COGEDE-548; NO OF PAGES 12 Please cite this article in press as: Madan Babu M, et al. Eukaryotic gene regulation in three dimensions and its impact on genome evolution, Curr Opin Genet Dev (2008), doi:10.1016/ j.gde.2008.10.002 Available online at www.sciencedirect.com Eukaryotic gene regulation in three dimensions and its impact on genome evolution M Madan Babu 1 , Sarath Chandra Janga 1 , Ines de Santiago 2,3 and Ana Pombo 2 Recent advances in molecular techniques and high-resolution imaging are beginning to provide exciting insights into the higher order chromatin organization within the cell nucleus and its influence on eukaryotic gene regulation. This improved understanding of gene regulation also raises fundamental questions about how spatial features might have constrained the organization of genes on eukaryotic chromosomes and how mutations that affect these processes might contribute to disease conditions. In this review, we discuss recent studies that highlight the role of spatial components in gene regulation and their impact on genome evolution. We then address implications for human diseases and outline new directions for future research. Addresses 1 MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK 2 MRC Clinical Sciences Centre, Imperial College School of Medicine, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK 3 Instituto Gulbenkian de Cie ˆ ncia, Oeiras, Portugal Corresponding author: Madan Babu, M ([email protected]) Current Opinion in Genetics & Development 2008, 18:1–12 This review comes from a themed issue on Genomes and evolution Edited by Sarah Teichmann and Nipam Patel 0959-437X/$ – see front matter # 2008 Elsevier Ltd. All rights reserved. DOI 10.1016/j.gde.2008.10.002 Introduction Although we observe an amazing diversity in the num- ber of chromosomes that eukaryotic organisms encode (e.g. 32 chromosomes in yeast, over 200 in butterflies, and 46 in humans), they are packaged in similar ways: each DNA molecule is wrapped around histone proteins to form nucleosomes, which are then condensed in a complex hierarchical manner to make up an entire chromosome (Figure 1). Such an intricate organization of genetic material within the eukaryotic nucleus pro- vides ample opportunities to regulate expression of the encoded genes at many different hierarchical levels. For instance, eukaryotic transcription is dynamically regulated at least at three major levels [1,2]. The first is at the level of DNA sequence (Figure 1) where DNA- binding proteins (e.g. transcription factors; TFs) associ- ate with cis-regulatory elements (e.g. TF-binding sites) to regulate transcription. The second is at the level of chromatin (Figure 1), which allows segments within a chromosomal arm to switch between different transcrip- tional states, that is, those that suppress transcription (heterochromatin) and those that allow for gene acti- vation (euchromatin). This involves changes in chro- matin structure and nucleosome occupancy, both of which are controlled by the interplay between several factors such as nucleosome remodeling complexes, histone modifications, and a variety of repressive and activating mechanisms [3,4]. The third is at the level of the entire chromosome (Figure 1) and includes posi- tioning of chromosomes within the nuclear space (e.g. closer to the nuclear periphery or next to internal nuclear compartments) and spatial organization of specific chromosomal loci within the nucleus, both of which are known to influence gene expression [5,6 ,7,8,9 ]. Several studies have investigated these mechanisms in detail and have revealed that such processes involve extensive physical and spatial association between dis- tantly located genomic elements and widespread cross- talk between the different levels. Advancements in molecular techniques and high-resolution imaging (Table 1) have facilitated investigation of the role of spatial component in gene regulation and have provided valuable insights into its importance in gene regulation [5,6 ,7,8,9 ]. These studies also raise fundamental ques- tions: Has the requirement for transcriptional regulation and its spatial considerations constrained the way in which genes are organized on chromosomes? If yes, in what ways does it affect genome evolution? In the first part of this review, we discuss recent studies that high- light the importance of spatial components in gene regulation. We then discuss some studies that address how the requirements for gene regulation could have constrained genome evolution. Finally, we discuss implications for human disease, outline open questions, and discuss how computational approaches can be help- ful in investigating the prevalence of spatial regulatory mechanisms and in understanding their impact on gen- ome evolution. We wish to stress that the studies dis- cussed have been carried out in different model systems and that further research is necessary to assess whether particular spatial mechanisms are universal or specific to each system. www.sciencedirect.com Current Opinion in Genetics & Development 2008, 18:1–12
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Available online at www.sciencedirect.com
Eukaryotic gene regulation in three dimensions and its impact ongenome evolutionM Madan Babu1, Sarath Chandra Janga1, Ines de Santiago2,3 andAna Pombo2
Recent advances in molecular techniques and high-resolution
imaging are beginning to provide exciting insights into the
higher order chromatin organization within the cell nucleus and
its influence on eukaryotic gene regulation. This improved
understanding of gene regulation also raises fundamental
questions about how spatial features might have constrained
the organization of genes on eukaryotic chromosomes and how
mutations that affect these processes might contribute to
disease conditions. In this review, we discuss recent studies
that highlight the role of spatial components in gene regulation
and their impact on genome evolution. We then address
implications for human diseases and outline new directions for
future research.
