Synthesis of potential shRNAs
The success of RNAi depends on the designing of the shRNA for specific target recognition and minimization of off-target effects. In the present study, unique/specific shRNA molecules were designed based on the Reynolds ranking criteria for the ACACB gene and also, the specificity of the shRNA sequences is important for the formation of RISC (Reynolds et al. 2004; Paddison et al. 2004). In addition to specificity, the G-C content plays an enormous role in the formation of duplex siRNA molecule. Low G-C content is known to decrease affinity for the target sequence, whereas higher G-C content interferes with RISC formation that eventually cleaves the mRNA molecules. The G-C content of the designed shRNA molecules in the present study was moderate for the duplex siRNA formation. In addition to the G-C content, the lack of internal repeats, an A/U-rich 5' end, Tuschl motifs, and other features were included which improves the silencing efficiency of siRNA (Fuchs et al. 2004). Finally, a simple local alignment search tool (BLAST) was also employed to ensure that shRNA had no significant homologies with genes other than the target to avoid possible off-target effects. Further, silencing performance was also positively associated with the siRNA-mRNA duplex (Gduplex) stability (Pascut et al. 2015). Similarly, 1 and 5 shRNAs had higher Gduplex values than shRNA 2, 3, and 4 (which had a low Gduplex value), meaning that 1 and 5 shRNAs could bind the target site more efficiently. The knockdown efficiency of 1 and 5 shRNAs was high, supporting the above predictions. The duplex asymmetry (DSSE) and target site accessibility could improve knockdown efficiency by about 26% and 40%, respectively (Shao et al. 2007). For enhanced RNAi potency, the siRNAs suitable disruption energy and DSSE is < − 10 kcal/mol and > 0.0 kcal/mol, respectively (Shao et al. 2007). We noticed that the expected disruption energies and DSSE for all of the modeled shRNAs were less than − 10 kcal/mol and greater than 0.0 kcal/mol, respectively, suggesting that all shRNAs have the ability to silence genes. It has been discovered that the development of self-structures in shRNA (both unimolecular and bimolecular shRNA folding) reduces the equilibrium affinity for the target mRNA (Lu and Mathews, 2007). For all of the shRNAs the predicted self-structure energies in this sample were low, indicating their efficiency in silencing.
Gene silencing caused by shRNAs is mostly due to sequence-specific mRNA degradation by antisense/guide strand of shRNA (Martinez et al. 2002). The 'guide strand' is inserted into the active RNA-induced silencing complex (RISC) to locate the mRNA, which has a complementary sequence leading to the endonucleolytic cleavage of the target mRNA leading to gene silencing (Hannon, 2002). The degree of secondary structure in the antisense strand was of utmost importance in determining the highly active shRNAs among the several factors controlling the efficiency of gene silencing (Patzel et al. 2005). The development of secondary structure in the antisense strand is a significant factor in shRNA-induced gene silencing (Wolfman et al. 2003; Qiao et al. 2008). The guide-RNA structures are categorized as those, greatest silencing caused by sequences that do not form secondary structures, second best are stem-loop structures with ≥ 2 free nucleotides at 5 'end and ≥ 4 free 3' nucleotides, followed by internal-loop, two stem-loop, and short free end stem-loop structures (Patzel et al. 2005). Therefore, it is understood that secondary structure formation correlates negatively with the efficient silencing of the gene. Hairpin-structured shRNAs are unable to fully open during their function, resulting in low gene silencing efficiency. As a result, the RISC-siRNA complex formed would not be that much effective while interacting with the complementary mRNA. The mRNA local structure is one of the key factors with a strong effect on silencing of the shRNA molecule (Schubert et al. 2005; Gredell et al. 2008; Overhoff et al. 2005; Pascut et al. 2015; Holen 2005; Matveeva et al. 2007). The mRNA contains loop structures that provide easy access to the guide strand for binding the target region which enhances the gene silencing efficiency but the presence of paired nucleotides and hairpins reduced the gene silencing, respectively (Schubert et al. 2005; Holen 2005; Li and Cha 2007). The GC content of the mRNA target region plays a crucial role in loading shRNA into RISC complex (Reynolds et al. 2004; Shah et al. 2007; Wang and Mu 2004; Kretschmer-Kazemi Far 2003; Bohula et al. 2003; Stewart et al. 2008; Luo and Chang 2004). In our study, all the ACACB mRNA target regions of shRNAs revealed stem-loop structures and optimum GC% content (42.86 to 47.6). However, there might be some other factors which also contributes to the different silencing efficiency of shRNA constructs.
