BACing up the interferon-gamma locus

Advances in bacterial artificial chromosome (BAC) transgenic mice for gene analysis and disease research

Transgenic mice, including those created using Bacterial Artificial Chromosomes (BACs), are artificial manipulations that have become critical tools for studying gene function. While conventional transgenic techniques face challenges in achieving precise expression of foreign genes in specific cells and tissues, BAC transgenic mice offer a solution by incorporating large DNA segments that can include entire expression units with tissue-specific enhancers. This review provides a thorough examination of BAC transgenic mouse technology, encompassing both traditional and humanized models. We explore the benefits and drawbacks of BAC transgenesis compared to other techniques such as knock-in and CRISPR/Cas9 technologies. The review emphasizes the applications of BAC transgenic mice in various disciplines, including neuroscience, immunology, drug metabolism, and disease modeling. Additionally, we address crucial aspects of generating and analyzing BAC transgenic mice, such as position effects, copy number variations, and strategies to mitigate these challenges. Despite certain limitations, humanized BAC transgenic mice have proven to be invaluable tools for studying the pathogenesis of human diseases, drug development, and understanding intricate gene regulatory mechanisms. This review discusses current topics on BAC transgenic mice and their evolving significance in biomedical research.

Crystal structure of the DNA binding domain of the transcription factor T-bet suggests simultaneous recognition of distant genome sites

The transcription factor T-bet (Tbox protein expressed in T cells) is one of the master regulators of both the innate and adaptive immune responses. It plays a central role in T-cell lineage commitment, where it controls the T_H1 response, and in gene regulation in plasma B-cells and dendritic cells. T-bet is a member of the Tbox family of transcription factors; however, T-bet coordinately regulates the expression of many more genes than other Tbox proteins. A central unresolved question is how T-bet is able to simultaneously recognize distant Tbox binding sites, which may be located thousands of base pairs away. We have determined the crystal structure of the Tbox DNA binding domain (DBD) of T-bet in complex with a palindromic DNA. The structure shows a quaternary structure in which the T-bet dimer has its DNA binding regions splayed far apart, making it impossible for a single dimer to bind both sites of the DNA palindrome. In contrast to most other Tbox proteins, a single T-bet DBD dimer binds simultaneously to identical half-sites on two independent DNA. A fluorescence-based assay confirms that T-bet dimers are able to bring two independent DNA molecules into close juxtaposition. Furthermore, chromosome conformation capture assays confirm that T-bet functions in the direct formation of chromatin loops in vitro and in vivo. The data are consistent with a looping/synapsing model for transcriptional regulation by T-bet in which a single dimer of the transcription factor can recognize and coalesce distinct genetic elements, either a promoter plus a distant regulatory element, or promoters on two different genes.

A detailed protocol for bacterial artificial chromosome recombineering to study essential genes in stem cells

Bacterial artificial chromosome (BAC) recombineering is a novel technique for DNA manipulation. It starts from an original chromosomal gene locus that is modified to introduce a transgene under the expression control of the original gene locus. In most cases a cell type specific promoter is chosen and the transgene is placed in a way that the exon containing the start codon is replaced. Alternatively, BACs such as the Rosa26 BAC are chosen because of their known open chromatin and ubiquitous promoter activity that allows a broad expression profile of the transgene in the whole body. Thus, transgenes can be overexpressed within their natural transcriptional regulatory circuit. BAC transgenes have a high tendency to maintain their appropriate chromatin status because the endogenous locus was expressed in different cell types. Here, we give a detailed protocol based on the original idea to choose a BAC approach until the injection of the modified BAC DNA that leads to the generation of novel transgenic mouse lines. As an example for a BAC mouse model suitable for the analysis of stem cell or hematopoietic stem cell functions, we chose modification of the locus for the transcription factor Stat3. Stat3 variants replace the wild-type Stat3 gene to study their function in particular in the earliest cell types of the body.