear matrix and
modified in promyelocytic leukemia cells (34
,
35
, 37
). In normal cells the PML protein
resides in discrete PML bodies. However, in leukemic cells the PML
protein is genetically rearranged and dispersed throughout the nucleus
(34
, 37
). Yet another example of chromosomal
translocations involving a locus encoding a nuclear matrix-associated
transcription factor occurs in acute lymphocytic leukemia (ALL/MLL).
Recently, a translocation has been described in which the ALL/MLL
protein is fused with a histone acetyltransferase. The chimeric protein
may promote leukemia by modifying histone acetylation of specific
genomic regions. Consequential modifications in the intranuclear
distribution of factors encoded by the rearranged ALL locus occur
(79-81)
while the chimeric transcription factors remain
nuclear matrix associated. Hence, these results suggest that
perturbations in subnuclear location and/or nuclear matrix association
of proteins may be related to modifications in gene expression that are
linked to leukemias.
|
CONCLUSIONS
|
|---|
Multiple lines of evidence suggest that components of nuclear
architecture contribute both structurally and enzymatically to control
of gene expression. Sequences have been identified that direct
transcription factors to nuclear matrix-associated sites that support
transcription. Insight is thereby provided into mechanisms linked to
the assembly and activities of subnuclear domains where transcription
occurs. In a restricted sense, the foundation has been provided for
experimentally addressing intranuclear trafficking of gene regulatory
factors and control of factor association with the nuclear matrix to
establish and sustain domains that are competent for transcription. The
unique sequences (14
, 15
) and crystal
structure for the 31-amino-acid nuclear matrix targeting signal of
CBF/AML transcription factors (82)
support specificity for
localization at intranuclear sites where the machinery for gene
expression is assembled, rendered operative, and/or suppressed. In a
broader context, there is growing appreciation for involvement of
nuclear architecture in a dynamic and bidirectional exchange of gene
transcripts and regulatory factors between the nucleus and cytoplasm,
as well as between regions and structures within the nucleus
(83
, 84
).
It is difficult to arbitrarily separate nuclear structure and function
or distinguish the regulated and regulatory parameters of control. The
challenges we now face are to further define the targeting of
transcription factors and control that reside at the level of nuclear
matrix-associated acceptor sites. The result will unquestionably be
further insight into fundamental processes that are involved with
directing components of gene expression to specific regions within the
nucleus. It would be presumptuous to propose a single model to account
for the specific pathways that direct transcription factors to sites
within the nucleus that support transcription. However, findings
suggest that parameters of nuclear architecture functionally interface
with components of transcriptional control. The involvement of nuclear
matrix-associated transcription factors with recruitment of regulatory
components to modulate transcription remains to be defined. However, a
framework for experimentally addressing components of transcriptional
control within the context of nuclear architecture is now realistic.
The diversity of targeting signals must be established to evaluate the
extent to which regulatory discrimination is mediated by encoded
intranuclear trafficking signals. It will also be important to
biochemically and mechanistically define the checkpoints that are
operative during subnuclear distribution of regulatory factors and the
editing steps that are invoked to ensure both structural and functional
fidelity of nuclear domains where replication and expression of genes
occur. There is emerging recognition that placement of regulatory
components of gene expression must be temporally and spatially
coordinated to optimally mediate biological control.
Breaches in nuclear structure-function interrelationships can occur as
a consequence of microgravity-mediated perturbations in cellular
architecture. Experimental approaches are available to evaluate
modifications in nuclear morphology and in the subnuclear distribution
of genes and regulatory factors under microgravity conditions. It is
realistic to assess the influences of microgravity on gene regulatory
mechanisms and on the integration of cellular regulatory signals that
control the activation and suppression of cell growth as well as
phenotypic genes.
|
ACKNOWLEDGMENTS
|
|---|
These studies were in part supported by grants from the National
Institutes of Health (AR42262, AR39588). The contents are solely the
responsibility of the authors and do not necessarily represent the
official views of the National Institutes of Health. The authors thank
Elizabeth Bronstein for editorial assistance with preparation of the
manuscript.
