The gene expression program of a cell encompasses the specific subset of the approximately 20,000 protein-coding genes in the genome that are actively transcribed and translated into their respective functional products, the subset of the estimated 20,000 to 25,000 ncRNA genes that are transcribed, the amount of products produced, and the particular sequence (alleles) of those products. The gene expression profile of any particular cell or cell type in a given individual at a given time (whether in the context of the cell cycle, early development, or one’s entire life span) and under a given set of circumstances (as influenced by environment, lifestyle, or disease) is thus the integrated sum of several different but interrelated effects, including the following: • The primary sequence of genes, their allelic variants, and their encoded products • Regulatory sequences and their epigenetic positioning in chromatin • Interactions with the thousands of transcriptional factors, ncRNAs, and other proteins involved in the control of transcription, splicing, translation, and post-translational modification • Organization of the genome into subchromosomal domains • Programmed interactions between different parts of the genome • Dynamic three-dimensional chromatin packaging in the nucleus
Gene Expression as the Integration of Genomic and Epigenomic Signals
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