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SPECIAL AT-RICH SEQUENCE-BINDING PROTEIN 2; SATB2

SPECIAL AT-RICH SEQUENCE-BINDING PROTEIN 2; SATB2

Alternative titles; symbolsKIAA1034HGNC Approved Gene Symbol: SATB2Cytogenetic location: 2q33.1 Genomic coordinates (GRCh38): 2:199,269,499-199,471,265 (from...

Alternative titles; symbols

  • KIAA1034

HGNC Approved Gene Symbol: SATB2

Cytogenetic location: 2q33.1 Genomic coordinates (GRCh38): 2:199,269,499-199,471,265 (from NCBI)

▼ Description
The SATB2 gene encodes a nuclear matrix DNA-binding protein that specifically binds to genomic nuclear matrix attachment regions and participates in transcription regulation and chromatin remodeling (summary by Leoyklang et al., 2013).

▼ Cloning and Expression
By sequencing clones obtained from a size-fractionated fetal brain cDNA library, Kikuno et al. (1999) cloned SATB2, which they designated KIAA1034. The deduced 761-amino acid protein shares 61% identity with SATB1 (602075). RT-PCR ELISA detected high expression in adult brain, moderate expression in fetal brain, and weak expression in adult liver, kidney, and spinal cord and in select brain regions, including amygdala, corpus callosum, caudate nucleus, and hippocampus. Little to no expression was detected in all other tissues and individual brain regions examined.

Dobreva et al. (2003) cloned mouse Satb2. The deduced 733-amino acid protein contains 2 central nuclear matrix attachment region (MAR) domains and a C-terminal homeobox domain. Unlike Satb1, Satb2 contains 2 consensus SUMO acceptor sites. Northern blot analysis detected Satb2 expression predominantly in brain and kidney, although transcripts of different sizes were detected at lower abundance in thymus and testis. Expression was also detected in several pre-B cell lines. Fluorescence-tagged Satb2 localized to the nuclear matrix of transfected human embryonic kidney cells.

In the developing embryonic mouse, Rainger et al. (2014) found expression of Satb2 in craniofacial tissues, including the palatal shelves, tongue, and mandible.

▼ Gene Structure
Leoyklang et al. (2013) stated that the SATB2 gene contains 11 exons.

▼ Gene Function
Dobreva et al. (2003) presented evidence that mouse Satb2 bound to the MAR of the immunoglobulin mu locus (147020) in pre-B cells and enhanced gene expression. Satb2 could be modified by the SUMO E3 ligase, Pias1 (603566). Mutations of the Satb2 SUMO conjugation sites enhanced its activation potential and its association with endogenous MARs in vivo, whereas N-terminal fusions with SUMO1 (601912) or SUMO3 (602231) decreased Satb2-mediated gene activation. Sumoylation also altered the targeting of Satb2 to the nuclear periphery, suggesting that this reversible modification may modulate the subnuclear DNA localization of SATB2.

Using chromatin immunoprecipitation (ChIP) analysis with primary mouse osteoblasts and electrophoretic mobility shift analysis (EMSA), Dobreva et al. (2006) found that mouse Satb2 bound to the EII enhancer of Hoxa2 (604685), an inhibitor of bone formation and regulator of branchial arch patterning. Satb2 repressed activity of the Hoxa2 EII enhancer in transfected osteoblasts. ChIP analysis and EMSA showed that Satb2 bound directly to the promoter of Bsp (IBSP; 147563) and indirectly to the promoter of Ocn (BGLAP; 112260), both of which are involved osteoblast differentiation. Expression of Satb2 in mouse myoblasts induced expression of endogenous Bsp directly and enhanced Atf4 (604064)- and Runx2 (600211)-induced expression of endogenous Ocn. Further analyses showed that Satb2 physically interacted with both Atf4 and Runx2, resulting in enhanced DNA binding and transactivation by these transcription factors. Satb2/Atf4 and Satb2/Runx2 double-heterozygous mutant mice displayed a severe defect in bone development that was not observed in single-heterozygous mutant mice, demonstrating that Satb2 interacted genetically with both Atf4 and Runx2 Dobreva et al. (2006) concluded that SATB2 represents a node of a transcriptional network underlying skeletal development in which SATB2 acts as both a transcriptional regulator by binding DNA directly and as a scaffolding protein that recruits other DNA-binding proteins to specific subnuclear sites.