|
REFERENCES
|
|---|
-
Kingston, R. E., Bunker, C. A., Imbalzano, A. N. (1996) Repression and activation by multiprotein complexes that alter chromatin structure. Genes Dev 10,905-920[Abstract/Free Full Text]
-
Zlatanova, J. S., van Holde, K. E. (1992) Chromatin loops and transcriptional regulation. Crit. Rev. Eukaryot. Gene Exp. 2,211-224[Medline]
-
Stein, G. S., van Wijnen, A. J., Stein, J. L., Lian, J. B., Montecino, M. (1997) Nuclear architecture in developmental transcriptional control of cell growth and tissue-specific genes. Bird, R. C. Stein, G. S. Lian, J. B. Stein, J. L. eds. Nuclear Structure and Gene Expression ,178-214 Academic Press New York.
-
Grunstein, M. (1997) Histone acetylation in chromatin structure and transcription. Nature 389,349-352[Medline]
-
Grunstein, M. (1997) Molecular model for telomeric heterochromatin in yeast. Curr. Opin. Cell Biol. 9,383-387[Medline]
-
Bidwell, J. P., Fey, E. G., van Wijnen, A. J., Penman, S., Stein, J. L., Lian, J. B., Stein, G. S. (1994) Nuclear matrix proteins distinguish normal diploid osteoblasts from osteosarcoma cells. Cancer Res 54,28-32[Abstract/Free Full Text]
-
Dworetzky, S. I., Fey, E. G., Penman, S., Lian, J. B., Stein, J. L., Stein, G. S. (1990) Progressive changes in the protein composition of the nuclear matrix during rat osteoblast differentiation. Proc. Natl. Acad. Sci. USA 87,4605-4609[Abstract/Free Full Text]
-
Getzenberg, R. H., Coffey, D. S. (1990) Tissue specificity of the hormonal response in sex accessory tissues is associated with nuclear matrix protein patterns. Mol. Endocrinol. 4,1336-1342[Abstract]
-
Nickerson, J. A., He, D. C., Krochmalnic, G., Penman, S. (1990) Immunolocalization in three dimensions: immunogold staining of cytoskeletal and nuclear matrix proteins in resinless electron microscopy sections. Proc. Natl. Acad. Sci. USA 87,2259-2263[Abstract/Free Full Text]
-
Pienta, K. J., and Coffey, D. S. (1991)
Correlation of nuclear morphometry with progression of breast cancer.
Cancer [Philadelphia] 68, 2012–2016
-
Getzenberg, R. H., Pienta, K. J., Huang, E. Y., Coffey, D. S. (1991) Identification of nuclear matrix proteins in the cancerous and normal rat prostrate. Cancer Res 51,6514-6520[Abstract/Free Full Text]
-
Berezney, R. (1991) The nuclear matrix: a heuristic model for investigating genomic organization and function in the cell nucleus. J. Cell. Biochem. 47,109-123[Medline]
-
Berezney, R., Coffey, D. S. (1975) Nuclear protein matrix: association with newly synthesized DNA. Science 189,291-292[Abstract/Free Full Text]
-
Zeng, C., van Wijnen, A. J., Stein, J. L., Meyers, S., Sun, W., Shopland, L., Lawrence, J. B., Penman, S., Lian, J. B., Stein, G. S., Hiebert, S. W. (1997) Identification of a nuclear matrix targeting signal in the leukemia and bone-related AML/CBF transcription factors. Proc. Natl. Acad. Sci. USA 94,6746-6751[Abstract/Free Full Text]
-
Zeng, C., McNeil, S., Pockwinse, S., Nickerson, J. A., Shopland, L., Lawrence, J. B., Penman, S., Hiebert, S. W., Lian, J. B., van Wijnen, A. J., Stein, J. L., Stein, G. S. (1998) Intranuclear targeting of AML/CBF regulatory factors to nuclear matrix-associated transcriptional domains. Proc. Natl. Acad. Sci. USA 95,1585-1589[Abstract/Free Full Text]
-
Dworetzky, S. I., Wright, K. L., Fey, E. G., Penman, S., Lian, J. B., Stein, J. L., Stein, G. S. (1992) Sequence-specific DNA-binding proteins are components of a nuclear matrix attachment site. Proc. Natl. Acad. Sci. USA 89,4178-4182[Abstract/Free Full Text]
-
