Genomic structure and chromosomal localization of the novel ETS factor, PE-2 (ERF)

ERF-Related Craniosynostosis in a Patient With Hypochondroplasia: A Case Report

We report a case of multiple suture craniosynostosis in a patient with hypochondroplasia. The patient presented with short stature marked by a relatively long trunk and short extremities. The clinical and radiological findings were suggestive of hypochondroplasia. Additionally, craniosynostosis was identified during the evaluation, which is an unusual finding in hypochondroplasia. To further investigate, exome sequencing was performed, revealing previously reported pathogenic heterozygous variants in FGFR3 and ERF genes. Exome sequencing not only enhances the accuracy of diagnosing individual cases of genetic skeletal disorders but also contributes to the collective knowledge base, advancing future research in the field.

0.1 THz exposure affects primary hippocampus neuron gene expression via alternating transcription factor binding

In recent years, many studies have been conducted to investigate the influence of terahertz (THz) radiation on the gene expression in various cell types, but the underling molecular mechanism has not yet been fully revealed. In this study, we explored the effects of 0.1 THz radiation on the gene expression in primary neuron cells through RNA-seq analysis. 111 up-regulated and 54 down-regulated genes were identified. Several biomolecule binding related categories such as "long-chain fatty acid binding", "tropomyosin binding", "BMP receptor binding", as well as "GTPase binding" and "phospholipid binding" were enriched by GO analysis. Moreover, the GSEA analysis indicated that genes encoding protein biosynthetic machinery ribosome were up-regulated by 0.1 THz irradiation. In addition, we demonstrated that the binding efficiency of a transcription factor (TF) AP-1 with its transcription factor binding site (TFBS) in DNA was reduced by THz irradiation, which suggested that THz irradiation might affect the interaction between TFs with DNA and consequently regulate the gene expression. Our results provide new insights into the biological effects of terahertz irradiation.

Structural Insight into the DNA Binding Function of Transcription Factor ERF

ETS family transcription factors control development of different cell types in humans, whereas deregulation of these proteins leads to severe developmental syndromes and cancers. One of a few members of the ETS family that are known to act solely as repressors, ERF, is required for normal osteogenesis and hematopoiesis. Another important function of ERF is acting as a tumor suppressor by antagonizing oncogenic fusions involving other ETS family factors. The structure of ERF and the DNA binding properties specific to this protein have not been elucidated. In this study, we determined two crystal structures of the complexes of the DNA binding domain of ERF with DNA. In one, ERF is in a distinct dimeric form, with Cys72 in a reduced state. In the other, two dimers of ERF are assembled into a tetramer that is additionally locked by two Cys72-Cys72 disulfide bonds across the dimers. In the tetramer, the ERF molecules are bound to a pseudocontinuous DNA on the same DNA face at two GGAA binding sites on opposite strands. Sedimentation velocity analysis showed that this tetrameric assembly forms on continuous DNA containing such tandem sites spaced by 7 bp. Our bioinformatic analysis of three previously reported sets of ERF binding loci across entire genomes showed that these loci were enriched in such 7 bp spaced tandem sites. Taken together, these results strongly suggest that the observed tetrameric assembly is a functional state of ERF in the human cell.

Variable pulmonary manifestations in Chitayat syndrome: Six additional affected individuals

Hand hyperphalangism leading to shortened index fingers with ulnar deviation, hallux valgus, mild facial dysmorphism and respiratory compromise requiring assisted ventilation are the key features of Chitayat syndrome. This condition results from the recurrent heterozygous missense variant NM_006494.2:c.266A>G; p.(Tyr89Cys) in ERF on chromosome 19q13.2, encoding the ETS2 repressor factor (ERF) protein. The pathomechanism of Chitayat syndrome is unknown. To date, seven individuals with Chitayat syndrome and the recurrent pathogenic ERF variant have been reported in the literature. Here, we describe six additional individuals, among them only one presenting with a history of assisted ventilation, and the remaining presenting with variable pulmonary phenotypes, including one individual without any obvious pulmonary manifestations. Our findings widen the phenotype spectrum caused by the recurrent pathogenic variant in ERF, underline Chitayat syndrome as a cause of isolated skeletal malformations and therefore contribute to the improvement of diagnostic strategies in individuals with hand hyperphalangism.

Chitayat syndrome: hyperphalangism, characteristic facies, hallux valgus and bronchomalacia results from a recurrent c.266A>G p.(Tyr89Cys) variant in the ERF gene

BACKGROUND

In 1993, Chitayat et al., reported a newborn with hyperphalangism, facial anomalies, and bronchomalacia. We identified three additional families with similar findings. Features include bilateral accessory phalanx resulting in shortened index fingers; hallux valgus; distinctive face; respiratory compromise.