Addresses1 MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2
0QH, UK2 MRC Clinical Sciences Centre, Imperial College School of Medicine,
Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK3 Instituto Gulbenkian de Ciencia, Oeiras, Portugal
Hierarchical organization of eukaryotic genetic material. Each DNA molecule is wrapped into nucleosomes, which form the chromatin and is ultimately
packaged into a chromosome that resides within the nucleus. The first level of regulation includes regulatory elements (e.g. enhancers and insulators),
DNA methylation and DNA structure (e.g. G-quadruplex and Z-DNA). The second level includes post-translational modification of nucleosomes (e.g.
histone methylation and acetylation) and remodeling of nucleosomes (e.g. histone chaperones and ATP-dependent remodeling complexes). The third
level of regulation includes chromosomal organization and the nuclear architecture (e.g. position of various loci and chromosomes within the nucleus).
Long-range interactions involving distalregulatory elementsRegulatory elements in eukaryotes can be spread over
several kilobases away from the associated gene. These
include binding sites for specific TFs, enhancer elements,
locus control regions (LCRs), and insulator elements
(Figure 2a). TF-binding sites are generally close to pro-
moter regions, but enhancer elements, LCRs, and insu-
lator elements can be present far away on the
chromosome and may influence the expression of more
than one gene simultaneously. Enhancers affect expres-
sion of nearby genes, whereas LCRs can affect several
genes that are distantly located within a genomic locus
spanning several kilobases [10]. Insulator elements can
block promiscuous enhancer–promoter interaction or act
as a barrier against the spreading of heterochromatin. The
former class of insulators functions by forming genomic
loops via long-range interactions and the latter class
prevents inappropriate gene expression by recruiting
nucleosome-modifying enzymes [11].
The formation of loops mediated by proteins bound to
specific elements along a chromosome appears to have a
central role in several processes as it can affect the
expression of several genes in a neighborhood [12�].Although only a few loops have been analyzed in detail
and the nature of the molecular forces that maintain them
remains unclear, recent evidence suggests that they are
found in several eukaryotes [10] and that the transcrip-
tional machinery itself could be a molecular tie [13–15]
(Figure 2b). Several studies that have used 3D-FISH,
chromosome conformation capture (3C; see Table 1)
[16��], and its variants 4C, 5C, and 6C [17] and live-cell
imaging [18] support the idea that active transcription
units are in close contact within the nuclear space
Please cite this article in press as: Madan Babu M, et al. Eukaryotic gene regulation in three d
j.gde.2008.10.002
Current Opinion in Genetics & Development 2008, 18:1–12
[14,19,20]. The results are consistent with a model for
genome organization in which active polymerases cluster
into transcription ‘factories’ bringing together distal genes
(Figure 2b) and where active genes are dynamically
organized into shared nuclear subcompartments [14,18–20]. They are also consistent with these cis-regulatory
elements functioning as insulators, enhancers or LCRs,
depending on their positions relative to other genes.
Interestingly, in a recent study, it has been shown that
specific ‘factories’ produce only a particular kind of tran-
script depending on the promoter type and whether or not
the gene contains an intron [21�]. These results support
the presence of ‘specialized’ transcription factories, which
transcribe specific transcription units depending on pro-
moter type or presence of introns [19,20,21�].