van Wijnen, A. J., Bidwell, J. P., Fey, E. G., Penman, S., Lian, J. B., Stein, J. L., Stein, G. S. (1993) Nuclear matrix association of multiple sequence-specific DNA binding activities related to SP-1, ATF, CCAAT, C/EBP, OCT-1, and AP-1. Biochemistry 32,8397-8402[Medline]
-
Nelkin, B. D., Pardoll, D. M., Vogelstein, B. (1980) Localization of SV40 genes within supercoiled loop domains. Nucleic Acids Res 8,5623-5633[Abstract/Free Full Text]
-
Robinson, S. I., Nelkin, B. D., Vogelstein, B. (1982) The ovalbumin gene is associated with the nuclear matrix of chicken oviduct cells. Cell 28,99-106[Medline]
-
Schaack, J., Ho, W. Y., Freimuth, P., Shenk, T. (1990) Adenovirus terminal protein mediates both nuclear matrix association and efficient transcription of adenovirus DNA. Genes Dev 4,1197-1208[Abstract/Free Full Text]
-
Stief, A., Winter, D. M., Stratling, W. H., Sippel, A. E. (1989) A nuclear DNA attachment element mediates elevated and position-independent gene activity. Nature 341,343-345[Medline]
-
Lawrence, J. B., Singer, R. H., Marselle, L. M. (1989) Highly localized tracks of specific transcripts within interphase nuclei visualized by in situ hybridization. Cell 57,493-502[Medline]
-
Zeitlin, S., Parent, A., Silverstein, S., Efstratiadis, A. (1987) Pre-mRNA splicing and the nuclear matrix. Mol. Cell Biol. 7,111-120[Abstract/Free Full Text]
-
Carter, K. C., Bowman, D., Carrington, W., Fogarty, K., McNeil, J. A., Fay, F. S., Lawrence, J. B. (1993) A three-dimensional view of precursor messenger RNA metabolism within the mammalian nucleus. Science 259,1330-1335[Abstract/Free Full Text]
-
Spector, D. L. (1990) Higher order nuclear organization: three-dimensional distribution of small nuclear ribonucleoprotein particles. Proc. Natl. Acad. Sci. USA 87,147-151[Abstract/Free Full Text]
-
Spector, D. L., Fu, X. D., Maniatis, T. (1991) Associations between distinct pre-mRNA splicing components and the cell nucleus. EMBO J 10,3467-3481[Medline]
-
Xing, Y., Johnson, C. V., Dobner, P. R., Lawrence, J. B. (1993) Higher level organization of individual gene transcription and splicing. Science 259,1326-1330[Abstract/Free Full Text]
-
Blencowe, B. J., Nickerson, J. A., Issner, R., Penman, S., Sharp, P. A. (1994) Association of nuclear matrix antigens with exon-containing splicing complexes. J. Cell Biol. 127,593-607[Abstract/Free Full Text]
-
Davie, J. R. (1997) Nuclear matrix, dynamic histone acetylation and transcriptionally active chromatin. Mol. Biol. Rep. 24,197-207[Medline]
-
van Holde, K. E. (1988) Chromatin Springer-Verlag New York.
-
Silver, P. A., Keegan, L. P., Ptashine, M. (1984) Amino terminus of the yeast GAL4 gene product is sufficient for nuclear localization. Proc. Natl. Acad. Sci. USA 81,5951-5955[Abstract/Free Full Text]
-
Ullman, K. S., Powers, M. A., Forbes, D. J. (1997) Nuclear export receptors: from importin to exportin [comment]. Cell 90,967-970[Medline]
-
Clemson, C. M., McNeil, J. A., Willard, H. F., Lawrence, J. B. (1996) XIST RNA paints the inactive X chromosome at interphase: evidence for a novel RNA involved in nuclear/chromosome structure. J. Cell Biol. 132,259-275[Abstract/Free Full Text]
-
Dyck, J. A., Maul, G. G., Miller, W. H., Chen, J. D., Kakizuka, A., Evans, R. M. (1994) A novel macromolecular structure is a target of the promyelocyte-retinoic acid receptor oncoprotein. Cell 76,333-343[Medline]
-
Nickerson, J. A., Blencowe, B. J., Penman, S. (1995) The architectural organization of nuclear metabolism. Berezney, R. Jeon, K. W. eds. Structural and Functional Organization of the Nuclear Matrix ,67-123 Academic Press New York.