OBJECTIVES

To identify the genetic aetiology of Chitayat syndrome and identify a unifying cause for this specific form of hyperphalangism.

METHODS

Through ongoing collaboration, we had collected patients with strikingly-similar phenotype. Trio-based exome sequencing was first performed in Patient 2 through Deciphering Developmental Disorders study. Proband-only exome sequencing had previously been independently performed in Patient 4. Following identification of a candidate gene variant in Patient 2, the same variant was subsequently confirmed from exome data in Patient 4. Sanger sequencing was used to validate this variant in Patients 1, 3; confirm paternal inheritance in Patient 5.

RESULTS

A recurrent, novel variant NM_006494.2:c.266A>G p.(Tyr89Cys) in ERF was identified in five affected individuals: de novo (patient 1, 2 and 3) and inherited from an affected father (patient 4 and 5). p.Tyr89Cys is an aromatic polar neutral to polar neutral amino acid substitution, at a highly conserved position and lies within the functionally important ETS-domain of the protein. The recurrent ERF c.266A>C p.(Tyr89Cys) variant causes Chitayat syndrome.

DISCUSSION

ERF variants have previously been associated with complex craniosynostosis. In contrast, none of the patients with the c.266A>G p.(Tyr89Cys) variant have craniosynostosis.

CONCLUSIONS

We report the molecular aetiology of Chitayat syndrome and discuss potential mechanisms for this distinctive phenotype associated with the p.Tyr89Cys substitution in ERF.

Expression profiles frame the promoter specificity dilemma of the ETS family of transcription factors

Sequence-specific DNA binding proteins that function as transcription factors are frequently encoded by gene families. Such proteins display highly conserved DNA binding properties, yet are expected to retain promoter selectivity. In this report we investigate this problem using the ets gene family, a group of metazoan genes whose members regulate cell growth and differentiation and are mutated in human cancers. We tested whether the level of mRNA can serve as a specificity determinant. The mRNA levels of the 27 paralogous human ets genes were measured in 23 tissues and cell lines. Real-time RT-PCR provided accurate measurement of absolute mRNA levels for each gene down to one copy per cell. Surprisingly, at least 16 paralogs were expressed in each cell sample and over half were expressed ubiquitously. Tissues and complementary cell lines showed similar expression patterns, indicating that tissue complexity was not a limitation. There was no unique, highly expressed gene for each cell type. Instead, one of only eight ets genes showed the highest expression in all samples. DNA binding studies illustrate both overlapping and unique specificities for ubiquitous ETS proteins. These findings establish the parameters of the promoter specificity dilemma within the ets family of transcription factors.

Stage-specific and tissue-specific expression characteristics of differentially expressed genes during mouse spermatogenesis

Spermatogenesis occurs in successive mitotic, meiotic, and post-meiotic phase, and involves a number of unique processes including meiosis and dramatic morphological changes. The unique differentiation mechanisms of spermatogenesis suggest the existence of germ-cell-specific molecules. The most straight forward strategy to elucidate differentiation mechanisms is to identify and characterize differentiation-specific molecules and their associated genes in germ cells. However, only a few genes specifically involved in spermatogenesis have been studied. In the present study, six different types of spermatogenic cells (primitive type A spermatogonia, type B spermatogonia, preleptotene spermatocytes, pachytene spermatocytes, round spermatids, and elongating spermatids) were isolated from Balb/c mice testes using velocity sedimentation and Atlas cDNA arrays containing 1,176 known mouse genes were used to determine the gene expression profiles of the spermatogenic cells. The expression of 260 genes were detected in six different stages of spermatogenic cells and a number of genes showed differential expression. The 23 differentially expressed genes were further analysed by reverse transcription polymerase chain reaction (RT-PCR) for their stage-specific and tissue-specific expression characteristics. Based on the results of RT-PCR, six genes highly express in both primitive type A and type B spermatogonia, four genes up-regulate in type B spermatogonia, two genes up-regulate in spermatocytes, two genes up-regulate in spermatids, three genes express constantly from primitive A spermatogonia to elongating spermatids, two genes express constantly from primitive A spermatogonia to round spermatids, two genes do not change in their expression during spermatogenesis, two genes can be detected highly in adult testis, but are undetectable in spermatogenic cells. The tissue-specific expression characteristics of the 23 genes showed that some of them specifically expressed in testes or other tissues. These data provide new information for further studies into spermatogenesis-related genes and may lead to the identification of genes with potential relevance to the differentiation of spermatogenic cells. In addition, some of these genes could be considered to be used as the molecular markers for different stages of spermatogenic cells.

