Role of the LIM domains in DNA recognition by the Lhx3 neuroendocrine transcription factor

Contrasting DNA-binding behaviour by ISL1 and LHX3 underpins differential gene targeting in neuronal cell specification

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The mechanisms by which ISL1 and LHX3 specify neuronal cell identity are unknown.

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EMSA/SPR data show ISL1 and LHX3 have markedly different DNA-binding behaviours.

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SAXS shows ISL1/LHX3:DNA complexes are flexible in nature.

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ISL1 binds DNA poorly but appears to modulate the DNA-binding specificity of LHX3.

The roles of ISL1 and LHX3 in the development of spinal motor neurons have been well established. Whereas LHX3 triggers differentiation into interneurons, the additional expression of ISL1 in developing neuronal cells is sufficient to redirect their developmental trajectory towards spinal motor neurons. However, the underlying mechanism of this action by these transcription factors is less well understood. Here, we used electrophoretic mobility shift assays (EMSAs) and surface plasmon resonance (SPR) to probe the different DNA-binding behaviours of these two proteins, both alone and in complexes mimicking those found in developing neurons, and found that ISL1 shows markedly different binding properties to LHX3. We used small angle X-ray scattering (SAXS) to structurally characterise DNA-bound species containing ISL1 and LHX3. Taken together, these results have allowed us to develop a model of how these two DNA-binding modules coordinate to regulate gene expression and direct development of spinal motor neurons.

The LIM protein complex establishes a retinal circuitry of visual adaptation by regulating Pax6 α-enhancer activity

The visual responses of vertebrates are sensitive to the overall composition of retinal interneurons including amacrine cells, which tune the activity of the retinal circuitry. The expression of Paired-homeobox 6 (PAX6) is regulated by multiple cis-DNA elements including the intronic α-enhancer, which is active in GABAergic amacrine cell subsets. Here, we report that the transforming growth factor ß1-induced transcript 1 protein (Tgfb1i1) interacts with the LIM domain transcription factors Lhx3 and Isl1 to inhibit the α-enhancer in the post-natal mouse retina. Tgfb1i1^-/- mice show elevated α-enhancer activity leading to overproduction of Pax6ΔPD isoform that supports the GABAergic amacrine cell fate maintenance. Consequently, the Tgfb1i1^-/- mouse retinas show a sustained light response, which becomes more transient in mice with the auto-stimulation-defective Pax6^ΔPBS/ΔPBS mutation. Together, we show the antagonistic regulation of the α-enhancer activity by Pax6 and the LIM protein complex is necessary for the establishment of an inner retinal circuitry, which controls visual adaptation.

DOI:http://dx.doi.org/10.7554/eLife.21303.001

The retina is a light-sensitive layer of tissue that lines the inside of the eye. This tissue is highly organized and comprises a variety of different nerve cells, including amacrine cells. Together, these cells process incoming light and then trigger electrical signals that travel to the brain, where they are translated into an image. Changes in the nerve cell composition of the retina, or in how the cells connect to each other, can alter the visual information that travels to the brain.

The nerve cells of the retina are formed before a young animal opens its eyes for the first time. Proteins called transcription factors – which regulate the expression of genes – tightly control how the retina develops. For example, a transcription factor called Pax6 drives the development of amacrine cells. Several other transcription factors control the production of Pax6 by binding to a section of DNA known as the “α-enhancer”. However, it is not clear how regulating Pax6 production influences the development of specific sets of amacrine cells.

Kim et al. reveal that a protein known as Tgfb1i1 interacts with two transcription factors to form a “complex” that binds to the α-enhancer and blocks the production of a particular form of Pax6. In experiments performed in mice, the loss of Tgfb1i1 led to increased production of this form of Pax6, which resulted in the retina containing more of a certain type of amacrine cell that produce a molecule called GABA. Mice lacking Tgfb1i1 show a stronger response to light and are therefore comparable to people who are too sensitive to light. On the other hand, mice with a missing a section of the α-enhancer DNA have fewer amacrine cells releasing GABA and become less sensitive to light and are comparable to people who have difficulty detecting weaker light signals.

The findings of Kim et al. suggest that an individual’s sensitivity to light is related, at least in part, to the mixture of amacrine cells found in their retina, which is determined by certain transcription factors that target the α-enhancer.

DOI:http://dx.doi.org/10.7554/eLife.21303.002

Contribution of LHX4 Mutations to Pituitary Deficits in a Cohort of 417 Unrelated Patients

CONTEXT

LHX4 encodes a LIM-homeodomain transcription factor that is implicated in early pituitary development. In humans, only 13 heterozygous LHX4 mutations have been associated with congenital hypopituitarism.

OBJECTIVE

The aims of this study were to evaluate the prevalence of LHX4 mutations in patients with hypopituitarism, to define the associated phenotypes, and to characterize the functional impact of the identified variants and the respective role of the 2 LIM domains of LHX4.

DESIGN AND PATIENTS

We screened 417 unrelated patients with isolated growth hormone deficiency or combined pituitary hormone deficiency associated with ectopic posterior pituitary and/or sella turcica anomalies for LHX4 mutations (Sanger sequencing). In vitro studies were performed to assess the functional consequences of the identified variants.

RESULTS

We identified 7 heterozygous variations, including p.(Tyr131*), p.(Arg48Thrfs*104), c.606+1G>T, p.Arg65Val, p.Thr163Pro, p.Arg221Gln, and p.Arg235Gln), that were associated with variable expressivity; 5 of the 7 were also associated with incomplete penetrance. The p.(Tyr131*), p.(Arg48Thrfs*104), p.Ala65Val, p.Thr163Pro, and p.Arg221Gln LHX4 variants are unable to transactivate the POU1F1 and GH promoters. As suggested by transactivation, subcellular localization, and protein-protein interaction studies, p.Arg235Gln is probably a rare polymorphism. Coimmunoprecipitation studies identified LHX3 as a potential protein partner of LHX4. As revealed by functional studies of LIM-defective recombinant LHX4 proteins, the LIM1 and LIM2 domains are not redundant.

