Introduction
Activation and repression of gene expression in both eukaryotes and prokaryotes is a complex process that many factors mediate. Scientists have formulated theories and hypotheses that elucidate a number of mechanisms through which activation and repression occur in both in vivo and in vitro environments. In the activation and repression of gene expression, histones play a central role, as they are proteins that associate with and bind to the DNA material in cells. The research questions sought to establish if acetylation of histones and chromatin remodeling complexes influence gene expression. According to the Agalioti, Chen, and Thanos, “chromatin modifying complexes recruited by transcription factors covalently modify the N-terminal tails of histones by adding or removing phosphate, methyl, or acetyl groups,” (381). On this basis, the research article hypothesizes that existence of chromatin modeling complexes and transcription factors that catalyze acetylation of histones, which have an overall impact of activating expression of genes. Hence, the histone code hypothesis predicts that a functional interaction exists between histone acetylase (GCN5) and chromatin remodeling complexes (SWI/SNF) in the cells. In proving the histone code hypothesis, the study hypothesized that histone acetylation is specific to certain residues that are responsible for gene activation through in vivo mechanism. The basis of the study is that modification of histones at the promoter and enhancer sites is critical in the activation of gene expression. Hence, to prove the hypothesis, the research sought to establish if acetylation of histones has a regular pattern that has a significant impact in enhancing activation of genes. Examination of the technologies employed in the study shows that they are appropriate in proving the histone code hypothesis.
Hypothesis
The major hypothesis of the study is that of histone code hypothesis. Histone code hypothesis states that functional interaction between histone acetylase (GCN5) and chromatin remodeling complexes (SWI/SNF) activates expression of genes. Modification of histones at the promoter and enhancer sites enhances gene expression. Agalioti, Chen, and Thanos state that the aim of the research paper is to “provide direct evidence for both the existence of a histone acetylation code and its interpretation by the transcriptional apparatus during human IFN-β gene activation” (381). Acetylation of lysine moieties in histones causes modification of histones, hence, bringing about activation of gene expression. Thus, the study assumes that acetylation of histones generates cascades of reactions that lead to enhanced expression of genes.
Punch Line
Acetylation of histones plays a significant role in regulation of gene expression. Specifically, “acetylation of histone H4K8 mediates recruitment of the SWI/SNF complex whereas acetylation of K9 and K14 in histone H3 is critical for the recruitment of TFIID” (Agalioti, Chen, and Thanos 381). Recruitment of transcriptional factors in a cascade manner explains the mechanism of gene expression via acetylation process. Acetylation of histones induces ATP-dependent process that causes SWI/SNF complexes to slide and initiate the transcription process at the downstream. Additionally, acetylation of histones causes recruitment of extra complexes such as TFIID, which are bromodomains that regulate interaction of transcription factors with the promoter and enhancer sites. According to Agalioti, Chen, and Thanos, acetylation of histones enhances activation of IFN-β gene expression by facilitating recruitment of SWI/SNF and TFIID complexes. Therefore, to prove acetylation of histones, the study sought to ascertain how Sendai virus induces acetylation of lysine residues present in histones H3 and H4 in the transcription of IFN-β gene.
Methodology
To determine the role of histone acetylation, the study employed the methodology of conducting an in vitro infection of cells with viruses and then assessing the extent of histone acetylation. In the in vitro experiment, the researchers infected the HeLa cells with Sendai virus. The virus infection then induced acetylation of lysine residues that are present in histones H4 and H3. After incubation for different periods, formaldehyde treatment was added to cause protein-DNA complexes and protein-protein cross-linkages to form. Immunoprecipitation of the linkages and complexes formed was then performed using antibodies that are specific to acetylated lysine residues in H4 and H3. While acetylation of H4 peaks at between 4-6 hours of incubation, H3 peaks at 6-10 hours after incubation. To determine the acetylated residues, electrophoresis by SDS-PAGE was performed to separate histone residues according to their sizes, thus separating acetylated ones. Eventually, Western blot was employed to identify acetylated lysine residues in histones using specific immunoprobes. The methodology used in ascertaining acetylation of lysine residues in histones due to virus infection is appropriate as it targets proteins, which are products of gene expression.