Human chromosomal localization, tissue/tumor expression, and regulatory function of the ets family gene EHF

Ets factors are members of an ancient multigene family of transcription factors including oncoproteins and possibly tumor suppressors. We previously characterized a novel divergent ets gene, Ehf (ets homologous factor) in mice. Here we report the cDNA sequence, chromosomal location, and tissue/tumor expression patterns of the human EHF gene and the regulatory activity of the EHF protein. EHF maps to 11p12, which is deleted in many prostate, breast, and lung carcinomas and is a hot spot for inherited deletion- or amplification-associated developmental defects. EHF is differentially expressed in normal tissues and carcinomas and between tumor stages and is most highly expressed in the organs known to form carcinomas upon 11p12 deletion. EHF protein represses the ETS-2 induced activity of both stromelysin-1 and collagenase-1 promoters. These data suggest that EHF may contribute to human development and carcinogenesis and is a candidate for the 11p12 tumor suppressor gene.

Exon 4-encoded acidic domain in the epithelium-restricted Ets factor, ESX, confers potent transactivating capacity and binds to TATA-binding protein (TBP)

The Ets gene family has a complex evolutionary history with many family members known to regulate genetic programs essential for differentiation and development, and some known for their involvement in human tumorigenesis. To understand the biological properties associated with a recently described epithelium-restricted Ets factor ESX, an 11 kb fragment from the 1q32.2 genomically localized human gene was cloned and analysed. Upstream of the ESX promoter region in this genomic fragment lies the terminal exon of a newly identified gene that encodes a ubiquitin-conjugating enzyme variant, UEV-1. Tissues expressing ESX produce a primary 2.2 kb transcript along with a 4.1 kb secondary transcript arising by alternate poly(A) site selection and uniquely recognized by a genomic probe from the 3' terminal region of the 11 kb clone. Endogenous expression of ESX results in a 42 kDa nuclear protein having fivefold greater affinity for the chromatin-nuclear matrix compartment as compared to other endogenous transcription factors like AP-2 and the homologous Ets factor, ELF-1. Exon mapping of the modular structure inferred from ESX cDNA and construction of GAL4(DBD)-ESX expression constructs were used to identify a transactivating domain encoded by exon 4 having comparable potency to the acidic transactivation domain of the viral transcription factor, VP16. This exon 4-encoded 31 amino acid domain in ESX was shown by mutation and deletion analysis to possess a 13 residue acidic transactivation core which, based on modeling and circular dichroism analysis, is predicted to form an amphipathic alpha-helical secondary structure. Using recombinant GST-ESX (exon 4) fusion proteins in an in vitro pull-down assay, this ESX transactivation domain was shown to bind specifically to one component of the general transcription machinery, TATA-binding protein (TBP). Transient transfection experiments confirmed the ability of this TBP-binding transactivation domain in ESX to squelch heterologous promoters independent of any promoter binding as efficiently as the transactivation domain from VP16.

Selective inhibition of prolactin gene transcription by the ETS-2 repressor factor

Regulation of prolactin gene transcription requires cooperative interactions between the pituitary-specific POU domain protein Pit-1 and members of the ETS transcription factor family. We demonstrate here that the ETS-2 repressor factor (ERF) is expressed in pituitary tumor cells and that overexpression of recombinant ERF inhibits prolactin promoter activity, but not the closely related growth hormone promoter. In non-pituitary cell lines, coexpression of ERF disrupts the cooperative interactions between Pit-1 and ETS-1 and blocks the induction of Pit-1-dependent prolactin promoter activity by cAMP. The potential role of ERF in the inhibitory response of the prolactin promoter to dopamine was examined using pituitary tumor cells stably expressing dopamine D2 receptors. The inhibitory responses of the prolactin promoter to ERF and dopamine are additive, suggesting that ERF has a complementary role in this hormonal response. A single Pit-1 DNA-binding element from the prolactin promoter is sufficient to reconstitute the inhibitory response to ERF. DNA binding analysis using either a composite Pit-1/ETS protein-binding site or a Pit-1 element with no known affinity for ETS proteins revealed that ERF interferes with Pit-1 binding. Together, these results demonstrate that ERF is a specific inhibitor of basal and hormone-regulated transcription of the prolactin gene and suggest a new level of complexity for the interaction of ETS factors with Pit-1 target genes.