CONCLUSION

This study, performed in the largest cohort of patients screened so far for LHX4 mutations, describes 6 disease-causing mutations that are responsible for congenital hypopituitarism. LHX4 mutations were found to be associated with variable expressivity, and most of them with incomplete penetrance; their contribution to pituitary deficits that are associated with an ectopic posterior pituitary and/or a sella turcica defect is ∼1.4% in the 417 probands tested.

Co-expression of the transcription factors CEH-14 and TTX-1 regulates AFD neuron-specific genes gcy-8 and gcy-18 in C. elegans

A wide variety of cells are generated by the expression of characteristic sets of genes, primarily those regulated by cell-specific transcription. To elucidate the mechanism regulating cell-specific gene expression in a highly specialized cell, AFD thermosensory neuron in Caenorhabditis elegans, we analyzed the promoter sequences of guanylyl cyclase genes, gcy-8 and gcy-18, exclusively expressed in AFD. In this study, we showed that AFD-specific expression of gcy-8 and gcy-18 requires the co-expression of homeodomain proteins, CEH-14/LHX3 and TTX-1/OTX1. We observed that mutation of ttx-1 or ceh-14 caused a reduction in the expression of gcy-8 and gcy-18 and that the expression was completely lost in double mutants. This synergy effect was also observed with other AFD marker genes, such as ntc-1, nlp-21and cng-3. Electrophoretic mobility shift assays revealed direct interaction of CEH-14 and TTX-1 proteins with gcy-8 and gcy-18 promoters in vitro. The binding sites of CEH-14 and TTX-1 proteins were confirmed to be essential for AFD-specific expression of gcy-8 and gcy-18 in vivo. We also demonstrated that forced expression of CEH-14 and TTX-1 in AWB chemosensory neurons induced ectopic expression of gcy-8 and gcy-18 reporters in this neuron. Finally, we showed that the regulation of gcy-8 and gcy-18 expression by ceh-14 and ttx-1 is evolutionally conserved in five Caenorhabditis species. Taken together, ceh-14 and ttx-1 expression determines the fate of AFD as terminal selector genes at the final step of cell specification.

Molecular characterization and expression patterns of the actinin-associated LIM protein (ALP) subfamily genes in porcine skeletal muscle

The actinin-associated LIM protein (ALP) subfamily has important functions in cell signal transduction, cell proliferation, and integration of cytoskeletal architecture. To detect their functions in pig skeletal muscle, we cloned and characterized the pig ALP subfamily genes, drew their genomic structure maps, and detected their tissue expression patterns. We identified a new spliced variant of PDLIM3 in pig skeletal muscle and named it as PDLIM3-4, which was only expressed in the heart and skeletal muscle. Our results showed that PDLIM3-4 was expressed in adult pig skeletal muscle with the highest expression level, and both PDLIM3-4 isoform and PDLIM4 had different expression profiles during the prenatal and postnatal stages of skeletal muscle development among the three pig breeds. These studies provide useful information for further research on the functions of pig ALP subfamily genes in skeletal muscle development.

LIM homeobox 8 (Lhx8) is a key regulator of the cholinergic neuronal function via a tropomyosin receptor kinase A (TrkA)-mediated positive feedback loop

Basal forebrain cholinergic neurons play an important role in cognitive functions such as learning and memory, and they are affected in several neurodegenerative diseases, including Alzheimer disease and Down syndrome. Despite their functional importance, the molecular mechanisms of functional maturation and maintenance of these cholinergic neurons after the differentiation stage have not been fully elucidated. This study demonstrates that the LIM homeobox 8 (Lhx8) transcription factor regulates cholinergic function in rat septal cholinergic neurons in primary cultures from E18.5 embryos and in the adult brain. Lhx8 expression modulated tropomyosin receptor kinase A (TrkA) expression in septal cholinergic neurons in vitro and in vivo, resulting in regulated acetylcholine release as an index of cholinergic function. In addition, Lhx8 expression and function were regulated by nerve growth factor (NGF), and the effect of NGF was potentiated by Lhx8-induced TrkA expression. Together, our findings suggest that positive feedback regulation between Lhx8, TrkA, and NGF is an important regulatory mechanism for cholinergic functions of the septum.

A human FSHB promoter SNP associated with low FSH levels in men impairs LHX3 binding and basal FSHB transcription

FSH production is important for human gametogenesis. In addition to inactivating mutations in the FSHB gene, which result in infertility in both sexes, a G/T single-nucleotide polymorphism (SNP) at -211 relative to the transcription start site of the 5' untranslated region of FSHB has been reported to be associated with reduced serum FSH levels in men. In this study, we sought to identify the potential mechanism by which the -211 SNP reduces FSH levels. Although the SNP resides in a putative hormone response element, we showed that, unlike the murine gene, human FSHB was not induced by androgens or progestins in gonadotropes. On the other hand, we found that the LHX3 homeodomain transcription factor bound to an 11-bp element in the human FSHB promoter that includes the -211 nucleotide. Furthermore, we also demonstrated that LHX3 bound with greater affinity to the wild-type human FSHB promoter compared with the -211 G/T mutation and that LHX3 binding was more effectively competed with excess wild-type oligonucleotide than with the SNP. Finally, we showed that FSHB transcription was decreased in gonadotrope cells with the -211 G/T mutation compared with the wild-type FSHB promoter. Altogether, our results suggest that decreased serum FSH levels in men with the SNP likely result from reduced LHX3 binding and induction of FSHB transcription.

