GENE TRAPPING Paras Yadav Jaspreet Singh Arora Sachinandan

GENE TRAPPING Paras Yadav*, Jaspreet Singh Arora*, Sachinandan De*, Tirtha Kumar Datta*, Surender Lal Goswami*, Aarti Bhardwaj$, Shalini Jain# and Hariom Yadav# *Animal Biotechnology, #Animal Biochemistry Division, National Dairy Research Institute, Karnal-132001, Haryana, India $Meerut Institute of Engeenering and Technology, Meerut, U. P. , India

What is gene trapping ? Gene trapping is a form of insertional mutagenesis specifically designed to disrupt gene function by producing intragenic integration events. Evans, M. J. (1998) Dev. Dyn. , 212, 167 -169

• A random integration of a reporter gene construct, called entrapment vector into genome. • Productive integration events bring the reporter gene under the transcriptional regulation of an endogenous gene.

Regulatory Components of a Gene – important for its expression Enhancer a set of short sequence elements which stimulate transcription of a gene. Promoter a combination of short sequence elements to which RNA polymerase binds in order to initiate transcription of a gene. Polyadenylation addition of typically 200 A residues to the 3' end of a m. RNA. The poly(A) tail is important for stabilizing m. RNA.

Basic Strategy in Gene Trap

Gene trap Strategy Choosing proper vector and delivery system Selecting the clones with markers Identification of location of the insert in the clone Studying biological questions: Production of chimeras

Components of gene trap: • Mouse or human embryonic stem cell (for mammalian model) • Entrapment vector construct having the reporter gene and selectable marker.

Reporter genes • The E. coli lac. Z gene • The E. coli. Chloramphenicol acetyltransferase (CAT) gene • The firefly luciferase gene • The jelly fish green flourecence protein (GFP) gene

Selectable Markers Positive selection: • Neomycin phosphotransferase gene (neo. R) • Puromycin selection (Puro) Negative selection: • Herpes Simplex Thymidine kinase gene (hsv-tk) • Diphtheria toxin gene

Types of vectors • • Enhancer trap vector Promoter trap vector Gene trap poly A trap

Enhancer Trap Endogenous gene X Vector promoter Enhancer Exon 1 Exon 2 DNA RNA protein. X lac Z neo lac Z p. A Exon 3 Vector Integration promoter P' neo lac Z neo β-gal Neo. R p. A

Promoter Trap Endogenous gene X P' lac Z neo p. A Vector Integration DNA lac Z RNA protein lac Z protein. X β-gal neo Neo. R p. A

Gene Trap Endogenous gene X P' lac Z SA Vector Integration SA DNA lac Z neo Spliced transcript RNA protein lac Z SA neo protein. X β-gal Neo. R neo p. A

Poly A Trap Endogenous gene X P' lac Z SA neo SD p. A Vector Integration SA DNA lac Z neo p. A SA RNA lac Z neo p. A protein. X β-gal Neo. R Nature Reviews Genet 2: 756 (2001)

Special types of Trapping (keeping functional objectives in view) 1. Secretory trap 2. Cre-lox. P system 3. Chromosomal deletion using Negative selection 4. Protein trap

1. Secretory Trap: Basic strategy

Secretory Trap: Improved strategy Protein

Identification of role of specific gene during development Trapped Gene name Coronal sections of forebrains showing PLAP expression in Secretory trap in mouse at birth Area of brain Nature 410: 174 (2001)

2. cre-lox. P mediated excision

Construct with lox. P site: lox. P DNA after integration RNA Exon from endogenous gene

3. Protein Trap Introns Brief Funct Genomic Proteomic. 2: 137 (2003)

Expression of trapped genes (GFP) in different developmental stages FEBS Letters 480: 63 (2000)

Vector Delivery 1. Chemical method: using reagents to package vector DNA 2. Electroporation: Applying electrical forces to enhance cell membrane pores 3. Biological system: Viral infection with adeno, lenti or retroviral vectors

Identification of insert location 1. Using a Rescue Vector strategy 2. Using a Expression of the reporter/marker gene- RACE

Applications of gene trap

Labeling Cell Lineages Effect of mutagenesis Gene Trap Identifying New Genes Chromosome Trap Induced Deletions

Gene trap helps in annotation of genome and identifying new genes with unknown function Nucleic Acids Research 32: 3995 (2004)

Studying X- chromosome Inactivation in Human Alleles Gel Nucleic Acids Research (2004)

Using gene trap method this study concluded that: In human extra-embryonic tissue (placenta), X inactivation is of non- random type. One can learn more about epigenetics using trapped clones and identify imprinted genes (those are expressed from one chromosome only). Nat Genet. 28: 310 (2001).

Should not be confused with gene targeting

What is gene targeting? • Integration of genomic DNA into mammalian cell genome by homologous sequence recombination. • It is usually used to create direct mutagenesis in mammalian cell particularly in mouse embryonic stem cell. • Phenotypic consequence of specific genetic modification can be assessed in the organism (e. g. loss of function ).

Gene Targeting Negative selection Positive selection TK neo x Vector x gene Chromosome Homologous recombination neo Targeted locus

Limitations of gene trap 1. Lack of effective prescreening of trapped genes. 2. Integration of multiple copies of the trap vector etc. 3. Biasness of the trapping vectors. 4. Cannot be used for genes which are permanently switched off. 5. Particular gene of interest may not be mutated. 6. Effect of Differential and Alternative Splicing.