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Key concepts Regulation of Transcription in Eukaryotes Because of the demands of development and of responding to environmental factors, the regulation of transcription is much more complex in eukaryotes than in viruses or bacteria. Promoter regions in eukaryotes are usually split into core and proximal elements; the core contains the polymerase docking site, while the proximal promoter region has regulatory functions. Distal DNA regulatory elements include enhancers, silencers, insulators, and locus control regions. Each of these elements acts through its own mechanisms. Eukaryotic transcription factors are molecular complexes that bind to DNA regulatory elements. Typically, they contain both DNA-binding and activation domains that act to bind to specific DNA sequences in specific genes and then activate transcription through recruitment of the basal transcriptional machinery. There are also protein factors that help polymerases to pass through nucleosomes. The mechanisms for transcription of DNA within nucleosomes are still not well understood. Transcription in eukaryotes is markedly influenced by post-translational modification or marking of histones on nucleosomes. These marks include acetylation, methylation, phosphorylation, ubiquitylation, and poly(ADP)ribosylation events. Specific enzymes exist for each of these modifications: the enzymes are highly specific for individual amino acid residues on individual histone molecules. There is also cross-talk between such modifications. Specific readers of these markings exist that, upon recognizing the marks, initiate the modification of gene expression. Certain modifications, like lysine acetylation, correlate strongly with gene activity. Others are associated with gene silencing. Histone replacement variants also play a role in gene regulation. For example, H2A.Z is often found in nucleosomes that flank nucleosome-free regions, which occur around transcription start sites. H3.3 and H2A.Bbd are often associated with active transcription. Chromatin structure must sometimes be remodeled to permit transcription. This can be accomplished by a battery of ATP-dependent chromatin remodelers. These may slide nucleosomes on DNA, modify their structure, or partly dissociate the nucleosomal particle. In addition to all the other mechanisms described above, it is now becoming clear that long noncoding RNAs can carry out a remarkable number of regulatory functions.