Question

A) (10pts) DNA methylation at CpGs sequences appears to cause gene silencing in both plants and mammals. Describe the mechanism by which this is thought to happen that involves histone modifications. Include in your answer any proteins/enzymes involved; please write out names of proteins/enzymes not just abbreviations and be clear about what that protein does. Also, describe the specific the histone modification that is influenced and how this affects chromatin organization/compaction. B)(3pts) The best method to determine all the regions in the human genome that are enriched for H3K4me3 epigenetic modification is (Choose ONE best): ChIP-PCR (Chromatin immunoprecipitation followed by PCR) ChIP-seq (Chromatin immunoprecipitation followed by sequencing) Digestion with methylation sensitive enzymes Semi-quantitative PCR C) (3pts) Histones can be methylated and acetylated on several different positions. Choose ONE best below where active genes active transcription: H3K4me3, H3K9me3 and H3K27me3 are all associated with inactive genes, while H3 acetylation is associated with active genes. H3K4me3 is associated with active genes while H3K9me3 and H3K27me3 are associated with inactive genes H3K9me3 and H3K27me3 are associated with active genes while H3K4me3are associated with inactive gene

Answer 1

A) DNA methylation at CpG sequences leads to gene silencing through a mechanism involving histone modifications. DNA methylation is catalyzed by DNA methyltransferases (DNMTs), which add a methyl group to CpG dinucleotides. This attracts methyl-binding proteins like MeCP2.

These proteins recruit histone deacetylases (HDACs), leading to histone deacetylation and chromatin compaction. The specific histone modification influenced is histone deacetylation (removal of acetyl groups), resulting in condensed chromatin that inhibits gene expression.

B) The best method to determine regions enriched for H3K4me3 epigenetic modification is ChIP-seq (Chromatin immunoprecipitation followed by sequencing). This technique allows for genome-wide profiling of specific histone modifications, providing a comprehensive view of H3K4me3-enriched regions.

C) H3K4me3 is associated with active genes, while H3K9me3 and H3K27me3 are associated with inactive genes. H3K9me3 and H3K27me3 are repressive marks, while H3K4me3 is an activating mark, promoting gene expression.

Step-by-step explanation:

A) DNA methylation at CpG sequences can lead to gene silencing through a complex mechanism involving histone modifications. Initially, DNA methyltransferases (DNMTs) add a methyl group to CpG dinucleotides. This methylated DNA attracts methyl-binding proteins like MeCP2, which serve as a bridge to histone deacetylases (HDACs). HDACs remove acetyl groups from histones, leading to histone deacetylation.

This change in histone modification results in condensed chromatin structure, making it inaccessible to transcription factors and RNA polymerase, thereby inhibiting gene expression. The interplay between DNA methylation and histone modifications contributes to the regulation of gene expression.

B) The most effective method for identifying regions enriched for H3K4me3 epigenetic modifications across the human genome is ChIP-seq (Chromatin immunoprecipitation followed by sequencing). ChIP-seq allows researchers to isolate DNA fragments associated with a specific histone modification (in this case, H3K4me3) and then sequence these fragments.

This provides a comprehensive, genome-wide map of H3K4me3-enriched regions, offering insights into active gene regulatory regions.

C) Among the given options, H3K4me3 is associated with active genes. It is a histone modification typically found in the promoter regions of actively transcribed genes. In contrast, H3K9me3 and H3K27me3 are repressive histone marks associated with gene silencing and inactive chromatin.

These marks are involved in maintaining a transcriptionally silent state. Therefore, H3K4me3 is the histone modification linked to active gene transcription, while H3K9me3 and H3K27me3 are associated with gene inactivity.