Using immunofluorescence studies, Leoyklang et al. (2013) showed that both wildtype and mutant R239X (608148.0001) SATB2 proteins were expressed and localized to the nucleus in HEK293 cells. The mutant protein retained the ability to dimerize with the wildtype protein. Luciferase expression studies demonstrated that wildtype SATB2 inhibited transcriptional activity, whereas mutant SATB2 was similar to empty vector. Overall, the findings suggested that mutant SATB2 has a dominant-negative effect on the wildtype protein. Since patients with mutation in the SATB2 gene have overlapping features with patients with MRXS14 (300676) carrying mutations in the UPF3B gene (300298), Leoyklang et al. (2013) explored whether the 2 genes could function in the same signaling pathway. Cells derived from the patient with mutant SATB2 as well as siRNA knockdown of SATB2 were associated with significantly decreased expression of UPF3B. Chromatin immunoprecipitation studies demonstrated that SATB2 binds to the UPF3B promoter, and a luciferase reporter assay confirmed that SATB2 expression significantly activates gene transcription using the UPF3B promoter. The findings associated SATB2 to the nonsense-mediated mRNA decay pathway.

▼ Mapping
By analysis of a YAC/BAC contig, Machado et al. (2000) mapped the SATB2 gene to chromosome 2q33.

▼ Molecular Genetics
In 1 of 59 unrelated Thai patients with craniofacial dysmorphism with or without mental retardation, Leoyklang et al. (2007) identified a heterozygous de novo mutation in the SATB2 gene (R239X; 608148.0001). The patient had isolated cleft palate, generalized osteoporosis, and profound mental retardation, consistent with Glass syndrome (612313). The findings suggested a role for the SATB2 gene in malformation syndromes involving craniofacial patterning and brain development.

Docker et al. (2014) identified a de novo heterozygous R239X mutation (rs137853127) in a 3-year-old girl with cleft palate, severely delayed speech, hypotonia, and mental retardation. The mutation was found by whole-exome sequencing and confirmed by Sanger sequencing. Dysmorphic facial features included hypotonic face with hypersalivation, hypertelorism, downslanting palpebral fissures, long eyelashes, upturned nose with broad tip, microretrognathia, long philtrum, low-set and posteriorly rotated ears, and crowded teeth. She also had severe sleeping disturbances, restlessness/hyperactivity, and recurrent temper tantrums. Mutant mRNA was present in the patient's cells, suggesting that it does not undergo nonsense-mediated mRNA decay. Docker et al. (2014) concluded that the SATB2 gene is essential for normal craniofacial patterning and cognitive development.

In a 20-year-old man with Glass syndrome, Lieden et al. (2014) identified a de novo heterozygous intragenic duplication of the SATB2 gene (608148.0002). The duplication was found by array CGH analysis. Functional studies and studies of patient cells were not performed.

In a 10-year-old girl with Glass syndrome, Kaiser et al. (2015) identified a de novo heterozygous intragenic duplication of the SATB2 gene (608148.0003), predicted to result in haploinsufficiency. The patient was born of unrelated parents and conceived via intracytoplasmic sperm injection.

▼ Cytogenetics
Brewer et al. (1999) reported 2 unrelated girls with cleft palate, facial dysmorphism, and mildly delayed development and learning difficulties associated with balanced, de novo cytogenetic rearrangements involving the same region of 2q. Molecular cytogenetic analyses localized both translocation breakpoints between markers D2S311 and D2S116 on chromosome 2q32. Facial features included prominent nasal bridge with underhanging columella, small mouth with distinctive upper lip, and long, slender fingers. FitzPatrick et al. (2003) determined that 1 of the breakpoints in the 2 girls reported by Brewer et al. (1999) localized to intron 2 of SATB2, and the other breakpoint was located 130 kb 3-prime to the SATB2 polyadenylation signal, within a conserved region of noncoding DNA. Whole-mount in situ hybridization to mouse embryos showed site- and stage-specific expression of SATB2 in the developing palate. Despite the strong evidence supporting an important role for SATB2 in palatal development, mutation analysis of an additional 70 unrelated patients with isolated cleft palate did not reveal any coding region variants.

Rosenfeld et al. (2009) reported 3 unrelated patients with small heterozygous deletions of chromosome 2q33.1, ranging from 173.1 to 185.2 kb, that affected only the SATB2 gene. Parental samples from the mother were available for only 2 patients, and neither mother carried the deletion; parental samples were not available for the third patient. All patients had severe developmental delay, mental retardation, and tooth anomalies, but other features varied. Dentofacial anomalies included delayed primary dentition and micrognathia in 1 patient; cleft palate, crowded teeth, and small mandible in the second; and fused mandibular central incisors without cleft palate in the third. Two patients had behavioral abnormalities and mild dysmorphic features. Rosenfeld et al. (2009) concluded that haploinsufficiency for SATB2 is responsible for some of the clinical features associated with the 2q32-q33 deletion syndrome (612313).

