Glossary, ESM
function as start and stop codons, flanking the
coding stretch on the messenger RNA.
allele One of two or more alternate versions of a
gene at the same location (locus) along a
chromosome; different alleles can be due to
mutations. Alleles contribute to the exhibited
phenotype. Humans are diploid organisms having
two alleles at each genetic locus, with one allele
received from each parent. Genotypes are
homozygous if there are two identical alleles at a
particular locus and heterozygous if the two alleles
differ.
degeneracy Gene networks exploit alternate
strategies to preserve the output ; they exemplify
degeneracy, by adjusting expression of different
genes and using multiple pathway combinations to
achieve functional plasticity, producing a similar
phenotypic outcome in one context and dissimilar
ones in other contexts. Degeneracy is a key
organizational feature of our genetic code; it greatly
increases the capacity of a limited and fixed number
of genes to yield remarkable morphomechanical
complexities.
allelic heterogeneity Different mutations in the
same gene at the same chromosomal locus that
cause a single phenotype.
alternative splicing The processing of an RNA
transcript into different mRNA molecules. Our genes
are usually organized as a series of alternating
exons that encode amino acids and introns that do
not. After the RNA transcript is synthesized, RNA
splicing enzymes remove the intron sequences and
attach the exon sequences together to produce the
final mRNA molecule. Sometimes an exon
sequence is treated as an intron and is removed,
producing an alternative form of the mRNA. For
many DNA sequences alternative splicing patterns
may occur under different circumstances (in
different cells, tissues, and organs), thus giving rise
to diverse proteins from the same DNA stretch.
assembly Computational reconstruction of a
longer DNA/RNA sequence from smaller sequence
reads
bioinformatics The study of collecting, sorting,
and analyzing DNA and protein sequence
information using computers and statistical
techniques.
chromatin Complex of DNA, RNA, histones, and
non-histone proteins from which eukaryotic
chromosomes are formed.
codon Each of the different nucleotide triplets in
DNA that, when transcribed into RNA, are then
translated into an amino acid in a protein. Since any
one of the four kinds of nucleotides of which a DNA
strand is built can occupy each of the three positions
of a codon, there is a totality of 43 = 64 different
codons as compared to only 20 available amino
acids; therefore, most amino acids are encoded by
more than one codon (the genetic code is
redundant) and most DNA sequence changes
affecting the third position in a codon do not change
the resulting protein. Some (noncoding) codons
DNA sequencing Processes determining the
exact order of the base pairs in a segment of DNA.
epigenetic inheritance (epigenetics) Inheritance
of a trait for one or more cell generations that is not
transmitted by the genetic material proper and is
reversible. A case of epigenetic inheritance is the
transmission of DNA methylation patterns.
epistasis Gene interaction and, particularly,
interaction between different alleles at different
genes. Epistasis is a phenomenon that consists of
the effect of one gene being dependent on the
presence of one or more modifier genes (genetic
background), and can occur at the same step or at
different stages of a pathway or process.
epistatic interaction The influence of the
interaction of multiple loci on phenotypic variation..
euchromatin State of chromatin in which the DNA
is partially or fully uncoiled and transcriptionally
active, in contrast to the inert heterochromatin.
exons Rather than forming a continuous stretch of
coding DNA, a gene may consist of a chain of
coding and noncoding sequences called exons and
introns, respectively. The RNA transcript of such a
gene goes through a process of splicing in which the
introns are excised yielding a "mature" messenger
RNA composed only of exons; each exon codes for
a specific portion of the complete protein.
gene expression General process by which the
information encoded in a gene is converted into an
observable phenotype, such as the production of
proteins. It pertains to DNA transcription into RNA,
RNA splicing/edition processes, translation, and
post-translational protein modifications.
gene network A graphical illustration for exploring
the functional interactive linkages and the potential
coordinate regulations of genes. Networks consist
of ‘‘nodes,’’ the genes and their regulators, joined
together by ‘‘edges,’’ which represent physical
and/or regulatory interactions.
genome All the genetic material in the chromosome
set of a particular organism. In diploid organisms
there are two genomic complements, one
complement inherited from each parent.
genotype The combination of alleles on the two
chromosomes of an individual, representing the
inherited genetic makeup or genetic constitution of
a cell or organism, which is modulated by the
environment before being expressed as a
phenotype.
haplotype A set of allelic states, or a series of
polymorphisms, found at neighboring loci in a
chromosome and tending to be inherited jointly. A
haplotype shared among unrelated individuals
affected with a genetic disease may indicate that a
gene causing the disease maps to that genomic
region.
heterochromatin Zones of chromatin with DNA
that remains condensed and transcriptionally
inactive or repressed.
homologous (or homolog) A gene or protein
inherited in two or more species by a common
ancestor. While homologous genes can be similar in
sequence, similar sequences are not inevitably
homologous.
