- In a transgenic mice line, lox P sites are introduced in the target A in the following manner
This transgenic mice line was mated with another transgenic mice line where Cre recombinase is expressed only in B cells. What will be the expression profile of gene A in Cre/lox recombinant mice?
(1) Gene will not be expressed in B cells, as orientation of exon I will be inverted by Cre.
(2) Gene will not be expressed in B cells, as exon 2 will be deleted by Cre.
(3) Gene will only be expressed in B cells of the recombinant mice where Cre removes the two lox P sites.
(4) Gene will not be expressed in B cells as orientation of exon 2 will be inverted.
The correct answer is option (2): in B cells, Cre recombinase will delete exon 2 because it is flanked by two loxP sites in the same orientation, so gene A will not be expressed in B cells.
Introduction
This CSIR NET June 2014 life sciences question tests understanding of the Cre–loxP recombination system, especially how the relative orientation of loxP sites determines whether a DNA segment will be deleted or inverted. In the problem, a transgenic mouse line carries gene A with exon 2 flanked by loxP sites, and it is crossed with another line expressing Cre recombinase only in B cells, leading to a B cell–specific change in gene expression.
Concept: Cre–loxP recombination and loxP orientation
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Cre recombinase recognizes 34 bp loxP sites and catalyzes recombination between two loxP sites.
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When loxP sites are on the same DNA molecule and in the same orientation, Cre excises (deletes) the intervening DNA as a circular fragment, leaving behind a single loxP site in the genome.
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When loxP sites are on the same molecule but in opposite orientations, Cre inverts the intervening DNA segment, flipping its orientation without deleting it.
In conditional knockout mice, a critical exon is often flanked by loxP sites (“floxed”) so that Cre expression in specific tissues deletes that exon and disrupts the gene only in those cells.
Applying the concept to this question
In the given construct, promoter–exon 1–loxP–exon 2–loxP are arranged with both loxP sites in the same direction, and exon 2 lies between them. When these mice are crossed with a line expressing Cre only in B cells, Cre will be present only in B cells, so recombination will occur only there, deleting exon 2 and leaving exon 1 joined to the downstream sequence with a single residual loxP site. Loss of exon 2 will generally truncate or frameshift gene A, so gene A will not be functionally expressed in B cells, while in other cell types without Cre, gene A remains intact.
Option-by-option explanation
Option (1)
Statement: Gene will not be expressed in B cells, as orientation of exon 1 will be inverted by Cre.
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Inversion requires loxP sites in opposite orientations flanking the segment to be inverted.
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In this construct, exon 1 is not between the two loxP sites; only exon 2 is flanked by them, and the loxP sites are drawn in the same direction, so exon 1 cannot be inverted by Cre.
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Therefore, this option is incorrect.
Option (2) – Correct
Statement: Gene will not be expressed in B cells, as exon 2 will be deleted by Cre.
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Exon 2 lies between two loxP sites that share the same orientation, the classic configuration for Cre-mediated deletion of the intervening sequence.
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In B cells, Cre excises exon 2, producing an mRNA missing exon 2; this usually disrupts the reading frame or removes an essential coding region, resulting in loss of functional gene A expression specifically in B cells.
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Hence option (2) correctly describes both the molecular event (exon 2 deletion) and the consequence (gene A not expressed in B cells), so it is the right answer.
Option (3)
Statement: Gene will only be expressed in B cells of the recombinant mice where Cre removes the two loxP sites.
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Cre does not simply “remove the loxP sites” without affecting the intervening exon; deletion of the region between identically oriented loxP sites removes that exon along with one of the loxP sites, leaving a single loxP behind.
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Removal of exon 2 in B cells inactivates gene A there, so gene A expression is actually lost, not gained, in B cells; it remains expressed in other tissues lacking Cre.
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Thus this option reverses the tissue-specific expression outcome and is incorrect.
Option (4)
Statement: Gene will not be expressed in B cells as orientation of exon 2 will be inverted.
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Inversion requires loxP sites in opposite orientations flanking exon 2, but in the diagram they are shown in the same orientation.
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With identically oriented loxP sites, Cre excises exon 2 rather than inverting it, so the mechanism stated in this option is wrong, even though the final statement “gene will not be expressed in B cells” matches the true phenotype.
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Because the question couples mechanism and outcome, a mechanistically incorrect explanation makes this option incorrect.
Key takeaway
This question illustrates that in Cre–loxP genetics, the orientation and position of loxP sites relative to exons determine whether Cre mediates deletion or inversion, which in turn defines where and how a gene is inactivated in conditional knockout mice.