-
Pombo, A., Cook, P. R. (1996) The localization of sites containing nascent RNA and splicing factors. Exp. Cell Res. 229,201-203[Medline]
-
Weis, K., Rambaud, S., Lavau, C., Jansen, J., Carvalho, T., Carmo-Fonseca, M., Lamond, A., Dejean, A. (1994) Retinoic acid regulates aberrant nuclear localization of PML-RAR alpha in acute promyelocytic leukemia cells. Cell 76,345-356[Medline]
-
Everett, R. D., Maul, G. G. (1994) HSV-1 IE protein Vmw110 causes redistribution of PML. EMBO J 13,5062-5069[Medline]
-
Grande, M. A., van der Kraan, I., van Steensel, B., Schul, W., de The, H., van der Voort, H. T., de Jong, L., van Driel, R. (1996) PML-containing nuclear bodies: their spatial distribution in relation to other nuclear components. J. Cell. Biochem. 63,280-291[Medline]
-
Bae, S. C., Yamaguchi-Iwai, Y., Ogawa, E., Maruyama, M., Inuzuka, M., Kagoshima, H., Shigesada, K., Satake, M., Ito, Y. (1993) Isolation of PEBP2B cDNA representing the mouse homolog of human acute myeloid leukemia gene, AML1. Oncogene 8,809-814[Medline]
-
Miyoshi, H., Shimizu, K., Kozu, T., Maseki, N., Kaneko, Y., Ohki, M. (1991) t(8;21) breakpoints on chromosome 21 in acute myeloid leukemia are clustered within a limited region of a single gene, AML1. Proc. Natl. Acad. Sci. USA 88,10431-10434[Abstract/Free Full Text]
-
Banerjee, C., McCabe, L. R., Choi, J.-Y., Hiebert, S. W., Stein, J. L., Stein, G. S., Lian, J. B. (1997) Runt homology domain proteins in osteoblast differentiation: AML-3/CBFA1 is a major component of a bone specific complex. J. Cell. Biochem. 66,1-8[Medline]
-
Levanon, D., Negreanu, V., Bernstein, Y., Bar-Am, I., Avivi, L., Groner, Y. (1994) AML1, AML2, and AML3, the human members of the runt domain gene family: cDNA structure, expression, and chromosomal localization. Genomics 23,425-432[Medline]
-
Meyers, S., Lenny, N., Sun, W.-H., Hiebert, S. W. (1996) AML-2 is a potential target for transcriptional regulation by the t(8;21) and t(12;21) fusion proteins in acute leukemia. Oncogene 13,303-312[Medline]
-
Satake, M., Nomura, S., Yamaguchi-Iwai, Y., Takahama, Y., Hashimoto, Y., Niki, M., Kitamura, Y., Ito, Y. (1995) Expression of the Runt domain-encoding PEBP2 alpha genes in T cells during thymic development. Mol. Cell. Biol. 15,1662-1670[Abstract]
-
Merriman, H. L., van Wijnen, A. J., Hiebert, S., Bidwell, J. P., Fey, E., Lian, J., Stein, J., Stein, G. S. (1995) The tissue-specific nuclear matrix protein, NMP-2, is a member of the AML/CBF/PEBP2/runt domain transcription factor family: interactions with the osteocalcin gene promoter. Biochemistry 34,13125-13132[Medline]
-
Banerjee, C., Hiebert, S. W., Stein, J. L., Lian, J. B., Stein, G. S. (1996) An AML-1 consensus sequence binds an osteoblast-specific complex and transcriptionally activates the osteocalcin gene. Proc. Natl. Acad. Sci. USA 93,4968-4973[Abstract/Free Full Text]
-
Rodan, G. A., Harada, S. (1997) The missing bone [comment]. Cell 89,677-680[Medline]
-
Ducy, P., Zhang, R., Geoffroy, V., Ridall, A. L., Karsenty, G. (1997) Osf2/Cbfa1: a transcriptional activator of osteoblast differentiation. Cell 89,747-754[Medline]
-
