Biology:CRISPR interference

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Short description: Genetic perturbation technique
Transcriptional repression via steric hindrance

CRISPR interference (CRISPRi) is a genetic perturbation technique that allows for sequence-specific repression of gene expression in prokaryotic and eukaryotic cells.[1] It was first developed by Stanley Qi and colleagues in the laboratories of Wendell Lim, Adam Arkin, Jonathan Weissman, and Jennifer Doudna.[2] Sequence-specific activation of gene expression refers to CRISPR activation (CRISPRa).

Based on the bacterial genetic immune system - CRISPR (clustered regularly interspaced short palindromic repeats) pathway,[3] the technique provides a complementary approach to RNA interference. The difference between CRISPRi and RNAi, though, is that CRISPRi regulates gene expression primarily on the transcriptional level, while RNAi controls genes on the mRNA level.

Background

Many bacteria and most archaea have an adaptive immune system which incorporates CRISPR RNA (crRNA) and CRISPR-associated (cas) genes.

The CRISPR interference (CRISPRi) technique was first reported by Lei S. Qi and researchers at the University of California at San Francisco in early 2013.[2] The technology uses a catalytically dead Cas9 (usually denoted as dCas9) protein that lacks endonuclease activity to regulate genes in an RNA-guided manner. Targeting specificity is determined by complementary base-pairing of a single guide RNA (sgRNA) to the genomic locus. sgRNA is a chimeric noncoding RNA that can be subdivided into three regions: a 20 nt base-pairing sequence, a 42 nt dCas9-binding hairpin and a 40 nt terminator (bacteria,[4] [5] [6] yeast,[7] fruit flies,[8] zebrafish,[9] mice[10]).

When designing a synthetic sgRNA, only the 20 nt base-pairing sequence is modified. Secondary variables must also be considered: off-target effects (for which a simple BLAST run of the base-pairing sequence is required), maintenance of the dCas9-binding hairpin structure, and ensuring that no restriction sites are present in the modified sgRNA, as this may pose a problem in downstream cloning steps. Due to the simplicity of sgRNA design, this technology is amenable to genome-wide scaling.[11] CRISPRi relies on the generation of catalytically inactive Cas9. This is accomplished by introducing point mutations in the two catalytic residues (D10A and H840A) of the gene encoding Cas9.[12] In doing so, dCas9 is unable to cleave dsDNA but retains the ability to target DNA. Together, sgRNA and dCas9 constitute a minimal system for gene-specific regulation.[2]

Transcriptional regulation

Repression

CRISPRi can sterically repress transcription by blocking either transcriptional initiation or elongation. This is accomplished by designing sgRNA complementary to the promoter or the exonic sequences. The level of transcriptional repression with a target within the coding sequence is strand-specific. Depending on the nature of the CRISPR effector, either the template or non-template strand leads to stronger repression.[13] For dCas9 (based on a Type-2 CRISPR system), repression is stronger when the guide RNA is complementary to the non-template strand. It has been suggested that this is due to the activity of helicase, which unwinds the RNA:DNA heteroduplex ahead of RNA pol II when the sgRNA is complementary to the template strand. Unlike transcription elongation block, silencing is independent of the targeted DNA strand when targeting the transcriptional start site. In prokaryotes, this steric inhibition can repress transcription of the target gene by almost 99.9%; in archaea, more than 90% repression was achieved;[14] in human cells, up to 90% repression was observed.[2] In bacteria, it is possible to saturate the target with a high enough level of dCas9 complex. In this case, the repression strength only depends on the probability that dCas9 is ejected upon collision with the RNA polymerase, which is determined by the guide sequence.[15] Higher temperatures are also associated with higher ejection probability, thus weaker repression.[15] In eukaryotes, CRISPRi can also repress transcription via an effector domain. Fusing a repressor domain to dCas9 allows transcription to be further repressed by inducing heterochromatinization. For example, the well-studied Krüppel associated box (KRAB) domain can be fused to dCas9 to repress transcription of the target gene up to 99% in human cells.[16]

Improvements on the efficiency

Whereas genome-editing by the catalytically active Cas9 nuclease can be accompanied by irreversible off-target genomic alterations, CRISPRi is highly specific with minimal off-target reversible effects for two distinct sgRNA sequences.[16] Nonetheless, several methods have been developed to improve the efficiency of transcriptional modulation. Identification of the transcription start site of a target gene and considering the preferences of sgRNA improves efficiency, as does the presence of accessible chromatin at the target site.[17]

