Badam Enkhmandakh

Essential functions of the Williams-Beuren syndrome-associated TFII-I genes in embryonic development

GTF2I and GTF2IRD1 encoding the multifunctional transcription factors TFII-I and BEN are clustered at the 7q11.23 region hemizygously deleted in Williams-Beuren syndrome (WBS), a complex multisystemic neurodevelopmental disorder. Although the biochemical properties of TFII-I family transcription factors have been studied in depth, little is known about the specialized contributions of these factors in pathways required for proper embryonic development. Here, we show that homozygous loss of either Gtf2ird1 or Gtf2i function results in multiple phenotypic manifestations, including embryonic lethality; brain hemorrhage; and vasculogenic, craniofacial, and neural tube defects in mice. Further analyses suggest that embryonic lethality may be attributable to defects in yolk sac vasculogenesis and angiogenesis. Microarray data indicate that the Gtf2ird1 homozygous phenotype is mainly caused by an impairment of the genes involved in the TGFβRII/Alk1/Smad5 signal transduction pathway. The effect of Gtf2i inactivation on this pathway is less prominent, but downregulation of the endothelial growth factor receptor-2 gene, resulting in the deterioration of vascular signaling, most likely exacerbates the severity of the Gtf2i mutant phenotype. A subset of Gtf2ird1 and Gtf2i heterozygotes displayed microcephaly, retarded growth, and skeletal and craniofacial defects, therefore showing that haploinsufficiency of TFII-I proteins causes various developmental anomalies that are often associated with WBS.

Diversity and complexity in chromatin recognition by TFII-I transcription factors in pluripotent embryonic stem cells and embryonic tissues.

GTF2I and GTF2IRD1 encode a family of closely related transcription factors TFII-I and BEN critical in embryonic development. Both genes are deleted in Williams-Beuren syndrome, a complex genetic disorder associated with neurocognitive, craniofacial, dental and skeletal abnormalities. Although genome-wide promoter analysis has revealed the existence of multiple TFII-I binding sites in embryonic stem cells (ESCs), there was no correlation between TFII-I occupancy and gene expression. Surprisingly, TFII-I recognizes the promoter sequences enriched for H3K4me3/K27me3 bivalent domain, an epigenetic signature of developmentally important genes. Moreover, we discovered significant differences in the association between TFII-I and BEN with the cis-regulatory elements in ESCs and embryonic craniofacial tissues. Our data indicate that in embryonic tissues BEN, but not the highly homologous TFII-I, is primarily recruited to target gene promoters. We propose a “feed-forward model” of gene regulation to explain the specificity of promoter recognition by TFII-I factors in eukaryotic cells.

PI3K/Akt-dependent functions of TFII-I transcription factors in mouse embryonic stem cells.

Activation of PI3K/Akt signaling is sufficient to maintain the pluripotency of mouse embryonic stem cells (mESC) and results in down‐regulation of Gtf2i and Gtf2ird1 encoding TFII‐I family transcription factors. To investigate how these genes might be involved in the process of embryonic stem cell differentiation, we performed expression microarray profiling of mESC upon inhibition of PI3K by LY294002. This analysis revealed significant alterations in expression of genes for specific subsets of chromatin‐modifying enzymes. Surprisingly, genome‐wide promoter ChIP‐chip mapping indicated that the majority of differently expressed genes could be direct targets of TFII‐I regulation. The data support the hypothesis that upregulation of TFII‐I factors leads to activation of a specific group of developmental genes during mESC differentiation. J. Cell. Biochem. 113: 1122–1131, 2012.

Epigenetic modulation by TFII-I during embryonic stem cell differentiation

TFII‐I transcription factors play an essential role during early vertebrate embryogenesis. Genome‐wide mapping studies by ChIP‐seq and ChIP‐chip revealed that TFII‐I primes multiple genomic loci in mouse embryonic stem cells and embryonic tissues. Moreover, many TFII‐I‐bound regions co‐localize with H3K4me3/K27me3 bivalent chromatin within the promoters of lineage‐specific genes. This minireview provides a summary of current knowledge regarding the function of TFII‐I in epigenetic control of stem cell differentiation. J. Cell. Biochem. 113: 3056–3060, 2012.