LHX3 interacts with inhibitor of histone acetyltransferase complex subunits LANP and TAF-1β to modulate pituitary gene regulation

LIM-homeodomain 3 (LHX3) is a transcription factor required for mammalian pituitary gland and nervous system development. Human patients and animal models with LHX3 gene mutations present with severe pediatric syndromes that feature hormone deficiencies and symptoms associated with nervous system dysfunction. The carboxyl terminus of the LHX3 protein is required for pituitary gene regulation, but the mechanism by which this domain operates is unknown. In order to better understand LHX3-dependent pituitary hormone gene transcription, we used biochemical and mass spectrometry approaches to identify and characterize proteins that interact with the LHX3 carboxyl terminus. This approach identified the LANP/pp32 and TAF-1β/SET proteins, which are components of the inhibitor of histone acetyltransferase (INHAT) multi-subunit complex that serves as a multifunctional repressor to inhibit histone acetylation and modulate chromatin structure. The protein domains of LANP and TAF-1β that interact with LHX3 were mapped using biochemical techniques. Chromatin immunoprecipitation experiments demonstrated that LANP and TAF-1β are associated with LHX3 target genes in pituitary cells, and experimental alterations of LANP and TAF-1β levels affected LHX3-mediated pituitary gene regulation. Together, these data suggest that transcriptional regulation of pituitary genes by LHX3 involves regulated interactions with the INHAT complex.

A structural basis for the regulation of the LIM-homeodomain protein islet 1 (Isl1) by intra- and intermolecular interactions

Islet 1 (Isl1) is a transcription factor of the LIM-homeodomain (LIM-HD) protein family and is essential for many developmental processes. LIM-HD proteins all contain two protein-interacting LIM domains, a DNA-binding homeodomain (HD), and a C-terminal region. In Isl1, the C-terminal region also contains the LIM homeobox 3 (Lhx3)-binding domain (LBD), which interacts with the LIM domains of Lhx3. The LIM domains of Isl1 have been implicated in inhibition of DNA binding potentially through an intramolecular interaction with or close to the HD. Here we investigate the LBD as a candidate intramolecular interaction domain. Competitive yeast-two hybrid experiments indicate that the LIM domains and LBD from Isl1 can interact with apparently low affinity, consistent with no detection of an intermolecular interaction in the same system. Nuclear magnetic resonance studies show that the interaction is specific, whereas substitution of the LBD with peptides of the same amino acid composition but different sequence is not specific. We solved the crystal structure of a similar but higher affinity complex between the LIM domains of Isl1 and the LIM interaction domain from the LIM-HD cofactor protein LIM domain-binding protein 1 (Ldb1) and used these coordinates to generate a homology model of the intramolecular interaction that indicates poorer complementarity for the weak intramolecular interaction. The intramolecular interaction in Isl1 may provide protection against aggregation, minimize unproductive DNA binding, and facilitate cofactor exchange within the cell.

Epigenetic obstacles encountered by transcription factors: reprogramming against all odds

Reprogramming of a somatic nucleus to an induced pluripotent state can be achieved in vitro through ectopic expression of Oct4 (Pou5f1), Sox2, Klf4 and c-Myc. While the ability of these factors to regulate transcription in a pluripotent context has been studied extensively, their ability to interact with and remodel a somatic genome remains underexplored. Several recent studies have begun to provide mechanistic insights that will eventually lead to a more rational design and improved understanding of nuclear reprogramming.

A recessive mutation resulting in a disabling amino acid substitution (T194R) in the LHX3 homeodomain causes combined pituitary hormone deficiency

BACKGROUND/AIMS

Recessive mutations in the LHX3 homeodomain transcription factor gene are associated with developmental disorders affecting the pituitary and nervous system. We describe pediatric patients with combined pituitary hormone deficiency (CPHD) who harbor a novel mutation in LHX3.

METHODS

Two female siblings from related parents were examined. Both patients had neonatal complications. The index patient had CPHD featuring deficiencies of GH, LH, FSH, PRL, and TSH, with later onset of ACTH deficiency. She also had a hypoplastic anterior pituitary, respiratory distress, hearing impairment, and limited neck rotation. The LHX3 gene was sequenced and the biochemical properties of the predicted altered proteins were characterized.

RESULTS

A novel homozygous mutation predicted to change amino acid 194 from threonine to arginine (T194R) was detected in both patients. This amino acid is conserved in the DNA-binding homeodomain. Computer modeling predicted that the T194R change would alter the homeodomain structure. The T194R protein did not bind tested LHX3 DNA recognition sites and did not activate the α-glycoprotein and PRL target genes.

CONCLUSION

The T194R mutation affects a critical residue in the LHX3 protein. This study extends our understanding of the phenotypic features, molecular mechanism, and developmental course associated with mutations in the LHX3 gene.

The diverse biofunctions of LIM domain proteins: determined by subcellular localization and protein-protein interaction

The LIM domain is a cysteine- and histidine-rich motif that has been proposed to direct protein-protein interactions. A diverse group of proteins containing LIM domains have been identified, which display various functions including gene regulation and cell fate determination, tumour formation and cytoskeleton organization. LIM domain proteins are distributed in both the nucleus and the cytoplasm, and they exert their functions through interactions with various protein partners.

A distal modular enhancer complex acts to control pituitary- and nervous system-specific expression of the LHX3 regulatory gene

Lin-11, Isl-1, and Mec-3 (LIM)-homeodomain (HD)-class transcription factors are critical for many aspects of mammalian organogenesis. Of these, LHX3 is essential for pituitary gland and nervous system development. Pediatric patients with mutations in coding regions of the LHX3 gene have complex syndromes, including combined pituitary hormone deficiency and nervous system defects resulting in symptoms such as dwarfism, thyroid insufficiency, infertility, and developmental delay. The pathways underlying early pituitary development are poorly understood, and the mechanisms by which the LHX3 gene is regulated in vivo are not known. Using bioinformatic and transgenic mouse approaches, we show that multiple conserved enhancers downstream of the human LHX3 gene direct expression to the developing pituitary and spinal cord in a pattern consistent with endogenous LHX3 expression. Several transferable cis elements can individually guide nervous system expression. However, a single 180-bp minimal enhancer is sufficient to confer specific expression in the developing pituitary. Within this sequence, tandem binding sites recognized by the islet-1 (ISL1) LIM-HD protein are essential for enhancer activity in the pituitary and spine, and a pituitary homeobox 1 (PITX1) bicoid class HD element is required for spatial patterning in the developing pituitary. This study establishes ISL1 as a novel transcriptional regulator of LHX3 and describes a potential mechanism for regulation by PITX1. Moreover, these studies suggest models for analyses of the transcriptional pathways coordinating the expression of other LIM-HD genes and provide tools for the molecular analysis and genetic counseling of pediatric patients with combined pituitary hormone deficiency.