The genomic loops involving regulatory elements are
dynamic, depend on the transcriptional status of a gene,
vary between cell types in the same organism and may
involve several proteins. The beta-globin locus in mouse
is the most studied one and involves the Hbb-b1 gene
(which encodes beta-globin), its LCR and the Eraf gene
(encoding an alpha-globin-stabilizing protein) on the
same chromosome. This LCR is thought to nucleate a
chromatin hub which correlates with expression of globin-
related genes. It has been confirmed, by 3C, 4C, and
RNA-TRAP that the contacts between Hbb-b1, the
LCR, and Eraf are seen only in erythroid nuclei (in which
all three are transcribed) but not in brain cell nuclei (in
which Hbb-b1 is inactive) [14,22�,23]. Moreover, the
contacts that Hbb-b1 makes with other genomic regions
depend on its transcriptional activity; in erythroid nuclei,
80% of contacts are with other active genes, but, in brain
cells, this falls to only 13% [22�]. Interestingly, the LCR
region itself is also transcribed and this might even be
imensions and its impact on genome evolution, Curr Opin Genet Dev (2008), doi:10.1016/
Eukaryotic gene regulation and its impact on genome evolution Madan Babu et al. 3
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j.gde.2008.10.002
Table 1
Experimental and computational approaches to study eukaryotic transcriptional regulation.
Experimental
approaches
Description
ChIP-chip Chromatin-bound proteins are covalently linked to DNA by using an in vivo crosslinking agent such as formaldehyde
(histones can be detected in unfixed chromatin preparations in native ChIP). Chromatin is then sheared and
immunoprecipitated (ChIP) using an antibody for a native protein, a tagged version, or a specific post-translational
modification. Reversal of the crosslink releases the bound DNA, allowing the enrichment of specific DNA fragments,
whose identity is determined by hybridization to a microarray (chip).
ChIP-seq In ChIP-seq experiments, the immunoprecipitated DNA is directly sequenced using high-throughput sequencing
technologies (e.g. Solexa or 454). The sequences are then computationally mapped back to the reference genome.
Fragments that were bound by the protein will be more abundant and sequenced several times, providing a direct
measure of enrichment.
DamID The DNA-binding protein of interest is fused to an E. coli protein, Dam. Dam methylates the N6 position of the adenine
in the sequence GATC, which is expected to occur once in every �256 bases. Upon binding DNA, the Dam protein
preferentially methylates adenine in the vicinity of binding. The DNA is digested by DpnI and DpnII restriction enzymes,
which cleave within the nonmethylated GATC sequence, and remove fragments that are not methylated. The remaining
methylated fragments are amplified by selective PCR and quantified using a microarray.
RNA-TRAP Newly made transcripts are detected in crosslinked cells by RNA-FISH using biotinylated probes and
probe–RNA–chromatin complexes are amplified with tyramide or directly immunoprecipitated, before PCR analyses.
Chromosome
conformation
capture (3C)
3C is used to determine which DNA sequences lie close together in 3D space in fixed cells. This typically involves
fixation to crosslink DNA sequences that lie next to each other (usually through DNA–protein–DNA links), before
cutting with a restriction enzyme, dilution, and ligation at low concentration. This favors the ligation of pairs of DNA
sequences that are crosslinked after which the reversing of crosslinks allows the ligated DNA to be detected by PCR.
4C 4C technology [chromosome conformation capture on chip (3C-on-chip) or circular chromosome conformation capture
(circular-3C)] allows for an unbiased genome-wide search for DNA loci that contact a given locus.
5C Chromosome conformation capture carbon copy (5C) is a massively parallel technique, which involves mapping physical
interactions between genomic elements and sequencing or microarray analysis of the ligated end products of the 3C
technique. 3C typically converts physical chromatin interactions into specific ligation products, which are quantified
using high-throughput microarrays or quantitative DNA sequencing using 454-technology as detection methods.
6C Combines ChIP for a specific chromatin bound protein with 3C-based methods to correlate specific long-range
chromatin interactions with the presence of a specific bound protein.