Following these findings, shRNA constructs 1 and 5 were devoid of any secondary structures in their antisense strands while shRNA constructs 2, 3, and 4 formed secondary structures. Accordingly, shRNA 1 and 5 had higher knockdown efficiency (67 and 69%) respectively, while shRNA 2, 3, and 4 had lower knockdown percentages (25–39%) which confirms the earlier reports (Patzel et al. 2005; Wolfman et al. 2003; Qiao et al. 2008). As compared to the control, all the shRNAs showed lower expression of the ACACB gene and among the five shRNAs, the shRNA 5 showed higher knockdown whereas shRNA 2 showed lower knockdown respectively.
ACACB gene silencing in chicken myoblast cells
Transfection of shRNA constructs into the CEM resulted in a notable down-regulation of ACACB mRNA, implying that CEM culture can be used as an in vitro model for some functional studies. Owing to the lack of secondary structures, shRNA 1 and 5 had a higher silencing efficiency than the other shRNAs. In the case of shRNA 2, intrinsic factors such as low duplex energy and high disruption energy may have made the mRNA-shRNA hybridization complex less stable, resulting in incomplete accessibility of the target mRNA region. Secondary structure formation in shRNA 2, 3, and 4 might have reduced their efficiency of silencing by influencing the hybridization of the siRNA/RISC to its target site (Schubert et al. 2005).
In goat fibroblast cells, observed that substantial silencing of ACTRIIB gene as 33–66 % (Patel et al. 2014). Besides, several researchers have carried out knockdown experiments on the MSTN gene in different animals, including chicken. However, the MSTN gene was silenced up to 68 and 75% in chicken embryo fibroblast cells (Sato et al. 2006; Tripathi et al. 2013). Later on, in the same chicken embryo fibroblast cells shRNA was used against MSTN, ACTRIIA, and ACTRIIB genes and observed the knockdown percentage of 68, 82 and 87, respectively (Tripathi et al. 2013; Satheesh et al. 2016; Guru Vishnu et al. 2019). Even in in vivo studies, MSTN knockdown chicken showed 28% more body weight during 42 days of age compared to the control broiler chicken (Bhattacharya et al. 2017). In duck embryonic fibroblasts, different lentivirus-mediated shRNA groups were compared and showed decreased the MSTN mRNA expression by 61.6, 76.9, and 79.1%, respectively (Tao et al. 2015). Further, in caprine foetal fibroblasts, transient transfection of anti-myostatin shRNA decreased the mRNA level by 89 and 72%, respectively (Kumar et al. 2014; Jain et al. 2015). The importance of using thermodynamic features in shRNA designing was highlighted by observing the relationship between shRNA thermodynamic parameters and the silencing performance of different shRNAs. Based on the findings, it is hypothesized that every designed shRNA with Goverall, Gduplex, Gbreaktarget, and Gends of shRNAs in the range of 25 to 32 kcal/mol, 31 to 35 kcal/mol, 1.0 to 1.9 kcal/mol, and > 0.0 Kcal/mol kcal/mol, respectively, would appease for maximum silencing efficiency.
Effect on immune response genes
Although RNA interference has promised to be a powerful experimental tool to manipulate gene function, there has been a growing concern about the use of shRNA due to off-target effects such as activation of immune response. Few studies have stated that both non-immune cells and immune cells can recognize shRNAs independent of the sequence leading to interferon (IFN) induction and inflammatory cytokines both in vivo and in vitro (Sledz et al. 2003; Judge et al. 2005). The IFN response caused by the activation of dsRNA-dependent protein kinase R (PKR) leads to the global inhibition of protein synthesis (Judge et al. 2005). The dsRNA (> 23-bp) can affect cell viability and induce a powerful interferon response (strong up-regulation of the dsRNA receptor, Toll-like receptor 3) in a cell type-specific manner (Reynolds et al. 2006). It was concluded that the length threshold of siRNA-induced interferon response was not constant, but it differed between various types of cells significantly. However, shRNAs shorter than 30 bp can evade PKR activation (Robbins et al. 2006) and some experiments exhibited a significant increase in the expression of immune response genes including Scramble shRNA. It was also observed that activation of interferon response in goat myoblast cells due to exogenous administration of shRNA against the ACTRIIB gene (Patel et al. 2014). Interferon modulation in chicken embryonic myoblast cells varied between 46–112 folds of OAS1 and 2-7.2 folds for IFNβ compared to mock-transfected control due to anti myostatin shRNA (Tripathi et al. 2013). It has been reported that the shRNA-mediated myostatin knockdown in transgenic sheep showed increased MHCI expression (Hu et al. 2013).