Molecular cloning of LIM homeodomain transcription factor Lhx2 as a transcription factor of porcine follicle-stimulating hormone beta subunit (FSHβ) gene

We cloned the LIM-homeodomain protein LHX2 as a transcription factor for the porcine follicle-stimulating hormone β subunit gene (Fshβ) by the Yeast One-Hybrid Cloning System using the upstream region of -852/-746 bases (b) from the transcription start site, called Fd2, as a bait sequence. The reporter assay in LβT2 and CHO cells revealed the presence of an LHX2-responsive region other than Fd2. A potential LHX2 binding sequence was confirmed as AATTAAT containing a consensus homeodomain binding core sequence AATT by Systematic Evolution of Ligands by Exponential Enrichment analysis. DNase I footprinting demonstrated three AATTAAT sequences located at regions -835/-829, -818/-812 and -806/-800 b in the Fd2 region and 12 binding sites in the distal and proximal regions mostly containing an AATT-core sequence. RT-PCR analysis of Lhx2 expression during porcine fetal and postnatal pituitary development showed a gradual increase from fetal day (f) 40 to postnatal day (p) 8 followed by a slight decrease to p230, suggesting that LHX2 may play its role largely in the late fetal and postnatal periods. The analyses of Lhx2 expression in pituitary tumor-derived cell lines showed their expressions in cell lines including αT31, LβT2 and others. Since LHX2 was previously identified as a transcription factor for Cga and the in vitro experiments in the present study suggested that LHX2 regulated the expression of Fshβ, it is possible that LHX2 controls the synthesis of FSH at the transcription level.

Multiple core homeodomain binding motifs differentially contribute to transcriptional activity of the murine gonadotropin-releasing hormone receptor gene promoter

Multiple homeodomain (Hbox) proteins have been shown to organize expression of key markers of gonadotropes. Nine putative Hbox-binding sites, characterized by the homeospecific TAAT motif, are located within the proximal 600 bp of the murine GnRHR promoter. Homeoproteins bind separate Hbox sites within this promoter, supporting basal- and endocrine-directed transcription. The function of the most proximal sites (Hbox1 and Hbox2) in the murine GnRHR is unknown; thus, understanding of the global contribution of homeospecific TAAT sites to promoter function is incomplete. Site-directed mutagenesis revealed that loss of Hbox2 reduced promoter activity in a cell-specific manner, having no effect in alphaT3-1 cells but reducing promoter function in LbetaT2 cells, another gonadotrope-derived cell line representing a later developmental stage. In contrast, eliminating Hbox1 reduced basal activity in both lines. This region displayed specific binding to homeoprotein Oct-1. Mutagenesis of a previously identified Oct-1-binding site in concert with Hbox1 led to further reduction in activity. We suggest that the two most proximal homeodomain-binding sites in the murine GnRHR promoter may regulate the promoter in a developmentally dependent fashion and that Oct-1 acts at multiple but distinct TAAT sites to support basal transcription.

Regulation of porcine pituitary glycoprotein hormone alpha subunit gene with LIM-homeobox transcription factor Lhx3

The aim of this study was to characterize the promoter activity of the porcine pituitary glycoprotein hormone common alpha gene (Cga) promoter (-1059/+12) and the role of LIM homeodomain transcription factor Lhx3. A transfection assay using Chinese hamster ovary (CHO) cells showed that the -1059/-101 region of the Cga promoter definitely responds to Lhx3 and that the -1059/-240 region exhibits a high basal transcriptional level in a pituitary-derived cell line, LbetaT2. A DNA binding and DNase I footprinting assay demonstrated that Lhx3 has seven binding sites in the -1059/+12 region of Cga, including a pituitary glycoprotein hormone basal element (PGBE) known as a LIM homeodomain factor-binding site. A transfection assay of the sequence of Lhx3-binding sites fused with minimal promoter vector confirmed their Lhx3-dependent stimulations in LbetaT2 cells. RT-PCR analysis of porcine pituitary ontogeny demonstrated that porcine Lhx3 showed striking changes of expression in both sexes during the fetal period but a stable high level of expression after birth. Thus, the porcine Cga promoter is regulated by Lhx3 through seven sites in the distal and proximal regions.

Intracellular localization of porcine single-strand binding protein 2

We have previously cloned cofactor CLIM2 (Ldb1/NL1) as a binding protein for LIM homeodomain transcription factor and now seek a protein interacting with CLIM2. Ultimately, SSBP2 was cloned as CLIM2 binding protein from the adult porcine pituitary cDNA library by the Yeast Two-Hybrid System. The amino acid sequence of porcine SSBP2 shows a high identity (99%) with those of other mammalian species, man, and mouse. Using fluorescence protein-fused SSBP2 and its deletion mutants, we observed that SSBP2 overexpressed in CHO cells predominantly localizes in mitochondria. Expression of mutant SSBP2s demonstrated that the first 241 amino acid residues are responsive for the mitochondrial localization. When CLIM2 vector was co-transfected, SSBP2 changed its location to nuclei. The similar translocation was also observed when CLIM2 vector was transfected 17 h after the transfection of SSBP2 vector. The first 120 residues of SSBP2 are responsible for the nuclear localization by guidance with CLIM2. RT-PCR demonstrated that SSBP2 was expressed in the porcine pituitary from fetal 40 days to postnatal 230 days in both genders and in the variety of pituitary and non-pituitary tumor cell lines, indicating that SSBP2 is present ubiquitously and plays a universal function during fetal and postnatal pituitary development.