Using comparative genomics, Rainger et al. (2014) identified 3 different functional enhancing cis-regulatory elements (CREs) in the gene desert between the PLCL1 (600597) and SATB2 genes, 3-prime to SATB2. Sites within these CREs were shown to bind the SOX9 (608160) transcription factor in cells derived from the mouse embryonic pharyngeal arch. Studies in zebrafish showed that CRE2 could drive SATB2-like expression in the embryonic craniofacial region, and this expression could be eliminated by mutating the SOX9-binding site. These findings suggested that the translocation breakpoints identified in patients with craniofacial defects disrupt the long-range cis regulation of SATB2 by SOX9, resulting in functional haploinsufficiency of SATB2.

Bengani et al. (2017) reported 19 different SATB2 mutations, of which 11 were loss-of-function and 8 missense (e.g., 608148.0004-608148.0006). SATB2 nuclear mobility was mutation-dependent. The clinical features in individuals with missense variants were indistinguishable from those with loss-of-function variants. Bengani et al. (2017) found that when mutant SATB2 protein is produced, the protein appears functionally inactive with a disrupted pattern of chromatin or matrix association.

▼ Animal Model
The identification of SATB2 as a candidate gene responsible for the craniofacial dysmorphologies associated with deletions and translocations at 2q32-q33, 1 of only 3 regions of the genome for which haploinsufficiency has been significantly associated with isolated cleft palate, led Britanova et al. (2006) to investigate the in vivo functions of murine Satb2. They found that, similar to the way in which SATB2 is perceived to act in humans, craniofacial defects due to haploinsufficiency of Satb2, including cleft palate (in approximately 25% of cases), phenocopy those seen with 2q32-q33 deletions and translocations in humans. Full functional loss of Satb2 resulted in amplification of these defects and led to increased apoptosis in the craniofacial mesenchyme where Satb2 is usually expressed and of changes in the pattern of expression of 3 genes implicated in the regulation of craniofacial development in humans and mice: Pax9 (167416), Alx4 (605420), and Msx1 (142983). The Satb2 dosage sensitivity in craniofacial development was conspicuous; along with its control of cell survival, pattern of expression, and reversible functional modification by sumoylation, the dosage sensitivity suggested that Satb2/SATB2 function in craniofacial development may prove to be more profound than had been previously thought. Because jaw development is Satb2 dosage-sensitive, the regulators of Satb2 expression and posttranslational modification become of critical importance both ontogenetically and evolutionarily, especially since such regulators plausibly play undetected roles in jaw and palate development and in the etiology of craniofacial malformations.

Dobreva et al. (2006) found that Satb2 +/- mice were phenotypically normal and fertile. Satb2 -/- mice were obtained at the expected mendelian frequency, but they died immediately after birth. Satb2 -/- embryos showed multiple craniofacial defects, including truncation of the mandible, shortening of the nasal and maxillary bones, malformations of the hyoid bone, and cleft palate. At later stages, Satb2 -/- embryos exhibited a delay in bone formation. Satb2 -/- osteoblasts showed a marked decrease in terminal differentiation, as determined by an absence of Bsp and Ocn expression. Quantitative RT-PCR showed decreased expression of Lhx7 (LHX8; 604425) and increased expression of several Hox genes, including Hoxa2, in cells from the head and branchial arch regions of Satb2 -/- mice. In situ hybridization revealed altered expression of Lhx7, Msx1, and Hoxa2 in Satb2 -/- mice. Microarray analysis showed deregulation of multiple genes, including Lhx7 and Hoxa2, in Satb2 -/- calvarial osteoblasts, and RT-PCR and in situ hybridization confirmed upregulation of Hoxa2 in Satb2 -/- calvarial osteoblasts. Loss of Hoxa2 rescued the calvarial bone formation defect in Satb2 -/- mice, suggesting that repression of HOXA2 by SATB2 is important for normal osteoblast differentiation.

▼ ALLELIC VARIANTS ( 6 Selected Examples):

.0001 GLASS SYNDROME
SATB2, ARG239TER (rs137853127)
In a Thai man with Glass syndrome (GLASS; 612313), characterized by cleft palate, gum hyperplasia, slight micrognathia, generalized osteoporosis, and mental retardation, Leoyklang et al. (2007) identified a heterozygous de novo 715C-T transition in exon 6 of the SATB2 gene, resulting in an arg239-to-ter (R239X) substitution. CT scan of the facial bones revealed multiple anomalies, including asymmetric mandibular hypoplasia, wide mandibular angles, anterior overbite of the upper teeth with marked anterior-pointing incisors, midline cleft palate, abnormal sinuses, short zygomatic arches, and flattened mandibular condylar heads. The patient also had profound mental retardation, seizures, and a jovial personality. Expression studies showed that the truncated protein was expressed. The mutation was not identified in 210 control alleles.

