Han, H.-J.; Russo, J.; Kohwi, Y. & Kohwi-Shigematsu, T.: SATB1 reprogrammes gene expression to promote breast tumour growth
nd metastasis.. In: Nature 452 (2008), Nr. 7184, S. 187-93
[Volltext]
Mechanisms underlying global changes in gene expression during tumour
rogression are poorly understood. SATB1 is a genome organizer that
ethers multiple genomic loci and recruits chromatin-remodelling
nzymes to regulate chromatin structure and gene expression. Here
e show that SATB1 is expressed by aggressive breast cancer cells
nd its expression level has high prognostic significance (P < 0.0001),
ndependent of lymph-node status. RNA-interference-mediated knockdown
f SATB1 in highly aggressive (MDA-MB-231) cancer cells altered the
xpression of >1,000 genes, reversing tumorigenesis by restoring
reast-like acinar polarity and inhibiting tumour growth and metastasis
n vivo. Conversely, ectopic SATB1 expression in non-aggressive (SKBR3)
ells led to gene expression patterns consistent with aggressive-tumour
henotypes, acquiring metastatic activity in vivo. SATB1 delineates
pecific epigenetic modifications at target gene loci, directly upregulating
etastasis-associated genes while downregulating tumour-suppressor
enes. SATB1 reprogrammes chromatin organization and the transcription
rofiles of breast tumours to promote growth and metastasis; this
s a new mechanism of tumour progression.

Ko, M.; Sohn, D. H.; Chung, H. & Seong, R. H.: Chromatin remodeling, development and disease.. In: Mutat Res 647 (2008), Nr. 1-2, S. 59-67
[Volltext]
Development is a stepwise process in which multi-potent progenitor
ells undergo lineage commitment, differentiation, proliferation
nd maturation to produce mature cells with restricted developmental
otentials. This process is directed by spatiotemporally distinct
ene expression programs that allow cells to stringently orchestrate
ntricate transcriptional activation or silencing events. In eukaryotes,
hromatin structure contributes to developmental progression as a
lueprint for coordinated gene expression by actively participating
n the regulation of gene expression. Changes in higher order chromatin
tructure or covalent modification of its components are considered
o be critical events in dictating lineage-specific gene expression
uring development. Mammalian cells utilize multi-subunit nuclear
omplexes to alter chromatin structure. Histone-modifying complex
atalyzes covalent modifications of histone tails including acetylation,
ethylation, phosphorylation and ubiquitination. ATP-dependent chromatin
emodeling complex, which disrupts histone-DNA contacts and induces
ucleosome mobilization, requires energy from ATP hydrolysis for
ts catalytic activity. Here, we discuss the diverse functions of
TP-dependent chromatin remodeling complexes during mammalian development.
n particular, the roles of these complexes during embryonic and
ematopoietic development are reviewed in depth. In addition, pathological
onditions such as tumor development that are induced by mutation
f several key subunits of the chromatin remodeling complex are discussed,
ogether with possible mechanisms that underlie tumor suppression
y the complex.

Richon, V. M.: A new path to the cancer epigenome.. In: Nat. Biotechnol. 26 (2008), Nr. 6, S. 655-6
[Volltext]

Yaragatti, M.; Basilico, C. & Dailey, L.: Identification of active transcriptional regulatory modules by the
unctional assay of DNA from nucleosome-free regions.. In: Genome Res 18 (2008), Nr. 6, S. 930-938
[Volltext]
The identification of transcriptional regulatory modules within mammalian
enomes is a prerequisite to understanding the mechanisms controlling
egulated gene expression. While high-throughput microarray- and
equencing-based approaches have been used to map the genomic locations
f sites of nuclease hypersensitivity or target DNA sequences bound
y specific protein factors, the identification of regulatory elements
sing functional assays, which would provide important complementary
ata, has been relatively rare. Here we present a method that permits
he functional identification of active transcriptional regulatory
odules using a simple procedure for the isolation and analysis of
NA derived from nucleosome-free regions (NFRs), the 2% of the cellular
enome that contains these elements. The more than 100 new active
egulatory DNAs identified in this manner from F9 cells correspond
o both promoter-proximal and distal elements, and display several
eatures predicted for endogenous transcriptional regulators, including
ocalization within DNase-accessible chromatin and CpG islands, and
roximity to expressed genes. Furthermore, comparison with published
hIP-seq data of ES-cell chromatin shows that the functional elements
e identified correspond with genomic regions enriched for H3K4me3,
histone modification associated with active transcriptional regulatory
lements, and that the correspondence of H3K4me3 with our promoter-distal
lements is largely ES-cell specific. The majority of the distal
lements exhibit enhancer activity. Importantly, these functional
NA fragments are an average 149 bp in length, greatly facilitating
uture applications to identify transcription factor binding sites
ediating their activity. Thus, this approach provides a tool for
he high-resolution identification of the functional components of
ctive promoters and enhancers.

