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     Quick Answer


    Yes, you will obtain mRNA products, but the levels and types may vary depending on the CRISPR modifications made.


     Long Answer


    Understanding CRISPR and mRNA Sequencing

    When you perform CRISPR gene editing in cells, you are typically targeting specific genes for modification, which can include knocking out genes, inserting new sequences, or altering existing ones. After CRISPR editing, if you extract mRNA and sequence it, you can expect to see several outcomes based on the nature of the edits made.

    Expected Outcomes in mRNA Sequencing

    • Retention of Wild-Type mRNA: If the CRISPR system does not affect the target gene's transcription, you will still see the wild-type mRNA in your sequencing results.
    • Altered mRNA Levels: If the CRISPR editing leads to a knockout or significant alteration of the target gene, you may observe a decrease in the corresponding mRNA levels. For instance, in a study involving CRISPR-Cas13a targeting the FGFR3-TACC3 fusion gene, significant reductions in mRNA expression were noted post-editing, indicating effective gene knockdown ().
    • Novel mRNA Products: If you introduce new sequences or modify existing ones, you may detect novel mRNA transcripts resulting from these edits. For example, CRISPR can be used to insert reporter genes, which would then be reflected in the mRNA sequencing data.
    • Compensatory Mechanisms: In some cases, the disruption of one gene may lead to compensatory upregulation of other related genes, which can also be observed in the sequencing results. For instance, in a study on zebrafish, the disruption of dact1 and dact2 led to compensatory changes in mRNA levels of these genes, indicating a complex regulatory network at play ().

    Conclusion

    In summary, after performing CRISPR in cells and sequencing the extracted mRNA, you can expect to see a mixture of wild-type mRNA, altered levels of target mRNA, and potentially novel mRNA products depending on the nature of the CRISPR modifications. The specific outcomes will depend on the target gene, the type of CRISPR system used, and the cellular context.



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    Updated: January 10, 2025

     Key Insight


    CRISPR can lead to complex changes in mRNA expression, including knockouts, compensatory upregulation, and novel transcript formation, reflecting the intricate regulatory networks in cells.

     Bioinformatics Wizard


    This code analyzes mRNA sequencing data to identify changes in expression levels post-CRISPR editing, utilizing relevant datasets for validation.


    import pandas as pd
import matplotlib.pyplot as plt

# Load mRNA sequencing data
mRNA_data = pd.read_csv('mRNA_sequencing_results.csv')

# Analyze expression levels
expression_changes = mRNA_data.groupby('gene').mean().reset_index()

# Plotting the results
plt.figure(figsize=(10,6))
plt.bar(expression_changes['gene'], expression_changes['expression_level'])
plt.title('mRNA Expression Levels Post-CRISPR Editing')
plt.xlabel('Gene')
plt.ylabel('Expression Level')
plt.xticks(rotation=45)
plt.tight_layout()
plt.show()

      

     Hypothesis Graveyard


    The assumption that CRISPR will only affect the targeted gene is overly simplistic, as off-target effects and compensatory mechanisms can significantly alter mRNA profiles.


    It was previously thought that CRISPR would always lead to a straightforward decrease in target mRNA levels, but compensatory mechanisms can complicate this outcome.

     Biology Art


    If I performed CRISPR in cells, extracted mRNA, and then sequenced it, what should I expect to see in the sequencing results? Will I still obtain an mRNA product despite using CRISPR? Biology Art

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