A regulatory network to segregate the identity of neuronal subtypes

Spinal motor neurons (MNs) and V2 interneurons (V2-INs) are specified by two related LIM-complexes, MN-hexamer and V2-tetramer, respectively. Here we show how multiple parallel and complementary feedback loops are integrated to assign these two cell fates accurately. While MN-hexamer response elements (REs) are specific to MN-hexamer, V2-tetramer-REs can bind both LIM-complexes. In embryonic MNs, however, two factors cooperatively suppress the aberrant activation of V2-tetramer-REs. First, LMO4 blocks V2-tetramer assembly. Second, MN-hexamer induces a repressor, Hb9, which binds V2-tetramer-REs and suppresses their activation. V2-INs use a similar approach; V2-tetramer induces a repressor, Chx10, which binds MN-hexamer-REs and blocks their activation. Thus, our study uncovers a regulatory network to segregate related cell fates, which involves reciprocal feedforward gene regulatory loops.

Three novel missense mutations within the LHX4 gene are associated with variable pituitary hormone deficiencies

CONTEXT

The LHX4 LIM-homeodomain transcription factor has essential roles in pituitary gland and nervous system development. Heterozygous mutations in LHX4 are associated with combined pituitary hormone deficiency.

OBJECTIVES

Our objectives were to determine the nature and frequency of LHX4 mutations in patients with pituitary hormone deficiency and to examine the functional outcomes of observed mutations.

DESIGN

The LHX4 gene sequence was determined from patient DNA. The biochemical and gene regulatory properties of aberrant LHX4 proteins were characterized using structural predictions, pituitary gene transcription assays, and DNA binding experiments.

PATIENTS

A total of 253 patients from 245 pedigrees with GH deficiency and deficiency of at least one additional pituitary hormone was included in the study.

RESULTS

In five patients, three types of heterozygous missense mutations in LHX4 that result in substitution of conserved amino acids were identified. One substitution is between the LIM domains (R84C); the others are in the homeodomain (L190R; A210P). The patients have GH deficiency; some also display reductions in TSH, LH, FSH, or ACTH, and aberrant pituitary morphology. Structural models predict that the aberrant L190R and A210P LHX4 proteins would have impaired DNA binding and gene activation properties. Consistent with these models, EMSAs and transfection experiments using pituitary gene promoters demonstrate that whereas the R84C form has reduced activity, the L190R and A210P proteins are inactive.

CONCLUSIONS

LHX4 mutations are a relatively rare cause of combined pituitary hormone deficiency. This report extends the range of phenotypes associated with LHX4 gene mutations and describes three novel exonic mutations in the gene.

Transgenic mice expressing LHX3 transcription factor isoforms in the pituitary: effects on the gonadotrope axis and sex-specific reproductive disease

The LHX3 transcription factor plays critical roles in pituitary and nervous system development. Mutations in the human LHX3 gene cause severe hormone deficiency diseases. The gene produces two mRNAs which can be translated to three protein isoforms. The LHX3a protein contains a central region with LIM domains and a homeodomain, and a carboxyl terminus with the major transactivation domain. LHX3b is identical to LHX3a except that it has a different amino terminus. M2-LHX3 lacks the amino terminus and LIM domains of LHX3a/b. In vitro experiments have demonstrated these three proteins have different biochemical and gene regulatory properties. Here, to investigate the effects of overexpression of LHX3 in vivo, the alpha glycoprotein subunit (alphaGSU) promoter was used to produce LHX3a, LHX3b, and M2-LHX3 in the pituitary glands of transgenic mice. Alpha GSU-beta galactosidase animals were generated as controls. Male alphaGSU-LHX3a and alphaGSU-LHX3b mice are infertile and die at a young age as a result of complications associated with obstructive uropathy including uremia. These animals have a reduced number of pituitary gonadotrope cells, low circulating gonadotropins, and possible sex hormone imbalance. Female alphaGSU-LHX3a and alphaGSU-LHX3b transgenic mice are viable but have reduced fertility. By contrast, alphaGSU-M2-LHX3 mice and control mice expressing beta galactosidase are reproductively unaffected. These overexpression studies provide insights into the properties of LHX3 during pituitary development and highlight the importance of this factor in reproductive physiology.

Mutations in the LHX3 gene cause dysregulation of pituitary and neural target genes that reflect patient phenotypes

The LHX3 LIM-homeodomain transcription factor is required for correct development of the mammalian pituitary gland and spinal motoneurons. Mutations in the LHX3 gene underlie complex diseases featuring combined anterior pituitary hormone deficiency and, in specific cases, loss of neck rotation considered to result from nervous system abnormalities. The molecular basis for LHX3 protein actions in both normal and aberrant pituitary and nervous system development is poorly understood. In this study, the gene regulatory abilities of mutant LHX3 proteins associated with distinct types of diseases (LHX3a A210V, LHX3a E173Ter, and LHX3a W224Ter) were investigated. The capacity of these proteins to activate pituitary hormone and transcription factor gene promoters, nervous system target genes, and to localize to the nucleus of pituitary cells was measured. Consistent with the symptoms of patients with these mutations, the abnormal proteins displayed diminished capacities to activate the promoters of genes expressed in the pituitary gland. On nervous system promoters, several mutant proteins retained some activity. The ability of the mutant proteins to concentrate in the nucleus of pituitary cells was correlated with the retention of defined nuclear localization signals in the protein sequence, except for the E173Ter protein which unexpectedly localizes to the nucleus, likely due to the insertion of cryptic nuclear localization signals by a frame shift caused by the mutation. This study extends the molecular characterization of the severe neuroendocrine diseases associated with LHX3 gene mutations.

Four novel mutations of the LHX3 gene cause combined pituitary hormone deficiencies with or without limited neck rotation

CONTEXT

The Lhx3 LIM-homeodomain transcription factor gene is required for development of the pituitary and motoneurons in mice. Human LHX3 gene mutations have been reported in five subjects with a phenotype consisting of GH, prolactin, TSH, LH, and FSH deficiency; abnormal pituitary morphology; and limited neck rotation.