Davuluri, R. V.: Bioinformatics tools for modeling transcription factor target genes
nd epigenetic changes.. In: Methods Mol Biol 408 (2007), S. 129-151

The combinatorial control of gene regulatory switches involves both
ranscription factor (TF) complexes and associated epigenetic modifications
o the chromatin template. The novel high-throughput technologies,
uch as Chromatin ImmunoPrecipitation ChIP-chip, have enabled genome-wide
n vivo identification of TF target regulatory regions and related
pigenetic modifications, which led to the view of highly dynamic
F-DNA interactions in activated or repressed promoters. Consequently,
odeling and elucidating the combinatorial interaction of TFs and
orresponding cis-regulatory modules in target promoters is of paramount
nterest. An estimated 5% of the genes in mammalian genomes code
or TF proteins, and computational modeling of cis-regulatory logic
ould rapidly increase the pace of experimental confirmation of TF
arget promoters at the bench. The purpose of this chapter is to
iscuss the use of different bioinformatics tools for predicting
he target genes of TFs of interest in mammalian genomes, and the
pplication of these methods in the analysis of ChIP-chip experimental
ata. The author describes most commonly used databases and prediction
rograms that are available on the World Wide Web and demonstrate
he use of some of these programs by an example. A list of these
rograms is provided along with their web Uniform Resource Locator
URLs) and guidelines for successful application are suggested.

Cai, S.; Lee, C. C. & Kohwi-Shigematsu, T.: SATB1 packages densely looped, transcriptionally active chromatin
or coordinated expression of cytokine genes.. In: Nat. Genet. 38 (2006), Nr. 11, S. 1278-88
[Volltext]
SATB1 (special AT-rich sequence binding protein 1) organizes cell
ype-specific nuclear architecture by anchoring specialized DNA sequences
nd recruiting chromatin remodeling factors to control gene transcription.
e studied the role of SATB1 in regulating the coordinated expression
f Il5, Il4 and Il13, located in the 200-kb T-helper 2 (T(H)2) cytokine
ocus on mouse chromosome 11. We show that on T(H)2 cell activation,
ATB1 expression is rapidly induced to form a unique transcriptionally
ctive chromatin structure at the cytokine locus. In this structure,
hromatin is folded into numerous small loops, all anchored to SATB1
t their base. In addition, histone H3 is acetylated at Lys9 and
ys14, and the T(H)2-specific factors GATA3, STAT6 and c-Maf, the
hromatin-remodeling enzyme Brg1 and RNA polymerase II are all bound
cross the 200-kb region. Before activation, the T(H)2 cytokine locus
s already associated with GATA3 and STAT6, showing some looping,
ut these are insufficient to induce cytokine gene expression. Using
NA interference, we show that on cell activation, SATB1 is required
ot only for compacting chromatin into dense loops at the 200-kb
ytokine locus but also for inducing Il4, Il5, Il13 and c-Maf expression.
hus, SATB1 is a necessary determinant for the hitherto unidentified
igher-order, transcriptionally active chromatin structure that forms
n T(H)2 cell activation.