Genome-wide Chromatin Mapping Defines AP2α in the Etiology of Craniofacial Disorders

Objective The aim of this study is to identify direct AP2α target genes implicated in craniofacial morphogenesis. Design AP2α, a product of the TFAP2A gene, is a master regulator of neural crest differentiation and development. AP2α is expressed in ectoderm and in migrating cranial neural crest (NC) cells that provide patterning information during orofacial development and generate most of the skull bones and the cranial ganglia. Mutations in TFAP2A cause branchio-oculofacial syndrome characterized by dysmorphic facial features including cleft or pseudocleft lip/palate. We hypothesize that AP2α primes a distinctive group of genes associated with NC development. Human promoter ChIP-chip arrays were used to define chromatin regions bound by AP2α in neural crest progenitors differentiated from human embryonic stem cells. Results High-confidence AP2α-binding peaks were detected in the regulatory regions of many target genes involved in the development of facial tissues including MSX1, IRF6, TBX22, and MAFB. In addition, we uncovered multiple single-nucleotide polymorphisms (SNPs) disrupting a conserved AP2α consensus sequence. Conclusions Knowledge of noncoding SNPs in the genomic loci occupied by AP2α provides an insight into the regulatory mechanisms underlying craniofacial development.

TFII-I and AP2α Co-occupy the Promoters of Key Regulatory Genes Associated With Craniofacial Development

Objectives: The aim of this study is to define the candidate target genes for TFII-I and AP2α regulation in neural crest progenitor cells. Design: The GTF2I and GTF2IRD1 genes encoding the TFII-I family of transcription factors are prime candidates for the Williams-Beuren syndrome, a complex multisystem disorder characterized by craniofacial, skeletal, and neurocognitive deficiencies. AP2α, a product of the TFAP2A gene, is a master regulator of neural crest cell lineage. Mutations in TFAP2A cause branchio-oculo-facial syndrome characterized by dysmorphic facial features and orofacial clefts. In this study, we examined the genome-wide promoter occupancy of TFII-I and AP2α in neural crest progenitor cells derived from in vitro-differentiated human embryonic stem cells. Results: Our study revealed that TFII-I and AP2α co-occupy a selective set of genes that control the specification of neural crest cells. Conclusions: The data suggest that TFII-I and AP2α may coordinately control the expression of genes encoding chromatin-modifying proteins, epigenetic enzymes, transcription factors, and signaling proteins.

Generation of a mouse model for a conditional inactivation of Gtf2i allele

The multifunctional transcription factor TFII‐I encoded by the Gtf2i gene is expressed at the two‐cell stage, inner cell mass, trophectoderm, and early gastrula stages of the mouse embryo. In embryonic stem cells, TFII‐I colocalizes with bivalent domains and depletion of Gtf2i causes embryonic lethality, neural tube closure, and craniofacial defects. To gain insight into the function of TFII‐I during late embryonic and postnatal stages, we have generated a conditional Gtf2i null allele by flanking exon 3 with loxP sites. Crossing the floxed line with the Hprt‐Cre transgenic mice resulted in inactivation of Gtf2i in one‐cell embryo. The Cre‐mediated deletion of exon 3 recapitulates a genetic null phenotype, indicating that the conditional Gtf2i line is a valuable tool for studying TFII‐I function during embryonic development. genesis 54:407–412, 2016.

3D genome architecture in the mammalian nucleus

Advances in DNA-sequencing technologies have made it possible to study the spatial hierarchy of genomic organization across different eukaryotic systems. Although genetic information is encrypted in the linear DNA sequence, a growing body of research suggests that the 3D genome plays an essential role in gene regulation [1]. The latest technological innovations associated with chromosome conformation capture methodologies (e.g., 3C, 4C, 5C, Hi-C and ChIA-PET) in mapping higher-order genomic communications have established new principles that describe spatial chromatin organization and its role in transcriptional control [2,3]. Experimental evidence indicates that the nuclear architecture is composed of a hierarchy of genomic interactions, from chromatin loops that connect genes and enhancers to larger chromosome territories and nuclear compartments [1,2,4].