Human Genome Project (HGP) An international
research project begun in 1990 and completed in
2003 that mapped and sequenced the three billion
DNA bases of the human genome.
monogenic (single gene) alterations. However, for
some phenotypes it is becoming clear that
mutations in a single gene can be insufficient to
cause a specific phenotype without sequence
alterations in other genes. Further variation in
phenotype or penetrance can be caused by loss or
alteration of contiguous genes. Modifier genes have
become increasingly recognized as an important
source of phenotypic variation that may explicate
the complex relationship of phenotype to genotype.
monogenic Involving a single gene. Monogenic
diseases are attributable to mutations in a single
gene; the defective gene is inherited from a parent
in most instances, but may also arise from
spontaneous mutation.
multifactorial
Traits/syndromes
that
are
determined by a combination of genetic as well as
non-genetic factors, each contributing to the overall
phenotype.
mutation A gene mutation is a permanent
alteration in the DNA sequence that makes up a
gene, such that the sequence differs from what is
found in most people. Mutations range in size; they
can affect anywhere from a single DNA building
block (base pair) to a large segment of a
chromosome that includes multiple genes.
Next Generation Sequencing (NGS) Highthroughput DNA and RNA (coding and non-coding)
sequencing methods which parallelize massively
the sequencing process, producing thousands or
millions of sequences at once; they can explore
gene expression changes, epigenomic pattern, etc,
on a genome-wide scale and with single base
precision.
introns Rather than forming a continuous stretch of
coding DNA, a gene may consist of a chain of
noncoding and coding sequences called introns and
exons, respectively. The RNA transcript of such a
gene goes through a process of splicing in which the
introns are excised yielding a "mature" messenger
RNA composed only of exons. The introns may
serve other functions, such as regulation of the
splicing and translation processes, or even may be
exons of other genes.
penetrance The likelihood, or probability, that a
particular genotype will be expressed in the
phenotype. A penetrance of 100% means that the
associated phenotype always occurs when the
corresponding genotype is present; similarly, if only
25% of those carrying a particular allele (such as a
disease-causing mutation) exhibit a phenotype (the
disease), the penetrance is 25%.
locus (pl. loci) In genetics, a specific site of a gene
on a chromosome. All the alleles of a particular gene
occupy the same locus.
phenotype Expressed morphomechanical traits or
other characteristics, including the presence or
absence of a disease, regardless of whether or to
what extent the traits are the result of genotype or
environment, or of the interaction of both.
modifier genes For many diseases, including
various genetic cardiomyopathies, no clear
relationship of phenotype to genotype can be
demonstrated. Most publications pertaining to the
genetics of pleiotropic syndromes have resulted
from the study of cases involving high-penetrance
pleiotropy (from the Gk. pleio and tropic, indicating
"more" and “forms, respectively.") A situation in
which mutations in one single gene can bring forth
various morphomechanical phenotypic traits/forms.
polygenic trait (multifactorial trait) Any
phenotype that results from the effect of multiple
genes at two or more loci, with possible modulating
environmental influences too. Cardiovascular
examples include hypertension, heart failure,
hypercholesterolemia, etc.
polymorphism Genome segment (locus), within or
outside a gene, in which alternate forms (alleles) are
present, having arisen from mutational events. A
genetic variation is polymorphic if all alleles are
found at frequencies >1% in the general population.
In clinical genetics, a polymorphism refers to any
genetic variation that, in contrast with a mutation, is
not known to be a direct cause of disease. However,
the distinction may be fuzzy, as the path from
genetic variation to disease can sometimes be
complicated.
remodeling The (mal)adaptive change of tissue
and organ morphology due to external or internal
stimuli.
single-nucleotide
polymorphism
(SNP)
Variation in a genetic sequence that affects only one
of the basic nucleotide building blocks—adenine,
guanine, thymine, or cytosine—in a segment of a
DNA molecule and occurs in more than 1 percent of
a population.
transcription The process by which RNA
polymerase assembles an RNA molecule
complementary to the template strand of the DNA.
The product may be messenger RNA, transfer RNA
or ribosomal RNA.
translation The process by which messenger RNA
directs a ribosome to assemble a polypeptide. As
specified in the genetic code each codon in the
mRNA corresponds to an amino acid. The assembly
of the protein stops when the ribosome encounters
one of three possible stop codons.