OBJECTIVE

The objective of the study was to determine the frequency and nature of LHX3 mutations in patients with isolated GH deficiency or combined pituitary hormone deficiency (CPHD) and characterize the molecular consequences of mutations.

DESIGN

The LHX3 sequence was determined. The biochemical properties of aberrant LHX3 proteins resulting from observed mutations were characterized using reporter gene and DNA binding experiments.

PATIENTS

The study included 366 patients with isolated GH deficiency or CPHD.

RESULTS

In seven patients with CPHD from four consanguineous pedigrees, four novel, recessive mutations were identified: a deletion of the entire gene (del/del), mutations causing truncated proteins (E173ter, W224ter), and a mutation causing a substitution in the homeodomain (A210V). The mutations were associated with diminished DNA binding and pituitary gene activation, consistent with observed hormone deficiencies. Whereas subjects with del/del, E173ter, and A210V mutations had limited neck rotation, patients with the W224ter mutation did not.

CONCLUSIONS

LHX3 mutations are a rare cause of CPHD involving deficiencies for GH, prolactin, TSH, and LH/FSH in all patients. Whereas most patients have a severe hormone deficiency manifesting after birth, milder forms can be observed, and limited neck rotation is not a universal feature of patients with LHX3 mutations. This study extends the known molecular defects and range of phenotypes found in LHX3-associated diseases.

Roles of the LHX3 and LHX4 LIM-homeodomain factors in pituitary development

The LHX3 and LHX4 LIM-homeodomain transcription factors play essential roles in pituitary gland and nervous system development. Mutations in the genes encoding these regulatory proteins are associated with combined hormone deficiency diseases in humans and animal models. Patients with these diseases have complex syndromes involving short stature, and reproductive and metabolic disorders. Analyses of the features of these diseases and the biochemical properties of the LHX3 and LHX4 proteins will facilitate a better understanding of the molecular pathways that regulate the development of the specialized hormone-secreting cells of the mammalian anterior pituitary gland.

A specific helical orientation underlies the functional contribution of the activin responsive unit to transcriptional activity of the murine gonadotropin-releasing hormone receptor gene promoter

Activin responsiveness of the murine GnRH receptor (GnRHR) gene promoter requires two spatially distinct regulatory elements termed the GnRH receptor activating sequence or GRAS and the downstream activin regulatory element or DARE. While GRAS interacts with multiple transcription factors, DARE activity requires tandem homeodomain binding motifs (TAAT) and displays specific binding to the LIM homeodomain protein LHX3. Herein, we find that both the murine GnRHR gene promoter and DARE fused to a minimal heterologous promoter are responsive to LHX3 overexpression. A dominant-repressor of LHX3 attenuates transcriptional activity of the murine GnRHR gene promoter but had no impact on activin responsiveness. Thus, LHX3 would not appear to be the protein mediating activin responsiveness of this promoter. Within DARE itself, the tandem TAAT motifs are separated by 4 bp. Although this arrangement differs from the prototypical P2 or P3 binding sites characterized for paired-like homeodomain proteins and from the directly abutting TAAT motifs found for LHX3, a LIM-class homeodomain protein, we find that separation of the TAAT sites by 5 and 10 bp decreases GnRHR promoter activity to a level similar to promoters containing loss of function mutations in either the proximal or distal TAAT motif. Thus, the juxtaposition of the TAAT sites is critical for the functional activity of DARE. That activin responsiveness of the GnRHR promoter requires both GRAS and DARE suggests that these elements may be both functionally and structurally coupled. As to the latter, GRAS and DARE are separated by 20 bp, thus placing the elements on the same side of the helical backbone. To determine if this spatial organization is functionally relevant, multiples of 5 bp were inserted or deleted between GRAS and DARE. Any insertion or deletion that resulted in a half-turn alteration in the helical positioning between the two elements reduced promoter activity. Thus, an important spatial relationship underlies functional cooperation between GRAS and DARE and the emergence of a complex activin responsive unit (ARU) within the mouse GnRHR promoter.

The LIM-homeodomain proteins Isl-1 and Lhx3 act with steroidogenic factor 1 to enhance gonadotrope-specific activity of the gonadotropin-releasing hormone receptor gene promoter

The GnRH receptor (GnRH-R) plays a central role in mammalian reproductive function throughout adulthood. It also appears as an early marker gene of the presumptive gonadotrope lineage in developing pituitary. Here, using transient transfections combined with DNA/protein interaction assays, we have delineated cis-acting elements within the rat GnRH-R gene promoter that represent targets for the LIM-homeodomain (LIM-HD) proteins, Isl-1 and Lhx3. These factors, critical in early pituitary development, are thus also crucial for gonadotrope-specific expression of the GnRH-R gene. In heterologous cells, the expression of Isl-1 and Lhx3, together with steroidogenic factor 1 (SF-1), culminates in the activation of both the rat as well as human GnRH-R promoter, suggesting that this combination is evolutionarily conserved among mammals. The specificity of these LIM-HD factors is attested by the inefficiency of related proteins, including Lhx5 and Lhx9, to activate the GnRH-R gene promoter, as well as by the repressive capacity of a dominant-negative derivative of Lhx3. Accordingly, targeted deletion of the LIM response element decreases promoter activity. In addition, experiments with Gal4-SF-1 fusion proteins suggest that LIM-HD protein activity in gonadotrope cells is dependent upon SF-1 binding. Finally, using a transgenic model that allows monitoring of in vivo promoter activity, we show that the overlapping expression of Isl-1 and Lhx3 in the developing pituitary correlates with promoter activity. Collectively, these data suggest the occurrence of a specific LIM-HD pituitary code and designate the GnRH-R gene as the first identified transcriptional target of Isl-1 in the anterior pituitary.

LIM-homeodomain genes in mammalian development and human disease

The human and mouse genomes each contain at least 12 genes encoding LIM homeodomain (LIM-HD) transcription factors. These gene regulatory proteins feature two LIM domains in their amino termini and a characteristic DNA binding homeodomain. Studies of mouse models and human patients have established that the LIM-HD factors are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs such as the pituitary gland and the pancreas. In this article, we review the roles of the LIM-HD proteins in mammalian development and their involvement in human diseases.