Other methods

Along with other improvements mentioned, factors such as the distance from the transcription start and the local chromatin state may be critical parameters in determining activation/repression efficiency. Optimization of dCas9 and sgRNA expression, stability, nuclear localization, and interaction will likely allow for further improvement of CRISPRi efficiency in mammalian cells.[2]

Applications

Gene knockdown

A significant portion of the genome (both reporter and endogenous genes) in eukaryotes has been shown to be targetable using lentiviral constructs to express dCas9 and sgRNAs, with comparable efficiency to existing techniques such as RNAi and TALE proteins.[16] In tandem or as its own system, CRISPRi could be used to achieve the same applications as in RNAi.

For bacteria, gene knockdown by CRISPRi has been fully implemented and characterized (off-target analysis, leaky repression) for both Gram-negative E. coli [4][6] and Gram-positive B. subtilis.[5]

Not only in bacteria but also in archaea (e.g., M. acetivorans) CRISPRi-Cas9 was successfully utilized to knockdown several genes/operons that related to nitrogen fixation.[14]

CRISPRi construction workflow

Allelic series

Differential gene expression can be achieved by modifying the efficiency of sgRNA base-pairing to the target loci.[11] In theory, modulating this efficiency can be used to create an allelic series for any given gene, in essence creating a collection of hypo- and hypermorphs. These powerful collections can be used to probe any genetic investigation. For hypomorphs, this allows the incremental reduction of gene function as opposed to the binary nature of gene knockouts and the unpredictability of knockdowns. For hypermorphs, this is in contrast to the conventional method of cloning the gene of interest under promoters with variable strength.

Genome loci imaging

Fusing a fluorescent protein to dCas9 allows for imaging of genomic loci in living human cells.[18] Compared to fluorescence in situ hybridization (FISH), the method uniquely allows for dynamic tracking of chromosome loci. This has been used to study chromatin architecture and nuclear organization dynamics in laboratory cell lines including HeLa cells.

Stem cells

Activation of Yamanaka factors by CRISPRa has been used to induce pluripotency in human and mouse cells providing an alternative method to iPS technology.[19][20] In addition, large-scale activation screens could be used to identify proteins that promote induced pluripotency or, conversely, promote differentiation to a specific cell lineage.[21]

Genetic screening

The ability to upregulate gene expression using dCas9-SunTag with a single sgRNA also opens the door to large-scale genetic screens, such as Perturb-seq, to uncover phenotypes that result from increased or decreased gene expression, which will be especially important for understanding the effects of gene regulation in cancer.[22] Furthermore, CRISPRi systems have been shown to be transferable via horizontal gene transfer mechanisms such as bacterial conjugation and specific repression of reporter genes in recipient cells has been demonstrated. CRISPRi could serve as a tool for genetic screening and potentially bacterial population control.[23]

Advantages and limitations

Advantages

  1. CRISPRi can silence a target gene of interest up to 99.9% repression.[11] The strength of the repression can also be tuned by changing the amount of complementarity between the guide RNA and the target. Contrary to inducible promoters, partial repression by CRISPRi does not add transcriptional noise to the target's expression.[15] Since the repression level is encoded in a DNA sequence, various expression levels can be grown in competition and identified by sequencing.[24]
  2. Since CRISPRi is based on Watson-Crick base-pairing of sgRNA-DNA and an NGG PAM motif, selection of targetable sites within the genome is straightforward and flexible. Carefully defined protocols have been developed.[11]
  3. Multiple sgRNAs can not only be used to control multiple different genes simultaneously (multiplex CRISPRi), but also to enhance the efficiency of regulating the same gene target. A popular strategy to express many sgRNAs simultaneously is to array the sgRNAs in a single construct with multiple promoters or processing elements. For example, Extra-Long sgRNA Arrays (ELSAs) use nonrepetitive parts to allow direct synthesis of 12-sgRNA arrays from a gene synthesis provider, can be directly integrated into the E. coli genome without homologous recombination occurring, and can simultaneously target many genes to achieve complex phenotypes.[25]
  4. While the two systems can be complementary, CRISPRi provides advantages over RNAi. As an exogenous system, CRISPRi does not compete with endogenous machinery such as microRNA expression or function. Furthermore, because CRISPRi acts at the DNA level, one can target transcripts such as noncoding RNAs, microRNAs, antisense transcripts, nuclear-localized RNAs, and polymerase III transcripts. Finally, CRISPRi possesses a much larger targetable sequence space; promoters and, in theory, introns can also be targeted.[16]
  5. In E. coli, construction of a gene knockdown strain is extremely fast and requires only one-step oligo recombineering.[6]