Bernstein, B. E.; Kamal, M.; Lindblad-Toh, K.; Bekiranov, S.; Bailey, D. K.; Huebert, D. J.; McMahon, S.; Karlsson, E. K.; Kulbokas, E. J.; Gingeras, T. R.; Schreiber, S. L. & Lander, E. S.: Genomic maps and comparative analysis of histone modifications in
uman and mouse.. In: Cell 120 (2005), Nr. 2, S. 169-81
[Volltext]
We mapped histone H3 lysine 4 di- and trimethylation and lysine 9/14
cetylation across the nonrepetitive portions of human chromosomes
1 and 22 and compared patterns of lysine 4 dimethylation for several
rthologous human and mouse loci. Both chromosomes show punctate
ites enriched for modified histones. Sites showing trimethylation
orrelate with transcription starts, while those showing mainly dimethylation
ccur elsewhere in the vicinity of active genes. Punctate methylation
atterns are also evident at the cytokine and IL-4 receptor loci.
he Hox clusters present a strikingly different picture, with broad
ysine 4-methylated regions that overlay multiple active genes. We
uggest these regions represent active chromatin domains required
or the maintenance of Hox gene expression. Methylation patterns
t orthologous loci are strongly conserved between human and mouse
ven though many methylated sites do not show sequence conservation
otably higher than background. This suggests that the DNA elements
hat direct the methylation represent only a small fraction of the
egion or lie at some distance from the site.

Seo, J.; Lozano, M. M. & Dudley, J. P.: Nuclear matrix binding regulates SATB1-mediated transcriptional repression.. In: J Biol Chem 280 (2005), Nr. 26, S. 24600-24609
[Volltext]
Special AT-rich binding protein 1 (SATB1) originally was identified
s a protein that bound to the nuclear matrix attachment regions
MARs) of the immunoglobulin heavy chain intronic enhancer. Subsequently,
ATB1 was shown to repress many genes expressed in the thymus, including
nterleukin-2 receptor alpha, c-myc, and those encoded by mouse mammary
umor virus (MMTV), a glucocorticoid-responsive retrovirus. SATB1
inds to MARs within the MMTV provirus to repress transcription.
o address the role of the nuclear matrix in SATB1-mediated repression,
series of SATB1 deletion constructs was used to determine protein
ocalization. Wild-type SATB1 localized to the soluble nuclear, chromatin,
nd nuclear matrix fractions. Mutants lacking amino acids 224-278
ad a greatly diminished localization to the nuclear matrix, suggesting
he presence of a nuclear matrix targeting sequence (NMTS). Transient
ransfection experiments showed that NMTS fusions to green fluorescent
rotein or LexA relocalized these proteins to the nuclear matrix.
ifficulties with previous assay systems prompted us to develop retroviral
ectors to assess effects of different SATB1 domains on expression
f MMTV proviruses or integrated reporter genes. SATB1 overexpression
epressed MMTV transcription in the presence and absence of functional
lucocorticoid receptor. Repression was alleviated by deletion of
he NMTS, which did not affect DNA binding, or by deletion of the
AR-binding domain. Our studies indicate that both nuclear matrix
ssociation and DNA binding are required for optimal SATB1-mediated
epression of the integrated MMTV promoter and may allow insulation
rom cellular regulatory elements.

Cai, S.; Han, H.-J. & Kohwi-Shigematsu, T.: Tissue-specific nuclear architecture and gene expression regulated
y SATB1.. In: Nat. Genet. 34 (2003), Nr. 1, S. 42-51
[Volltext]
Eukaryotic chromosomes are packaged in nuclei by many orders of folding.
ittle is known about how higher-order chromatin packaging might
ffect gene expression. SATB1 is a cell-type specific nuclear protein
hat recruits chromatin-remodeling factors and regulates numerous
enes during thymocyte differentiation. Here we show that in thymocyte
uclei, SATB1 has a cage-like 'network' distribution circumscribing
eterochromatin and selectively tethers specialized DNA sequences
nto its network. This was shown by fluorescence in situ hybridization
n wild-type and Satb1-null thymocytes using in vivo SATB1-bound
equences as probes. Many gene loci, including that of Myc and a
rain-specific gene, are anchored by the SATB1 network at specific
enomic sites, and this phenomenon is precisely correlated with proper
egulation of distant genes. Histone-modification analyses across
gene-enriched genomic region of 70 kb showed that acetylation of
istone H3 at Lys9 and Lys14 peaks at the SATB1-binding site and
xtends over a region of roughly 10 kb covering genes regulated by
ATB1. By contrast, in Satb1-null thymocytes, this site is marked
y methylation at H3 Lys9. We propose SATB1 as a new type of gene
egulator with a novel nuclear architecture, providing sites for
issue-specific organization of DNA sequences and regulating region-specific
istone modification.