DNA recognition properties of the LHX3b LIM homeodomain transcription factor

LHX3 is a LIM homeodomain transcription factor with established roles in pituitary and nervous system development. Mutations in the human LHX3 gene are associated with severe hormone deficiency diseases. Previous studies have shown that the human LHX3 gene produces at least three protein isoforms: LHX3a, LHX3b, and M2-LHX3. In gene activation assays, LHX3a and M2-LHX3 are significantly more active than LHX3b because the actions of LHX3b are repressed by an inhibitory domain in its amino terminus. In this report, we investigate the molecular characteristics that result in reduced transcriptional capacity of LHX3b by determining the optimal DNA binding preference of LHX3b. Site selection experiments using purified human LHX3b reveal that it selects AT-rich sequences that contain ATTA/TAAT motifs. The pool of sequences selected by LHX3b is similar to that selected by LHX3a but does not conform to as strict a consensus. Further, the LHX3b-selected sites are bound more avidly by LHX3a and M2-LHX3 suggesting that LHX3b does not act by recognizing LHX3b-specific binding sites in target genes. We conclude that the amino terminal repression domain of LHX3b mostly acts to reduce the transcriptional potency of LHX3 by inhibiting the DNA binding affinity of the homeodomain, with some reduction in DNA binding specificity.

Serine/threonine/tyrosine phosphorylation of the LHX3 LIM-homeodomain transcription factor

LHX3 is a LIM homeodomain transcription factor with essential roles in pituitary and motor neuron development in mammals. Patients with mutations in the LHX3 gene have combined pituitary hormone deficiency and other symptoms. In this study, we show that the LHX3 protein can be modified post-translationally by phosphorylation. LHX3 can serve as a substrate for protein kinase C and casein kinase II. Overexpression of these kinases reduces the transcriptional capacity of LHX3 to activate target genes. Following exposure of LHX3 to cellular kinases, mass spectrometry was used to map the phosphorylation of five amino acid residues within the human LHX3a isoform. Two phosphorylated residues (threonine 63 and serine 71) lie within the first LIM domain of the protein. Three other modified amino acids (tyrosine 227, serine 234, and serine 238) are located in the carboxyl terminus. Targeted replacement of these amino acids with non-modifiable residues significantly reduced the ability of LHX3 to activate both synthetic and pituitary hormone reporter genes. However, the amino acid replacements did not significantly affect the capability of LHX3 to interact with the NLI, PIT1, and MRG1 partner proteins, or its ability to bind to a high affinity DNA site. In conclusion, we have identified unique amino acids within LHX3 that are important for its transcriptional activity and are phosphorylated.

Mouse GnRH receptor gene expression is mediated by the LHX3 homeodomain protein

Appropriate expression of GnRH receptor (GnRHR) is necessary for the correct regulation of the gonadotropins, LH and FSH, by GnRH. GnRHR is primarily expressed in the gonadotrope cells of the anterior pituitary, and a number of regulatory elements important for both basal and hormonal regulation of the gene have been identified. Using the gonadotrope-derived cell line, alpha T3-1, that endogenously expresses GnRHR, we have identified an ATTA element located at -298 relative to the transcriptional start site that is essential for basal expression of the GnRHR gene. LHX3, a member of the LIM homeodomain family, binds the -298 ATTA site in vitro as well as to the endogenous GnRHR promoter in vivo. Additionally, LHX3 specifically activates through this -298 ATTA site in transient transfection assays. LHX3 is essential for pituitary development and has been implicated in the regulation of a number of pituitary specific genes; however, this is the first report identifying its role in the regulation of GnRHR.

Making very similar embryos with divergent genomes: conservation of regulatory mechanisms of Otx between the ascidians Halocynthia roretzi and Ciona intestinalis

Ascidian embryos develop with a fixed cell lineage into simple tadpoles. Their lineage is almost perfectly conserved, even between the evolutionarily distant species Halocynthia roretzi and Ciona intestinalis, which show no detectable sequence conservation in the non-coding regions of studied orthologous genes. To address how a common developmental program can be maintained without detectable cis-regulatory sequence conservation, we compared in both species the regulation of Otx, a gene with a shared complex expression pattern. We found that in Halocynthia, the regulatory logic is based on the use of very simple cell line-specific regulatory modules, the activities of which are conserved, in most cases, in the Ciona embryo. The activity of each of these enhancer modules relies on the conservation of a few repeated crucial binding sites for transcriptional activators, without obvious constraints on their precise number, order or orientation, or on the surrounding sequences. We propose that a combination of simplicity and degeneracy allows the conservation of the regulatory logic, despite drastic sequence divergence. The regulation of Otx in the anterior endoderm by Lhx and Fox factors may even be conserved with vertebrates.

Regulation of the follicle-stimulating hormone beta gene by the LHX3 LIM-homeodomain transcription factor

FSH is a critical hormone regulator of gonadal function that is secreted from the pituitary gonadotrope cell. Human patients and animal models with mutations in the LHX3 LIM-homeodomain transcription factor gene exhibit complex endocrine diseases, including reproductive disorders with loss of FSH. We demonstrate that in both heterologous and pituitary gonadotrope cells, specific LHX3 isoforms activate the FSH beta-subunit promoter, but not the proximal LHbeta promoter. The related LHX4 mammalian transcription factor can also induce FSHbeta promoter transcription, but the homologous Drosophila protein LIM3 cannot. The actions of LHX3 are specifically blocked by a dominant negative LHX3 protein containing a Kruppel-associated box domain. Six LHX3-binding sites were characterized within the FSHbeta promoter, including three within a proximal region that also mediates gene regulation by other transcription factors and activin. Mutations of the proximal binding sites demonstrate their importance for LHX3 induction of the FSHbeta promoter and basal promoter activity in gonadotrope cells. Using quantitative methods, we show that the responses of the FSHbeta promoter to activin do not require induction of the LHX3 gene. By comparative genomics using the human FSHbeta promoter, we demonstrate structural and functional conservation of promoter induction by LHX3. We conclude that the LHX3 LIM homeodomain transcription factor is involved in activation of the FSH beta-subunit gene in the pituitary gonadotrope cell.