Nuchprayoon, I., Meyers, S., Scott, L. M., Suzow, J., Hiebert, S. W., Friedman, A. D. (1994) PEBP2/CBF, the murine homolog of the human myeloid AML1 and PEBP2ß/CBFß proto-oncoproteins, regulates the murine myeloperoxidase and neutrophil elastase genes in immature myeloid cells. Mol. Cell. Biol. 14,5558-5568[Abstract/Free Full Text]
-
Ho, I.-C., Yang, L.-H., Morle, G., Leiden, J. M. (1989) A T-cell-specific transcriptional enhancer element 3' of C in the human T-cell receptor a locus. Proc. Natl. Acad. Sci. USA 86,6714-6718[Abstract/Free Full Text]
-
Gottschalk, L. R., Leiden, J. M. (1990) Identification and functional characterization of the human T-cell receptor gene transcriptional enhancer: common nuclear proteins interact with the transcriptional regulatory elements of the T-cell receptor and ß genes. Mol. Cell. Biol. 10,5486-5495[Abstract/Free Full Text]
-
Hernandez-Munain, C., Krangel, M. S. (1994) Regulation of the T cell receptor delta enhancer by functional cooperation between c-Myb and core-binding factors. Mol. Cell. Biol. 14,473-483[Abstract/Free Full Text]
-
Frank, R., Zhang, J., Uchida, H., Meyers, S., Hiebert, S. W., Nimer, S. D. (1995) The AML1/ETO fusion protein blocks transactivation of the GM–CSF promoter by AML1B. Oncogene 11,2667-2674[Medline]
-
Takahashi, A., Satake, M., Yamaguchi-Iwai, Y., Bae, S. C., Lu, J., Maruyama, M., Zhang, Y. W., Oka, H., Arai, N., Arai, K.-I., Ito, Y. (1995) Positive and negative regulation of granulocyte-macrophage colony stimulating factor promoter activity by AML1-related transcription factor, PEBP2. Blood 86,607-616[Abstract/Free Full Text]
-
Nimer, S., Zhang, J., Avraham, H., Miyazaki, Y. (1996) Transcriptional regulation of interleukin-3 expression in megakaryocytes. Blood 88,66-74[Abstract/Free Full Text]
-
Wang, S., Wang, Q., Crute, B. E., Melnikova, I. N., Keller, S. R., Speck, N. A. (1993) Cloning and characterization of subunits of the T-cell receptor and murine leukemia virus enhancer core-binding factor. Mol. Cell. Biol. 13,3324-3339[Abstract/Free Full Text]
-
Meyers, S., Downing, J. R., Hiebert, S. W. (1993) Identification of AML-1 and the t(8;21) translocation protein (AML-1/ETO) as sequence-specific DNA-binding proteins, the runt homology domain is required for DNA binding and protein-protein interactions. Mol. Cell. Biol. 13,6336-6345[Abstract/Free Full Text]
-
Meyers, S., Lenny, N., Hiebert, S. W. (1995) The t(8;21) fusion protein interferes with AML-1B-dependent transcriptional activation. Mol. Cell. Biol. 15,1974-1982[Abstract]
-
Ogawa, E., Maruyama, M., Kagoshima, H., Inuzuka, M., Lu, J., Satake, M., Shigesada, K., Ito, Y. (1993) PEBP2/PEA2 represents a family of transcription factors homologous to the products of the Drosophila runt gene and the human AML1 gene. Proc. Natl. Acad. Sci. USA 90,6859-6863[Abstract/Free Full Text]
-
Stein, G. S., Stein, J. L., Lian, J. B., van Wijnen, A. J., Montecino, M. (1996) Functional interrelationships between nuclear structure and transcriptional control: contributions to regulation of cell cycle– and tissue–specific gene expression. J. Cell. Biochem. 62,198-209[Medline]
-
