1
|
Pandey GK, Vadlamudi S, Currin KW, Moxley AH, Nicholas JC, McAfee JC, Broadaway KA, Mohlke KL. Liver regulatory mechanisms of noncoding variants at lipid and metabolic trait loci. HGG Adv 2024; 5:100275. [PMID: 38297830 PMCID: PMC10881423 DOI: 10.1016/j.xhgg.2024.100275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 01/23/2024] [Accepted: 01/23/2024] [Indexed: 02/02/2024] Open
Abstract
Genome-wide association studies (GWASs) have identified hundreds of risk loci for liver disease and lipid-related metabolic traits, although identifying their target genes and molecular mechanisms remains challenging. We predicted target genes at GWAS signals by integrating them with molecular quantitative trait loci for liver gene expression (eQTL) and liver chromatin accessibility QTL (caQTL). We predicted specific regulatory caQTL variants at four GWAS signals located near EFHD1, LITAF, ZNF329, and GPR180. Using transcriptional reporter assays, we determined that caQTL variants rs13395911, rs11644920, rs34003091, and rs9556404 exhibit allelic differences in regulatory activity. We also performed a protein binding assay for rs13395911 and found that FOXA2 differentially interacts with the alleles of rs13395911. For variants rs13395911 and rs11644920 in putative enhancer regulatory elements, we used CRISPRi to demonstrate that repression of the enhancers altered the expression of the predicted target and/or nearby genes. Repression of the element at rs13395911 reduced the expression of EFHD1, and repression of the element at rs11644920 reduced the expression of LITAF, SNN, and TXNDC11. Finally, we showed that EFHD1 is a metabolically active gene in HepG2 cells. Together, these results provide key steps to connect genetic variants with cellular mechanisms and help elucidate the causes of liver disease.
Collapse
Affiliation(s)
- Gautam K Pandey
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | | | - Kevin W Currin
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Anne H Moxley
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Jayna C Nicholas
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Jessica C McAfee
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - K Alaine Broadaway
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Karen L Mohlke
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA.
| |
Collapse
|
2
|
Fernandes LGV, Foltran BB, Teixeira AF, Nascimento ALTO. LipL41 and LigA/LigB Gene Silencing on a LipL32 Knockout Leptospira interrogans Reveals the Impact of Multiple Mutations on Virulence. Pathogens 2023; 12:1191. [PMID: 37887707 PMCID: PMC10610384 DOI: 10.3390/pathogens12101191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 09/15/2023] [Accepted: 09/21/2023] [Indexed: 10/28/2023] Open
Abstract
Leptospirosis is a global zoonosis caused by pathogenic bacteria of the genus Leptospira. The application of the CRISPR/Cas9 system has facilitated the generation of mutants and subsequent evaluation of phenotypes. Since DNA breaks induced by RNA-guided Cas9 nuclease are lethal to Leptospira, different methodologies were implemented to overcome this limitation. Initially, CRISPR interference (CRISPRi) was employed to create knockdown mutants, utilizing a catalytically inactive Cas9 (dCas9). Subsequently, the co-expression of CRISPR/Cas9 and a DNA repair system from Mycobacterium smegmatis enabled the generation of scarless knockout mutants. We eliminated plasmids from the lipL32 knockout L. interrogans strain and further achieved multiple gene mutations via gene silencing in this knockout background. Strains lacking both LipL41 and LipL32 and LigA, LigB, and LipL32, were evaluated. The absence of proteins LipL32 and LipL41 had no effect on leptospiral virulence. On the other hand, mutants lacking LigA, LigB, and LipL32 were unable to cause acute disease. The expanded apparatus for genetic manipulation of pathogenic leptospires via the CRISPR/Cas9 system has allowed the evaluation of multiple mutations upon leptospiral virulence. This work shows that LipL32 and LipL41 are not required for acute disease and consolidates LigA and LigB proteins as virulence factors.
Collapse
Affiliation(s)
- Luis Guilherme V. Fernandes
- Laboratório de Desenvolvimento de Vacinas, Instituto Butantan, Avenida Vital Brazil, 1500, São Paulo 05503-900, SP, Brazil; (B.B.F.); (A.F.T.)
| | - Bruno B. Foltran
- Laboratório de Desenvolvimento de Vacinas, Instituto Butantan, Avenida Vital Brazil, 1500, São Paulo 05503-900, SP, Brazil; (B.B.F.); (A.F.T.)
- Programa de Pos-Graduacao Interunidades em Biotecnologia, Instituto de Ciencias Biomedicas, São Paulo 05508-900, SP, Brazil
| | - Aline F. Teixeira
- Laboratório de Desenvolvimento de Vacinas, Instituto Butantan, Avenida Vital Brazil, 1500, São Paulo 05503-900, SP, Brazil; (B.B.F.); (A.F.T.)
| | - Ana Lucia Tabet Oller Nascimento
- Laboratório de Desenvolvimento de Vacinas, Instituto Butantan, Avenida Vital Brazil, 1500, São Paulo 05503-900, SP, Brazil; (B.B.F.); (A.F.T.)
