Table 1 Glossary of technical terms
From: Dark matter RNA illuminates the puzzle of genome-wide association studies
Term | Meaning |
Chromatin signaling | A system of regulation of gene activity in a cell that works by affecting the immediate surroundings of DNA, for example, by modifying various proteins that coat DNA inside the nucleus. Depending on the exact nature of the modification, DNA becomes either more or less accessible to cellular machinery that activates genes |
Enhancer | A sequence of DNA that can regulate a target gene or genes over long distances |
DNAse I hypersensitivity region | A region of DNA identified in an assay where chromatin is digested with DNAse I, an enzyme that degrades DNA. More accessible regions of chromatin, typically containing regulatory elements such as promoters and enhancers, are more susceptible to DNAse digestion and thus are enriched in DNAse I hypersensitivity regions |
Gene Ontology (GO) term | GO is a an international initiative aimed at assigning controlled vocabulary, consisting of terms such as ‘regulation of apoptosis’ that define the functional property of each gene. This vocabulary is often very useful in understanding the biological meaning of a genomics experiment. For example, a list of genes activated during a disease would have a list of specific terms associated with each gene. Enrichment of specific terms in the list would suggest general cellular functions in which these genes participatem and give clues to the molecular functions underlying the disease |
H1 embryonic stem cells | A line of human embryonic stem cells maintained in culture |
H3K27 trimethylation | A certain type of chemical modification of a protein that binds DNA. Important for reversible deactivation oftargeted portions of the genome |
Intron | Part of an RNA molecule that is included immediately after transcription and removed during maturation of that molecule |
Intronic RNA | RNA encoded by a DNA sequence that also encodes an intron of another transcript |
lincRNA-p21 | A non-coding RNA activated upon DNA damage and in various tumor cell lines |
MYC gene | A gene encoding an important regulator controlling activity of many genes. This gene has been associated with many cancers |
Normal human epidermal keratinocytes (NHEK) | A line of primary keratinocytes maintained in culture |
Non-coding RNA | RNA that is not used as a template for protein synthesis |
Pervasive transcription | Massive transcription from unannotated regions of the genome |
PolyA+ RNA | A molecule of RNA containing a long stretch of adenosine residues at the end |
PRC2 chromatin signaling complex | A complex composed of multiple protein molecules that reversibly modifies chromatin and silences target genes |
Promoter | A sequence of DNA that is located immediately adjacent to a target gene and regulates its activity |
Pseudogene | A copy of a gene, presumed to be non-functional, although a number of recent examples describe both non-coding functions and occasionally coding functions for some of these loci |
Regulation in trans | Regulation via interaction with molecules encoded by distal regions of the genome |
RNA Pol II | A complex composed of multiple protein molecules responsible for synthesis of RNA, which is used as template for protein synthesis |
Transcript | A molecule of RNA produced by transcription, that is, copying of RNA from the DNA template |
Transcription factor | A protein that regulates expression of genes by binding to their promoters and/or enhancers |
Transcription factor motif | A short DNA sequence recognized by a transcription factor or group of transcription factors, typically found in promoters and enhancers |
Transcriptome | A collection of all the RNA molecules (transcripts) in a cell or a tissue |
Transcriptomics | Study of the transcriptome |
Xenopus oocytes | Oocytes from frogs of genus Xenopus, an important model system for study of developmental biology, cell biology, molecular biology, toxicology, and neuroscience |