Stein, G. S., van Wijnen, A. J., Stein, J. L., Lian, J. B., Bidwell, J. P., Montecino, M. (1994) Nuclear architecture supports integration of physiological regulatory signals for transcription of cell growth and tissue-specific genes during osteoblast differentiation. J. Cell. Biochem. 55,4-15[Medline]
-
Mancini, M. A., Shan, B., Nickerson, J. A., Penman, S., Lee, W.-H. (1994) The retinoblastoma gene product is a cell cycle-dependent, nuclear matrix-associated protein. Proc. Natl. Acad. Sci. USA 91,418-422[Abstract/Free Full Text]
-
Bidwell, J. P., van Wijnen, A. J., Fey, E. G., Dworetzky, S., Penman, S., Stein, J. L., Lian, J. B., Stein, G. S. (1993) Osteocalcin gene promoter-binding factors are tissue-specific nuclear matrix components. Proc. Natl. Acad. Sci. USA 90,3162-3166[Abstract/Free Full Text]
-
Ogawa, E., Inuzuka, M., Maruyama, M., Satake, M., Naito-Fujimoto, M., Ito, Y., Shigesada, K. (1993) Molecular cloning and characterization of PEBP2ß, the heterodimeric partner of a novel Drosophila runt-related DNA binding protein PEBP2. Virology 194,314-331[Medline]
-
Giese, K., Kingsley, C., Kirshner, J. R., Grosschedl, R. (1995) Assembly and function of a TCR alpha enhancer complex is dependent on LEF-1-induced DNA bending and multiple protein-protein interactions. Genes Dev 9,995-1008[Abstract/Free Full Text]
-
Zhang, D. E., Hetherington, C. J., Meyers, S., Rhoades, K. L., Larson, C. J., Chen, H. M., Hiebert, S. W., Tenen, D. G. (1996) CCAAT enhancer-binding protein (C/EBP) and AML1 (CBF2) synergistically activate the macrophage colony-stimulating factor receptor promoter. Mol. Cell. Biol. 16,1231-1240[Abstract]
-
Berezney, R., Mortillaro, M., Ma, H., Meng, C., Samarabandu, J., Wei, X., Somanathan, S., Liou, W. S., Pan, S. J., Cheng, P. C. (1996) Connecting nuclear architecture and genomic function. J. Cell Biochem. 62,223-226[Medline]
-
Jackson, D. A. (1997) Chromatin domains and nuclear compartments: establishing sites of gene expression in eukaryotic nuclei. Mol. Biol. Reprod. 24,209-220[Medline]
-
Guo, B., Odgren, P. R., van Wijnen, A. J., Last, T. J., Nickerson, J., Penman, S., Lian, J. B., Stein, J. L., Stein, G. S. (1995) The nuclear matrix protein NMP-1 is the transcription factor YY1. Proc. Natl. Acad. Sci. USA 92,10526-10530[Abstract/Free Full Text]
-
Lindenmuth, D. M., van Wijnen, A. J., Hiebert, S., Stein, J. L., Lian, J. B., Stein, G. S. (1997) Subcellular partitioning of transcription factors during osteoblast differentiation: developmental association of the AML/CBF/PEBP2-related transcription factor-NMP-2 with the nuclear matrix. J. Cell. Biochem. 66,123-132[Medline]
-
Grande, M. A., van der Kraan, I., de Jong, L., van Driel, R. (1997) Nuclear distribution of transcription factors in relation to sites of transcription and RNA polymerase II. J. Cell Sci. 110,1781-1791[Abstract]
-
Alvarez, M., Long, H., Onyia, J., Hock, J., Xu, W., Bidwell, J. (1997) Rat osteoblast and osteosarcoma nuclear matrix proteins bind with sequence specificity to the rat type I collagen promoter. Endocrinol 138,482-489[Abstract/Free Full Text]
-
Chen, H. Y., Sun, J. M., Hendzel, M. J., Rattner, J. B., Davie, J. R. (1996) Changes in the nuclear matrix of chicken erythrocytes that accompany maturation. Biochem. J. 320,257-265