Shannon, M. F.: A nuclear address with influence.. In: Nat. Genet. 34 (2003), Nr. 1, S. 4-6
[Volltext]

Liu, J.; Bramblett, D.; Zhu, Q.; Lozano, M.; Kobayashi, R.; Ross, S. R. & Dudley, J. P.: The matrix attachment region-binding protein SATB1 participates in
egative regulation of tissue-specific gene expression.. In: Mol Cell Biol 17 (1997), Nr. 9, S. 5275-5287

The nuclear matrix has been implicated in several cellular processes,
ncluding DNA replication, transcription, and RNA processing. In
articular, transcriptional regulation is believed to be accomplished
y binding of chromatin loops to the nuclear matrix and by the concentration
f specific transcription factors near these matrix attachment regions
MARs). A number of MAR-binding proteins have been identified, but
ew have been directly linked to tissue-specific transcription. Recently,
e have identified two cellular protein complexes (NBP and UBP) that
ind to a region of the mouse mammary tumor virus (MMTV) long terminal
epeat (LTR) previously shown to contain at least two negative regulatory
lements (NREs) termed the promoter-proximal and promoter-distal
REs. These NREs are absent from MMTV strains that cause T-cell lymphomas
nstead of mammary carcinomas. We show here that NBP binds to a 22-bp
equence containing an imperfect inverted repeat in the promoter-proximal
RE. Previous data showed that a mutation (p924) within the inverted
epeat elevated basal transcription from the MMTV promoter and destabilized
he binding of NBP, but not UBP, to the proximal NRE. By using conventional
nd affinity methods to purify NBP from rat thymic nuclear extracts,
e obtained a single major protein of 115 kDa that was identified
y protease digestion and partial sequencing analysis as the nuclear
atrix-binding protein special AT-rich sequence-binding protein 1
SATB1). Antibody ablation, distamycin inhibition of binding, renaturation
nd competition experiments, and tissue distribution data all confirmed
hat the NBP complex contained SATB1. Similar types of experiments
ere used to show that the UBP complex contained the homeodomain
rotein Cux/CDP that binds the MAR of the intronic heavy-chain immunoglobulin
nhancer. By using the p924 mutation within the MMTV LTR upstream
f the chloramphenicol acetyltransferase gene, we generated two strains
f transgenic mice that had a dramatic elevation of reporter gene
xpression in lymphoid tissues compared with reporter gene expression
n mice expressing wild-type LTR constructs. Thus, the 924 mutation
n the SATB1-binding site dramatically elevated MMTV transcription
n lymphoid tissues. These results and the ability of the proximal
RE in the MMTV LTR to bind to the nuclear matrix clearly demonstrate
he role of MAR-binding proteins in tissue-specific gene regulation
nd in MMTV-induced oncogenesis.

Nakagomi, K.; Kohwi, Y.; Dickinson, L. A. & Kohwi-Shigematsu, T.: A novel DNA-binding motif in the nuclear matrix attachment DNA-binding
rotein SATB1.. In: Mol. Cell. Biol. 14 (1994), Nr. 3, S. 1852-60

The nuclear matrix attachment DNA (MAR) binding protein SATB1 is a
equence context-specific binding protein that binds in the minor
roove, making virtually no contact with the DNA bases. The SATB1
inding sites consist of a special AT-rich sequence context in which
ne strand is well-mixed A's, T's, and C's, excluding G's
ATC sequences), which is typically found in clusters within different
ARs. To determine the extent of conservation of the SATB1 gene among
ifferent species, we cloned a mouse homolog of the human STAB1 cDNA
rom a cDNA expression library of the mouse thymus, the tissue in
hich this protein is predominantly expressed. This mouse cDNA encodes
764-amino-acid protein with a 98% homology in amino acid sequence
o the human SATB1 originally cloned from testis. To characterize
he DNA binding domain of this novel class of protein, we used the
ouse SATB1 cDNA and delineated a 150-amino-acid polypeptide as the
inding domain. This region confers full DNA binding activity, recognizes
he specific sequence context, and makes direct contact with DNA
t the same nucleotides as the whole protein. This DNA binding domain
ontains a novel DNA binding motif: when no more than 21 amino acids
t either the N- or C-terminal end of the binding domain are deleted,
he majority of the DNA binding activity is lost. The concomitant
resence of both terminal sequences is mandatory for binding. These
wo terminal regions consist of hydrophilic amino acids and share
omologous sequences that are different from those of any known DNA
inding motifs. We propose that the DNA binding region of SATB1 extends
ts two terminal regions toward DNA to make direct contact with DNA.