FISH Fluorescent in situ hybridization (FISH) detects specific DNA sequences and localizes them on cytogenetic preparations of
chromosomes or interphase cell nuclei. Cells are hypotonically swollen and dropped on glass slides before hybridization,
such that fine structural details might be lost. It uses tagged probes amplified from specific DNA fragments up to single
chromosomes, to detect the target sequences. The genomic regions bound by the probe are visualized by
fluorescence microscopy.
3D-FISH A modified FISH procedure that improves the preservation of 3D nuclear structure (3D-FISH), important for spatial
mapping of the position of specific genomic sequences within the interphase nuclei. This technique can be slow as it
requires imaging of multiple image stacks on a small number of nuclei and 3D reconstruction. It can also be
combined with protein and RNA localization.
Cryo-FISH A modified FISH procedure that uses ultra-thin cryosections from sucrose-embedded fixed samples. Sections are 100 to
200-nm thick. Preservation of ultrastructure is optimized, signal-to-noise ratios are improved and imaging artifacts are
minimized. It is ideal for imaging short-range interactions between specific loci or their associations with specific landmarks
with higher resolution and faster data collection. Specific cells in their tissue context can be easily investigated.
Single molecule
imaging
(fluorescence
microscopy)
In single molecule imaging (SMI) of live cells, the molecules of interest are conjugated with fluorophores and introduced
into cells. The behavior of multiple fluorescent molecules in cells is then visualized using high-sensitivity video microscopy.
The observables in SMI are the position or movement of the fluorescent spots, the fluorescence intensity of individual
spots, the fluorescence spectrum or color of individual spots, and the number and distribution of the spots.
Lac-binding-site
array
In this approach, in vivo visualization of chromatin dynamics is based on lac repressor recognition of direct repeats of
the lac operator. The method allows tagging of specific chromosomal sites and thus in situ localization in vivo. Detection
by light microscopy, using GFP–lac–repressor fusion proteins or immunofluorescence, can be complemented by higher
resolution electron microscopy using immunogold staining. This method facilitates the investigation of interphase
chromosome dynamics, as well as chromosome segregation during cell division in organisms that lack cytologically
condensed chromosomes.
Computational
approaches
Description
Boolean modeling In qualitative modeling, kinetic processes are simulated by tracking over discrete time, the state of the system, defined in
terms of a coarse range for each variable. The weak specification of such models conserves computer resources needed
to explore the space of possible behaviors. Moreover, it provides high-level predictions applying to a whole family of
systems. Although simulation of qualitative models can be fast, even a rough exploration of parameter space can become
intractable as the size of the system increases, highlighting the need for increasing computer resources and methods
to accelerate the parameters’ search space. For genes that are naturally found in only two states (e.g. on or off), the
trade-off in accuracy may not be high. On the contrary, simple models can, in some cases, predict behaviors that
are far from reality.
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Eukaryotic gene regulation and its impact on genome evolution Madan Babu et al. 5
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Figure 2
Features of genome architecture in 3D. (a) The DNA is shown as a black line, a gene is represented as an arrow and the different classes of regulatory
elements are shown in various shapes and colors. Insulator elements (blue rectangles) block spread of heterochromatin (red circles) and prevent
inappropriate interaction between enhancers (green oval) and unrelated genes. Enhancers can facilitate regulation of nearby genes that may still be a
few kilobases away. Locus control region (gray oval) can bring genomic loci that are several kilobases away close to each other to coordinate gene
expression. The bottom panel shows various aspects of the spatial component in eukaryotic gene regulation. The nucleus is shown in the center. (b)
Different active regions of the same or different chromosomes can associate with the same transcription factory (yellow domain). (c) Enhancers from
one chromosome may regulate the expression of genes present on another chromosome via inter-chromosomal interactions. (d) Chromosomes
occupy defined volumes within the nucleus, called chromosomal territories, which are depicted in different colors with significant intermingling mostly
at the edges. (e) Genetic material residing near the nuclear periphery has been correlated with gene silencing and gene activity. One theme that stands
out is that regions of the chromosome that interact with the lamina and the nuclear inner membrane are largely inactive in both mammals and yeast,
whereas loci that interact with the components of the nuclear pore appear to be transcriptionally active.
locus. Another interesting example is the regulation of
olfactory receptor genes. Dual RNA and DNA FISH
revealed that the expression of a specific olfactory gene
is accompanied by inter-chromosomal or intra-chromoso-
mal interactions between the active gene and a genomic
region on chromosome 14 containing an enhancer
sequence, referred to as the H element [28].
