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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