Limitations

  1. The requirement of a protospacer adjacent motif (PAM) sequence limits the number of potential target sequences. Cas9 and its homologs may use different PAM sequences, and therefore could theoretically be utilized to expand the number of potential target sequences.[11]
  2. Sequence specificity to target loci is only 14 nt long (12 nt of sgRNA and 2nt of the PAM), which can recur around 11 times in a human genome.[11] Repression is inversely correlated with the distance of the target site from the transcription start site. Genome-wide computational predictions or selection of Cas9 homologs with a longer PAM may reduce nonspecific targeting.
  3. Endogenous chromatin states and modifications may prevent the sequence-specific binding of the dCas9-sgRNA complex.[11] The level of transcriptional repression in mammalian cells varies between genes. Much work is needed to understand the role of local DNA conformation and chromatin in relation to binding and regulatory efficiency.
  4. CRISPRi can influence genes that are in close proximity to the target gene. This is especially important when targeting genes that either overlap other genes (sense or antisense overlapping) or are driven by a bidirectional promoter.[26]
  5. Sequence-specific toxicity has been reported in eukaryotes, with some sequences in the PAM-proximal region causing a large fitness burden.[27] This phenomenon, called the "bad seed effect", is still unexplained but can be reduced by optimizing the expression level of dCas9.[28]