Recently, two different studies showed that inter-chro-
mosomal interactions may involve several factors and can
be induced upon exposure to specific stimuli or upon viral
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infection. The dynamics of gene association with tran-
scription factories was investigated during immediate
early gene induction in mouse B lymphocytes and was
shown to result in a rapid relocation of the Myc proto-
oncogene on chromosome 15 to the same factory that
transcribed the Igh gene located on chromosome 12 [29].
The study on the investigation of the interferon (IFN-
beta) gene-locus upon viral infection reported that the
stochastic and monoallelic expression of the IFN-beta
gene depends on inter-chromosomal associations with
distinct genetic loci that could mediate binding of the
imensions and its impact on genome evolution, Curr Opin Genet Dev (2008), doi:10.1016/
Current Opinion in Genetics & Development 2008, 18:1–12
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Figure 3
The interplay between spatial component in gene regulation and genome evolution, normal physiology, and disease states. *Although several factors
(e.g. functional relatedness of genes, replication origin sites, etc.) are known to influence genome organization, several studies clearly provide support
that transcriptional regulation is an important factor. +Position effect is defined as a change in the level of gene expression brought about by an
alteration in the position of the gene relative to its normal chromosomal environment, but not associated with an intragenic mutation or deletion.
consequences of repositioning the immunoglobulin loci
in mouse fibroblasts to the nuclear periphery supports
the notion that such molecular interactions may be a
mechanism to limit the accessibility to proteins that
facilitate recombination or transcription [54�].
While the nuclear periphery has been generally associ-
ated with repressed genes, several studies have shown a
correlation with active genes being associated with com-
ponents of the nuclear pore complexes (NPCs), which
serve as gates for the transport of molecules between the
nucleus and cytoplasm. ChIP experiments in yeast for
NPC components revealed an enrichment for active
genes [55]. Several inducible genes such as INO1,
HXK1, GAL1, GAL2, and HSP104 become stably posi-
tioned at the nuclear periphery when activated and
remain there after the transcription is shut off [55–58].
In the case of Gal1 and Ino1, the relocalization to pores
was found to be dependent upon the SAGA acetyl-trans-
ferase complex [58,59]. In humans and Drosophila, the
MSL complex can recruit transcriptionally active loci to
the nuclear pore [60], although another study revealed
that the association of silent genes is just as likely as for
active genes [61]. Most of these results have to be
reconciled with the observation that many (if not most)
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transcribed genes, in both yeast [62] and mammals [63],
do not associate stably with pores. Despite this, one
common theme that is emerging is a tendency for the
inner nuclear membrane to be associated with less active
genes, whereas the NPCs tend to associate with tran-
scriptionally active loci, at least in yeast, possibly in order
to facilitate efficient transport of mRNAs (Figure 2e).
Implications for genome evolutionGiven that eukaryotic gene regulation involves several
events, including the spatial association between differ-
ent genomic loci and micro-compartmentalization within
the nuclear space to be coordinated in space and time, this
raises a fundamental question: have the spatial processes
involved in gene regulation constrained genome evol-
ution? If so, has this affected (i) the way in which genes
are organized on the chromosomes (ii) the evolution of
gene expression patterns between species and (iii) the
evolution of gene regulatory networks underlying specific
phenotypes? There are now several examples which
provide evidence that all of this has happened.