Technologies Employed
The experiment employed in vitro culture of HeLa cells as a technology for assessing the impact of virus infection on gene expression via acetylation of histones. The acetylation mechanism that occurs in an in vivo environment is similar to the one that occurs in an in vitro environment. Therefore, the use of HeLa cells reflects the actual mechanism that occurs in the cells. Activation of gene expression due to virus infection was then detected using RT-PCR, which measures the message level of IFN-β gene (IFN-β mRNA). Immunoprecipitation technology was also applicable in cross-linking chromatin material that is rich in acetylated lysine residues. To separate different types of histones depending on their size, SDS-PAGE was a critical technology. After separation of histones based on their sizes, Western blotting was essential as a technology that uses immunoprobes, which are very specific to acetylated lysine residues in histones. Thus, Western blotting is an important technology that aided detection of acetylated lysine residues in histones, following activation of IFN-β gene in human.
Data Analysis
The data show that acetylation of histones activates expression of IFN-β gene. The virus infection induces expression of the IFN-β gene, thus causing enhanced transcription process in cells. After infection of HeLa cells with Sendai virus, there was increased expression of IFN-β gene in both H3 and H4 histones. Agalioti, Chen, and Thanos report that acetylation of H3 and H4 histones occur in different patterns, as acetylation of H3 peaks at 6-10 hours after incubation while acetylation of H4 peaks at 4-6 hours after incubation (382). However, the acetylation process begins at 3 hours after incubation in both H3 and H4 histones. Since the virus induces acetylation of histone at the IFN-ß promoter, it enhances gene expression leading to the increased message level of the IFN-β in the HeLa cells. RT-PCR done indicated the IFN-β mRNA increased with time after infection, thus peaking at 4-6 hours in H4 and 6-10 hours for H3. SDS-PAGE electrophoresis and Western blotting do support the histone code hypothesis that acetylation of histones activates expression of IFN-β gene in human.
Derived Conclusions
Histone code is critical in regulation of IFN-β gene, which is in human. The acetylation of histones enhances expression of IFN-β gene as shown by RT-PCR analysis. According to Agalioti, Chen, and Thanos, GCN5 acetyltranferase causes acetylation of H3 and H4 histones leading to activation of the IFN-β gene in human. Acetylation of histones causes recruitment of SWI/SNF complexes and TFIID complexes, which are responsible for triggering a series of mechanisms that lead to activation of IFN-β gene. Thus, the study proved that the histone code hypothesis is applicable in elucidating the activation of IFN-β gene in human.
Interpretation of Figures
In the article, figure 1 depicts how virus infection induces activation of IFN-β in human by acetylation of histones. RT-PCR shows that there is an increased message level following infection by the Sendai virus. Immunoprecipitation techniques also indicate that proteins associated with H3 and H4 increase due to the infection. Ultimately, SDS-PAGE and Western blot confirmed that lysine residues in H3 and H4 histones were acetylated, thus promoting expression of IFN-β gene in human. The figure 4 elucidates the mechanism of acetylation from a functional perspective. Since recombinant nucleosome cannot undergo acetylation process, the IFN-β gene activation cannot occur, as in the case with native nucleosome. Hence, these findings proved that acetylated histones initiate recruitment of SWI/SNF and TFIID complexes necessary for translation of histone code as shown in the model, figure 5.
Summary
Histone code helps in regulation IFN-β gene expression in human. Specifically, acetylation of H3 and H4 histones activates expression of the IFN-β gene. Acetylated histones initiate the recruitment of SWI/SNF and TFIID complexes, which are essential in the downstream activation of gene expression cooperatively. The use of recombinant nucleaosomes proved that lysine residues in histones are critical regions of acetylation, because, without them, acetylation will not take place. Hence, acetylation of histone code is central in activation of IFN-β gene in human.
Recommendation
- Histone code hypothesis predicts that acetylation of histones in IFN-β gene provides means through which activation of gene expression occurs. As the study hypothesizes that acetylation of histone activates expression of IFN-β gene in human, more studies are necessary to establish if other factors that mediate remodeling of histone structures exist.
- Viruses have the ability to induce acetylation of histones. Since Sendai virus induces acetylation of histones in HeLa cells, other viruses and stem cells should be used to ascertain the role of histone code in gene expression.
- Transcription factors and other complexes determine the expression of genes. Given that acetylation of histones initiates downstream processes that are critical in recruitment of SWI/SNF and TFIID complexes, a study is necessary to determine if additional complexes that mediate IFN-β gene expression exist.
Works Cited
Agalioti, Theodora, Guoying Chen, and Dimitris Thanos. “Deciphering the Transcriptional Histone Code for a Human Gene.” Cell 111.3 (2002): 381-392. Web.