-
Nardozza, T. A., Quigley, M. M., Getzenberg, R. H. (1996) Association of transcription factors with the nuclear matrix. J. Cell Biochem. 61,467-477[Medline]
-
Spelsberg, T. C., Lauber, A. H., Sandhu, N. P., Subramaniam, M. (1996) A nuclear matrix acceptor site for the progesterone receptor in the avian c-myc gene promoter. Recent Prog. Horm. Res. 51,63-96
-
Matera, A. G., Ward, D. C. (1993) Nucleoplasmic organization of small nuclear ribonucleoproteins in cultured human cells. J. Cell Biol. 121,715-727[Abstract/Free Full Text]
-
Hiebert, S. W., Sun, W., Davis, J. N., Golub, T., Shurtleff, S., Buijs, A., Downing, J. R., Grosveld, G., Roussell, M. F., Gilliland, D. G., Lenny, N., Meyers, S. (1996) The t(12;21) translocation converts AML-1B from an activator to a repressor of transcription. Mol. Cell. Biol. 16,1349-1355[Abstract]
-
Sobulo, O. M., Borrow, J., Tomek, R., Reshmi, S., Harden, A., Schlegelberger, B., Housman, D., Doggett, N. A., Rowley, J. D., Zeleznik-Le, N. J. (1997) MLL is fused to CBP, a histone acetyltransferase, in therapy-related acute myeloid leukemia with a t(11;16)(q23;p13.3). Proc. Natl. Acad. Sci. USA 94,8732-8737[Abstract/Free Full Text]
-
Yano, T., Nakamura, T., Blechman, J., Sorio, C., Dang, C. V., Geiger, B., Canaani, E. (1997) Nuclear punctate distribution of ALL-1 is conferred by distinct elements at the N terminus of the protein. Proc. Natl. Acad. Sci. USA 94,7286-7291[Abstract/Free Full Text]
-
Rogaia, D., Grignani, F., Carbone, R., Riganelli, D., LoCoco, F., Nakamura, T., Croce, C. M., Di Fiore, P. P., Pelicci, P. G. (1997) The localization of the HRX/ALL1 protein to specific nuclear subdomains is altered by fusion with its eps15 translocation partner. Cancer Res 57,799-802[Abstract/Free Full Text]
-
Tang, L., Guo, B., van Wijnen, A. J., Lian, J. B., Stein, J. L., Stein, G. S., Zhou, G. W. (1998) Preliminary crystallographic study of the glutathione S-transferase fused with the nuclear matrix targeting signal of the transcription factor AML-1/CBF2. J. Struct. Biol. 123,83-85[Medline]
-
Wei, X., Samarabandu, J., Devdhar, R. S., Siegel, A. J., Acharya, R., Berezney, R. (1998) Segregation of transcription and replication sites into higher order domains. Science 281,1502-1505[Abstract/Free Full Text]
-
Lamond, A. I., Earnshaw, W. C. (1998) Structure and function in the nucleus. Science 280,547-553[Abstract/Free Full Text]
This article has been cited by other articles:
|
|
|
|
 
T. K. Chatterjee and R. A. Fisher
RGS12TS-S Localizes at Nuclear Matrix-Associated Subnuclear Structures and Represses Transcription: Structural Requirements for Subnuclear Targeting and Transcriptional Repression
Mol. Cell. Biol.,
June 15, 2002;
22(12):
4334 - 4345.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
Y. Wang, D. C. Newton, T. L. Miller, A.-M. Teichert, M. J. Phillips, M. S. Davidoff, and P. A. Marsden
An Alternative Promoter of the Human Neuronal Nitric Oxide Synthase Gene Is Expressed Specifically in Leydig Cells
Am. J. Pathol.,
January 1, 2002;
160(1):
369 - 380.
[Abstract]
[Full Text]
[PDF]
|
|
|
TOP
ABSTRACT
INTRODUCTION