Computational analyses of genome sequence data and
gene expression datasets have revealed a general prin-
ciple that is applicable to several organisms: gene order is
imensions and its impact on genome evolution, Curr Opin Genet Dev (2008), doi:10.1016/
Current Opinion in Genetics & Development 2008, 18:1–12
Eukaryotic gene regulation and its impact on genome evolution Madan Babu et al. 9
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aging process; cells harboring mutant lamin proteins have
altered nuclear morphology and display increased geno-
mic instability because of perturbation of the DNA
damage response and repair pathway [89,90]. For an
excellent account of how the disruption of long-range
control of gene expression could result in disease, please
see a recent review by Kleinjan and van Heyningen
[91��].
Conclusions and outlookAlthough it is clear that the spatial components have been
exploited in eukaryotic gene regulation, its prevalence in
a genome, its occurrence in different organisms and how it
affects genome organization and evolution are only now
being addressed in detail. Future experiments from sev-
eral model systems coupled with analysis of genome-wide
datasets [92,93] are likely to provide insights into the
prevalence and universality of these mechanisms and
their impact on genome evolution.
Experimental advances in microscopy (e.g. multicolor
immuno-FISH [94] and thin section cryo-FISH [95])
and innovative techniques (e.g. magnetic nanoparticles
[96]) could allow to accelerate such studies in different
model organisms, cell types, different stages of develop-
ment such as cellular differentiation and in disease cell
types. With advances in high-throughput techniques,
such as ChIP-seq and variants of 3C, it is now possible
to investigate the interaction between different loci
within the nucleus at high resolution (Table 1). Such
studies will not only provide a deeper understanding of
the principles that govern long-range interactions but will
also facilitate generation of a physical map of the network
of interaction between different genomic loci within the
eukaryotic nucleus.
This is an exciting time for computational biologists who
aim to understand the impact of spatial component in
gene regulation on genome organization, evolution of
gene expression, and regulatory networks. New directions
in this area include objective treatment of the data by
developing statistical models at various levels of resol-
ution within the hierarchical framework of gene regula-
tion, 3D network representations of interacting loci in
different cell types, computational procedures for inte-
grating diverse datasets and comparative analysis across
different organisms [15,97–102] (Table 1). Such advances
can have direct applications in genetic engineering exper-
iments and gene therapy. For instance, describing the
map of spatial interactions between genomic loci in
higher eukaryotes will have implications in gene therapy
and in rationally identifying suitable sites to incorporate
reporter genes while producing transgenic organisms.
While the advances in experimental and computational
approaches provide new roads to address these problems,
we believe that a combined approach will accelerate our
Please cite this article in press as: Madan Babu M, et al. Eukaryotic gene regulation in three d
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efforts and take us closer towards understanding the
contribution of the spatial component for gene regulation
in different cell types, disease states, development, and
ultimately genome evolution.
AcknowledgementsMMB and SCJ acknowledge MRC-LMB. SCJ acknowledges support fromCCT and MMB thanks Darwin College and Schlumberger Ltd for generoussupport. AP and IS thank the MRC-CSC for support. IS acknowledgesfunding from Fundacao para a Ciencia eTecnologia (SFRH/BD/33205/2007). We thank K Weber, A Wuster, R Janky, H Braberg, D Jani, DRhodes, A Emili, M Murthy, V Pisupati, A Cristino, L Costa, S Michnick, ATravers, and A Klug for providing comments on this manuscript.
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The authors report that the stochastic and monoallelic expression of theIFN-beta gene depends on inter-chromosomal associations with threeidentified genetic loci that could mediate binding of the transcriptionfactor NF-kappaB to the IFN-beta enhancer, thus triggering enhanceo-some assembly and activation of transcription from this allele.
31.��
Augui S, Filion GJ, Huart S, Nora E, Guggiari M, Maresca M,Stewart AF, Heard E: Sensing X chromosome pairs before X
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The authors demonstrate homologous associations driven by a novel X-pairing region (Xpr) of the Xic and propose that they enable cells to sensewhen more than one X chromosome is present and to coordinatereciprocal Xist/Tsix expression.
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41. Kupper K, Kolbl A, Biener D, Dittrich S, von Hase J, Thormeyer T,Fiegler H, Carter NP, Speicher MR, Cremer T et al.: Radialchromatin positioning is shaped by local gene density, not bygene expression. Chromosoma 2007, 116:285-306.