References

  1. ↑ "Targeted regulation of transcription in primary cells using CRISPRa and CRISPRi". Genome Research 31 (11): 2120–2130. November 2021. doi:10.1101/gr.275607.121. PMID 34407984. 
  2. ↑ 2.0 2.1 2.2 2.3 2.4 "Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression". Cell 152 (5): 1173–1183. February 2013. doi:10.1016/j.cell.2013.02.022. PMID 23452860. 
  3. ↑ "CRISPR provides acquired resistance against viruses in prokaryotes". Science 315 (5819): 1709–1712. March 2007. doi:10.1126/science.1138140. PMID 17379808. Bibcode: 2007Sci...315.1709B. 
  4. ↑ 4.0 4.1 "RNA-guided editing of bacterial genomes using CRISPR-Cas systems". Nature Biotechnology 31 (3): 233–239. March 2013. doi:10.1038/nbt.2508. PMID 23360965. 
  5. ↑ 5.0 5.1 "A Comprehensive, CRISPR-based Functional Analysis of Essential Genes in Bacteria". Cell 165 (6): 1493–1506. June 2016. doi:10.1016/j.cell.2016.05.003. PMID 27238023. 
  6. ↑ 6.0 6.1 6.2 "tCRISPRi: tunable and reversible, one-step control of gene expression". Scientific Reports 6: 39076. December 2016. doi:10.1038/srep39076. PMID 27996021. Bibcode: 2016NatSR...639076L. 
  7. ↑ "Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems". Nucleic Acids Research 41 (7): 4336–4343. April 2013. doi:10.1093/nar/gkt135. PMID 23460208. 
  8. ↑ "Genome engineering of Drosophila with the CRISPR RNA-guided Cas9 nuclease". Genetics 194 (4): 1029–1035. August 2013. doi:10.1534/genetics.113.152710. PMID 23709638. 
  9. ↑ "Efficient genome editing in zebrafish using a CRISPR-Cas system". Nature Biotechnology 31 (3): 227–229. March 2013. doi:10.1038/nbt.2501. PMID 23360964. 
  10. ↑ "One-step generation of mice carrying mutations in multiple genes by CRISPR/Cas-mediated genome engineering". Cell 153 (4): 910–918. May 2013. doi:10.1016/j.cell.2013.04.025. PMID 23643243. 
  11. ↑ 11.0 11.1 11.2 11.3 11.4 11.5 11.6 "CRISPR interference (CRISPRi) for sequence-specific control of gene expression". Nature Protocols 8 (11): 2180–2196. November 2013. doi:10.1038/nprot.2013.132. PMID 24136345. 
  12. ↑ "A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity". Science 337 (6096): 816–821. August 2012. doi:10.1126/science.1225829. PMID 22745249. Bibcode: 2012Sci...337..816J. 
  13. ↑ "CRISPR Tools To Control Gene Expression in Bacteria". Microbiology and Molecular Biology Reviews 84 (2). May 2020. doi:10.1128/MMBR.00077-19. PMID 32238445. 
  14. ↑ 14.0 14.1 "A CRISPRi-dCas9 System for Archaea and Its Use To Examine Gene Function during Nitrogen Fixation by Methanosarcina acetivorans". Applied and Environmental Microbiology 86 (21): e01402–20. October 2020. doi:10.1128/AEM.01402-20. PMID 32826220. Bibcode: 2020ApEnM..86E1402D. 
  15. ↑ 15.0 15.1 15.2 "Tuning dCas9's ability to block transcription enables robust, noiseless knockdown of bacterial genes". Molecular Systems Biology 14 (3): e7899. March 2018. doi:10.15252/msb.20177899. PMID 29519933. 
  16. ↑ 16.0 16.1 16.2 16.3 "CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes". Cell 154 (2): 442–451. July 2013. doi:10.1016/j.cell.2013.06.044. PMID 23849981. 
  17. ↑ "Optimizing sgRNA position markedly improves the efficiency of CRISPR/dCas9-mediated transcriptional repression". Nucleic Acids Research 44 (18): e141. October 2016. doi:10.1093/nar/gkw583. PMID 27353328. 
  18. ↑ "Dynamic imaging of genomic loci in living human cells by an optimized CRISPR/Cas system". Cell 155 (7): 1479–1491. December 2013. doi:10.1016/j.cell.2013.12.001. PMID 24360272. 
  19. ↑ "Cas9 effector-mediated regulation of transcription and differentiation in human pluripotent stem cells". Development 141 (1): 219–223. January 2014. doi:10.1242/dev.103341. PMID 24346702. 
  20. ↑ "Direct activation of human and mouse Oct4 genes using engineered TALE and Cas9 transcription factors". Nucleic Acids Research 42 (7): 4375–4390. April 2014. doi:10.1093/nar/gku109. PMID 24500196. 
  21. ↑ "Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors". Cell 126 (4): 663–676. August 2006. doi:10.1016/j.cell.2006.07.024. PMID 16904174. 
  22. ↑ "A protein-tagging system for signal amplification in gene expression and fluorescence imaging". Cell 159 (3): 635–646. October 2014. doi:10.1016/j.cell.2014.09.039. PMID 25307933. 
  23. ↑ "Specific gene repression by CRISPRi system transferred through bacterial conjugation". ACS Synthetic Biology 3 (12): 929–931. December 2014. doi:10.1021/sb500036q. PMID 25409531. 
  24. ↑ "Modulated efficacy CRISPRi reveals evolutionary conservation of essential gene expression-fitness relationships in bacteria". bioRxiv: 805333. 2019-10-15. doi:10.1101/805333. https://www.biorxiv.org/content/10.1101/805333v1. Retrieved 2020-01-16. 
  25. ↑ "Simultaneous repression of multiple bacterial genes using nonrepetitive extra-long sgRNA arrays". Nature Biotechnology 37 (11): 1294–1301. November 2019. doi:10.1038/s41587-019-0286-9. PMID 31591552. 
  26. ↑ "Challenges of CRISPR/Cas9 applications for long non-coding RNA genes". Nucleic Acids Research 45 (3): e12. February 2017. doi:10.1093/nar/gkw883. PMID 28180319. 
  27. ↑ "A CRISPRi screen in E. coli reveals sequence-specific toxicity of dCas9". Nature Communications 9 (1): 1912. May 2018. doi:10.1038/s41467-018-04209-5. PMID 29765036. Bibcode: 2018NatCo...9.1912C. 
  28. ↑ "Gene silencing with CRISPRi in bacteria and optimization of dCas9 expression levels". Methods. Methods for characterizing, applying, and teaching CRISPR-Cas systems 172: 61–75. February 2020. doi:10.1016/j.ymeth.2019.07.024. PMID 31377338. https://hal-pasteur.archives-ouvertes.fr/pasteur-02476079/file/Depardieu_Bikard_2020_Gene_silencing.pdf. 



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