Using immunofluorescence studies, Leoyklang et al. (2013) showed that the mutant R239X protein localized to the nucleus in HEK293 cells and was able to dimerize with the wildtype protein. Luciferase expression studies demonstrated that wildtype SATB2 inhibited transcriptional activity, whereas mutant SATB2 was similar to empty vector. Overall, the findings suggested that mutant SATB2 has a dominant-negative effect on the wildtype protein.

Docker et al. (2014) identified a de novo heterozygous R239X mutation (rs137853127) in a 3-year-old girl with cleft palate, severely delayed speech, hypotonia, and mental retardation. The mutation was found by whole-exome sequencing and confirmed by Sanger sequencing. Dysmorphic facial features included hypotonic face with hypersalivation, hypertelorism, downslanting palpebral fissures, long eyelashes, upturned nose with broad tip, microretrognathia, long philtrum, low-set and posteriorly rotated ears, and crowded teeth. She also had severe sleeping disturbances, restlessness/hyperactivity, and recurrent temper tantrums. Mutant mRNA was present in the patient's cells, suggesting that it does not undergo nonsense-mediated mRNA decay.

.0002 GLASS SYNDROME
SATB2, 35-KB DUP, EX5-7
In a 20-year-old man with Glass syndrome (GLASS; 612313), Lieden et al. (2014) identified a de novo heterozygous intragenic duplication (chr2:200,233,354-200,255,458, GRCH37) of the SATB2 gene; the breakpoints were intronic and resulted in the duplication of exons 5, 6, and 7. The duplication was found by array CGH analysis. Functional studies and studies of patient cells were not performed. The phenotype in this patient was similar to that observed in other patients with this disorder.

.0003 GLASS SYNDROME
SATB2, 54-KB DUP, EX3
In a 10-year-old German girl with Glass syndrome (GLASS; 612313), Kaiser et al. (2015) identified a de novo heterozygous 54-kb duplication (c.169+9407_347-10003dup, NM_001172509.1) of exon 3 in the SATB2 gene. Sanger sequence analysis and studies of patient transcripts confirmed that the duplication was in tandem and resulted in an in-frame duplication of exon 3. The patient was born of unrelated parents and conceived via intracytoplasmic sperm injection. Further molecular studies were not performed; the authors postulated that the mutation resulted in haploinsufficiency.

.0004 GLASS SYNDROME
SATB2, ARG389CYS
In a female (patient 271044) with Glass syndrome (GLASS; 612313) characterized by severe intellectual disability and a cleft palate due to Pierre-Robin sequence, Bengani et al. (2017) identified a de novo heterozygous C-to-T transition at nucleotide c.1165 (c.1165C-T, ENST00000417098) of the SATB2 gene, resulting in an arginine-to-cysteine substitution at codon 386 (R389C), in the CUT1 domain. Hamosh (2018) noted that the c.1165C-T variant was not present in the ExAC or gnomAD databases (June 14, 2018). Transient transfection of mutant constructs revealed that SATB2 nuclear mobility was increased by this mutation.

.0005 GLASS SYNDROME
SATB2, GLY515SER
In a male (patient 262240) with Glass syndrome (GLASS; 612313) with severe intellectual disability but absent cleft palate, Bengani et al. (2017) identified a de novo heterozygous G-to-A transition at nucleotide c.1543 (c.1543G-A, ENST00000417098) of the SATB2 gene resulting in a glycine-to-serine substitution at codon 515 (G515S), between the CUT2 and HOX domains. Hamosh (2018) noted that the c.1543G-A variant was not present in the ExAC or gnomAD databases (June 14, 2018). Transient transfection of mutant constructs revealed that this variant resulted in decreased nuclear mobility of SATB2. This patient was reported in the Deciphering Developmental Disorders Study (2015) with clinical features of seizures; delayed speech and language development; frontal bossing; deeply set eyes; abnormal hair pattern; strabismus; and smooth philtrum.

.0006 GLASS SYNDROME
SATB2, GLU566LYS
In a female (patient 264840) with Glass syndrome (GLASS; 612313), Bengani et al. (2017) identified a de novo heterozygous G-to-A transition at nucleotide c.1696 (c.1696G-A, ENST00000417098) of the SATB2 gene resulting in a glutamic acid-to-lysine substitution at codon 566 (E566K). Hamosh (2018) noted that the c.1696G-A variant was not present in the ExAC or gnomAD databases (June 14, 2018). The mutation occurred between the CUT2 and HOX domains; transient transfection of mutant constructs revealed that this variant resulted in reduced SATB2 nuclear mobility. This variant also appeared as Gln566Lys in the text and figures of the report by Bengani et al. (2017).

Tags: 2q33.1