- Programa de Pos-Graduacao Interunidades em Biotecnologia, Instituto de Ciencias Biomedicas, São Paulo 05508-900, SP, Brazil
| |
Collapse
|
3
|
Brackett K, Mungale A, Lopez-Isidro M, Proctor DA, Najarro G, Arias C. CRISPR Interference Efficiently Silences Latent and Lytic Viral Genes in Kaposi's Sarcoma-Associated Herpesvirus-Infected Cells. Viruses 2021; 13:783. [PMID: 33924938 PMCID: PMC8146339 DOI: 10.3390/v13050783] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 04/22/2021] [Accepted: 04/22/2021] [Indexed: 12/28/2022] Open
Abstract
Uncovering viral gene functions requires the modulation of gene expression through overexpression or loss-of-function. CRISPR interference (CRISPRi), a modification of the CRISPR-Cas9 gene editing technology, allows specific and efficient transcriptional silencing without genetic ablation. CRISPRi has been used to silence eukaryotic and prokaryotic genes at the single-gene and genome-wide levels. Here, we report the use of CRISPRi to silence latent and lytic viral genes, with an efficiency of ~80-90%, in epithelial and B-cells carrying multiple copies of the Kaposi's sarcoma-associated herpesvirus (KSHV) genome. Our results validate CRISPRi for the analysis of KSHV viral elements, providing a functional genomics tool for studying virus-host interactions.
Collapse
Affiliation(s)
- Kevin Brackett
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA 93106, USA; (K.B.); (A.M.); (M.L.-I.); (D.A.P.); (G.N.)
| | - Ameera Mungale
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA 93106, USA; (K.B.); (A.M.); (M.L.-I.); (D.A.P.); (G.N.)
| | - Mary Lopez-Isidro
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA 93106, USA; (K.B.); (A.M.); (M.L.-I.); (D.A.P.); (G.N.)
| | - Duncan A. Proctor
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA 93106, USA; (K.B.); (A.M.); (M.L.-I.); (D.A.P.); (G.N.)
| | - Guillermo Najarro
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA 93106, USA; (K.B.); (A.M.); (M.L.-I.); (D.A.P.); (G.N.)
| | - Carolina Arias
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA 93106, USA; (K.B.); (A.M.); (M.L.-I.); (D.A.P.); (G.N.)
- Neuroscience Research Institute, University of California, Santa Barbara, CA 93106, USA
- Center for Stem Cell Biology and Engineering, University of California, Santa Barbara, CA 93106, USA
| |
Collapse
|
4
|
Fu BXH, Wainberg M, Kundaje A, Fire AZ. High-Throughput Characterization of Cascade type I-E CRISPR Guide Efficacy Reveals Unexpected PAM Diversity and Target Sequence Preferences. Genetics 2017; 206:1727-1738. [PMID: 28634160 PMCID: PMC5560783 DOI: 10.1534/genetics.117.202580] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 05/29/2017] [Indexed: 12/18/2022] Open
Abstract
Interactions between Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) RNAs and CRISPR-associated (Cas) proteins form an RNA-guided adaptive immune system in prokaryotes. The adaptive immune system utilizes segments of the genetic material of invasive foreign elements in the CRISPR locus. The loci are transcribed and processed to produce small CRISPR RNAs (crRNAs), with degradation of invading genetic material directed by a combination of complementarity between RNA and DNA and in some cases recognition of adjacent motifs called PAMs (Protospacer Adjacent Motifs). Here we describe a general, high-throughput procedure to test the efficacy of thousands of targets, applying this to the Escherichia coli type I-E Cascade (CRISPR-associated complex for antiviral defense) system. These studies were followed with reciprocal experiments in which the consequence of CRISPR activity was survival in the presence of a lytic phage. From the combined analysis of the Cascade system, we found that (i) type I-E Cascade PAM recognition is more expansive than previously reported, with at least 22 distinct PAMs, with many of the noncanonical PAMs having CRISPR-interference abilities similar to the canonical PAMs; (ii) PAM positioning appears precise, with no evidence for tolerance to PAM slippage in interference; and (iii) while increased guanine-cytosine (GC) content in the spacer is associated with higher CRISPR-interference efficiency, high GC content (>62.5%) decreases CRISPR-interference efficiency. Our findings provide a comprehensive functional profile of Cascade type I-E interference requirements and a method to assay spacer efficacy that can be applied to other CRISPR-Cas systems.
Collapse
Affiliation(s)
- Becky Xu Hua Fu
- Department of Genetics, Stanford University School of Medicine, California 94305
| | - Michael Wainberg
- Department of Computer Science, Stanford University, California 94305
| | - Anshul Kundaje
- Department of Genetics, Stanford University School of Medicine, California 94305
- Department of Computer Science, Stanford University, California 94305
| | - Andrew Z Fire
- Department of Genetics, Stanford University School of Medicine, California 94305
- Department of Pathology, Stanford University School of Medicine, California 94305
| |
Collapse
|