Cloning and analysis of axolotl ISL2 and LHX2 LIM-homeodomain transcription factors

We cloned and characterized the ISL2 and LHX2 LIM-homeodomain transcription factors of the Mexican salamander, or axolotl, Ambystoma mexicanum. Using a degenerate PCR approach, partial cDNAs representing five LIM-homeodomain genes were cloned, indicating conservation of this class of transcription factors in urodeles. Full-length cDNAs for Isl2 and Lhx2 were identified and sequenced. The predicted ISL2 and LHX2 proteins are well conserved, especially in the LIM and DNA-binding domains. The Isl2 and Lhx2 genes are expressed at all examined stages of embryogenesis and display tissue-restricted expression patterns in adults. In functional tests, axolotl LHX2 was inactive compared to homologous mammalian factors and adopted unusual DNA/protein complexes. However, axolotl ISL2 bound and induced transcription from the rat insulin gene. These experiments demonstrate conservation of key developmental regulatory proteins in salamanders and will allow future studies of their potential roles in the molecular regulation of tissue regeneration in such species.

Specification of Drosophila motoneuron identity by the combinatorial action of POU and LIM-HD factors

In both vertebrates and invertebrates, members of the LIM-homeodomain (LIM-HD) family of transcription factors act in combinatorial codes to specify motoneuron subclass identities. In the developing Drosophila embryo, the LIM-HD factors Islet (Tailup) and Lim3, specify the set of motoneuron subclasses that innervate ventral muscle targets. However, as several subclasses express both Islet and Lim3, this combinatorial code alone cannot explain how these motoneuron groups are further differentiated. To identify additional factors that may act to refine this LIM-HD code, we have analyzed the expression of POU genes in the Drosophila embryonic nerve cord. We find that the class III POU protein, Drifter (Ventral veinless), is co-expressed with Islet and Lim3 specifically in the ISNb motoneuron subclass. Loss-of-function and misexpression studies demonstrate that the LIM-HD combinatorial code requires Drifter to confer target specificity between the ISNb and TN motoneuron subclasses. To begin to elucidate molecules downstream of the LIM-HD code, we examined the involvement of the Beaten path (Beat) family of immunoglobulin-containing cell-adhesion molecules. We find that beat Ic genetically interacts with islet and Lim3 in the TN motoneuron subclass and can also rescue the TN fasciculation defects observed in islet and Lim3 mutants. These results suggest that in the TN motoneuron context, Islet and Lim3 may specify axon target selection through the actions of IgSF call-adhesion molecules.

Transcriptional control during mammalian anterior pituitary development

The mammalian anterior pituitary gland is a compound endocrine organ that regulates reproductive development and fitness, growth, metabolic homeostasis, the response to stress, and lactation, by actions on target organs such as the gonads, the liver, the thyroid, the adrenals, and the mammary gland. The protein and peptide hormones that control these physiological parameters are secreted by specialized pituitary cell types that derive from a common origin in the early ectoderm. Collectively, the broad physiological importance of the pituitary gland, its intriguing organogenesis, and the clinical and agricultural significance of its actions, have established pituitary development as an excellent model system for the study of the gene-regulatory cascades that guide vertebrate cell determination and differentiation. We review the transcriptional pathways that regulate the commitment of the individual pituitary cell lineages and that subsequently modulate trophic hormone gene activity in the differentiated cells of the mature gland.

Isolation and characterization of the follicle-stimulating hormone beta subunit gene and 5' flanking region of the Chinook salmon

In this study we have isolated the follicle-stimulating hormone beta subunit gene from the Chinook salmon (csFSHbeta). This gene encodes for a protein that is highly similar to those isolated from other salmonids and shares all of the structural constraints seen in mammalian gonadotropins, including twelve conserved cysteines and a putative N-linked glycosylation site. The organization of the gene follows the conserved pattern regarding the numbers and positions of the introns, although the csFSHbeta gene contains a particularly large 6.2-kb first intron due to the inclusion of several transposon-like elements. Isolation of 1.2 kb of the 5' flanking region of the csFSHbeta gene and subsequent analysis in silico have revealed a number of putative elements which appear highly conserved in teleost FSHbeta gene promoters and are thus likely involved in basal and hormone-induced transcriptional regulation. The functionality of this 1.2-kb fragment in driving expression of a reporter gene and its response to GnRH was shown in gonadotropes, while the overexpression of AP-1 factors, Sf-1, estrogen receptor or Smad1 revealed that the promoter is responsive to these transcription factors. Our current study has opened the way for future analysis to verify the role of these factors in mediating hormonally induced transcription of this gene.

Context-dependent transcription: all politics is local

An organism ultimately reflects the coordinate expression of its genome. The misexpression of a gene can have catastrophic consequences for an organism, yet the mechanics of transcription is a local phenomenon within the cell nucleus. Chromosomal and nuclear position often dictate the activity of a specific gene. Transcription occurs in territories and in discrete localized foci within these territories. The proximity of a gene or trans-acting factor to heterochromatin can have profound functional significance. The organization of heterochromatin changes with cell development, thus conferring temporal changes on gene activity. The protein-protein interactions that engage the trans-acting factor also contribute to context-dependent transcription. Multi-protein assemblages known as enhanceosomes govern gene expression by local committee thus dictating regional transcription factor function. Local DNA architecture can prescribe enhancesome membership. The local bending of the double helix, typically mediated by architectural transcription factors, is often critical for stabilizing enhanceosomes formed from trans-acting proteins separated over small and large distances. The recognition element to which a transcription factor binds is of functional significance because DNA may act as an allosteric ligand influencing the conformation and thus the activity of the transactivation domain of the binding protein, as well as the recruitment of other proteins to the enhanceosome. Here, we review and attempt to integrate these local determinants of gene expression.