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Kosak ST, Scalzo D, Alworth SV, Li F, Palmer S, Enver T, Lee JS,Groudine M: Coordinate gene regulation during hematopoiesisis related to genomic organization. PLoS Biol 2007, 5:e309.
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It is shown here that identical GFP reporter constructs integrated at 90different chromosomal positions obtain expression levels that corre-spond to the activity of the domains of integration. 3D-FISH showedthat active domains of integration have a more open chromatin structurethan integration domains with weak activity. On the basis of theseobservations, the authors propose the existence of a novel domain-wideregulatory mechanism that, together with transcription factors, exerts adual control over gene transcription.
76.��
Xiao H, Jiang N, Schaffner E, Stockinger EJ, van der Knaap E: Aretrotransposon-mediated gene duplication underliesmorphological variation of tomato fruit. Science 2008,319:1527-1530.
An excellent study which shows that a retrotransposon-mediated changein genomic context of a key regulator, SUN, resulted in an alteredexpression level relative to that of the ancestral state, thereby resultingin variation in tomato fruit shape.
77. Doebley JF, Gaut BS, Smith BD: The molecular genetics of cropdomestication. Cell 2006, 127:1309-1321.
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78. Otto SP: The evolutionary consequences of polyploidy. Cell2007, 131:452-462.
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Janga S, Collado-Vides J, Madan Babu M: Transcriptionalregulation constrains the organization of genes on eukaryoticchromosomes. Proc Natl Acad Sci U S A 2008, 105:15761-15766.
The authors present evidence for the existence of a higher order orga-nization of genes across and within chromosomes that is constrained bytranscriptional regulation. They suggest that specific organization ofgenes that allowed for efficient control of transcription within the nuclearspace has been selected during evolution.
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Brianna Caddle L, Grant JL, Szatkiewicz J, van Hase J, Shirley BJ,Bewersdorf J, Cremer C, Arneodo A, Khalil A, Mills KD:Chromosome neighborhood composition determinestranslocation outcomes after exposure to high-dose radiationin primary cells. Chromosome Res 2007, 15:1061-1073.
It is shown that chromosomal territory (CT) neighborhoods compriseheterologous chromosomes, within which inter-CT distances directlyrelate to translocation partner choice. Their findings demonstrate thatinterphase chromosome arrangement is a principal factor in genomicinstability outcomes in primary lymphocytes, providing a structural con-text for understanding the biological effects of radiation exposure, and themolecular etiology of tumor-specific translocation patterns.
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89. Liu B, Wang J, Chan KM, Tjia WM, Deng W, Guan X, Huang JD,Li KM, Chau PY, Chen DJ et al.: Genomic instability inlaminopathy-based premature aging. Nat Med 2005,11:780-785.
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Kleinjan DA, van Heyningen V: Long-range control of geneexpression: emerging mechanisms and disruption in disease.Am J Hum Genet 2005, 76:8-32.
An excellent and timely review providing an account of several humandiseases which arise owing to mutations that disrupt long-range controlof gene expression.
92. Babu MM, Balaji S, Iyer LM, Aravind L: Estimating the prevalenceand regulatory potential of the telomere looping effect in yeasttranscription regulation. Cell Cycle 2006, 5:2354-2363.
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96. Kanger JS, Subramaniam V, van Driel R: Intracellularmanipulation of chromatin using magnetic nanoparticles.Chromosome Res 2008, 16:511-522.
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98. Dodd IB, Micheelsen MA, Sneppen K, Thon G: Theoreticalanalysis of epigenetic cell memory by nucleosomemodification. Cell 2007, 129:813-822.
99. Bon M, Marenduzzo D, Cook PR: Modeling a self-avoidingchromatin loop: relation to the packing problem, action-at-a-distance, and nuclear context. Structure 2006, 14:197-204.
100. Balaji S, Iyer LM, Babu MM, Aravind L: Comparison oftranscription regulatory interactions inferred from high-throughput methods: what do they reveal? Trends Genet 2008,24:319-323.
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imensions and its impact on genome evolution, Curr Opin Genet Dev (2008), doi:10.1016/