There are several reports regarding shRNA-induced interferon responses suggested that a high level of shRNA expression might be due to the accumulation of unprocessed or aberrantly processed transcripts triggering interferon response (Stewart et al. 2008; Cao et al. 2005; Watanabe et al. 2006). The shRNA transfected porcine embryo cells, showed induction of the OAS1 and IFNβ genes by 1000 and 50 folds respectively (Stewart et al. 2008). Further, reported that the introduction of H1 and U6 promoter-based shRNA constructs by pronuclear microinjection led to induction of OAS1 gene and early embryo lethality (Bridge et al. 2003). In the present experiment, the expression of interferon genes IFN α, IFN β, and BLB1 were analyzed in control (scrambled shRNA treatment) and knockdown cells possessing different shRNA molecules to explore the impact of shRNA on immune function. It was observed that there was no significant difference of expression of IFN α, IFN β, BLB1 genes between knockdown and scrambled shRNA treated cells. Hence, shRNA molecules used in the present study have not been captured by the interferon mechanism in vitro as any foreign DNA fragment of a specific length is normally detected and destroyed by the interferons. It may therefore be construed that these shRNA molecules have been very much effective to silence ACACB expression without interfering with the body’s immune system. However, the introduction of short (< 30 nt) dsRNAs with 2-base 3 overhangs resembling dicer processing does not activate the interferon pathway and also shRNA expression from vectors in the nucleus resemble endogenous miRNA (Elbashir et al. 2001). The administration of naked, synthetic siRNAs in mice showed down-regulation of endogenous or exogenous targets without inducing an interferon response (Heidel et al. 2004). Similarly, the in vitro siRNA study showed the absence of IFN induction in human CD34 + progenitor cells (Robbins et al. 2006). On the contrary, activation of PKR, OAS, RIG-1, TLR 7, and TLR 8 by sequences shorter than 19 bp (Gantier et al. 2007).
Effect of ACACB gene silencing on de novo fat synthetic genes
Now-a-days, researchers are more focused on ACACA and ACACB to understand the chemistry and biological activity because they are very important enzymes in fatty acid synthesis and oxidation. The ACACB gene is localized subcellularly on the mitochondrial membrane and is involved in the synthesis of malonyl-CoA, and this inhibits the CPT1, which plays an important role for controlling the two opposing pathways i.e. fatty acid synthesis and oxidation. In this study, we knocked down the ACACB gene in chicken myoblast cells and tracked the expression of key fatty acid metabolism genes such as ACACA, FASN, SCD, ELOVL2, and CPT1. We observed down-regulation of ACACA, FASN, SCD, and CPT1 gene and up-regulation of ELOVL2 in ACACB knockdown myoblast cells. The down-regulation of ACACA, FASN, SCD genes indicates suppression of the fatty acid synthesis, and up-regulation of ELOVL2 indicates the enhancement of long-chain fatty acids formation (Fig. 6). The CPT1 is a rate-limiting enzyme and down-regulation of this enzyme indicates blocking the β-oxidation for balancing the fatty acid synthesis and oxidation because of fewer fats accumulation in the tissues.
Effect of ACACB gene silencing on cholesterol and triglyceride synthesis
In chicken egg and meat the high cholesterol and triglycerides are most undesired components and which compels us to eat chicken products in less quantity. The ACVR2B knockdown chicken showed significantly low cholesterol (Bhattacharya et al. 2019). In mice, LNP-formulated siRNAs were used for knockdown of the ApoB gene resulted in significant reduction of total cholesterol and LDL cholesterol, which suggested that targeting ApoB is a therapeutic approach for hyperlipidaemia treatment (Tadin-Strapps et al. 2011). In this study, we observed a significant reduction of cholesterol and triglycerides at 47.71% and 34.91%, respectively in ACACB knockdown cell lysate compared to the control. Based on these results, we suggest that the ACACB knockdown chicken may produce low cholesterol and triglycerides.
In conclusion, from the present study we have identified potential shRNA molecules against the ACACB gene where shRNA1 and shRNA5 showed more than 60% knockdown efficiency on the expression of the ACACB gene under in vitro myoblast cell culture system. The silencing of the ACACB gene showed to have a direct effect on the down-regulation of ACACA, FASN, SCD, and CPT1 genes, and up-regulation of ELOVL2 gene in myoblast cells. We suggest that these shRNA molecules may be used under in vivo system for the development of knockdown chicken having a potential of producing lean meat by silencing of expression of the ACACB gene.